derives_from
Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
ro_bfo_bridge
relationship
OBO_REL:0000015
derived_from
Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
derived_from
Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
Description
An account of the content of the resource.
Description may include but is not limited to: an abstract,
table of contents, reference to a graphical representation
of content or a free-text account of the content.
Contributor
An entity responsible for making contributions to the
content of the resource.
Examples of a Contributor include a person, an
organisation, or a service. Typically, the name of a
Contributor should be used to indicate the entity.
annotation property domain
PERSON:Alan Ruttenberg
PERSON:Alan Ruttenberg
Relates an Annotation Property to a the class that a subject is inferred to be. Can't use owl:domain else we create OWL Full.
preceded_by
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
ro_bfo_bridge
OBO_REL:0000017
relationship
P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
Creator
An entity primarily responsible for making the content
of the resource.
Examples of a Creator include a person, an organisation,
or a service. Typically, the name of a Creator should
be used to indicate the entity.
definition
GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
PERSON:Daniel Schober
The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
definition
editor note
GROUP:OBI:<http://purl.obfoundry.org/obo/obi>
PERSON:Daniel Schober
An administrative note intended for its editor. It will not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
editor note
definition editor
GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
PERSON:Daniel Schober
Name of editor entering the definition
definition editor
alternative term
GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
PERSON:Daniel Schober
An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent)
alternative term
preferred term
GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
PERSON:Daniel Schober
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
preferred term
example of usage
GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
PERSON:Daniel Schober
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
example
Subject and Keywords
The topic of the content of the resource.
Typically, a Subject will be expressed as keywords,
key phrases or classification codes that describe a topic
of the resource. Recommended best practice is to select
a value from a controlled vocabulary or formal
classification scheme.
in branch
OBI_0000277
has curation status
OBI_0000281
agent_in
relationship
OBO_REL:0000022
ro_bfo_bridge
precedes
OBO_REL:0000018
relationship
ro_bfo_bridge
Resource Identifier
An unambiguous reference to the resource within a given context.
Recommended best practice is to identify the resource by means
of a string or number conforming to a formal identification
system.
Example formal identification systems include the Uniform
Resource Identifier (URI) (including the Uniform Resource
Locator (URL)), the Digital Object Identifier (DOI) and the
International Standard Book Number (ISBN).
Date
A date associated with an event in the life cycle of the
resource.
Typically, Date will be associated with the creation or
availability of the resource. Recommended best practice
for encoding the date value is defined in a profile of
ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
definition source
GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
PERSON:Daniel Schober
definition source
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
participates_in
relationship
OBO_REL:0000020
ro_bfo_bridge
Title
Typically, a Title will be a name by which the resource is
formally known.
A name given to the resource.
Relation
Recommended best practice is to reference the resource by means
of a string or number conforming to a formal identification
system.
A reference to a related resource.
transformed_into
Obsoleted
relationship
OBO_REL:0000014
ro_bfo_bridge
derived_into
OBO_REL:0000016
relationship
ro_bfo_bridge
has_participant
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
OBO_REL:0000019
ro_bfo_bridge
relationship
P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
Language
A language of the intellectual content of the resource.
Recommended best practice is to use RFC 3066 [RFC3066],
which, in conjunction with ISO 639 [ISO639], defines two-
and three-letter primary language tags with optional
subtags. Examples include "en" or "eng" for English,
"akk" for Akkadian, and "en-GB" for English used in the
United Kingdom.
Resource Type
The nature or genre of the content of the resource.
Type includes terms describing general categories, functions,
genres, or aggregation levels for content. Recommended best
practice is to select a value from a controlled vocabulary
(for example, the DCMI Type Vocabulary [DCMITYPE]). To
describe the physical or digital manifestation of the
resource, use the Format element.
transformation_of
When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.
ro_bfo_bridge
OBO_REL:0000013
relationship
Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
location_of
ro_bfo_bridge
OBO_REL:0000009
relationship
Source
A reference to a resource from which the present resource
is derived.
The present resource may be derived from the Source resource
in whole or in part. Recommended best practice is to reference
the resource by means of a string or number conforming to a
formal identification system.
has_agent
OBO_REL:0000021
ro_bfo_bridge
relationship
As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
Publisher
An entity responsible for making the resource available
Examples of a Publisher include a person, an organisation,
or a service.
Typically, the name of a Publisher should be used to
indicate the entity.
annotation property range
PERSON:Alan Ruttenberg
PERSON:Alan Ruttenberg
Relates an Annotation Property to the class that the object is inferred to be. Can't use owl:domain else we create OWL Full.
annotation property range
Coverage
Coverage will typically include spatial location (a place name
or geographic coordinates), temporal period (a period label,
date, or date range) or jurisdiction (such as a named
administrative entity).
Recommended best practice is to select a value from a
controlled vocabulary (for example, the Thesaurus of Geographic
Names [TGN]) and that, where appropriate, named places or time
periods be used in preference to numeric identifiers such as
sets of coordinates or date ranges.
The extent or scope of the content of the resource.
alternative term tag
GROUP:OBI:<http://obi.sourceforge.net>
PERSON:Daniel Schober
alternative term tag
tag to indicate sets of alternative terms Example: toxicogenomics_community, abbreviation
alternative term source
GROUP:OBI:<http://obi.sourceforge.net>
PERSON:Daniel Schober
alternative term source
An unambiguous and traceable reference to the source of the alternative term. Examples: ISBN, URI plus date, MeSH Term, PUBMED ID, DOI.
imported from
GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
For external terms/classes, the ontology from which the term was imported
imported from
has validation method
PERSON:Alan Ruttenberg
PERSON:Alan Ruttenberg
Relates an annotation property to a method which can be used to validate whether the value of the annotation property is valid.
located_in
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
relationship
OBO_REL:0000008
ro_bfo_bridge
C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
Format
The physical or digital manifestation of the resource.
Typically, Format may include the media-type or dimensions of
the resource. Format may be used to determine the software,
hardware or other equipment needed to display or operate the
resource. Examples of dimensions include size and duration.
Recommended best practice is to select a value from a
controlled vocabulary (for example, the list of Internet Media
Types [MIME] defining computer media formats).
Rights Management
Typically, a Rights element will contain a rights
management statement for the resource, or reference
a service providing such information. Rights information
often encompasses Intellectual Property Rights (IPR),
Copyright, and various Property Rights.
If the Rights element is absent, no assumptions can be made
about the status of these and other rights with respect to
the resource.
Information about rights held in and over the resource.
specifically denotes
c specifically denotes r =def
r is a portion of reality
& c is a particular quality
& c depends specifically on some independent continuant b
& b acquired c as the result of the achievement of an objective to enable pointing to r repeatedly.
Marked means there is a changed or additional quality of the bearer - the quality is the information carrier.
Case 1
Memory trace as mark created when reading some description of some friend. The trace can denote.
Case 2
Pattern of ink arrayed on paper as mark when writing down a friend's name
Case 3
Pattern of magnetic domains on scattered pieces of a hard disk platter as mark when saving a file.
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
The process of creation is, for example, writing down on paper the name of a friend by deliberately creating a certain pattern using ink.
Here the ink + paper is the independent continuant and the carrier is the pattern in the ink.
c = pattern in the ink
b = paper + ink
r = friend
Alan Ruttenberg
is about
This document is about information artifacts and their representations
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
a representation is_about anything exactly when some part of the information_artifact denotes the entity
person:Alan Ruttenberg
generically denotes
person:Alan Ruttenberg
g generically denotes r =def
r is a portion of reality
there is some c that is a concretization of g
every c that is a concretization of g specifically denotes r
The word Boston on a traffic signn in Massachusetts generically denotes the city of Boston
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
materially denotes
is quality measurement of
m is a quality measurement of q at t when
q is a determinable quality
there is a measurement process p that has_output m
m has a value part that together with the units of the value of q at t.
p is a assay
assay:
process and has_input some material entity
and has_output some information content entity
and which is such that instances of this process type reliably generate outputs that describes the input.
a is a magnitude means a is a determinate quality particular inhering in some bearer b existing at a time t that can be represented/denoted by an information content entity e that has parts denoting a unit of measure, a number, and b. The unit of measure is an instance of the determinable quality.
unit of measure is a quality, e.g. the length of a ruler.
a represents b means either a denotes b or a describes
describe:
a describes b means a is about b and a allows an inference of at least one quality of b
Example:
q = height of barry
p is the process using a tape measure extend across the longer part of barry and reading off the number at the far end.
v is that number
# dimension is height
unit of measure is inches
We have had a long discussion about denotes versus describes.
This one is the one we are struggling with at the moment. The issue is what a measurement measures. On the one hand saying that it measures the quality would include it "measuring" the bearer = referring to the bearer in the measurement. However this makes comparisons of two different things not possible. On the other hand not having it inhere in the bearer, on the face of it, breaks the audit trail.
Werner suggests a solution based on "Magnitudes" a proposal for which we are awaiting details.
describes
represents
has_specified_input
FG: Due to the fact that only material entities can play roles under BFO. The range of this relation has been tighted to be material entity. If BFO relaxes its principles and allows information entities to play roles then the range should be expanded back to continuant.
PERSON: Larry Hunter
PERSON: Melanie Coutot
has_specified_input
A relation between a process and a participant present at the beginning of that process. The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). The continuant realizes specified_Input_Role for that process. In general, not all participants present at the beginning of the process are specified_inputs.
PERSON: Alan Ruttenberg
see is_input_of example_of_usage
is_concretization_of
Is a relationship between a generically dependent continuant and a specifically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.
PERSON: Alan Ruettenburg
PERSON: Barry Smith
is_concretization_of
is_specified_input_of
Alan Ruttenberg
Relationship between a participant and a protocol application. The input is, at a minimum, present at the beginning of the protocol application, but not all participants present at the beginning of the protocol applications are input, only those that are viewed as inputs according to the plan, and hence realize InputRole.
some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
is_concretized_as
Is a relationship between a specifically dependent continuant and a generically dependent continuant. A generically dependent continuant may inhere in more than one entity. It does so by virtue of the fact that there is, for each entity that it inheres, a specifically dependent *concretization* of the generically dependent continuant that is specifically dependent. For instance, consider a story, which is an information artifact that inheres in some number of books. Each book bears some quality that carries the story. The relation between this quality and the generically dependent continuant is that the former is the concretization of the latter.
PERSON: Alan Ruettenburg
PERSON: Barry Smith
has_quality
A relation between an entity and a quality. For types: E has_quality Q iff:
for any eEt, exists qQt such that q inheres_in e at t.
For instances: e has_quality q at t iff q inheres_in e at t and q instance-of Quality" [GOC:cjm]
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungall
has_quality
has_specified_output
PERSON: Larry Hunter
PERSON: Melanie Courtot
has_specified_output
A relation between a process and a participant present at the end of that process. The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). The continuant realizes specified_output_role for that process. In general, not all participants present at the end of the process are specified_outputs.
PERSON: Alan Ruttenberg
is_realized_by
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungall
Relation between a realizable and a process. Reciprocal relation of realizes" [GOC:cjm]
executed_during
has_realization
is_realized_as
outputs_specified_data
PERSON: Frank Gibson
outputs_specified_data
A relation between a device, which is a participant in a process, that produces a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the end of the process are specified_data.
PERSON: Alan Ruttenberg
is_manufactured_by
Alan Ruttenberg
Liju Fan
c is_manufactured_by o means that there was a process p in which c was built in which a person, or set of people or machines did the work(bore the "Manufacturer Role", and those people/and or machines were members or of directed by the organization to do this.
has_make
has_manufacturer
http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
http://www.affymetrix.com/products/arrays/specific/hgu133.affx is_manufactered_by http://www.affymetrix.com/ (if we decide to use these URIs for the actual entities)
is_manufactured_by
has_function
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungall
Relation between an independent continuant and a function.
heart has_function to-pump-blood
is_reagent_in
Alan Ruttenberg
Relationship between a substance and a protocol application in which it participates, where the substance has a ReagentRole
some Triton X-100 (Sigma-Aldrich) is_reagent_in instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
realizes
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungal
Relation between a process and a function, where the unfolding of the
process requires the execution of the function. Class level: P realizes F iff:
given any p that instantiates P, there exists some f, t such that f instantiates
F at t and p *realizes* f. Here, *realizes* is the primitive
instance level relation" [GOC:cjm]
example of usage: The process of 'histidine catabolism' (GO:0006548) realizes the
function 'histidine ammonia lyase activity' (GO:0004397) (note: here 'activity'
denotes a function and not a process). We leave open the possibility of defining
in future the sub-relations directly_realizes (as bewteen a function and it's
functioning) and indirectly_realizes.
executes
has_function_part
involves_execution_of
is_realization_of
utilizes_reagent
Alan Ruttenberg
Relationship between a protocol application and a substance that has role reagent that participates in the protocol application
see example_of_usage for is_reagent_in
is_device_for
Alan Ruttenberg
Relationship between a device and a protocol application in which it participates
some LKB 1272 Clinigamma counter is_device_for instance of Chromium Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
is_specified_output_of
is_specified_output_of
Alan Ruttenberg
Relationship between a participant and a protocol application. The output is, at a minimum, present at the end of the protocol application, but not all participants present at the end of the protocol applications are input, only those that are viewed as outputs according to the plan, and hence realize OutputRole.
utilizes_device
Alan Ruttenberg
Relationship between protocol application and an intrument in which it participates
see example_of_usage for is_device_for
is_proxy_for
A relation between continuant instances c1 and c2 where within a protocol
application, measurement of c1 is related to a what would be the
measurement of c2.
A relation between continuant instances c1 and c2 where within an experiment/ protocol application, measurement of c1 is used to determine what a measurement of c2 would be.
Alan Ruttenberg
position on a gel is_proxy_for mass and charge of molecule in an western blot. Florescent intensity is_proxy_for amount of protein labeled with GFP. Examples:
A260/A280 (of a DNA sample) is_proxy_for DNA-purity. NMR Sample scan is a proxy for sample quality.
Within the assay mentioned here: https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay
level of radioactivity is_proxy_for level of toxicity
inputs_specified_data
PERSON: Frank Gibson
consumes data
inputs specified data
A relation between a process and a device, which is a participant of that process, that consumes a data set . The process is the realization of a concretization of a realizable information entity (objective specification or plan specification). In general, not all data present at the beginning of the process are specified_data.
PERSON:Alan Ruttenberg
See note for outputs_data
has_role
A relation between a continuant C and a role R. The reciprocal relation of role_of.
GROUP:OBI:<http://obi.sourceforge.net>
PERSON:Chris Mungal
has_role
results_from
has_objective
still under discussion
bearer_of
A relation between an entity and a dependent continuant; the reciprocal relation of inheres_in" [GOC:cjm]
example of usage: red eye bearer_of redness
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungal
bearer_of
function_of
A relation between a function F and an entity E. F function_of E iff: Q inheres_in E and Q is a function
Example: 'to blood pump' function_of 'heart'
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungall
function_of
inheres_in
A relation between a dependent continuant D and an entity E. D inheres_in E iff: given any d that instantiates D at t, there exists some e that instantiates E at t and d *inheres_in* e at t. Here *inheres_in* is the primitive instance level relation.
This relation links qualities, functions, dispositions and other dependent continuants to their bearers. Examples: A particular shape that inheres in a lung; The redness that ineres in a Drosophila eye; Catalytic activity function inheres_in catalytic molecule. Note that inherence is a functional relation: if x inheres_in y at t and x inheres_in z at t, then y=z. We leave open the possibility of a relation multiply_inheres_in, such as between a gene sequence and the multiple chromosomes it multiply inheres in. The super-relation of both inheres_in and multiply_inheres_in would be depends_on
has_bearer
quality_of
A relation between a quality Q and an entity E. Q quality_of E iff: Q inheres_in E and Q is a quality
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungall
quality_of
role_of
A relation between a role R and an entity E. R role_of E iff: R inheres_in E and R is a role
GROUP:OBI:<http://obi.sourceforge.net>
PERSON: Chris Mungall
role_of
adjacent_to
Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum
OBO_REL:0000012
relationship
C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
agent_in
relationship
OBO_REL:0000022
ro_bfo_bridge
contained_in
Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition):
relationship
OBO_REL:0000010
C contained_in C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
C contained_in C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.)
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
contains
relationship
OBO_REL:0000011
derived_into
OBO_REL:0000016
relationship
ro_bfo_bridge
derives_from
Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant.
ro_bfo_bridge
relationship
OBO_REL:0000015
derived_from
Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
derived_from
Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
has_agent
OBO_REL:0000021
ro_bfo_bridge
relationship
As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
As for has_participant, but with the additional condition that the component instance is causally active in the relevant process
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
has_improper_part
See reasons for obsoletion of improper_part_of
relationship
OBO_REL:0000024
has_integral_part
relationship
OBO_REL:0000005
has_part
relationship
OBO_REL:0000003
has_participant
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
OBO_REL:0000019
ro_bfo_bridge
relationship
P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
has_proper_part
relationship
OBO_REL:0000007
improper_part_of
OBSOLETE. The definition is "As for part_of, with the additional constraint that subject and object may be identical". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as "improper_part_of is part_of but not proper_part_of",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf]
relationship
OBO_REL:0000025
As for part_of, with the additional constraint that subject and object may be identical
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
As for part_of, with the additional constraint that subject and object may be identical
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
integral_part_of
relationship
OBO_REL:0000004
C integral_part_of C' if and only if: C part_of C' AND C' has_part C
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
C integral_part_of C' if and only if: C part_of C' AND C' has_part C
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
located_in
Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus
relationship
OBO_REL:0000008
ro_bfo_bridge
C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.)
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
location_of
ro_bfo_bridge
OBO_REL:0000009
relationship
part_of
Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell.
There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else
relationship
OBO_REL:0000002
For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.)
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
participates_in
relationship
OBO_REL:0000020
ro_bfo_bridge
preceded_by
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
ro_bfo_bridge
OBO_REL:0000017
relationship
P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
precedes
OBO_REL:0000018
relationship
ro_bfo_bridge
proper_part_of
OBO_REL:0000006
relationship
As for part_of, with the additional constraint that subject and object are distinct
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
As for part_of, with the additional constraint that subject and object are distinct
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
relationship
this relation was superfluous, so it has been obsoleted
relationship
A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances.
GOC:cjm
http://purl.org/obo/owl/GOC#GOC_cjm
A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances.
GOC:cjm
http://purl.org/obo/owl/GOC#GOC_cjm
transformation_of
When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.
ro_bfo_bridge
OBO_REL:0000013
relationship
Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2.
PMID:15892874
http://purl.org/obo/owl/PMID#PMID_15892874
transformed_into
Obsoleted
relationship
OBO_REL:0000014
ro_bfo_bridge
has measurement value
has_feature_value
James Malone
has_feature_value datatype proprty is used to describe the feature values which the feature class can contain, for example has_base can have feature values of nonNegativeInteger values.
conditional specification
OBI branch derived
OBI_0000349
PlanAndPlannedProcess Branch
instruction trigger
is a plan to carry out a process or an event if the trigger condition is fulfilled
measurement unit label
remove? See unit of measure.
A measurement unit label is an label that is part of a measurement datum and denotes a unit of measure.
Examples of measurement unit labels are liters, inches, weight per volume.
OBI_0000176
measurement unit label
person:Alan Ruttenberg
objective specification
IAO
OBI_0000217
Answers the question, why did you do this experiment?
Jennifer Fostel /Barry Smith
objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed. (note: achievement
objective specification
purpose of a study; support of hypothesis, discovery of new information
source pending
narrative object
group:OBI
OBI_0000013
A narrative object is an information content entity that is a set of propositions.
Examples of narrative objects are reports, journal articles, and patents submission.
agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
narrative object
person:Chris Stoeckert
artifact
There is not yet consensus this term
An artifact is an independent continuant that is the intended output of an objective driven process
label
A label is a symbol that is part of some other datum and is used to either partially define the denotation of that datum or to provide a means for identifying the datum as a member of the set of data with the same label
http://www.golovchenko.org/cgi-bin/wnsearch?q=label#4n
software
digital entity
group:OBI
OBI_0000261
A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
digital entity
person:Chris Stoeckert
journal article content
group:OBI
OBI_0000159
Examples of encodings of journal article content are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
Journal article content is a narrative object that is the information content encoded in a article published in a serious, scholarly publication, most often peer-reviewed.
journal article content
person:Alan Ruttenberg
person:Chris Stoeckert
information carrier
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
an information carrier is that quality of an information bearer that imparts the information content
Alan Ruttenberg
The pattern in ink on a page of a paperback novel.
material entity
binary digital entity
group:OBI
A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
MS Word document, ZIP file, DICOM file, JPEG file
OBI_0000244
binary digital entity
digital_entity
person:Chris Stoeckert
unit of measure
Smith, Ceusters, Ruttenberg, 2000 years of philosophy
The length of a ruler.
a unit of measure is the quality of some material entity compared to which another quality is some multiple of.
Alan Ruttenberg
programming language
group:OBI
A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
OBI_0000058
R, Perl, Java
person:Alan Ruttenberg
person:Chris Stoeckert
programming language
datum
Jonathan Rees
datum -- well, this will be very tricky to define, but maybe some
information-like stuff that might be put into a computer and that is
meant, by someone, to denote and/or to be interpreted by some
process... I would include lists, tables, sentences... I think I might
defer to Barry, or to Brian Cantwell Smith
symbol
Jonathan Rees
a smallish, word-like datum...
numeral
Jonathan Rees
a symbol that denotes a number
information content entity
OBI_0000142
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
information content entity
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
integer numeral
Jonathan Rees
a numeral that denotes an integer
information entity about a realizable
OBI branch derived
OBI_0000337
PlanAndPlannedProcess Branch
Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan
guide
instruction
is the specification of a plan that can be concretized and realized by an actor.
time trigger
OBI_0000331
OBI branch derived
PlanAndPlannedProcess Branch
revisit?
time trigger
conclusion
A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application.
Jennifer Fostel
OBI_0000005
conclusion
text based digital entity
group:OBI
A text based digital entity is a digital entity that is encoded so that it only contains text characters.
OBI_0000132
XML file, C++ source code file
digital_entity
person:Chris Stoeckert
text based digital entity
rule
OBI_0500021
MSI
PRS
PRS
a rule is an executable which guides, defines, restricts actions
example to be added
rule
algorithm
OBI_0000270
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
algorithm
an algorithm is a plan which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
software interpreter
group:OBI
OBI_0000199
A software interpreter is a generically dependent realizable entity that takes, as input, some digital entity, and takes action driven by the information content of that digital entity
Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
R program, Perl interpreter, Java virtual machine
person:Alan Ruttenberg
person:Chris Stoeckert
software interpreter
curation status specification
Better to represent curation as a process with parts and then relate labels to that process (in IAO meeting)
GROUP:OBI:<http://purl.obofoundry.org/obo/obi>
OBI_0000266
PERSON:Bill Bug
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
curation status specification
report of results
group:OBI
OBI_0000099
A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
person:Chris Stoeckert
report of results
report display element
group:OBI
OBI_0000001
A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
person:Alan Ruttenberg
person:Allyson Lister
report display element
binary executable
group:OBI
OBI_0000222
Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
binary executable
person:Jennifer Fostel
source code module
group:OBI
OBI_0000039
A source code module is an information content entity that specifies, using a programming language, some algorithm.
The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
person:Alan Ruttenberg
person:Chris Stoeckert
source code module
report table
group:OBI
A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
OBI_0000265
person:Alan Ruttenberg
person:Allyson Lister
report table
data format specification
A data format specification is the information content borne by the document published defining the specification.
blah:
for organizing information artifacts. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
OBI branch derived
OBI_0000187
PlanAndPlannedProcess Branch
data format specification
data set
group:OBI
OBI_0000042
A data set is an information content entity that is an aggregate of other information_content_entities that have something in common and are considered to form a unit.
data set
person:Allyson
person:Chris Stoeckert
image
group:OBI
An image is an information content entity which provides a visual representation of for the result of a measurement.
OBI_0000030
image
person:Allyson
person:Chris Stoeckert
plan specification
OBI_0000344
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
OBI branch derived
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
Part of range for an object property is_potentially_realizable_as in obi before split (LF 040907)
PlanAndPlannedProcess Branch
a plan specification is a specification of a process that an actor can engage in to achieve the objective specified as part of the plan
plan specification
digital document
group:OBI
OBI_0000195
A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
digital document
person:Jennifer Fostel
measurement datum
group:OBI
OBI_0000305
A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by an instrument.
Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}.
measurement datum
person:Chris Stoeckert
was measurement. (alan) Is this the old quantitative value? If so need to change cardinal part of stuff. I think the value and units should be on special relations and that the value should not be a BFO entity.
_identifier
_identifier is a container under information content entity for collecting types of terms to indicate a specific instance or clas of what was used or participated in an investigation. Identifiers are borne by a product or its packaging, and can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
Note: everybody agreed that identifier is probably a too general term. We however felt that it would be appropriate to group "identifiying" terms under some kind of umbrella. We therefore propose to use _identifier for that purpose. As per OBI conventions, the _ prefixing identifier indicates that this is a helper class and shouldn't be considered as final.
version number
Note: we feel that at the moment we are happy with a general version number, and that we will subclass as needed in the future. For example, see 7. genome sequence version
A version number is an information content entity which is a sequence of characters borne by part of each of a class of manufactured products or its packaging and indicates its order within a set of other products having the same name.
serial number
A serial number is an information content entity which is a unique sequence of characters borne by part of manufactured product or its packaging that is assigned to each individual in some class of products, and so can serve as a way to identify an individual product within the class. Serial numbers can be encoded in a variety of other information objects, such as bar codes, numerals, or patterns of dots.
Note: during the call there was some confusion between serial number and model number. We agreed that it would be very helpful for all those terms to have example of usages - please add if you have any :-)
lot number
batch number
A lot number is an information content entity which is an identical sequence of character borne by part of manufactured product or its packaging for each instances of a product class in a discrete batch of an item. Lot numbers are usually assigned to each separate production run of an item. Manufacturing as a lot might be due to a variety of reasons, for example, a single process during which many individuals are made from the same portion of source material. Lot numbers can be encoded in a pattern of other information objects, such as bar codes, numerals, or patterns of dots.
setting datum
Alan grouped these in placeholder for the moment. Name by analogy to measurement datum.
A settings datum is a datum that denotes some configuration of an instrument.
digital quality
Need to rework digital entity. Digital quality was suggested by Barry.
material information bearer
An information bearer is an artifact, such as a hard drive, upon which an information content entity generically depends.
obsolete_report display element
group:OBI
A report display element is a narrative object that is part of a report. Report display elements are set off from the textual parts of a report and are typically given a label(e.g. Figure 2) which is used to refer to the element from the text. Typically the 2d layout is part of the identity of such elements.
There will be some issue here about whether these are defined classes. As intended these are meant to denote the parts of the report that are not textual but are typically boxed and set within the text, labelled with some identifier, and referred to in the text
person:Alan Ruttenberg
person:Allyson Lister
replaced by IAO_0000091
report display element
study population role
Jennifer Fostel
Study population
obsolete_Statistical factor
Jennifer Fostel
Statistical factor
Statistical factor is an outcome role consisting of being a variable used in the main analysis of the study
example_of_usage to be added
source pending
role of being first subject screened
First person interviewed about study enrollment criteria
First subject screened
First subject screened is a potential study participant role played by a single individual first to have the inclusion / exclusion criteria applied
Jennifer Fostel
first subject screened. First subject who signs the informed consent form and is screened for potential enrollment and randomization into a study, but has not yet been determined to meet the inclusion/exclusion criteria for the trial. who signs the informed consent form and is screened for potential enrollment and randomization into a study, but has not yet been determined to meet the inclusion/exclusion criteria for the trial.
obsolete_Conclusion
A conclusion is a narrative object which can be published in a paper summerizing and interpreting a protocol application.
Conclusion
Jennifer Fostel
example_of_usage to be added
replaced by IAO_0000035
source pending
role of being consumer safety officer
Consumer safety officer; Consumer Safety Officer Positions at FDA http://69.20.19.211/jobs/cso.htm
FDA official who coordinates the review
Jennifer Fostel
OBI, CDISC
Person charged with serving as CSO
obsolete_Surrogate marker
CDISC definition: surrogate marker. A measurement of a drug's biological activity that substitutes for a clinical endpoint such as death or pain relief.
Jennifer Fostel
Surrogate marker
Surrogate marker is an indirect experimental factor role assigned to a variable shown to be a substitute for an adverse reaction
Transcript level changes associated with cancer outcomes
source pending
obsolete_Experimental factor
A variable is a Study role assigned to a particular measurable or observable outcome; also marker, biomarker, biological marker
Dosage; time of exposure; serum ALT level; blood pressure
Experimental factor
Experimental factor is a role played by any study variable which is hypothesized to contribute to a study outcome, such as (1) a protocol parameter which is systematically or deliberately varied within the study or (2) selection of study participants with different characteristics or that are from different environments
Jennifer Fostel
source pending
technology provider role
CDISC definition: technology provider. A person, company or other entity who develops, produces and sells software applications and/or hardware for use in conducting clinical trials and/or in analyzing clinical trial data and or submitting clinical trial information for regulatory approval
Jennifer Fostel
Technology provider
Technology provider is a supplier who provides software, instruments or computational devices used in a study; this role generally occurs before the study, but could occur during the study
fluorescent reporter intensity
group:OBI
From the DT branch: This term and definition were originally submitted by the community to our branch, but we thought they best fit DENRIE. However we see several issues with this. First of all the name 'probe' might not be used in OBI. Instead we have a 'reporter' role. Also, albeit the term 'probe intensity' is often used in communities such as the microarray one, the name 'probe' is ambiguous (some use it to refer to what's on the array, some use it to refer to what's hybed to the array). Furthermore, this concept could possibly be encompassed by combining different OBI terms, such as the roles of analyte, detector and reporter (you need something hybed to a probe on the array to get an intensity) and maybe a more general term for 'measuring intensities'. We need to find the right balance between what is consistent with OBI and combinations of its terms and what is user-friendly. Finally, note that 'intensity' is already in the OBI .owl file and is also in PATO. Why didn't OBI import it from PATO? This might be a problem.
The fluorescent reproter intensity is a datum that represents the output of a scanner measuring the intensity value for each fluorescent reporter.
fluorescent reporter intensity
person:Chris Stoeckert
objective driven process
Bjoern Peters
I (BP) felt the need for this upper class, as processes like planning or interpreting data clearly have an objective but do not have a plan. This distinction may get tricky.
is a process which is initiataed by one or more human participants with an overall objective they wish to achieve. The participantes do not necessarily have to have a plan how to achieve it.
obsolete_organization_role
general consensus is that organization_role is not correct; we need organization as an entity. Feb 29, 2008
obsolete_narrative object
group:OBI
A narrative object is an information content entity that is a set of propositions.
Examples of narrative objects are reports, journal articles, and patents submission.
agree - DENRIE. Issue(alan) do we only mean text? What about a story told by mime. Does music count? (no) what about an oral report. Regarding definition, saying it is a set of propositions means we loose the idea that wording matters. Maybe adjust saying a narrative object has some relationshop to a set of propositions
narrative object
person:Chris Stoeckert
replaced by IAO_0000006
regulator role
Fact sheet - Regulating the companies The role of the regulator. Ofwat is the economic regulator of the water and sewerage industry in England and Wales. http://www.ofwat.gov.uk/aptrix/ofwat/publish.nsf/Content/roleofregulator_factsheet170805
Jennifer Fostel
OBI
Regulator
Regulator role is a regulatory role involved with making and/or enforcing relevant legislation and governmental orders
biological feature identification objective
Biological_feature_identification_objective is an objective role carried out by the proposition defining the aim of a study designed to examine or characterize a particular biological feature.
Jennifer Fostel
biological feature identification objective
example_of_usage to be added
source pending
regulation-assigned role
Approval letter
Jennifer Fostel
Regulation-assigned role
Regulation-assigned role is a regulatory role defined by legislation or governmental orders
regulatory role
Jennifer Fostel
OBI, CDISC
Regulatory agency, Ethics committee, Approval letter; example: Browse these EPA Regulatory Role subtopics http://www.epa.gov/ebtpages/enviregulatoryrole.html Feb 29, 2008
Regulatory role
Regulatory role is a role of making, enforcing or defined by legislation or orders issued by a governmental body.
govt agents responsible for creating regulations; proxies for enforcing regulations. CDISC definition: regulatory authorities. Bodies having the power to regulate. NOTE: In the ICH GCP guideline the term includes the authorities that review submitted clinical data and those that conduct inspections. These bodies are sometimes referred to as competent
supplier role
CDISC definition: Supplier. An organization that enters into a contract with the acquirer for the supply of a system, software product, or software service under the terms of a contract.
Jennifer Fostel
Supplier
Supplier is a worker who provides reagents, subjects and other materials used in a study; this role generally occurs before the study, but could occur during the study
example_of_usage to be added
source pending
obsolete_radioactive
OBI Biomaterial derived
Philippe Rocca-Serra
a quality of chemical entity which indicates its ability to desintegrate and emit energetic particles (photon, electron, neutron)
chromium 51 is a radioactive isotope of chromium
contract research organization role
Contract research organization
Contract research organization is a worker role of carrying out the study according to the protocol document or study plan delivered by the PI, under the control of the study director. This role cannot make decisions about the study execution
Jennifer Fostel
list-mode data file
group:Flow Cytometry community
A list-mode data file is a digital entity where events are stored sequentially, parameter by parameter.
An example of a list-mode data file is a file following list-mode Flow Cytometry Standard (FCS) format. Since FCS files can be in histogram mode or list-mode we have to specify which data format specifically. List-mode format in the overwhelming (even universal) option used.
One example of usage is in the context of flow cytometry, however is not restricted to this community and is more widely used, e.g. by imaging people.
list-mode data file
person:Chris Stoeckert
specified_input_role
OBI
data can be an entity that plays an input role
examples include a scale and mouse play input role in a process to determine weight; reagents for measuring glucose and a specimen of blood have input role in a glucose-measuring assay.
Specified input role is a study participant role which is played by an entity at the beginning of a process and which is specified as input to the process.
role of data or material entity played at the start of a process; must be specified.
reagents for measuring glucose and a specimen of blood are inputs in a glucose-measuring assay.
the input must be specified, for example, the reagents will be in tubes which aslo contain air; the air is not an input unless it is specified in the assay protocol
specified_output_role
OBI
data can be an entity that plays an output role
Specified output role is a study participant role which is played by an entity at the end of a process and which is specified as output to the process
The role must be specified by the process protocol. Example, in an assay measuring glucose in blood, the blood specimen is input to the assay, and is discarded after the assay. In this case, unless the blood is sepcified as an output of the assay it does not play the role output role.
obsolete_Data transformation role
Data transformation role
Data transformation role is a role whereby a data analysis entity is transformed into a different data analysis entity
Integrated dataset, normalized dataset, clustered dataset
Jennifer Fostel
source pending
reference substance role
Calibration standard, positive control substance, vehicle Good Laboratory Practices: Questions and Answers - Test Control and Reference Substance Characterization http://www.epa.gov/enforcement/monitoring/programs/fifra/glpqanda-character.html
Jennifer Fostel
OBI
Reference substance
Reference substance is a reference role in which the characteristics or responses elicited by the substance playing the reference substance role are used for comparison or reference.
cytological stain role
Cytological stain
Jennifer Fostel
report figure
group:OBI
A report figure is a report display element that has some aspect of illustration, but may be a composite of figures, images, and other elements
I prepended the 'report ' to make it clear that we mean parts of reports here. We may want a more generic version of 'figure', in which case this would become a defined class - figure and part_of some report
person:Alan Ruttenberg
person:Allyson Lister
report figure
patent content
group:OBI
A patent content is a report for the purpose of obtaining a license from a government conferring for a set period the sole right to make, use, or sell some process or invention
need to distinguish the patent submission (which I think the term refers to) and the patent itself, which is what confers the rights. (Alan) Renamed from patent to patent submission. [Isn't the submission like a recipe, i.e. a realizable information entity, in that it tells you how to do something? no] Cristian: what is the difference b/w some document that has been patented, and the same document that has not been patented? The (informational) content is the same. It is just that the former has been encapsulated within some social mechanism, hence it has acquired some role. Hence 'patent' is a role.
patent content
person:Chris Stoeckert
pellet role
a pellet role is a biological specimen role in which the specimen is separated into two parts
obsolete_image
group:OBI
An image is an information content entity which provides a visual representation of for the result of a measurement.
image
person:Allyson
person:Chris Stoeckert
replaced by IAO_0000101
obsolete_Time interval variable
A time course study design
Jennifer Fostel
Time interval variable
Time interval variable is a direct experimental factor in which the varying parameter is a time interval describing the time of exposure of study participants to a treatment, intervention or other perturbational protocol.
source pending
clinical research coordinator role
A clinical research coordinator is a worker role comprised of handling the administrative duties of a trial or study.
Clinical research coordinator
Jennifer Fostel
obsolete_sex_effect
A variable in an experiment that is designed to look at differences between organisms of different genders, mating types etc.
supernatant role
_cloning placeholder
OBI branch derived
Place holder class, see editor note
Placeholder class. The terms beneath this need to play nice with each other. Needs to be done by someone with cloning experience
PlanAndPlannedProcess Branch
_cloning placeholder
Global assessment variable
CDISC definition: global assessment variable. A single variable, usually a scale of ordered categorical ratings, which integrates objective variables and the investigator's overall impression about the state or change in state of a subject.
Global assessment variable
Global assessment variable is a finding describing in a categorical variable the investigator's overall impression about the state or change in state of a subject.
Jennifer Fostel
example_of_usage to be added
source pending
vitamin role
Jennifer Fostel
Vitamin
thiamine; A vitamin is an organic compound required as a nutrient in tiny amounts by an organism Wikipedia, March 2008
chromatography column
Column chromatography in chemistry is a tube (typically glass) used to purify individual chemical compounds from mixtures of compounds. It is often used for preparative applications on scales from micrograms up to kilograms.
Frank Gibson
chromatography column
example_of_usage to be added
http://en.wikipedia.org/wiki/Column_chromatography
obsolete_source code module
group:OBI
A source code module is an information content entity that specifies, using a programming language, some algorithm.
The written source code that implements part of an algorithm. Test - if you know that it was written in a specific language, then it can be source code module. We mean here, roughly, the wording of a document such as a perl script.
person:Alan Ruttenberg
person:Chris Stoeckert
replaced by IAO_0000096
source code module
drug role
Drug role
Drug role is a role assigned to an entity by a regulatory agency that is designed to diagnose, treat or prevent an abnormal medical condition
Jennifer Fostel
OBI, CDISC
pump valve switch
A pump valve switch is a cardinal part of a liquid chromatography instrument that controls the flow.
FG:I would assume this should be a pump valve control switch and it would not be specific to a liquid chromatography instrument
OBI
OBI Instrument branch
example_of_usage to be added
pump valve switch
obsolete_data set
group:OBI
A data set is an information content entity that is an aggregate of other information_content_entities that have something in common and are considered to form a unit.
data set
person:Allyson
replaced by IAO_0000100
xenotransplantation
OBI branch derived
PlanAndPlannedProcess Branch
is the transplantation of living cells, tissues or \norgans from one species to another such as from pigs to humans
xenotransplantation
physical document
OBI
a book is a physical document
A physical document is an object serving as a record of information by means of symbolic marks.
BP: moved and renamed for BFO
information_content_entity "is_encoded_in" some physical_document in obi before split (040907).
waiting
BP: I have doubts about the utility of this.
OBI branch derived
PERSON:Alan Ruttenberg
We need a better handling/modeling of time (January 2008)
not actively doing anything to a material for a duration of time.
waiting
obsolete_non-realizable information entity
IAO
group:OBI
A non-realizable information entity is a generically dependent continuant which conveys meaning that can be communicated but whose meaning does necessarily imply that some process might follow from that meaning.
An essay on the history of the euro. Contrast: A recipe to bake a bread
person:Alan Ruttenberg
replaced by IAO_0000100
top level
artifact object
An artefact_object is an object that is produced or shaped by human craft, especially a tool, weapon, or ornament of archaeological or historical interest, i.e. something that is manufactered.
Examples include the siblings of device and other objects such as gel matrices; used in gel electrophoresis, filter paper, parafilm and buffer solutions.
Frank Gibson
artifact object
editor_note pending
http://www.answers.com/artefact
chromatography device
chromatography instrument
A Chromatography device is a device that facilitates the separation of mixtures. The function of a chromatography device involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture and allows it to be isolated.
Frank Gibson
chromatography device
http://en.wikipedia.org/wiki/Chromatography
mass spectrometer
A mass spectrometer is an instrument which is used to measure the mass to charge ratio of ions. All mass spectrometers consist of three basic parts: an ion source, a mass analyzer, and a detector system. The stages within the mass spectrometer are: 1. Production of ions from the sample 2. Separation of ions with different masses 3. Detection of the number of ions of each mass produced 4.Collection of data to generate the mass spectrum
Frank Gibson
LCQ Fleet Ion Trap MSn manufactured by thermo fisher scientific
http://en.wikipedia.org/wiki/Mass_spectrometry
mass spectrometer
platform
OBI Instrument branch
OBI Instrument branch
platform
A platform is an object_aggregate that is the set of instruments and software needed to perform a process. definition_source: OBI.
rem1: We decided at the Philly workshop that consumables do not include reagents.
FG: we could actully add a relation to platform which would be "has_part some instrument"
DS: Sounds fine to me, with the restriction that I would assume a min. cardinality of 2 to be applicable for this crossproduct, so at least 2 instruments make it a platform... at least one is not enough
AR:has_part is transitive, and transitive properties can't have cardinality constraints in OWL-DL. We can always put this particular constraint in the owl-full file.
We need to make this a defined class when the class software is in the ontology
liquid chromatography mass spectrometry platform
OBI Instrument branch
OBI instrument branch
liquid chromatography mass spectrometry platform
A liquid chromatography mass spectrometry platform is a platform that is the collection of instrument, software and reagents needed to perform a liquid chromatography mass spectrometry protocol. definition_source: OBI.
microarray platform
OBI Instrument branch
OBI Instrument branch
microarray platform
A microarray platform is a platform that contains the instruments, software and reagents needed to perform a microarray protocol. definition_source: OBI.
antibody role
Antibody
Jennifer Fostel
ratio of collected to emitted light
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
10%
A ratio of collected to emitted light is a datum measuring the amount of light collected s compared to the total amount of emitted light in the detector component of a flow cytometer instrument. The datum has a qualitative role
person:Chris Stoeckert
person:Kevin Clancy
quantity
ratio of collected to emitted light
software optimization
Jennifer Fostel
Software_optimization is a software_testing_objective role describing a study designed to identify the best software or parameters of the software.
example_of_usage to be added
software optimization
source pending
Notified_Body role
Jennifer Fostel
Notified Body
Notified Body (NB). A private institution charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive. This process, called Conformity Assessment, has EU-wide validity once completed by the NB.
Notified body is regulator of consumables and medical devices charged by the Competent Authority with verifying compliance of medical devices (not drugs) with the applicable Essential Requirements stated in the Medical Device Directive
OBI, CDISC
The role of notified bodies presentation: http://ec.europa.eu/enterprise/electr_equipment/emc/revision/notified_bodies.pdf
allotransplantation
OBI branch derived
PlanAndPlannedProcess Branch
allotransplantation
is the transplantation of organs between members of the same species.
obsolete_programming language
group:OBI
A language in which source code is written, intended to executed/run by a software interpreter. Programming languages are ways to write instructions that specify what to do, and sometimes, how to do it.
R, Perl, Java
person:Alan Ruttenberg
person:Chris Stoeckert
programming language
replaced by IAO_0000025
gamma counter
A gamma counter is an instrument which measures gamma radiation emitted by a radionuclide.
Frank Gibson
gamma counter
http://en.wikipedia.org/wiki/Gamma_counter
trial monitor role
CDISC definition: Person employed by the sponsor or CRO who is responsible for determining that a trial is being conducted in accordance with the protocol and GCP guidance. NOTE: A monitor's duties may include, but are not limited to, helping to plan and initiate a trial, assessing the conduct of trials, and assisting in data analysis, interpretation and extrapolation. Clinical Research Associate: Primary representative of the sponsor; monitors progress of investigator sites participating in a clinical study.
Jennifer Fostel
Trial monitor
Trial monitor is a responsible party involved in planning, overseeing the conduct of a study or study component, and interpreting data from a study
obsolete_Surgical intervention
Jennifer Fostel
Surgical intervention
Surgical intervention device is an intervention variable in which the varying parameter is a surgical procedure or medical device
Test of a new pacemaker
source pending
obsolete_Environmental characteristic variable
Environmental characteristic variable
Environmental characteristic variable is a direct experimental factor (role) in which the component which varies is a part of the environment or the environmental history of study participants
Jennifer Fostel
Varying the collection location for environmental samples in study of chromium levels and effects
source pending
obsolete_Reference medical device
Insertion of approved cardiac pace maker
Jennifer Fostel
Reference medical device
Reference medical device is a reference treatment used in a clinical investigation of medical device behavior; it is played by an approved medical device.
source pending
positive reference substance role
Jennifer Fostel
MMS mutagen
Positive reference substance
polyethylene glycol p-(1,1,3,3-tetramethylbutyl)-phenyl ether
PMID: 30799. J Histochem Cytochem. 1978 Sep;26(9):696-712. Acid lipase: a histochemical and biochemical study using triton X100-naphtyl palmitate micelles.
Philippe Rocca-Serra
adapted from Wikipedia before possible import from CHEBI
triton X100 is a chemical entity which belongs to the group of The pluronics which are triblock copolymers of ethylene oxide and propylene oxide. Triton x-100 is_used_as detergent due to its non-ionic surfactant properties
investigation
this definition is meant to clarify what differentiates an investigation from a single protocol_application
Altdef: A set of studies that are designed to address a related question. It may include individual studies that are domain specific(?) , microarray, proteomics.
An investigation is a planned process with the objective to generate an
'information entity of scientific value' by planning protocol applications, carrying them out and documenting the results. In addition, an investigation can include a sub process of interpreting the data to draw conclusions.
Bjoern Peters
OBI branch derived
investigation
evaluant role
Evaluant role is a specified input role played by an entity in an assay such that the output data describes a feature of the material entity playing the evaluant role
Role call - 17nov-08: JF and MC think an evaluant role is always specified input of a process. Even in the case where we have an assay taking blood as evaluant and outputing blood, the blood is not the specified output at the end of the assay (the concentration of glucose in the blood is)
a specimen of blood was assayed for glucose (output data = glucose concentration); a specimen of liver was assayed using microarray for gene expression levels (output data = gene expression data + MIAME annotation); a specimen of soil was assayed for heavy metal concentration.
evaluant role
examples of features that could be described in an evaluant: quality.... e.g. "contains 10 pg/ml IL2", or "no glucose detected")
reporting party role
Jennifer Fostel
OBI
Reporting party
Reporting party role is a study personnel role played by a party who reports the outcome of a study component
The first section has been pre-designated as the “Reporting Party” section and should be filled with the Reporting Party’s personal information. http://www.mercedsheriff.com/SelfReporting.htm
protocol application
A protocol application is a process carried out to bring about the objective defined in the protocol applied. Every protocol_application has one or more inputs and outputs definition_source: OBI. a protocol_application is a planned process realizes a process in which the objective of the protocol is achieved. The manipulation of materials and information on materials as part of an investigation
OBI
PlanAndPlannedProcess Branch
protocol application
protocol_application part_of_process some sample_preparation_for_assay in obi before split (LF 040907)
rem1: This is an actual part of the experiment. It includes the protocol that the experimenter intends to carry out, deviations from this and unintended variables, such as the earthquake that occurred while the experiment was taking place.
assay
AltDef: An assay is a protocol application which is a process of measuring. rem1: Imaging is covered by this definition. rem2: material: used in the context of studying some biological problem, example: hybridization
An assay is a process with the objective to create as an output information about a material entity (bearing evaluant role).
OBI branch derived
PlanAndPlannedProcess Branch
assay
quantitative confidence value
group:OBI
A quantitative confidence value is a information content entity which is used to indicate the degree of uncertainty about a measurement.
person:Chris Stoeckert
quantitative confidence value
obsolete_parameter_value_application
OBI
A parameter value application is part of a protocol application in which the values of the parameter are set.
Setting the centrifuge to 1200 RPM.
sample preparation for assay
A sample_preparation_for_assay is a protocol_application including material_enrollments and biomaterial_transformations. definition_source: OBI.
Nutrigenomics
OBI branch derived
PlanAndPlannedProcess Branch
move to defined class
rem1: the 'relates to a set of biological materials' covers environmental samples and data
sample preparation for assay
study
Hypothesis
Darwin's theory of evolution
Hypothesis
Hypothesis is a role played by a proposition describing a reasoned proposal suggesting a possible correlation between multiple phenomena.
Jennifer Fostel
discussion on the tracker
http://sourceforge.net/tracker/index.php?func=detail&aid=1887478&group_id=177891&atid=886178
source pending
Diagnosis
Diagnosis
Diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
Jennifer Fostel
The act or process of identifying or determining the nature and cause of a disease or injury through evaluation
example_of_usage to be added
source pending
spontaneous process
OBI
An extraneous process is a process which is external in origin to the investigation that has an impact on the outcome.
Earthquake that destroys the lab, an outside investigator discovering an adverse effect of the reagants used
role of being member of special population
CDISC Definition: special populations. Subsets of study populations of particular interest included in clinical trials to ensure that their specific characteristics are considered in interpretation of data [e.g., geriatric].
Geriatric subset of eligible population
Jennifer Fostel
Special population
Special population is an eligible population role played by a population with characteristics that make it especially important to target for enrollment
eMedical record
article-without-pmid-or-doi:CDISCglossary
An eMedical record is a digital document derived from a computer system used primarily for patient care in a clinical setting. Not required to be compliant with requirements of 21 CFR Part 11.
eMedical record
person:Jennifer Fostel
culture medium role
A growth medium or culture medium is a substance in which microorganisms or cells can grow. Wikipedia, growth medium, Feb 29, 2008
Culture medium
Jennifer Fostel
OBI
obsolete_information artifact
IAO
BFO to do
BFO to do
PlanAndPlannedProcess Branch
replaced by IAO_0000030
obsolete_Psychological intervention
Jennifer Fostel
Psychological intervention
Psychological intervention is an intervention variable in which the varying parameter is a psychological therapy
Test of new psychological therapy
source pending
role of acclimating subject
Acclimating potential subject is a potential subject kept in controlled physical conditions prior to the study
Acclimating subject
Fish captured in the wild being acclimated to the housing conditions of the laboratory; lab animals being temporally progressed so that their night occurs during normal daylight hours
Jennifer Fostel
electronic case report tabulation
CDISC glossary
An electronic case report tabulation is a digital document containing tabular data about multiple trial participants which is part of a clinical regulatory submission. An eCRT has the property that it can be audited and compliant with requirements of 21 CFR Part 11 and has format suited to review by regulators.
electronic case report tabulation
person:Jennifer Fostel
polystyrene tube
OBI
definition pending
editor_note pending
example_of_usage to be added
polystyrene tube
scintillation_tubes
source pending
concretized protocol
BFO to do
OBI branch derived
PlanAndPlannedProcess Branch
concretized protocol
reagent role
Reagent role is a study participant role played by a biological or chemical entity used to produce a chemical reaction to detect, measure, and produce other substances
www.answers.com/topic/reagent; November 2008
Jennifer Fostel
Reagent
obsolete_Metabolite
A metabolite is a role characterized by being the product of catabolism or metabolism by a living organism
Jennifer Fostel
Metabolite
N-acetyl-benzoquinoneimine (NAPQI) produced from acetaminophen
output of a process
output of a process
source pending
administrative unit role
Administrative unit
Administrative unit is a study personnel role consisting of scientific and support personnel who are engaged in carrying out a biomedical or biological investigation and are members of a biomedical organization such as a hospital. This role occurs during the study timeline although the biomedical organization and membership exists before and after the study.
Generally, a local administrative unit (LAU) is an area of governmental administration below a province, region, state or other major national subdivision. Wikipedia march 2008
Jennifer Fostel
OBI
role of regulator of chemical manufacture
A regulator of chemical manufacture is a regulator involved with making and enforcing legislation and governmental orders relevant to chemical manufacture
EPA; John Mollison is the registrar of chemical products in Tasmania, the body that administers the Act that regulates chemical use in that State. http://www.abc.net.au/rn/science/earth/stories/s1160346.htm
Jennifer Fostel
OBI
Regulator of chemical manufacture
treated role
detector reagent role
role of being certified IRB professional
CIP= Certified IRB Professional; http://acronyms.thefreedictionary.com/Certified+IRB+Professional
Certified IRB Professional
Jennifer Fostel
patient role
CDISC definition: patient. Person under a physician's care for a particular disease or condition. NOTE: A subject in a clinical trial is not necessarily a patient, but a patient in a clinical trial is a subject. See also subject, trial subject, healthy volunteer. Often used interchangeably
Jennifer Fostel
OBI, CDISC
Patient
Patient is a role played by a person under the care of a physician or health care provider
a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778
material transformation
A material transformation is a protocol_application carried out to generate output material from the input material
Bjoern Peters
OBI branch derived
a material_application is protocol_application which has the objective to
produce output material(s) from input material(s)
material transformation
we may not need this one in the long term, and just keep the children? (TC 14 June)
obsolete_number
A number is an information content entity which provides a magnitude for the result of a measurement.
PERSON:Chris Stoeckert
Was 'value'
protocol testing objective
Jennifer Fostel
Protocol_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different protocols.
example_of_usage to be added
protocol testing objective
source pending
study subject role
Jennifer Fostel
Study subject
Study subject is a Study participant role that is played by the objects of the study during the study timeline. In most cases, a study subject is considered to be a population representative
subject/trial subject. An individual who participates in a clinical trial, either as recipient of the investigational product(s)) or as a control. [ICH] See also healthy volunteer, human subject.; human subject. Individual who is or becomes a participant in research, either as a recipient of the test article or as a control. A subject may be either a healthy human or a patient. [21 CFR50.3]. Synonym: subject/trial subject.
obsolete__biomaterial(deprecated)
A biomaterial entity is an object of biological origin. definition_source: OBI.
Alan Ruttenberg
Bjoern Peters
Daniel Schober
Domain of an object property "has_role_which_can_only_be_played_by_biomaterial_entity" in obi before split, Range: ?role_which_can_only_be_played_by_biomaterial_entity (LF 040907).
Helen Parkinson
James Malone
Jennifer Fostel
Melanie Courtot
Philippe Rocca-Serra
Susanna Sansone
Tina Boussard
_biomaterial(deprecated)
_biomaterial(deprecated)
call Jan11 2008: Proposal to keep Biomaterial as name of the branch, but with the following definition: object and has_role (sample role or reagent role).. While Device would be an object and ((has_role some instrument_role) or (has_part some (has_role some instrument_role)))
example_of_usage to be added
obsolete_report of results
group:OBI
A report is a narrative object that is a formal statement of the results of an investigation, or of any matter on which definite information is required, made by some person or body instructed or required to do so.
Examples of reports are gene lists and investigation reports. These are not published (journal) articles but may be included in a journal article.
disagreement about where reports go. alan: only some gene lists are reports. Is a report all the content of some document? The example of usage suggests that a report may be part of some article. Term needs clarification
person:Chris Stoeckert
replaced by IAO_0000065
report of results
role of being first subject treated
First subject treated
First subject treated is a subject role played by the subject first to have treatment applied
Jennifer Fostel
Rat 1A; first enrolled patient to receive treatment
first subject treated. First subject who receives the test article or placebo in a clinical trial.
measured expression level
OBI Data Transformation branch
A measured expression level is a datum that is the outcome of the quantification of an assay for the activity of a gene, or the number of RNA trancsripts.
Examples are quantified data from an expression microarray experiment, PCR measurements, etc.
measured expression level
person:Chris Stoeckert
responsible party role
A responsible party role is a study personnel role played by a party who is accountable for the execution of a study component and can make decisions about the conduct of the study
Jennifer Fostel
OBI
Responsible party
he THERAPIST has the ability to print a separate statement for the patient and each responsible party. http://www.beaverlog.com/therapist/ez_support/billing/responsible_party_statements.htm
principal investigator role
CDISC definition: A person responsible for the conduct of the clinical trial at a trial site. If a trial is conducted by a team of individuals at a trial site, the investigator is the responsible leader of the team and may be called the principal investigator. 2. The individual principal investigator. 2. The individual under whose immediate direction the test article is administered or dispensed to, or used involving, a subject, or, in the event of an investigation conducted by a team of individuals, is See also sponsor-investigator.; Leiter der klinischen Prufung.Under the German Drug Law, the physician who is head of the clinical investigation (CDISC): coordinating investigator (CDISC) (also study coordinator, MUSC); sponsor-investigator. An individual who both initiates and conducts, alone or with others, a clinical trial, and under whose immediate direction the investigational product is administered to, dispensed to, or used by a subject.NOTE: The term does not include any person other than an individual, hence not a corporation, agency (CDISC)
Jennifer Fostel
Principal investigator
Principal investigator is a responsible party role played by a person responsible for the overall conduct of a study
protocol application role
transplantation
OBI branch derived
PlanAndPlannedProcess Branch
a protocol application to replace an organ or tissue of an organism
transplantation
role of being vulnerable subject
Jennifer Fostel
Person who believes the trial medication will cure them of cancer
Vulnerable subject
Vulnerable subject is a potential study participant role characterized by being unduly influenced by the expectation that participation in the trial will provide direct benefit
vulnerable subjects. Individuals whose willingness to volunteer in a clinical trial may be unduly influenced by the expectation, whether justified
obsolete_variables
Jennifer Fostel
Variables are specifications, part of plan
obsolete_Sham treatment
Jennifer Fostel
Sham treatment
Sham treatment is a reference treatment designed to mimic the harmless portion of an intervention; e.g. treatment with vehicle alone, placebo or sham surgery.
Shave animals but do not apply treatment to skin
source pending
biological vector role
1983 Sci. Amer. Jan. 58/2 Plasmids are routinely used as vectors for introducing foreign DNA into bacteria.
Some epidemiological aspects and vector role of tick infestation on layers in the Faisalabad district (Pakistan). http://journals.cambridge.org/action/displayAbstract;jsessionid=0373164489D00868AEEF2C556EB4FD29.tomcat1?fromPage=online&aid=624280
pH indicator dye role
Jennifer Fostel
pH indicator dye
phenol red in RPMI; pH=4 indicator dye (also carries reference role)
study participant role
Jennifer Fostel
Study participant
Study participant is a role of actual or potential entities of, used in or produced by a study; NB: this does not include the study personnel who perform the study
biological specimen role
sequence feature identification objective
Jennifer Fostel
Sequence_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features exhibited at the level of a macromolecular sequence, e.g. nucleic acid, protein, polysaccharide.
example_of_usage to be added
sequence feature identification objective
source pending
clinical laboratory role
Clinical laboratory
Clinical laboratory is a worker role involved in carrying out assay protocols on specimens derived from a study; this activity occurs outside the study timeline
Jennifer Fostel
intervention design
OBI branch derived
PMID: 18208636.Br J Nutr. 2008 Jan 22;:1-11.Effect of vitamin D supplementation on bone and vitamin D status among Pakistani immigrants in Denmark: a randomised double-blinded placebo-controlled intervention study.
Philppe Rocca-Serra
an intervention design is a study design in which treatments (perturbations or intervention) defined as a combination of values taken by independant variable manipulated by the experimentalists are applied to the recruited subjects assigned (possibly by applying specific methods) to treatment groups. The specificity of intervention design is the fact that independent variables are being manipulated and a response of the biological system is evaluated via response variables as monitored by possibly a series of assays.
intervention design
worker role
Jennifer Fostel
OBI
Public sector workers in states that run their own OSHA programs are covered by those states. http://www.osha.gov/as/opa/worker/index.html
Worker
Worker is a personnel role played by a party who executes a component of the study plan; this can occur before, during, after or outside the study timeline
Bernoulli trial
Bernoulli trial
OBI branch derived
PlanAndPlannedProcess Branch
is an assay where the output data is a datum with one of two values denoted success and failure.
gene list
group:OBI
A gene list is a report of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis.
Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis.
gene list
kind of report. (alan) need to be careful to distinguish from output of a data transformation or calculation. A gene list is a report when it is published as such? Relates to question of whether report is a whole, or whether it can be a part of some other narrative object.
person:Chris Stoeckert
number of particles in subset
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
500, 200, 0
A number of particles in subset is a datum measuring the the number of subjects in a defined subset in a flow cytometer instrument. The datum has a qualitative role
number of particles in subset
person:Kevin Clancy
quantity
Finding
CDISC definition: a meaningful interpretation of data or observations resulting from planned evaluations.
Finding
Finding is an assessment of data, observations or evaluations from a clinical study which can be used to form a diagnosis
Jennifer Fostel
example_of_usage to be added
source pending
obsolete_High-level analysis
Examples: (a) Clustering of microarray data for class discovery; (b) Identification of differentially expressed genes.
High-level analysis
High-level analysis is a data transformation role which results in conclusions drawn from a data analysis element
Jennifer Fostel
source pending
obsolete_Mock surgery
Jennifer Fostel
Liver sparing sham hepatectomy
Mock surgery
Mock surgery is a sham treatment designed to imitate the harmless portion of a surgical intervention
source pending
dot plot
group:OBI
A dot plot is a report graph which is a graphical representation of data where each data point is represented by a single dot placed on coordinates corresponding to data point values in particular dimensions.
Dot plot of SSC-H and FSC-H.
dot plot
generically_dependent_continuants
person:Allyson
person:Chris Stoeckert
role of being healthy volunteer
Healthy volunteer
Healthy volunteer is a potential study participant role played by a person who is healthy in all aspects relevant to the trial
Jennifer Fostel
Person with controlled diabetes but high blood pressure (with respect to a study of blood pressure therapy)
volunteer. A person volunteering to participate as a subject in a clinical trial, often a healthy person agreeing to participate in a Phase 1 trial. See
number of lost events electronic
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
74, 0, 14 events lost due to data acquisition electronic coincidence.
A number of lost events electronic is a datum measuring the the number of analysis events lost due to errors in data acquisition electronic coincidence in a flow cytometer insturment. The datum has a qualitative role.
number of lost events electronic
person:Kevin Clancy
quantity
_induction of natural processes
OBI branch derived
Place holder class, see editor note
PlanAndPlannedProcess Branch
This is a placeholder class to collect all protocl applications where the name conflicts with natural processes that could be classes in other ontologies. The fact that it is induced experimetnally by following a protocol makes it a protocol application. Need to make sure that labels don't conflict with natural processes.\nThe terms: translation and transcription were also requested.
_induction of natural processes
epitope role
Epitope
Jennifer Fostel
source pending
medical institution role
External definitions. CDISC: Any public or private entity or agency or medical or dental facility where clinical trials are conducted. [ICH]. An independent body constituted of medical, scientific, and non-scientific members; study-site (RCT schema)
Jennifer Fostel
Medical institution
Medical institution is an administrative unit role played by an organization and its members who perform clinical assays or trials
calibration substance role
Calibration substance
Jennifer Fostel
ice water (calibrates a thermometer)
obsolete_in-vitro_state
An in-vitro state is a state in which the entity is in an artificial environment outside the living organism. definition_source: http://wordnet.princeton.edu/perl/webwn?s=in%20vitro, Jan 3, 2007.
molecular feature identification objective
Jennifer Fostel
Molecular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize molecular features of a biological system, e.g. expression profiling, copy number of molecular components, epigenetic modifications.
example_of_usage to be added
molecular feature identification objective
source pending
obsolete_text based digital entity
group:OBI
A text based digital entity is a digital entity that is encoded so that it only contains text characters.
XML file, C++ source code file
digital_entity
person:Chris Stoeckert
replaced by IAO_0000047
text based digital entity
reference role
Jennifer Fostel
OBI
Reference
Reference is a role that can support the observation of similarities, differences, relative magnitude or change
control
hardware testing objective
Hardware_testing_objective is a methodology_testing_objective role describing a study designed to examine the effects of using different hardware, e.g. scanner.
Jennifer Fostel
example_of_usage to be added
hardware testing objective
source pending
role of medical monitor
Jennifer Fostel
Medical monitor
Medical monitor is a trial monitor role with medical authority for the evaluation of the safety aspects of a clinical trial
incubator
An incubator is an instrument in which environmental conditions (light, photoperiod, temperature, humidity, etc.) can be controlled
Frank Gibson
Incubators are used in microbiology for culturing (growing) bacteria and other microorganisms. Incubators in tissue culture rooms are used for culturing stem cells, lymphocytes, skin fibroblasts and other types of cells
http://www.medterms.com/script/main/art.asp?articlekey=18426
incubator
obsolete_state
OBI
a state is a quality indicating the condition in which an entity exists, e.g. immortalized, frozen, cellular_state (in-vivo, in-vitro), macromolecular state, 'ectopic in-vivo', 'denatured or native for protein'.
obsolete_in-vivo_state
OBI
An in-vivo state is a state in which the entity remains part of the living organism.
obsolete_frozen_state
OBI
A frozen state is a state in which the entity is kept below its freezing point.
reporter reagent role
Jennifer Fostel
Reporter
obsolete_material entity
OBI BIomaterial derived
to be added
Because OBI spans many levels of granularity, we can't effectively use the BFO three level granularity model. Thus we erase the difference using this strategy of saying it is any of the material like entities in BFO
Material is any of bfo:Object, bfo:ObjectAggregate, or bfo:FiatObjectPart.
PERSON:Alan Ruttenberg
replaced by IAO_0000018
obsolete_information content entity
group:OBI
An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity.
Examples of information content entites include journal articles, data, graphical layouts, and graphs.
information content entity
information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907).
person:Chris Stoeckert
replaced by IAO_0000030
baseline participant role
Baseline participant
Jennifer Fostel
Subject at time = 0; subject before a stress test.
role of independent data monitoring committee
Independent data monitoring committee
Independent data monitoring committee is a trial monitor role charged recommending whether to continue, modify, or end the trial
Jennifer Fostel
pathologist role
Jennifer Fostel
Pathologist
Pathologist is a worker role of being responsible for making the histopathology diagnoses associated with data from a study; this activity occurs outside the study timeline
supernatant collection system harvesting frame
Daniel Schober
The Supernatant Collection system is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125.
editor_note pending
example_of_usage to be added
google
supernatant collection system harvesting frame
role of being member of recruited population
CDISC definition: The group of eligible participants that agreed to participate in the trial and signed the informed consent.
Group of people who have agreed to participate, before they are completely enrolled
Jennifer Fostel
Recruited population
Recruited population is an eligible population role played by the set of members who have signed the informed consent form
vehicle role
Corn oil, ethanol
Jennifer Fostel
Vehicle
role of nutritional supplement
Jennifer Fostel
Nutritional supplement
Nutritional supplement is a nutrient role played by additives to feed or culture medium which enhance its nutritive properties
growth factor, vitamin; http://www.nutritionalsupplements.com/ "NutritionalSupplements.com is the Internet's premier source for unbiased information about nutritional supplements and prescription drugs."
Assessment
Assessment
Assessment is a conclusion derived from the processes used to learn about a patient's condition. In part from NCI
Jennifer Fostel
example_of_usage to be added
source pending
filter paper
Fliter paper is a device manufacture with the intent to provide a porous unsized paper used for filtering.
Frank Gibson
filter paper
sep:00107
obsolete_Intervention variable
CDISC definition: intervention. The drug, device, therapy or process under investigation in a clinical trial which has an effect on outcome of interest in a study: e.g., health-related quality of life, efficacy, safety, pharmacoeconomics. Synonyms: therapeutic intervention, medical product. See also: test articles; devices;. medicinal product. Synonym for therapeutic intervention, but usually a drug.
Intervention is a direct experimental factor role assigned to a study variable in a clinical study
Intervention variable
Jennifer Fostel
Variable in a clinical trial
source pending
cell co-culturing
2
A material combination in which cell cultures of two or more different types are are combined and allowed to culture as one.
Culturing cytotoxic T-lymphocytes together with target cells in order to study lysis of the target cells. See chromium_release_assay
OBI branch derived
PlanAndPlannedProcess Branch
cell co-culturing
role of Internal Review Board
An institutional review board/independent ethics committee (IRB/IEC) (also known as ethical review board) is a group that has been formally designated to approve, monitor, and review biomedical and behavioral research involving humans with the alleged aim to protect the rights and welfare of the subjects. Wikipedia March 2008
CDISC definition: institutional review board; independent ethics committee (IEC). An independent body (a review board or a committee, institutional, regional, national, or supranational) constituted of medical/scientific professionals and non-scientific members, whose responsibility it is to ensure the protection of the rights, safety and well-being of human subjects involved in a trial.
Internal Review Board
Jennifer Fostel
OBI, CDISC
disease
moved from TheRest.OWL to Quality branch by James M 2/6/08
Place_holder for disease ontology
rem0: BS did not view disease as a process, and indeed it is now a child of dependent continuant.
rem1: BP - placed into quality. needs to be discussed
obsolete_trial site role
A hospital
AR: to move under processual context? + relation located, as it is the physical location
CDISC definition: trial site. The location(s) where trial related activities are actually conducted.
Jennifer Fostel
Trial site
Trial site is an investigation site played by the physical location wherein a clinical study occurs
source pending
obsolete_?chromium 51
Bjoern Peters
Chromium 51
Philippe Rocca-Serra
Will be imported from CHEBI
placeholder for future import from CHEBI
to be added
eSource document
article-without-pmid-or-doi:CDISCglossary
an eSource document is a digital document consisting of a logical collection of Source data and other eSource documents that can be presented in an ordered way and capture the time of completion, change, and any signatures
eSource document
person:Jennifer Fostel
obsolete_journal article content
group:OBI
Examples of encodings of journal article content are articles published in the journals, Nature and Science. The content can often be cited by reference to a paper based encoding, e.g. Authors, Title of article, Journal name, date or year of publication, volume and page number.
Journal article content is a narrative object that is the information content encoded in a article published in a serious, scholarly publication, most often peer-reviewed.
journal article content
person:Alan Ruttenberg
person:Chris Stoeckert
replaced by IAO_0000013
obsolete_Treatment variable
A test of exposure to different compounds or procedures
CDISC definition: investigational treatment. An intervention under investigation in a clinical trial.
Jennifer Fostel
Treatment variable
Treatment variable is a direct experimental factor in which the varying parameter is a component of a treatment, intervention or perturbational protocol.
source pending
crossover population role
Crossover population
Jennifer Fostel
complete nutrient role
Complete nutrient
Jennifer Fostel
Rat chow; RPMI medium + serum; use example: CNS17 (Complete Nutrient System) Grow 3-2-4, http://www.kalyx.com/store/proddetail.cfm/ItemID/552307/CategoryID/12000/SubCatID/2755/file.htm
radiolabel role
Jennifer Fostel
Label_role
Radiolabel
Radiolabel is a reporter role which uses radiological decay as the signal
cDNA library
Luisa Montecchi
Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
ALT DEF:: a cDNA library is a collection of host cells, typically E.Coli cells but not exclusively. modified by transfer of plasmid DNA molecule used as vector containing a fragment or totality of cDNA molecule (the insert) . cDNA library may have an array of role and applications.
PMID:6110205. collection of cDNA derived from mouse splenocytes.
PRS: 22022008. class moved under population,
modification of definition and replacement of biomaterials in previous definition with 'material'
addition of has_role restriction
PSI
Philippe Rocca-Serra (ALT DEF)
cDNA library
obsolete_Direct experimental factor
Direct experimental factor
Direct experimental factor is an experimental factor role played by any study variable which is directly varied in the protocol application, such as (1) a protocol parameter which is systematically or deliberately varied within the study or (2) selection of study participants with different characteristics or that are from different environments
Dosage; sex; disease state; collection location
Jennifer Fostel
source pending
obsolete_Indirect experimental factor
Indirect experimental factor
Indirect experimental factor is an experimental factor role of any measurement or observation correlated with the effects of a parameter that is directly varied
Jennifer Fostel
Serum cholesterol as marker of coronary stress
source pending
electronic case report form
CDISC glossary
An electronic case report form is a digital document used to record all of the protocol required information to be reported for each trial subject. An eCRF has the property that it can be audited and compliant with requirements of 21 CFR Part 11.
electronic case report form
person:Jennifer Fostel
obsolete_Surrogate variable
CDISC definition: surrogate variable. A variable that provides an indirect measurement of effect in situations where direct measurement of clinical effect is not feasible or practical.
Following serum lipase levels as predictor of pancreatic failure
Jennifer Fostel
Surrogate variable
Surrogate variable is an indirect experimental factor role assigned to behavior which varies in a known relationship to a variable of interest that is more difficult to measure
source pending
placebo role
CDISC definition placebo. A pharmaceutical preparation that does not contain the investigational agent. In blinded studies, it is generally prepared to be physically indistinguishable from the preparation containing the investigational product.
Jennifer Fostel
Pill consisting of inert materials
Placebo
obsolete_Outcome
Data resulting from a measurement; conclusions from a study
Jennifer Fostel
Outcome
Outcome is a role describing the result of a process, protocol, plan or analysis
source pending
autotransplantation
OBI branch derived
PlanAndPlannedProcess Branch
autotransplantation
is the transplantation of tissue from one part of \nthe body to another in the same individual. )
parameter threshold
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
0.01, 0.03
A parameter threshold is a datum measuring the minimal signal that must be detected to generate an electrical event, as comparewd to the maximal detected signal in a flow cytometer insturment. The datum has a qualitative role
parameter threshold
person:Kevin Clancy
quantity
role of being excluded study participant
CDISC definition: screen failure. Potential subject who did not meet one or more criteria required for participation in a trial. See also screening of subjects. screen/screening (of substances). Screening is the process by which substances are evaluated in a
Excluded study participant
Excluded study participant is a study participant role of not meeting the inclusion criteria or being excluded by the exclusion criteria
Jennifer Fostel
Person too old for trial inclusion
study group role
Jennifer Fostel
Study group population
The group of randomized participants that are assigned to a treatment arm of the trial
p-value
group:OBI
A p-value is a quantitative confidence value which represents the probability of obtaining a result at least as extreme as that actually obtained, assuming that the actual value was the result of chance alone.
ask data transformation. Are they thinking about this too? What is this, in reality. Quality of the measurement? Quality of a population of measurements? Issue: How to avoid having numbers being an easy way to miss connections with reality
p-value
person:Chris Stoeckert
obsolete_measurement unit
group:OBI
A measurement unit is an information content entity associated with a physical magnitude that has been conventionally assigned a number.
Examples of measurement unit are liters, inches, weight per volume.
agree
measurement unit
person:Chris Stoeckert
person:Cristian Cocos
replaced by IAO_0000003
obsolete_Reference treatment
Jennifer Fostel
Reference treatment
Reference treatment is a reference role in which a protocol is applied that can produce a result which may be used as a reference or standard for comparison
Treat flies with MMS to elucidate maximal mutagenesis; apply sham surgery to subjects to compare with hepatectomized subjects
source pending
enrolled population role
Enrolled population
Enrolled population is a study population played by subjects who have completed the enrollment process
Jennifer Fostel
The group of eligible participants that agreed to participate in the trial and signed the informed consent.
density plot
group:Flow Cytometry community
A density plot is a report graph which is a graphical representation of data where the tint of a particular pixel corresponds to some kind of function corresponding the the amount of data points relativelly with their distance from the the pixel.
Density plot of SSC-H and FSC-H.
density plot
generically_dependent_continuants
person:Allyson
person:Chris Stoeckert
reagent supplier role
Jennifer Fostel
Reagent supplier
population
PMID12564891. Environ Sci Technol. 2003 Jan 15;37(2):223-8. Effects of historic PCB exposures on the reproductive success of the Hudson River striped bass population.
Philippe Rocca-Serra
a population is a collection of individuals from the same taxonomic class living, counted or sampled at a particular site or in a particular area
adapted from Oxford English Dictionnary
population
rem1: collection somehow always involve a selection process
nuclear magnetic resonance assay
A nuclear magnetic resonance assay is an assay used to identify the chemical structure of a compound or biological macromolecule. definition_source: www.nature.com/nrd/journal/v2/n5/glossary/nrd1086_glossary.html
OBI branch derived
PlanAndPlannedProcess Branch
nuclear magnetic resonance assay
mass spectrometry assay
A mass spectrometry assay is an assay to measure and analyze the molecules of a sample based on it's mass and charge. definition_source: OBI.
OBI branch derived
PlanAndPlannedProcess Branch
mass spectrometry assay
laboratory role
Jennifer Fostel
Laboratory
Laboratory is an administrative unit role played by an organization and its members who perform clinical assays or non-clinical trials
imaging assay
An imaging assay is an assay to produce a picture of an entity. definition_source: OBI.
OBI branch derived
PlanAndPlannedProcess Branch
imaging assay
protocol optimization
Jennifer Fostel
Protocol_optimization is a protocol_testing_objective role describing a study designed to identify the best protocol. This may be carried out by comparing different protocols or by modifying the parameters used within a single protocol.
example_of_usage to be added
protocol optimization
source pending
obsolete_data format specification
A data format specification is a plan which organizes information. Example: The ISO document specifying what encompasses an XML document; The instructions in a XSD file
OBI branch derived
PlanAndPlannedProcess Branch
data format specification
replaced by IAO_0000098
role of pathology review board
Jennifer Fostel
Pathology review board
Pathology review board is a worker role comprised of providing a confirmed and consensus diagnosis for histopathology results obtained during the investigation
obsolete_liquid_state
OBI
A liquid state is a state in which the entity has no fixed shape but a fixed volume, generally at a temperature between its freezing and boiling points.
obsolete_solid_state
A solid state is a state in which the entity has no tendency to flow under moderate stress; resists forces (such as compression) which tend to deform it; and retains a definite size and shape. definition_source: http://wordnet.princeton.edu/perl/webwn?s=solid%20state, Jan 3, 2007.
obsolete_gaseous_state
A gaseous state is a state in which the entity is distinguished from the solid and liquid states by: relatively low density and viscosity; relatively great expansion and contraction with changes in pressure and temperature; the ability to diffuse readily; and the spontaneous tendency to become distributed uniformly throughout any container. definition_source: http://wordnet.princeton.edu/perl/webwn?s=gaseous%20state, Jan 3, 2007.
microtiter plate
A microtiter plate with 6, 24, 96, 384 or 1536 sample wells used in the enzyme-linked immunosorbent assay (ELISA)
A microtiter_plate is a flat plate with multiple wells used as small test tubes.
Melanie Courtot
http://en.wikipedia.org/wiki/Microtiter_plate
microplate
microtiter plate
study committee role
Coordinating committee is a responsible party role overseeing the progress of a multicenter trial
Jennifer Fostel
Study committee
coordinating committee (also executive committee, steering committee MUSC; study-committee, RCT schema)
obsolete_Historic value
Historic control value is a reference value consisting of measurements or observations of unperturbed or baseline subjects averaged over a period of time by the lab making the measures for the study
Historic value
Jennifer Fostel
Lab average values for ALT assay done in Sprague Dawley rats
source pending
obsolete_digital document
group:OBI
A digital document is a digital entity consisting of an electronic file which can be rendered into human-readable form by one or more computational applications. The digital document does not refer to the information content of the document but to an instance of the file.
digital document
person:Jennifer Fostel
replaced by IAO_0000105
role of being impartial witness
According to GCP , an impartial witness should be present for an
illiterate subject. PharmPK Discussion, http://www.boomer.org/pkin/PK06/PK2006253.html
Impartial witness
Jennifer Fostel
impartial witness. A person, who is independent of the trial, who cannot be unfairly influenced by people involved with the trial, who attends the informed consent process if the subject or the subject's legally acceptable representative cannot read, and who
obsolete_Data pre-processing
Data pre-processing
Data pre-processing is a data transformation role which results in a data analysis element ready for higher-level analysis
Examples: (a) Filtering of input data; (b) Microarray data normalization.
Jennifer Fostel
source pending
biological replicate role
A member of a dose-time group; a patient in a given arm of a trial
Biological replicate
Jennifer Fostel
OBI
obsolete_software interpreter
group:OBI
A software interpreter is a generically dependent realizable entity that takes, as input, some digital entity, and takes action driven by the information content of that digital entity
Do we care? Jennifer: Yes, there was a particular version of R that had a bug and it was fixed later. That would imply that we mean specific version of an interpreter. So an instance of this would be a particular version of the interpreter
R program, Perl interpreter, Java virtual machine
person:Alan Ruttenberg
person:Chris Stoeckert
replaced by IAO_0000065
software interpreter
obsolete__unclassified
All classes yet to be suitably placed in a hierarchy
James Malone
example_of_usage to be added
source pending
this class should eventually be removed
radioactivity detection
An assay in which a material's radioactivity is measured.
Measurment of the radioactivity of a supernatant, as in chromium_release_assay.
OBI branch derived
PlanAndPlannedProcess Branch
radioactivity detection
study personnel role
Jennifer Fostel
OBI
Study director; funding agency; animal technician; Add/Remove/Change IRB Study Personnel. www.research.umn.edu/irb/download/addchange_personnel.doc
Study personnel
Study personnel is a role carried out by a person or organization who is performing the study involved in any of the following activities: planning, overseeing, reviewing, reporting and implementing a study.
obsolete_Placebo treatment
Delivery of a pill consisting of inert materials
Jennifer Fostel
Placebo treatment
Placebo treatment is a sham treatment role played in a clinical investigation by a treatment appearing similar to an investigational product but lacking the active chemical component
source pending
nutrient role
A nutrient role is a role played by a substance used in an organism's metabolism which is taken in from the environment and provides nourishment.
Jennifer Fostel
Luria broth; vitamin A; A nutrient is a substance used in an organism's metabolism which must be taken in from the environment. Wikipedia.
Nutrient
Wikipedia, feb 29, 2008
dropout role
CDISC definition: dropout. A subject in a clinical trial who for any reason fails to continue in the trial until the last visit or observation required of him/her by the protocol
Dropout
Dropout is a study subject role characterized by leaving the study earlier than the protocol specified; the bearer was a study participant prior to being a dropout.
Escaped rat; human who moved to another city
Jennifer Fostel
obsolete_format standard
PERSON:Chris Stoeckert
PERSON:Jennifer Fostel
a format standard is a digital entity that consists of rules applied to information, as opposed to rules applied to objects (which are termed plans)
health care provider role
Health care provider
Healthcare provider is a worker role of providing medical care either within or outside the study timeline
Jennifer Fostel
methodology testing objective
Jennifer Fostel
Methodology_testing_objective is an objective role carried out by a proposition defining the aim of the study is to examine the effect of using different methodologies.
example_of_usage to be added
methodology testing objective
source pending
inactive isomer role
Inactive isomer
Jennifer Fostel
analytical cytology data file
group:Flow Cytometry community
A digital entity intended to capture data in analytical cytology domain.
FCS file, ACS file, foo.fcs, foo.asc
analytical cytology data file
binary_digital_entity
person:Chris Stoeckert
proxy respondent role
Jennifer Fostel
Proxy respondent
Proxy respondent is a worker role of describing patient's symptoms or condition to medical personnel
obsolete_funder
fluorescence compensation matrix
group:Flow Cytometry community
((1.053096, -0.22476), (-0.24877, 1.053096))
A fluorescence compensation matrix is a square matrix which is used as the left multiplier of the vector of fluorescence values while performing digital fluorescence compensation. Also, fluorescence compensation matrix is the inverse of the fluorescence spillover matrix.
fluorescence compensation matrix
generically_dependent_continuants
person:Chris Stoeckert
negative reference substance role
Jennifer Fostel
Negative reference substance
Saline solution
role of legally acceptable representative
Jennifer Fostel
Legally acceptable representative
OBI, CDISC
Parent of minor patient; Definition of legally acceptable representative
An individual or juridicial or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject`s participation in the clinical trial. http://www.geneed.com/website/catalog/glossary_search.php?id=2134&search_term=legally%20acceptable%20representative&select=TRUE
legally acceptable representative. An individual or juridical or other body authorized under applicable law to consent, on behalf of a prospective subject, to the subject's participation in the clinical trial. [ICH, E6 Glossary]
obsolete_Reference value
Jennifer Fostel
Magnitude of response or quality of a subject a subject at time 0
Reference value
Reference value is a reference role in which the reference value is used for comparison or reference.
source pending
obsolete_objective specification
IAO
Answers the question, why did you do this experiment?
Jennifer Fostel /Barry Smith
objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed. (note: achievement
objective specification
purpose of a study; support of hypothesis, discovery of new information
replaced by IAO_0000005
source pending
investigation results report
group:OBI
An investigation report is a report on the results of an investigation.
There's probably a role that it plays. Would this be considered an outcome? (alan)
investigation results report
person:Chris Stoeckert
cellular feature identification objective
Cellular_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the cellular level, e.g. stage of cell cycle, stage of differentiation.
Jennifer Fostel
cellular feature identification objective
example_of_usage to be added
source pending
reference participant role
Jennifer Fostel
OBI
Reference participant
Reference participant role is a reference role in which the characteristics or responses of the participant playing the reference participant role are used for comparison or reference.
Saline treated rat; one of three identically-treated subjects
vital dye role
Jennifer Fostel
Vital dye
obsolete_binary executable
group:OBI
Binary executable is a digital entity consisting of the binary representation of machine instructions of a specific processor or they may be binary pseudocode for a virtual machine. A non-source executable file is also called an object program. It is assumed that the binary executable file contains properly-formatted computer instructions. (derived from Wikipedia, Nov 1, 2007)
binary executable
person:Jennifer Fostel
replaced by IAO_0000222
blinded medication role
Blinded medication
CDISC definition (in part): blinded (masked) medications. Products that appear identical in size,
Inert pill shaped like aspirin tablet
Jennifer Fostel
sub-investigator role
CDISC definition: Sub-investigator. Any member of the clinical trial team designated and supervised by the investigator at a trial site to perform critical trial-related procedures and/or to make important trial-related decisions (e.g., associates, residents, research fellows) [ICH] See associates, residents, research fellows
Jennifer Fostel
Sub-investigator
Sub-investigator is a worker authorized to make study-related decisions and carry out tasks related to the study; this role occurs during the study timeline
obsolete_investigation site role
A field, a laboratory, a medical institute, a pharmaceutical company
Investigation site
Jennifer Fostel
site is a material (building) having the role site
solution1: is a physical location, should maybe go under processual context, and then be used in conjunction with the located relation
solution2: site is related to trial used located_in relation - site can bear the role
source pending
obsolete_precipitate role
data encoding
OBI branch derived
PlanAndPlannedProcess Branch
We (protocol application branch) placed this term because it kept getting bounced from data transformation and DENRIE
data encoding
is a process to encode an information entitiy into a digital document
storage of measurement results from an assay into a text file, such as
role of being member of screened population
Group of potential subjects who pass the screening criteria
Jennifer Fostel
Screened population
Screened population is a potential study participant role of individuals who have been interviewed or screened for participation eligibility
role of potential study participant
Jennifer Fostel
People with diabetes in range of a trial site for a new diabetes therapy; SD rats living in Charles River Labs when an order for rats is placed there
Potential study participant
obsolete_Baseline value
Baseline value
Baseline value is a reference value produced by a measurement or observation of a study participant at rest or prior to the study
Jennifer Fostel
Value of a test measuring a subject at time 0, or at rest
source pending
enzymatic cleavage
Polymorphism R62W results in resistance of CD23 to enzymatic cleavage in cultured cells. Genes Immun. 2007 Apr;8(3):215-23. Epub 2007 Feb 15. PMID: 17301828
OBI branch derived
PlanAndPlannedProcess Branch
enzymatic cleavage
enzymatic cleavage is a protocol application to digest the fraction of input material that is susceptible to that enzyme
hardware optimization
Hardware_optimization is a hardware_testing_objective describing a study designed to identify the best hardware.
Jennifer Fostel
example_of_usage to be added
hardware optimization
source pending
trial statistician role
CDISC definition: trial statistician. A statistician who has a combination of education/training and experience sufficient to implement the principles in the ICH E9 guidance and who is responsible for the statistical aspects of the trial. [ICH E9]
Jennifer Fostel
Trial statistician
Trial statistician is a worker who analyzes data obtained during a trial or study; this role occurs after the trial or study is completed or terminated.
standard error
group:OBI
Standard error is a quantitative confidence value which is the standard deviations of the sample in a frequency distribution, obtained by dividing the standard deviation by the total number of cases in the frequency distribution.
person:Chris Stoeckert
see P-Value
standard error
_under_discussion
placeholder for under discussion classes
antigen role
Antigen
Antigen is a role played by material which when introduced into an immune-competent organism causes an immune response
Jennifer Fostel
obsolete_Vehicle control treatment
Deliver saline solution via gavage
Jennifer Fostel
Vehicle control treatment
Vehicle treatment is a sham treatment in which the solvent is delivered without the active test compound
source pending
obsolete_Subject characteristic variable
Jennifer Fostel
Selection of subjects of different sexes for testing
Subject characteristic variable
Subject characteristic variable is a direct experimental factor in which the component which varies results from the selection of subjects with non-uniform characteristics
source pending
report graph
group:OBI
A report graph is a report figure that presents one or more tuples of information my mapping those tuples in to a two dimensional space in a non arbitrary way.
person:Alan Ruttenberg
person:Allyson Lister
report graph
animal care technician role
Animal care technician
Animal care technician is a worker role involved in day-to-day care of lab animals; this role occurs before and during the study
Jennifer Fostel
software testing objective
Jennifer Fostel
Software_testing_objective is a hardware_optimization role describing a study designed to examine the effects of using different software or software parameters, e.g. data processing software.
example_of_usage to be added
software testing objective
source pending
sponsor role
CDISC definition: sponsor. 1. An individual, company, institution, or organization that takes responsibility for the initiation, management, and/or financing of a clinical trial. 2. A corporation or agency whose employees conduct the investigation is considered a sponsor; employees are considered investigators
Jennifer Fostel
Sponsor
Sponsor is a responsible party role involved with any of the following activities: initiating, managing and funding a study
obsolete_binary digital entity
group:OBI
A binary digital entity is a digital entity that is encoded in a way that is not easily human readable and that contains other than text characters.
MS Word document, ZIP file, DICOM file, JPEG file
binary digital entity
digital_entity
person:Chris Stoeckert
replaced by IAO_0000019
organization
Alan Ruttenberg
BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based:
1) there are organization_member_roles (president, treasurer, branch
editor), with individual persons as bearers
2) there are organization_roles (employer, owner, vendor, patent holder)
3) an organization has a charter / rules / bylaws, which specify what roles
there are, how they should be realized, and how to modify the
charter/rules/bylaws themselves.
It is debatable what the organization itself is (some kind of dependent
continuant or an aggregate of people). This also determines who/what the
bearer of organization_roles' are. My personal favorite is still to define
organization as a kind of 'legal entity', but thinking it through leads to
all kinds of questions that are clearly outside the scope of OBI.
Interestingly enough, it does not seem to matter much where we place
organization itself, as long as we can subclass it (University, Corporation,
Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO,
W3C, University of Oklahoma), and have it play roles.
This leads to my proposal: We define organization through the statements 1 -
3 above, but without an 'is a' statement for now. We can leave it in its
current place in the is_a hierarchy (material entity) or move it up to
'continuant'. We leave further clarifications to BFO, and close this issue
for now.
Bjoern Peters
OBI Developer derived
PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods.
Philippe Rocca-Serra
Susanna Sansone
An organization is a continuant entity which can play roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can play specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members.
contour plot
group:Flow Cytometry community
A contour plot is a report graph which is a graphical representation of a 3-dimensional surface by plotting constant z slices, called contours, on a 2-dimensional format. That is, given a value for z, lines are drawn for connecting the (x,y) coordinates where that z value occurs.
Contour plot of SSC-H, FSC-H, and FL1-H.
contour plot
generically_dependent_continuants
person:Allyson
person:Chris Stoeckert
role of being member of eligible population
Eligible population
Eligible population is a study population role characterized by meeting the inclusion / exclusion criteria
Group of people passing the inclusion criteria for the investigation
Jennifer Fostel
feed role
Feed
Jennifer Fostel
OBI
Purina rat chow; cited use: Control; F = feed (rat chow); W = water; F. g. = feed-ginger concentrate. www.academicjournals.org/AJB/PDF/pdf2007/19Sep/Egwurugwu%20et%20al.pdf - Feb 29, 2008
technical replicate role
Aliquots of a tissue subjected to parallel assays
Jennifer Fostel
Technical replicate
dye role
Jennifer Fostel
dye
cluster
group:OBI
A data cluster is a data set which is a subset of data that are a similar to each other in some way.
Cluster of the lymphocytes population.
cluster
generically_dependent_continuants
person:Allyson
person:Chris Stoeckert
cohort role
# a group of individuals in a study who share a demographic, clinical, or other statistical characteristic (eg, age, study site).
www.thebody.org/content/treat/art2612.html
# a group of individuals having a statistical factor (as age or class membership) in common in a demographic study, such as a cohort of students.
www.sceoc.com/glossaryofterms/
# A cohort is a group of people with a common characteristic that is studied over a period of time as part of a scientific or medical investigation.
www.uhhospitals.org/tabid/591/Default.aspx
In statistics and demography, a cohort is a group of subjects — most often humans from a given population — defined by experiencing an event (typically birth) in a particular time span. Wikipedia "cohort", Feb 29 2008
Jennifer Fostel
a cohort role is a biological replicate role played by a group of study participants who share a common charactreristic of interest to the study.
artifically induced nucleic acid hybridization
Is a material transformation in which strands of nucleic acids that are (somewhat) complementary form a double-stranded molecule. Has input at least two single stranded molecules of nucleic acid molecules.
OBI branch derived
PlanAndPlannedProcess Branch
artifically induced nucleic acid hybridization
www.ornl.gov/sci/techresources/Human_Genome/publicat/97pr/09gloss.html, http://www.accessexcellence.org/RC/VL/GG/nucleic.html, http://omrf.ouhsc.edu/~frank/HYBNOTES.html. http://en.wikipedia.org/wiki/Nucleic_acid_hybridization,http://www.pnas.org/cgi/reprint/46/8/1044.pdf
obsolete_specimen_role
OBI
A specimen role is an investigation object role where the object is a piece of a material.
organism "has_role_which_can_only_be_played_by_biomaterial_entity" some specimen_role in obi before split (LF 040907).
rem: not necessarily played by biomaterial entities, also include material entity
subject provider role
Jennifer Fostel
Subject provider
Subject provider does not provide clinical subjects
Subject provider is a supplier of animals, cultures, other living material in a form suitable for use in a study. This role occurs before the study timeline.
environmental matter
(formerly known as environmental sample)
Norman Morrison
OBI Biomaterial derived
PRS: 110508: Possible Import from ENVO:00010483
PRS:19032008: change label from site_sample to environmental sample to match definition. site_sample demoted to alternative term
site_sample
Matter in or on which organisms may live (From ENVO) OR an environmental sample is an object that contains an array of objects that may or may not contain a biomaterial. definition_source: OBI.
PMID: 3109018.Schriftenr Ver Wasser Boden Lufthyg. 1987;71:71-82. German. An environmental sample bank for human organ samples in Munster--hair analyses (NOTE: Only 2 occurences in Pubmed Title line)
A dirt sample containing different populations of bacteria. A sample of martian water. A sample of gut flora.
DNA extraction
A DNA extraction is a nucleic acid extration where the desired output material is DNA.
DNA extraction
OBI branch derived
PlanAndPlannedProcess Branch
obsolete_Control value
Control value
Control value is a reference value produced by a measurement or observation of a study participant in a designated control treatment group
Jennifer Fostel
Value of test done on solvent-treated control animal at time = 6 in a study where the same test is also done on groups of treated animals at time = 6
source pending
obsolete_ex-vivo_state
An ex-vivo state is a state in which the entity is in an artificial environment outside the living organism. definition_source: http://wordnet.princeton.edu/perl/webwn?s=in%20vitro, Jan 3, 2007.
rem0: (AL) One of in-vitro state/ex-vivo state should be deleted, and made a synonym of the remaining term.
concretized information entity
BFO
BFO to do
BFO to do
concretized information entity
obsolete_digital entity
group:OBI
A digital entity is an information entity which is a collection of bits that can be interpreted by a computer. Two digital entities are the same if they are bitwise identical.
digital entity
person:Chris Stoeckert
replaced by IAO_0000012
obsolete_Chemical stressor
A dose response study design
Chemical stressor
Chemical stressor is a treatment variable role in a non-clinical study; varying parameter may be concentration of or exposure to a chemical, chemical mixture, biological extract, aerosol, undefined chemical substance
Jennifer Fostel
source pending
person
Alan Ruttenberg
PMID: 18333287.AIDS Read. 2008 Feb;18(2):100-4.Progression of Kaposi sarcoma associated with iatrogenic Cushing syndrome in a person with HIV/AIDS.
PRS: a person is material entity instantiating an organism human
Philippe Rocca-Serra
Susanna Sansone
adapted from OED and OBI
a human being regarded as an individual
sample population
Jennifer Fostel
OBI Biomaterial derived
Patterns of benzylpiperazine/trifluoromethylphenylpiperazine party pill use and adverse effects in a population sample in New Zealand. Drug Alcohol Rev. 2008 Mar 31:1-7. PMID: 18608458
Philippe Rocca-Serra
recruited population
A sample population is an object aggregate that is selected from the population, e.g. the fish in the net that were sampled from the lake, the people that responded to the call for volunteers.
PRS 22-02-2008: this is still a population. may be we need qualifiers for this entity e.g. 'screened population, recruited population or we need to use the following label: sample of population, subpopulation
obsolete_report table
group:OBI
A report table is a report display element consisting of a matrix of cells layed out in a grid, some set of which are filled with some information content
person:Alan Ruttenberg
person:Allyson Lister
replaced by IAO_0000097
report table
obsolete_curation status
GROUP:OBI:<http://obi.sourceforge.net>
PERSON:Bill Bug
curation status
The curation status of the term. The allowed values come from an enumerated list of predefined terms. See the specification of these instances for more detailed definitions of each enumerated value.
replaced by IAO_0000078
obsolete_Biologic
Biologic
Biologic is an intervention variable in which the varying parameter is a drug or investigational compound
CDISC: variable. 1. Any quantity that varies; any attribute, phenomenon or event that can have different qualitative or quantitative values. 2. In SDTM variables are used to describe observations. Such describing variables have roles that determine the type of information conveyed by the variable about each observation and how it can be used; FCR: Variables concepts that can be assigned values and thus must be defined operationally by the methods for measuring or evaluating them; CDISC: study variable. A term used in trial design to denote a variable to be captured on the CRF. See also variable, supporting variable
Jennifer Fostel
Test of investigational drug
source pending
organism feature identification objective
Jennifer Fostel
Organism_feature_identification_objective is a biological_feature_identification_objective role describing a study designed to examine or characterize a biological feature monitored at the level of the organism, e.g. height, weight, stage of development, stage of life cycle.
example_of_usage to be added
organism feature identification objective
source pending
number of lost events computer
Submitted by the Flow Cytometry community in DigitalEntity-FlowCytometry-2007-03-30.txt
0, 125, 787 events lost due to computer busy.
A number of lost events is a datum recording the the number of measurement events lost due to overloading of the analysis chip in a flow cytometer insturment. The datum has a qualitative role
number of lost events computer
person:Kevin Clancy
quantity
obsolete_algorithm
PMID: 18378114.Genomics. 2008 Mar 28. LINKGEN: A new algorithm to process data in genetic linkage studies.
Philippe Rocca-Serra
PlanAndPlannedProcess Branch
adapted from discussion on OBI list (Matthew Pocock, Christian Cocos, Alan Ruttenberg)
algorithm
an algorithm is a plan which describes inputs, output of mathematical functions as well as workflow of execution for achieving an predefined objective. Algorithms are realized usually by means of implementation as computer programs for execution by automata.
replaced by IAO_0000064
Causality assessment
Causality assessment
Causality assessment is an assessment role in which the contribution of a study factor towards causing the observed outcome or data is estimated and reported
Jennifer Fostel
example_of_usage to be added
source pending
protocol
OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29)
PMID: 18388943.Nat Protoc. 2008;3(4):612-8.Protocol for the induction of arthritis in C57BL/6 mice.
PlanAndPlannedProcess Branch
protocol
protocol is a plan which outlines a set of instructions to achieve a specific objective relevant to the biomedical domain and which can be realized as a protocol application.
role of regulator of consumables and medical devices
A regulator of consumables and medical devices is a regulator involved with making and enforcing legislation and governmental orders relevant to the development, testing, manufacture and use of food, drugs and medical devices
Drug regulatoy authority
FDA, EMEA; http://www.fda.gov/; The International Conference of Drug Regulatory Authorities (ICDRAs) provide drug regulatory authorities of WHO Member States with a forum to meet and discuss ways to strengthen collaboration.http://www.who.int/medicines/areas/quality_safety/regulation_legislation/icdra/en/index.html
Jennifer Fostel
OBI, CDISC
administering substance
is a process to place an administered material into a target location
analyte role
is the role of the substance that is being detected in a analyte measuring assay
_positional quality
OBI
Philippe Rocca-Serra
a positional quality is quality which inheres in an independent continuant located in another
_disease stage
Stage II breast cancer, The timepoint of recovery from a disease
is a fiat_process_part which is part_of a disease_process which is associated with position in the normal progression of the disease
intrajugular
OBI Biomaterial
Philippe Rocca-Serra
Restoration of lactation in bromocriptine-treated rats by prolactin replacement: comparison of constant versus pulsatile infusion and intrahepatic versus intrajugular routes of delivery.
J Endocrinol Invest. 1993 Jan;16(1):29-35. PMID: 8445154
intrajugular is a positional quality which inheres in a material entity located in the jugular vein
intraperitoneal injection
obsolete__GO molecular function placeholder
This placeholder is a stub for molecular functions from GO that OBI will need for assay reagent (BB:2008-01-30).
_GO molecular function
precipitate
OBI
Philippe Rocca-Serra
Physicochemical properties and antibacterial activity of the precipitate of vancomycin and ceftazidime: implications in the management of endophthalmitis. Retina. 2008 Feb;28(2):320-5. PMID: 18301038
a precipitate is a material entity which is output of a precipitation process
precipited material
intraventricular
Endoscopic surgery for intraventricular brain tumors in patients without hydrocephalus.
Neurosurgery. 2008 Jun;62(6 Suppl 3):1042-8.PMID: 18695524
OBI Biomaterial
Philippe Rocca-Serra
intraventricular is a positional quality which inheres in a ventricule site (e.g. heart ventricule or brain ventricule)
protein-protein interaction detection
obsolete_reporter_role
this role was added as a sibling of reporter, which is not sensible. we will keep one term for reporter, and use the one with a definition provided. The original term contained a child "dye-role" which is equivalent to label role
transcription factor binding site identification
OBI
Philippe Rocca-Serra
Transcription factor binding site identification in yeast: a comparison of high-density oligonucleotide and PCR-based microarray platforms.
Funct Integr Genomics. 2007 Oct;7(4):335-45. Epub 2007 Jul 19. PMID: 17638031
transcription binding site identification is a process which aims at finding DNA region specifically recognized by proteins whose function is
transcription factors
enrollment
Bjoern Peters
Enrollment of patients in a study.
Short-term outcome of neuropsychiatric events in systemic lupus erythematosus upon enrollment into an international inception cohort study. Arthritis Rheum. 2008 May 15;59(5):721-9. PMID: 18438902
IEDB
enrollment
enrollment is a process of identifying a set of objects for further use in an investigation based on a set of criteria or rules
obsolete__PATO_quality
instrument_function
A function inhering an instrument enabling it to participate in critical process in the context of a specific investigation plan.
Bill Bug
E.g. the function of a analytical centrifuge to sediment very large material objects out of a liquid suspension.
PERSON:William Bug@2007/07/10
instrument_function
obsolete_datum
group:OBI
A datum is an information content entity that is a recording of the output of a measurement such as produced by an instrument.
Examples of data are the recoding of the weight of a mouse, the recording of an observation of the behavior of the mouse, the recording of the expression level of a gene as measured through the process of microarray experiment. Instance level information is information describing a specific instance of an entity
datum
person:Chris Stoeckert
replaced by IAO_0000109
was measurement. (alan) Is this the old quantitative value? If so need to change cardinal part of stuff. I think the value and units should be on special relations and that the value should not be a BFO entity.
adverse event trigger
OBI branch derived
PERSON:Alan Ruttenberg
adverse event trigger
revisit?
eluate
OBI Bionaterial
Philippe Rocca-Serra
Raman spectroscopic detection of haemoproteins in the eluate from high-performance liquid chromatography. J Chromatogr. 1983 Jan 7;254:285-8. PMID: 6298263
a eluate is a material entity which results from an elution, e.g. from a chromatography column. it has as part a material entity with role mobile phase
eluted material
need to add restriction to indicate: has_part some (material entity has_role mobile phase)
need to add mobile phase as role
administered material role
intracardiac
Intracardiac thrombus and pulmonary aneurysms in an adolescent with Behçet disease.
Rheumatol Int. 2008 Oct 11. PMID: 18850100
OBI Biomaterial
Philippe Rocca-Serra
intracardiac is a positional quality which inheres in a material entity located in organism part heart
peritoneum
BP: should be imported in the future, but I need it now to demonstrate how to define intraperitoneal injection
is the serous membrane that forms the lining of the abdominal cavity
intraoccular
Longterm results after phacovitrectomy and foldable intraocular lens implantation.
Acta Ophthalmol. 2008 Oct 3. PMID: 18937822
OBI Biomaterial
Philippe Rocca-Serra
intraoccular is a positional quality which inheres in a material entity located in the eye
obsolete_time trigger
OBI branch derived
PlanAndPlannedProcess Branch
replaced by IAO_0000034
revisit?
time trigger
obsolete_specification
A specification is an information entity, which can be used to classify entities into conforming or non-conforming in respect to the specification
OBI branch derived
PlanAndPlannedProcess Branch
specification
obsolete__to_be_fixed
investigation design
Investigation_design is a plan for an investigation. definition_source: OBI.
OBI branch derived
PlanAndPlannedProcess Branch
investigation design
obsolete__chemical entity (import_from ChEBI)
Import of ChEBI ontology
OBI
_ChEBI_object
example_of_usage to be added
objects of chemical or biological interest
source pending
obsolete_realizable information entity
OBI branch derived
PlanAndPlannedProcess Branch
instruction
is the specification of a process that can be concretized and realized by an actor
realizable information entity
replaced by IAO_0000033
interpreting data
Bjoern Peters
Bjoern Peters
is the process of evaluating the data gathered in an investigation with the objective to generate more general conclusions or to identify what additional data is necessary to draw conclusions
planning
Bjoern Peters
Bjoern Peters
planning is the process of creating or modifying a plan.
documenting
Bjoern Peters
the process of capturing information in a digital or physical representation with the capacity and intend to communicate
wikipedia http://en.wikipedia.org/wiki/Documenting
histological sample preparation
BP added following request from biomaterial branch.
OBI branch derived
PERSON:Bjoern Peters
histological sample preparation
histological sample preparation is the preparation of an input tissue via slicing and labeling to make tissue microstructure of interest visible in a future histology assay
investigation planning
Bjoern Peters
Bjoern Peters
a planning process with the objective to create or modify an investigation design
choosing an ELISPOT protocol to measure IFN-gamma T cell responses.
inductive reasoning
Based on the observation that all lung cancer patients treated with aspirin in our clinical trial survived longer than the control group, we conclude by inductive reasining that aspirin has a therapeutic effect on lung cancer.
Bjoern Peters
It is used to ascribe properties or relations to types based on an observation instance (i.e., on a number of observations or experiences); or to formulate laws based on limited observations of recurring phenomenal patterns.
wikipedia: http://en.wikipedia.org/wiki/Inductive_reasoning
obsolete_plan specification
Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved
OBI branch derived
PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice.
Part of range for an object property is_potentially_realizable_as in obi before split (LF 040907)
PlanAndPlannedProcess Branch
a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan
replaced by IAO_0000104
mass analyzer
A Mass analyzer is a device that separates ions according to their mass-to-charge ratio. All mass spectrometers are based on dynamics of charged particles in electric and magnetic fields iin vacuum where the two laws of Lorentz force law and Newton's second law of motion apply.
Frank Gibson
PERSON: Daniel Schober
The mass analyzer of the Voyager-DE™ STR Biospectrometry Workstation
http://en.wikipedia.org/wiki/Mass_spectrometry#Mass_analyzer
mass analyzer
conferred quality
Alan Ruttenberg
BFO-discuss, IAO discussions
Bjoern Peters, Philippe Rocca-Serra
Former Definition: historical role is a dependant continuant that exist by virue of something having been the case or having happened to the entity it inheres in
This is an experiemental class, to be passed upward to BFO should it be successful. The goal is to gather a number of such roles and see if they seem a coherent classification
a conferred quality is a quality inhering in an entity as a result of a process having been applied to it. Such qualities may be used to track the history of event having affected an entity
changed to confered quality on 24102008, used to be historical role
conferred quality
digested is a conferred quality resulting from a digestion process affecting a material entity
_roles
historically not part
A historical role inhering in a part that is commonly independent entity - not a direct part of something.
Not quite satisfactory because part_of is transitive.
PERSON:Alan Ruttenberg
obsolete_instruction trigger
OBI branch derived
PlanAndPlannedProcess Branch
instruction trigger
is a plan to carry out a process or an event if the trigger condition is fulfilled
replaced by IAO_0000001
_why
For each of these I didn't understand what the purpose of the term was. Have these been requested? For what purpose
historically part
A historical role of something that was formerly a part of something else. Relational, as what it was part of is important.
One is tempted to make this a relationship historical_part_of following Alan Rector. Jury is out at the moment, but perhaps all relational dependents are equivalent to relations.
PERSON:Alan Ruttenberg
_results_from
A review of Philippes results_from classes, put into bins by similarity by Alan and Melanie, for subsequent review.
_qualities
_disease course
is a process through which a disease manifests itself
hypothesis driven investigation
OBI branch derived
PlanAndPlannedProcess Branch
hypothesis driven investigation
is an investigation with the goal to test one or more hypothesis
hypothesis generating investigation
OBI branch derived
PlanAndPlannedProcess Branch
hypothesis generating investigation
is an investigation in which data is generated and analyzed with the purpose of generating new hypothesis
author role
An author_role is a role attributed to someone creating an information_object
_still
These are called "still", as the terms denote dependents that still remain with the entity they depend on. In this sense they are different from historical entities which represent things that are not necessarily the case "now". These are further subdivided into entities which seem to be other sorts of dependents.
_related_to_material_separation
Each of these are related to material separation. I'm not sure if they should be named or not, and whether any of them are historical in the sense described in historical role
_uncertain
ion source
An ion source is a device that is part of a mass
spectrometer that ionizes the material under analysis. The ions are
then transported by magnetic or electric fields to the mass analyzer.
Techniques for ionization have been key to determining what types of
samples can be analyzed by mass spectrometry. Electron ionization and
chemical ionization are used for gases and vapors. In chemical
ionization sources, the materila is ionized by chemical ion-molecule
reactions during collisions in the source. Two techniques often used
with liquid and solid biological samples include electrospray
ionization (due to John Fenn PMID 2675315.) and matrix-assisted laser
desorption/ionization (MALDI, due to M. Karas and F. Hillenkamp
(Measuring Mass: From Positive Rays to Proteins by Michael A. Grayson
(Editor) (ISBN 0-941901-31-9))).
Frank Gibson
The ion source of a Voyager-DE™ STR Biospectrometry Workstation
http://en.wikipedia.org/wiki/Mass_spectrometry#Ion_source
ion source
_dependent_bearers
The question of each of these, is what is the bearer. It seems that these might not be independent continuants and therefore not reasonable bearers of dependents.
_dispositions
ion detector
An ion detector is a device that measures and records
the charge induced or current produced when an ion passes by or hits a
surface. In a scanning instrument the signal produced in the detector
during the course of the scan versus where the instrument is in the
scan (at what m/Q) will produce a mass spectrum, a record of ions as a
function of m/Q.
Frank Gibson
The ion detector of the Voyager-DE™ STR Biospectrometry Workstation
http://en.wikipedia.org/wiki/Mass_spectrometry#Detector
ion detector
metabolite profiling
Metabolite profiling of human colon carcinoma - deregulation of TCA cycle and amino acid turnover. Mol Cancer. 2008 Sep 18;7(1):72. PMID: 18799019
OBI
Philippe Rocca-Serra
metabolite profiling is a process which aims at detecting and identifying chemical entities resulting from biochemical and cellular metabolism
light emmision function
A light emmision function is an excitation function to excite a material to a specific excitation state that it emits light.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
light emmision function
record function
A record function is a function that registers or collects information in a particular format on a particular recording medium. For example on paper or a digital representation
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
record function
magnify function
A magnify function is a function to increase the size of a transmitted object image through the precise arrangement of energy diffraction elements along an imaging path.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
magnify function
contain function
A contain function is a function to bound or constrain some quantity of material to fixed volume and minimize interaction of the bounded material with the environment outside of the containing device.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
contain function
heat function
A heat function is a function that increases the internal kinetic energy of a material
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
heat function
separation function
A separation function is a function that increases the resolution between two or more material entities. The to distinction between the entities is usually based on some associated physical quality.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
separation function
ionize process
excitation function
A excitation function is a function to inject energy by bombarding a material with energetic particles (e.g., photons) thereby imbuing internal material components such as electrons with additional energy. These internal, 'excited' particles may lead to the rupturing of covalent chemical bonds or may quickly relax back to there unexcited state with an exponential time course thereby locally emitting energy in the form of photons.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
excitation function
freeze function
A freeze function is a function to decrease the internal kinetic energy of a material below the freezing point of that type of material.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
freeze function
synthesizing function
A synthesizing function is a function to assemble new output materials from distinct input materials. The output materials typically consist of chemically distinct monomeric objects or object aggregate polymers.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
synthesizing function
perturbe function
A perturbe function is a function that disrupts the normal function of a system induced through either internal or external means. External means of perturbation include: (1) displacement fields in the physical sense - e.g., temperature change, osmotic shock, pressure change; (2) application of small molecules such as drugs or toxins to perturb the function of specific pathways or application of surfactants to perturb the normal function of plasma membrane. Internal means of perturbation include: (1) manipulation of gene function via gene knockout or transcript knockdown via RNAi; (2) directed genetic mutation leading to minimal aa alterations that interfere with peptide function.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
http://en.wikipedia.org/wiki/Perturbation_biology
perturbe function
filter function
A filter function is a function to prevent the flow of certain entities based on a quality or qualities of the entitiy while allowing entities which have different qualities to pass through
Frank Gibson
filter function
mechanical function
A mechanical function is a function that is realised via mechanical work (through an certain amount of energy transferred by some force.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
http://en.wikipedia.org/wiki/Mechanical_work
mechanical function
gas filter function
A gas filter function is a filter function which prevents the flow of solid objects, defined by specifc qualities, in a gas-solid mixture
Frank Gibson
gas filter function
liquid filter function
A liquid filter function is a filter function which prevents the flow of solid objects, defined by specifc qualities, in a liquid-solid mixture
Frank Gibson
liquid filter function
measure function
A mass spectrometer measure the mass to charge ration of excited ions.
A measure function is a function that estimates the magnitude of some object attribute, such as that object's length or weight given according to a specific unit of measure
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
http://en.wikipedia.org/wiki/Measurement
measure function
transfer function
A transfer function is a function to displace a material from one location to another.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
transfer function
electricity supply function
An electricity supply function is an energy supply function to transfer electricity from one source to another, typically a consumer of the electricity.
Daniel Schober
Frank Gibson
Melanie Courtot
electricity supply function
power supply
ionization function
An ionization function is a function to physically convert an atom or molecule into an ion by adding or removing charged particles such as electrons or other ions.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
The ion source in amass spectrometer
http://en.wikipedia.org/wiki/Ionization
ionization function
count function
A count function is a measure function to numerically quantify an entitiy with certain qualities
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
count function
cool function
A cool function is a function to decrease the internal kinetic energy of a material below the initial kinetic energy of that type of matterial.
Daniel Schober
Frank Gibson
Melanie Courtot
cool function
connection function
A connection function is a function to couple two or more flow channels so that material or signals can be transported from one set of channels to another.
An electricity cable
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
connection function
isoelectric focussing device
An isoelectric focussing device is a device in which isoelectric focusing can be performed. An isoelectric focussing device had the function to contain and control the contained environment and transfer electrical energy from a power supply to a separateion medium and the charged material to be separated.
Frank Gibson
isoelectric focussing device
isoelectric focussing unit
sep:00097
thermostatic circulator
A thermostatic circulator is a device which cools or heats a circulating liquid. It has the function to contain control the contained environment and transfer energy from or to the circulating liquid
Frank Gibson
sep:00098
thermostatic circulator
energy supply function
An energy supply function is a function to supply or transfer energy from an energy source to a consumer of the energy
Frank Gibson
information processor function
An information processor function is a function that converts information from one form to another, by a lossless process or an extraction process.
Frank Gibson
data processor function
signal conversion function
A signal conversion function is an information processor function which transforms a signal into another type of signal. For example an analog-to-digital_converter, Ac/Ac converter, a synapse converts electrical action potentials into an intermediate chemical signal. The post synapse converts it back into an electric one passed on to the axon.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
signal conversion function
blot module
A blot module is a device which has the function to conatin and facilitate the material transfer process blotting to be realised
Frank Gibson
blot module
sep:00092
signal amplifcation function
A signal amplification function is a signal conversion function to inject energy into an input signal so as to produce an output signal with increased differntial magnitude while also seeking to minimize increases in the signal to noise ratio. For example, to produce a 0.1 KW output signal from a 1 mW RMS input signal.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
signal amplification function
measuring
image aquisition function
An image aquisition function is a function to aquire an image of a material
Frank Gibson
image aquisition function
image aquisition device
An image acquisition device is a device which captures a digitiesed image of an object
Frank Gibson
image acquisition device
sep:00096
immobilize function
An immobilize function is a contain function to fix an entity in a defined position and prevent its movement
Daniel Schober
Frank Gibson
Melanie Courtot
immobilize funtion
display function
A display function is a function to present information by translating that information through some lookup process into visual form.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
display function
environment control function
An environmentl control function is a function that regulates a contained environment within specified parameter ranges. For example the control of light exposure, humidity and temperature.
Bill Bug
Daniel Schober
Frank Gibson
Melanie Courtot
environment control function
canonical realisation of device function
sort function
A sort function is a function to distinguish material components based on some associated physical quality or entity and to partition the separate components into distinct fractions according to a defined order.
Daniel Schober
Frank Gibson
Melanie Courtot
gel dryer
A gel dryer is a device which has the function to contain and to control the contained environment to facilitate the drying of gels
Frank Gibson
gel dryer
sep:00094
primer_role
PCR product
is double stranded DNA that is the output of a polymerase chain reaction
should we use PCR (or the written out words)? These are also in the Sequence Ontology, should we take them from there? Needs DNA added to the logical definition
viral RNA extraction
cloning_vector_plus_insert
template_role
recombinant plasmid
cloning vector role
A cloning vector role is a vector role played by a small, self-replicating DNA or RNA molecule - usually a plasmid or chromosome - and realized in a process whereby foreign DNA or RNA is inserted into the vector during the process of cloning.
recombinant plasmid construction
A recombinant plasmid construction is a process with the objective to create a plasmid that contains an artificial combination of DNA
cell cycle synchronization
Bjoern Peters and Nicole Washington
Elimination of serum from the culture medium for about 24 hours results in the accumulation of cells at G1 phase. This effect of nutritional deprivation can be restored by their addition by which time the cell synchrony occurs.
OBI PA
cell cycle synchronization is a process with the objective to obtain a cell culture in which all cells are in the same stage of the cell cycle
_instrument by virtue of part
polymerase chain reaction
OBI Plan
Opisthorchis viverrini: Detection by polymerase chain reaction (PCR) in human stool samples. Exp Parasitol. 2008 Sep 9. PMID: 18805413
PCR
PCR is the process in which a DNA polymerase is used to amplify a piece of DNA by in vitro enzymatic replication. As PCR progresses, the DNA thus generated is itself used as a template for replication. This sets in motion a chain reaction in which the DNA template is exponentially amplified.
adapted from wikipedai
cloning insert role
is the role a DNA or RNA fragment plays that is inserted into a cloning vector in a cloning process.
measuring glucose concentration in blood serum
reverse transcriptase
enzyme and has_function some GO:0003964 (RNA-directed DNA polymerase
activity)
group:OBI
person:Melanie Courtot
reverse transcriptase
trypsinized material
Test Class: to evaluate OBI design pattern
_relative position
Philippe Rocca-Serra
syringe
Accuracy of oral liquid measuring devices: comparison of dosing cup and oral dosing syringe.Ann Pharmacother. 2008 Jan;42(1):46-52. Epub 2007 Dec 4. PMID: 18056832
OBI Instrument adapted from Wikipedia
Philippe Rocca-Serra
a syringe is a device which is used to introduce or draw fluids from a material entity. Syringe is made of a piston and body. the movement of the piston in the body determines the amount/volume of fluid to inject or draw
extract
OBI
Philippe Rocca-Serra
Up-regulation of inflammatory signalings by areca nut extract and role of cyclooxygenase-2 -1195G>a polymorphism reveal risk of oral cancer. Cancer Res. 2008 Oct 15;68(20):8489-98. PMID: 18922923
an extract is a material entity which results from an extraction process
extracted material
transcription profiling
OBI
Philippe Rocca-Serra
Whole genome transcription profiling of Anaplasma phagocytophilum in human and tick host cells by tiling array analysis. BMC Genomics. 2008 Jul 31;9:364. PMID: 18671858
gene expression profiling
trancription profiling is a process which aims to provide information about gene expression and transcription activity using ribonucleic acids collected froma entity of organismal origin using a range of techniques and instrument such as DNA sequencers, DNA microarrays, Northern Blot
averaging objective
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
A mean calulcation which has averaging objective is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the “center of gravity” for the data set. It is also known as the first moment.
An averaging objective is a data transformation objective where the aim is to perform mean calculations on the input of the data transformation.
James Malone
averaging objective
injection
Multiple Small-Dose Injections Can Reduce the Passage of Sclerosant Foam into Deep Veins During Foam Sclerotherapy for Varicose Veins. Eur J Vasc Endovasc Surg. 2008 Oct 13. PMID: 18922712
OBI Biomaterial
Philippe Rocca-Serra
injection is process which aims at introducing a compound or a mixture into a material entity (either biological entity or instrument) by relying on devices such as synringe or injector connected,attached or forced into a vascular system (veins of an organism or tubes of a machine) or in a tissue.
enzyme
(protein or rna) or has_part (protein or rna) and
has_function some GO:0003824 (catalytic activity)
GROUP:OBI
enzyme
person: Melanie Courtot
latitude
intraperitoneal administration
plasmid
group:OBI
person:Melanie Courtot
plasmid
plasmid = DNA and has_quality circular and has_function
(is_realized_as some gene expression) GO:0010467
injection into organ section
polyacrylamide gel
Assessing CMT cell line stability by two dimensional polyacrylamide gel electrophoresis and mass spectrometry based proteome analysis. J Proteomics. 2008 Jul 21;71(2):160-7. PMID: 18617143
OBI Biomaterial
Philippe Rocca-Serra
agarose gel is a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
DNA sequence feature detection
OBI
Philippe Rocca-Serra
should be a defined class where interpretation of data generated by assay qualifies a DNA sequence
administrating substance objective
is the specification of an objective to place an administered substance (role) in a target (role) location
genotyping
High-throughput genotyping of oncogenic human papilloma viruses with MALDI-TOF mass spectrometry. Clin Chem. 2008 Jan;54(1):86-92. Epub 2007 Nov 2.PMID: 17981923
OBI Biomaterial
Philippe Rocca-Serra
genotype profiling
genotyping is a process which generates a genotype from genomic DNA isolated from an entity of organismal origin. A variety of techniques and instruments can be used to produce information about sequence variation at particular genomic positions
needle
OBI Instrument
Ovarian carcinoma presenting with axillary lymph node metastasis: A case diagnosed by fine-needle aspiration and brief review of the literature.
Diagn Cytopathol. 2008 Oct 16. PMID: 18925569
Philippe Rocca-Serra
a needle is a sharp, hollow device used to penetrate tissue or soft material. When attached to a syringe. it allows delivery of a specific volume of liquid or gaseous mixture.
needle
analyte measurement objective
is an assay objective to determine the presence or concentration of an analyte in the evaluant
DNA sequence variation detection
Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform. Nucleic Acids Res. 2006;34(18):e121. PMID: 17000641
DNA sequence variation detection is a process which aims at finding changes (expansion, amplification, deletion, mutation) in sequence of DNA molecule.
OBI Biomaterial
Philippe Rocca-Serra
agarose gel
OBI biomaterial
Performance comparison of capillary and agarose gel electrophoresis for the identification and characterization of monoclonal immunoglobulins. Am J Clin Pathol. 2008 Mar;129(3):451-8. PMID: 18285269
Philippe Rocca-Serra
agarose gel is a material entity resulting from the polymerization of agarose after heating agarose suspended in some buffer solution
longitude
assay objective
is the specification of an objective to determine a specified type of information about an evaluated entity (independent continuant bearing evaluant role)
heart
analyte measuring assay
Is an assay with the objective to determine a quality: the presense, concentration, or amount of one substance (bearer of analyte role) that is present in another(bearer of the evaluant role).
Note: is_realization of some analyte role isn't always true, for example when there is none of the analyte in the evaluant. For the moment we are writing it this way, but when the information ontology is further worked out this will be replaced with a condition discussing the measurement.
Philippe will add that the datum is about a concentration of the analyte towards the evaluant.
datum here will be replaced by measurement_datum when the IAO is imported into OBI
example of usage: In lab test for blood glucose, the test is the assay, the blood bears evaluant_role and glucose bears the analyte role. The evaluant is considered an input to the assay and the information entity that records the measurement of glucose concentration the output
target role
weight measurement assay
a process to determine the weight of an evaluant
identification
DNA cleavage assay for the identification of topoisomerase I inhibitors.
Nat Protoc. 2008;3(11):1736-50. PMID: 18927559
Philippe Rocca-Serra
a process by which the identity (what a thing is) of a material entity is established within a certain confidence interval
obsolete_biomaterial
OBI Biomaterial derived
Philippe Rocca-Serra
obsolete_genetic information content
example_of_usage to be added
genetic information content
obsolete_allele
An allele is a viable DNA coding that occupies a given locus (position) on a chromosome. It represents one of two or more alternative forms of a gene or marker sequence at a given locus and differing from other alleles at one or more mutational sites based on phenotype or sequence.
Helen Parkinson
MO_58
Melanie Courtot
PMID: 18241317, Alcohol Clin Exp Res. 2008 Jan 30. Association of the Epsilon2 Allele of Apoe Gene to Hypertriglyceridemia and to Early-Onset Alcoholic Cirrhosis.
Philippe Rocca-Serra
Susanna Sansone
allele
bin under common 'Genotype' Placeholder. Do we also want recessive_allele etc? as Children or are these qualities. HP will check with PATO
http://en.wikipedia.org/wiki/Allele
obsolete_diplotype
A diplotype is the association of two alleles of a haplotype (or simple gene allele) in a diploid organism.
Helen Parkinson
MC: is diplotype a diploid genotype? (cf haplotype)
PMID: 11842208. Proc Natl Acad Sci U S A. 2002 Feb 19;99(4):2228-33. "...Theory to estimate the covariance D for a random sample of haplotypes or disomic genotypes (diplotypes) may be extended to the association probability...."
PMID:15274749. BMC Genet. 2004 Jul 26;5:20."..The combination of two haplotypes is called the diplotype..."
TCCG/CCTG at the ADH1B
PRS: see reference, it stands for disomic genotype and it is also referred to as " The combination of two haplotypes is called the diplotype" from PMID:15274749 even though no details are given on the type of combinaition
Philippe Rocca-Serra
Susanna Sansone
Tina Boussard/PharmGBK
diplotype
disomic genotype
haplotype pair
obsolete_haplotype
A haplotype, or ""haploid genotype"", is a set of allelic states found at neighbouring loci on a chromosome, as inherited from a parent. Haplotype can be determined also as the genetic constitution of an individual chromosome. In the case of diploid organisms such as humans, the haplotype will contain one member of the pair of alleles for each site.
Addition :
A haplotype is a genetic information content which corresponds to the genetic constitution of an individual chromosome (in diploid species); one member of a pair of alleles for each loci.
When haplotypes are defined with relation to SNPs, the definition changes: a haplotype is a set of SNPs found to be statistically associated on a single chromatid. That is, adjacent SNPs that are inherited together on the basis of linkage disequilibrium.
Addition from http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=haplotype&rid=helpsnpfaq.section.Info.Information_about_Ha
MC: definition says it is a haploid genotype. Should be a subclass of genotype then
MO_146
PMID: 18193213 ,Immunogenetics. 2008;60;1-18.Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project. "...The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database..."
other example: The AMH 1.15 haplotype is also referred to as the Atlantic Modal Cluster or AMC
Philippe Rocca-Serra
Susanna Sansone
adapted from en.wikipedia.org/wiki/Haplotype
haplotype
obsolete_genotype
Genotype is a genetic information content which corresponds to the total sum of the genetic information of an organism that is known and relevant to the experiment being performed, including chromosomal, plasmid, viral or other genetic material which has been introduced into the organism either prior to or during the experiment.
MO_51
Philippe Rocca-Serra
THIS ALSO SOUNDS LIKE NON-REALIZABLE INFORMATION ENTITY TO ME, HENCE DENRIE. JAMES
IT IS CURRENTLY A PLACEHOLDER. Philippe
genotype
p53 codon 72 genotype
obsolete_natural biomaterial
OBI Biomaterial derived
DS: Assign metadata and ID
THIS IS NOT A GOOD PARENT CONCEPT - THIS SHOULD BE A QUALITY. JAMES
definition pending
example_of_usage to be added
natural biomaterial
obsolete_unicellular organism
Bjoern Peters (added term)
E Coli
MC: should be a child of organism?
I THINK THIS IS LIKELY A QUALITY. JAMES
Organism made up of a single cell
added as hierarchy term
none
unicellular organism
Epstein Barr virus transformed B cell
OBI Biomaterial derived
Susanna Sansone
an EBV transformed B cell is an entity of organismal entity which results from viral transformation process using EBV as transformation agent when applied to B-cell entity
PMID: 8777380. Expression of thyroid peroxidase in EBV-transformed B cell lines using adenovirus.Thyroid. 1996 Feb;6(1):23-8.
obsolete_cytotoxic T-cell
A cytotoxic T-cell belongs to a sub-group of T lymphocytes (a type of white blood cell) which are capable of inducing the death of infected somatic or tumor cells; they kill cells that are infected with viruses (or other pathogens), or are otherwise damaged or dysfunctional.
CD8+ T cells are recognized as cytotoxic T-cells once they become activated
Melanie Courtot
T-Killer cell
cytotoxic T-cell
http://en.wikipedia.org/wiki/Cytotoxic_T-cell
killer T cell
obsolete_ecotype
PRS: Following discussion on biomaterial branch related to taxonomic order,strain and species, this class might get deprecated or submitted to role branch
A. thaliana Ecotype Ler
An ecotype of a species is subgroup of members of that species characterized by the ecological surroundings it inhabits.
Helen Parkinson
MO_71
Melanie Courtot
ecotype
http://en.wikipedia.org/wiki/Ecotype
chimera
An organism which contains cells or tissues with a different genotype
DS: Is a chimaera a natural_biomaterial? Not sure here.
Helen Parkinson
chimera
example_of_usage to be added
source pending
macroscopic part of multicellular organism
BP: The purpose of this class is to be different from 'entity of organismal orgin' to refer to ONLY those entities that are still part of the organism. The label 'organism part' instead of 'anatomical entity was chosen to make this more explicit.
Bjoern Peters
No OBI class should be here, they should all be imported from FMA / CARO etc.
PRS: Possible Import from CARO:0000000
Philippe Rocca-Serra
not super happy about liquids (blood, sperm), as they seem to be 'granular' somewhat, and not form a structure.
A macroscopic part of a multicellular organism is a material entity that is part of a multicelluar organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it.
MO
Tina Boussard
Tissue, organ, system, sperm, blood or body location (arm).
organism part
blood plasma
PRS:19032008-moved under entity of organismal origin ->modification to definition to reflect change + addition of pubmed based example
Philippe Rocca-Serra
Maura Gasparetto
Melanie Courtot
PMID: 18217225.Sex Transm Dis. 2008 Jan;35(1):55-60. Review.Human immunodeficiency virus viral load in blood plasma and semen: review and implications of empirical findings.
This is in FMA
WEB: http://en.wikipedia.org/wiki/Blood_plasma
blood plasma
blood plasma is an entity of organismal origin which corresponds to the liquid component of blood, in which the blood cells are suspended.
plasma
blood serum
Philippe Rocca-Serra
Blood serum is an entity of organismal origin which derives from blood and corresponds to blood plasma without fibrinogen or the other clotting factors.
Maura Gasparetto
Melanie Courtot
PMID: 18229666.Adv Med Sci. 2007;52 Suppl 1:204-6.Antioxidant activity of blood serum and saliva in patients with periodontal disease treated due to epilepsy.
PRS:19032008-moved under entity of organismal origin ->modification to definition to reflect change + addition of pubmed based example
WEB: http://en.wikipedia.org/wiki/Blood_plasma
blood serum
obsolete_cohort
10/02/2008: PRS - Should be a child of population (we now do away with agregate object for the moment)
A cohort is a group of individuals, identified by a common characteristic, who are studied over a period of time as part of an epidemiological investigation.
Cancer Medicine. 6th ed.
Kufe, Donald W.; Pollock, Raphael E.; Weichselbaum, Ralph R.; Bast, Robert C., Jr.; Gansler, Ted S.; Holland, James F.; Frei III, Emil, editors.
Hamilton (Canada): BC Decker Inc; c2003.ISBN 1–55009–213–8.
Helen Parkinson
PMID: 18260175. J Rheumatol. 2008 Feb 1."...Miami, Florida, and Midwestern US (Missouri) Caucasian MCTD cohorts were studied. Clinical and laboratory features of the 2 MCTD cohorts were compared. A concurrently collected cohort of Sm-positive patients with systemic lupus erythematosus (SLE) was studied as a control..."
Philippe Rocca-Serra
Susanna Sansone
Tina Boussard/PharmGBK
cohort
obsolete_serotype
A serotype is a subdivision of a species of microorganism, eg, a bacteria, based upon its particular antigens.
MO_159
Melanie Courtot
Streptococcus pyogenes M3 serotype
Tina Boussard
allograft
serotype
obsolete_strain
A strain is the collective descendants of a common ancestor; synonyms: race, stock, line, or breed.
Canton S is a strain of Drosophila
MO
Tina Boussard
strain
obsolete_biomolecule
A biomolecule is a molecule that naturally occurs in living organisms and biological systems.
James Malone
MC: do we want a sibling to include chemicals for example?
WEB: http://en.wikipedia.org/wiki/Biomolecule
biomolecule
keratin
obsolete_enzyme
Enzymes are proteins that catalyze (i.e. accelerate) chemical reactions. They work by lowering the activation energy (Ea or ΔG‡) for a reaction, thus dramatically accelerating the rate of the reaction.
MC: should be child of a class protein
Melanie Courtot
Oxidoreductases
Transferases
WEB: http://en.wikipedia.org/wiki/Enzyme
enzyme
obsolete_DNA polymerase
A DNA polymerase is an enzyme that assists in DNA replication. Such enzymes catalyze the polymerization of deoxyribonucleotides alongside a DNA strand, which they "read" and use as a template. The newly-polymerized molecule is complementary to the template strand and identical to the template's partner strand.
DNA polymerase
Melanie Courtot
Taq polymerase is a commonly used DNA polymerase to copy DNA templates in PCR reactions.
WEB: http://en.wikipedia.org/wiki/DNA_polymerase
obsolete_reverse transcriptase
A reverse transcriptase is a DNA polymerase enzyme that transcribes single-stranded RNA into single-stranded DNA.
Avian reverse transcriptase transcribes RNA into complementary DNA.
MC: should be a child of DNA polymerase
Melanie Courtot
RNA-dependent DNA polymerase
WEB: http://en.wikipedia.org/wiki/Reverse_transcriptase
reverse transcriptase
organism
An organism is biomaterial entity that is an individual living system, such as animal, plant or micro-organism, that is capable of reproduction, growth and maintenance. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
Melanie Courtot
WEB: http://en.wikipedia.org/wiki/Organism
animal
examples: Archaea, Bacteria,Eukaryota,Viroids, Viruses rem1: OBI should link to an external resource (e.g. NCBI Taxonomy) Altdef: an organism is a biomaterial entity which is self-contained
MC: virus and viroid are not organisms
fungus
micro-organism
organism
organism "has_role_which_can_only_be_played_by_biomaterial_entity" some specimen_role, organism "has_role" some investigation_object_role in obi before split (LF 040907).
plant
obsolete_virus
A virus (from the Latin virus meaning toxin or poison) is a sub-microscopic infectious agent that is unable to grow or reproduce outside a host cell. Each viral particle, or virion, consists of genetic material, DNA or RNA, within a protective protein coat called a capsid. The capsid shape varies from simple helical and icosahedral (polyhedral or near-spherical) forms, to more complex structures with tails or an envelope. Viruses infect cellular life forms and are grouped into animal, plant and bacterial types, according to the type of host infected. Viruses must replicate in a living cell, as they cannot carry out metabolic processes on their own.
HPV
Immunobiology by Janeway & Travers 1997
Maura Gasparetto
Melanie Courtot
WEB: http://en.wikipedia.org/wiki/Virus
merged Maura Gasparetto _ Helen Parkinson
MC: A virus is not an orgnism
virus
obsolete_archaea
An archaea is an organism that is a single-celled prokaryote. In this they are similar to bacteria but these two groups evolved differently, and are classified as different domains in the three-domain system.
Halobacterium
Melanie Courtot
WEB: http://en.wikipedia.org/wiki/Archaea
archaea
obsolete_bacterium
A bacterium is an organism that is a single-celled prokaryote.
Melanie Courtot
PERSON: Melanie Courtot
Staphylococcus
Streptococcus
Thiomargarita namibiensis
bacterium
obsolete_eukaryote
James Malone
An eukaryote is an organism whose cells are organized into complex structures by internal membranes and a cytoskeleton. The most characteristic membrane-bound structure is the nucleus. This feature gives them their name, also spelled "eucaryote," which comes from the Greek ??, meaning good/true, and ??????, meaning nut, referring to the nucleus.
Melanie Courtot
WEB: http://en.wikipedia.org/wiki/Eukaryote
animals
eukaryote
fungi
plants
protists
obsolete_viroid
Melanie Courtot
Viroids are plant pathogens that consist of a short stretch (a few hundred nucleobases) of highly complementary, circular, single-stranded RNA without the protein coat that is typical for viruses.
WEB: http://en.wikipedia.org/wiki/Viroid
rice yellow mottle sobemovirus (RYMV)
viroid
obsolete_in vivo biomaterial
OBI Biomaterial derived
Philippe Rocca-Serra
This is a place holder, indicating that we have trouble dealing with the state / site of biomaterials, i.e. in vivo, ex vivo, in vitro
THIS IS NOT A CONCEPT FOR BIOMATERIAL - LIKELY A QUALITY. JAMES
example_of_usage to be added
placeholder, to be moved/submitted to Site/Location
obsolete_cell derived from multicellular organism
A cell derived from a multicellular organism
Bjoern Peters
added as hierarchy term
HMMM.. THE CONCEPT HERE IS CELL, ITS ORIGIN IS A DIFFERENT CONCEPT LINKED BY A RELTION SUCH AS ORIGNATED_FROM OR SIMILAR. SUGGEST REMOVE THIS AND ADD APPROPRIATE RELATION. JAMES
cell derived from multicellular organism
lymphocyte
none
immortal cell
Bjoern Peters
PRS: 22-02-2008: need to submit immortal to PATO
a cell derived from a multicellular organism that has the potential to replicate indefinately
a single Hela cell
added as hierarchy term
immortal cell
none
obsolete_supernatant
Bjoern Peters
Liquid portion of complex biomaterial resulting from a separation from a solid portion
MC: should be a role
added as hierarchy term
none
none
supernatant
obsolete_artificially engineered biomaterial
Laboratory created combination of discrete biomaterials not usually found in nature. Created with the purpose of facilitating laboratory research.
THIS IS NOT A GOOD PARENT CONCEPT - THIS SHOULD BE A QUALITY. JAMES
Bjoern Peters
IEDB
artificially engineered biomaterial
chimeric mAb, chimeric mouse, GST-Rho protein
obsolete_vector
A vector is a vehicle for transferring genetic material into a cell. It is an autonomous replicating vehicle which can be modified by the insertion of foreign DNA and when introduced into recipient cells does not alter the viability of those cells.
Adapted from http://en.wikipedia.org/wiki/Vector_%28biology%29
Melanie Courtot
PRS: Vector should treated as a role ->submission to tracker
Philippe Rocca-Serra
Susanna Sansone
The DNA expressing the protein of interest was inserted within pM13 which was then transfected into a cell line to facilitate expression of the protein.
plasmid vector
vector
viral vector
fragment derived from protein
Bjoern Peters
IEDB
PRS:22022008. result from protocol_application where input=protein and output=polypeptide or peptide (to capture: derives_from protein)
a fragment derived from protein is an entity of organismal origin which is derived from a protein
fragment derived from protein
original term: protein fragment split into synthetic polypeptide and fragment derived from protein
THE DEFINITION OF THIS SUGGESTS WE COVER THIS ALREADY IN PEPTIDE/POLYPETIDE. DO WE NEED THIS AND CAN WE DEAL WITH IT IN SOME OTHER WAY? JAMES
the peptide with sequence SIINFEKL, which is eluted from a cell expressing hen egg lysozyme
obsolete_biosource provider
Helen Parkinson
MO_230
THIS IS A ROLE. James
The Jackson Laboratory is a biosource_provider
The resource or individual (e.g. company, hospital, commerical supplier) used to obtain or purchase the biomaterial.
biosource provider
obsolete_cultivar
A cultivar is a cultivated plant that has been selected and given a unique name because it has desirable characteristics (decorative or useful) that distinguish it from otherwise similar plants of the same species. When propagated it retains those characteristics.
Helen Parkinson
MO_124
Melanie Courtot
Solanum tuberosum has a virus resistant cultivar Alcmaria
WEB: http://en.wikipedia.org/wiki/Cultivar
cultivar
obsolete_differentiation state
ArrayExpress
Helen Parkinson
PRS: Should be 'cellular differentiation state' and should be moved to quality or dependent continuant branch
Philippe Rocca-Serra
Prostate epithelial transit amplifying cells
The differentiation state is a descriptor of a cell's properties at some defined point in the differentiation process recognisable by some observable characteristic such as morphology.
differentiation state
obsolete_genetic modification
"GENETIC MODIFICATION" TO ME SOUNDS LIKE AN ACTION - NOT SURE HOW WE DEAL WITH THIS ONE.
Examples of genetic modification include specification of a transgene or the gene knocked-out or details of transient transfection. A deletion
MO_122
PRS: move to plan and planned processes and possibly send to dependentcontinuant branch or PATO a quality such as 'genetically modified'
The genetic modification is a process in which genetic material into introduced,added or removed into the organism from which the biomaterial was derived in order to introduce, repair or remove a particular locus and possibly altering biological function of the targeted genetic structure.
genetic modification
modified by Philippe Rocca-Serra
obsolete_molecular mixture
A molecular mixture is an unspecified collection of heterogeneous molecules, e.g. lipids, carbohydrate , nucleic acids and proteins
MO_889
PRS:22022008
from the current definition, it sounds like an bfo:agregate object with a possibility to become a child of collection-> hence change curation status by adding temporary graph position
The material obtained upon homogenizing a biomaterial
Tina Boussard
molecular mixture
obsolete_liquid chemical solution
moved here following BM140308-call from molecular mixture (a class which has been deprecated, i.e. moved to obsolete.owl
Bjoern Peters
PBS, RPMI
a liquid solvent containing one or more solutes
added as hierarchy term
liquid chemical solution
phosphate buffered saline solution
Philippe Rocca-Serra
Melanie Courtot
PBS buffer
PMID: 16279733.Dent Mater J. 2005 Sep;24(3):414-21.PBS buffer solutions with different pH values can change porosity of DNA-chitosan complexes.
Phosphate buffered saline (abbreviated PBS) is a buffer solution commonly used in biochemistry. It is a salty solution containing sodium chloride, sodium phosphate and potassium phosphate. The buffer helps to maintain a constant pH. The concentration usually matches the human body (isotonic).
Tina Boussard
http://en.wikipedia.org/wiki/Phosphate_buffered_saline
phosphate buffered saline solution
obsolete_emulsion
A mixture of immiscible (unblendable) substances, that are finely dispersed and not separate through the action of gravity alone
MC: should be a state
PSI
Susanna
emulsion
lipid emulsion, oil in water emulsion, perfluoro-chemical emulsion, photographic emulsion
obsolete_solution
A homogeneous mixture of two or more substances
MC: should be a state
PSI
Susanna
solution
obsolete_suspension
MC: should be a state
PSI
Substance floating in a liquid medium
Susanna
suspension
obsolete_?organism status
?organism status
E.g. premortem or postmortem
MO
Organism_status is the stage premortem or postmortem at which the sample was processed for extraction of biomaterials.
THIS IS PROBABLY A QUALITY. JAMES
Tina Boussard
entity of organismal origin
PERSON: James Malone
Philippe Rocca-Serra
An entity of organismal origin is a biomaterial entity which is obtained from an organism.
OBI Biomaterial derived
entity of organismal origin
example_of_usage to be added
cell of organismal origin
OBI Biomaterial derived
OBI Biomaterial derived
A cell of organismal origin is an entity of organismal origin that contains nuclear and cytoplasmic material enclosed by a semipermeable membrane.
cell of organismal origin
hepatocyte
rem1:link to Cell Type Ontology (CO)
obsolete_cell component
possible import: CARO:0000014
Anatomical structure that is a direct part of the cell.[From CARO]
Old:A cell component is an entity of organismal origin which has a definable shape, bounded predominantly by bonafide boundaries.
CARO
PMID: 1046421. Regulation of cell component production by growth rate in the group B Streptococcus. J Bacteriol. 1999 Sep;181(17):5389-94.
cell component
obsolete_cellular compartment
James Malone
OBI Biomaterial derived
Philippe Rocca-Serra
possible import from GO or From CARO
PMID: 15342780 .The PEN1 syntaxin defines a novel cellular compartment upon fungal attack and is required for the timely assembly of papillae. Mol Biol Cell. 2004 Nov;15(11):5118-29. Epub 2004 Sep 1.
a cellular compartment is a cellular component which is defined or enlosed by a lipidic membrane (golgi) and nucleic acid material (nucleole).
cellular compartment
cell line cell
Susanna Sansone
A cell line is an entity of organismal origin that represents generations of a primary culture.
OBI Biomaterial derived
cell line cell
example_of_usage to be added
immortalized cell line
Susanna Sansone
An immortalized cell line is a cell line that is able to replicate indefinitely as a result of an immortalization process
Isolation and characterization of an immortalized oral keratinocyte cell line of mouse origin.
Arch Oral Biol. 2008 Nov;53(11):1091-100. Epub 2008 Aug 21. PMID: 1872191
OBI Biomaterial derived
immortalized cell line
obsolete_multicellular entity of organismal origin (Should be deprecated!)
OBI Biomaterial
A multicellular entity of organismal origin is an entity of organismal origin that is a heterogeneous biomaterial entity which is either part of an organism or which is obtained from an organism by "material transformation process"
OBI Biomaterial derived
PRS: The class definition does not reflect its position anymore . Should be removed/obsoleted as reliance on CARO is expanded.
multicellular entity of organismal origin
multicellular entity of organismal origin "has role" some ex-vivo state in obi before split (LF 040907).
xenograft
Philippe Rocca-Serra
Human xenotransplantation (e.g. from pig to human) offers a potential treatment for end-stage organ failure, a significant health problem in parts of the industrialized world
MC: xenotransplantation should be submited to material_transformation
Melanie Courtot
WEB: http://en.wikipedia.org/wiki/Xenograft
a xenograft is an entity of organismal origin which results from the transplantation of living cells, tissues or organs from on organism of one species to an organism of another species.
xenograft
xenotransplant
obsolete_experimental biomateral entity
DS: what is this? Does the 'experimental' here refer to the biomaterials role in an experiment? Or does this refer to the metadata level, e.g. indicating this class' experimental status?
example_of_usage to be added
experimental biomateral entity
cell culture
OBI Biomaterial derived
Bjoern Peters (added term)
Jurkat cell line in RPMI w/ 10% FCS. PBMCs were purified from blood sample and put into tissue culture media.
Purification of recombinant human growth hormone from CHO cell culture supernatant by Gradiflow preparative electrophoresis technology.
Protein Expr Purif. 2003 Nov;32(1):126-34.
PMID: 14680949
PRS:22-02-2008: cell entity has input_role in culturing or growth protocol application, has_site=in-vitro
a cell culture is an entity of organismal origin which corresponds to a population of cells and cell culture medium maintained in vitro and grown from a particular cell isolate. Can be homogeneous (monoclonal), heterogenous (oligoclonal, polyclonal)
added as hierarchy term
cell culture
primary cell culture
OBI Biomaterial derived
Susanna Sansone
a primary cell culture is a cell culture where the cells derive from a fresh tissue source.
primary cell culture
spleen cells put directly into culture
Cold storage of biopsies from wild endangered native Chilean species in field conditions and subsequent isolation of primary culture cell lines. In Vitro Cell Dev Biol Anim. 2008 Jul 2. PMID: 18594934
cell line culture
OBI Biomaterial derived
Susanna Sansone
HeLa cells
Changes in ultrastructure and endogenous ionic channels activity during culture of HEK 293 cell line. Eur J Pharmacol. 2007 Jul 12;567(1-2):10-8. PMID: 17482592
a cell line culture is a cell culture where the cells grown are from a cell line, long term culture of cells that are replicating continuously. The cell population is homogenous but not clonal
cell line culture
clonal cell culture
OBI Biomaterial derived
Susanna Sansone
a clonal cell culture is a cell culture in which all cells can be assumed to be identical, tracking back to a single ancestor cell.
cell cut
Stem cell functions assessed in clonal culture. Soc Gen Physiol Ser. 1988;43:39-45. Review. PMID: 3077557
clonal cell culture
screening library
IEDB
Bjoern Peters
PMID: 15615535.J Med Chem. 2004 Dec 30;47(27):6864-74.A screening library for peptide activated G-protein coupled receptors. 1. The test set. [cdna_library, phage display library]
PRS: 22-02-2008: while working on definition of cDNA library and looking at current example of usage, a screening library should be a defined class -> any material library which has input_role in a screening protocol application
change biomaterial to material in definition
a screening library is a collection of materials engineered to identify qualities of a subset of its members during a screening process?
added as hierarchy term
screening library
synthetic polypeptide
Bjoern Peters
IEDB
PRS:22-02-2008: a chebi entity which has output role in a synthesis protocol application
a synthetic polypeptide is an material entity which is artificially engineered and results from the synthesis of a chain of amino acids which may also be found in natural protein and be identical in sequence to a protein fragment
original term: protein fragment split into synthetic polypeptide and fragment derived from protein
DS: Is this synthetic an oxymoron to the biomaterial?
synthetic polypeptide
the synthesized peptide SIINFEKL which also occurs in hen-egg lysozyme
organ section
Philippe Rocca-Serra
A liver slice used in a perfusion experiment.
Thyroidectomy during laryngectomy for advanced laryngeal carcinoma--whole organ section study with long-term functional evaluation. Clin Otolaryngol Allied Sci. 1995 Apr;20(2):145-9. PMID: 7634521
An organ_section is entity of organismal origin which derives from an organ and results from a process of dissection or histological sample preparation a portio(formerly an organ section is portionn of an organ removed from the context of the organ)
CEBS + OBI Biomaterial
Helen Parkinson
organ section
section needs to be added as process
PRS 22-02-2008: organ has input_role in protocol_application histological preparation.
Also how different it is from a fragment
bronchial alveolar lavage
BAL
Bjoern Peters
Group of biomaterials present in the bronchial aveolar space of an organism which are collected through lavage including the reagents used to for the lavage process, organisms, cells, and cellular secretions present in the bronchial aveolar space.
IEDB
PRS:22-02-2008: output role in protocol application lavage and need to submit protocol application
bronchial alveolar lavage
solution containing lung derived T cells, eosinophils, and TNFa.
monomer
OBI Biomaterial derived
PRS 210608: moved from biomaterial branch following deprecation of biomolecule class (note: polymer has been moved under quality (since polymer describes the result of a polymerization process where as monomer indicates that a chemical entity has the potential to be used as a monomer such polymerization reaction)
placeholder, possible import from CHEBI
to be added (possibly)
Susanna Sansone
TEMP FOR NOW FOR STRUCTURE - MAY NEED TO REMOVE THIS. JAMES
monomer
polymer
PRS:210608: moved here following deprecation of biomolecule - to be discussed in branch role
A macromolecule is a molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass.
James Malone
Philippe Rocca-Serra
TEMP FOR NOW FOR STRUCTURE - MAY NEED TO REMOVE THIS. JAMES
TERM: CHEBI:33839
polymer
obsolete_amino acid
CHEBI:33709
Carboxylic acids containing one or more amino groups.
James Malone
PMID: 18215123. Biochem J. 2008 Jan 23.Human topoisomerase I (Top1) relaxes supercoiled DNA during cell division and transcription. Top1 is composed of 765 amino acids (aa) and contains an unstructured N-terminal domain of 200 aa, and a structured functional domain of 565 aa that binds and relaxes supercoiled DNA
Susanna Sansone
TEMP FOR NOW FOR STRUCTURE - MAY NEED TO REMOVE THIS. JAMES
amino acid
obsolete_prokaryote
James Malone
Melanie Courtot
The prokaryotes are a group of organisms that lack a cell nucleus (= karyon), or any other membrane-bound organelles.
WEB: http://en.wikipedia.org/wiki/Prokaryote
bacteria
prokaryote
obsolete_DNA virus
A DNA virus is a virus that has DNA as its genetic material and replicates using a DNA-dependent DNA polymerase.
DNA virus
James Malone
Melanie Courtot
WEB: http://en.wikipedia.org/wiki/DNA_virus
papillomavirus
obsolete_RNA virus
An RNA virus is a virus that has ribonucleic acid (RNA) as its genetic material and does not replicate using a DNA intermediate.
James Malone
Melanie Courtot
RNA virus
Susanna Sansone
WEB: http://en.wikipedia.org/wiki/RNA_viruses
hepatitis C virus
yellow fever virus
obsolete_reverse transcribing virus
A reverse transcribing virus is any virus which replicates using reverse transcription, the formation of DNA from an RNA template.
James Malone
Melanie Courtot
Susanna Sansone
WEB: http://en.wikipedia.org/wiki/Reverse_transcribing_viruses
hepatitis B virus
reverse transcribing virus
obsolete_plant
Any of various photosynthetic, eukaryotic, multicellular organisms of the kingdom Plantae characteristically producing embryos, containing chloroplasts, having cellulose cell walls, and lacking the power of locomotion.
James Malone
Melanie Courtot
WEB: http://www.answers.com/topic/plant?cat=biz-fin
plant
tree
obsolete_animal
A multicellular organism of the kingdom Animalia, differing from plants in certain typical characteristics such as capacity for locomotion, nonphotosynthetic metabolism, pronounced response to stimuli, restricted growth, and fixed bodily structure.
James Malone
MC: definition not satisfying, it tells more about the difference between plant and animal than what is an animal.
Melanie Courtot
WEB: http://www.answers.com/animal?cat=health
animal
human
obsolete_fungus
A fungus is any eukaryotic organism that is a member of the kingdom Fungi. The fungi are heterotrophic organisms characterized by a chitinous cell wall, and in the majority of species, filamentous growth as multicellular hyphae forming a mycelium; some fungal species also grow as single cells.
James Malone
Melanie Courtot
Saccharomyces cerevisiae
WEB: http://en.wikipedia.org/wiki/Fungus
fungus
obsolete_protist
James Malone
Melanie Courtot
Protists are a diverse group of organisms, comprising those eukaryotes that cannot be classified in any of the other kingdoms as fungi, animals, or plants.
WEB: http://en.wikipedia.org/wiki/Protist
algae
protist
protozoa
obsolete__move to role?
All classes yet to be suitably placed in a hierarchy
James Malone
example_of_usage to be added
source pending
this class should eventually be removed
obsolete__move to quality?
All classes yet to be suitably placed in a hierarchy
James Malone
example_of_usage to be added
source pending
this class should eventually be removed
obsolete__move to relations?
All classes yet to be suitably placed in a hierarchy
James Malone
example_of_usage to be added
source pending
this class should eventually be removed
obsolete_peptide
Amides derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid.
James Malone
Philippe Rocca-Serra
Susanna Sansone
TEMP FOR NOW FOR STRUCTURE - MAY NEED TO REMOVE THIS. JAMES
HAS PART_OF RELATION WITH POLYPEPTIDE CONCEPT
HAS MADE_UP_OF RELATION WITH AMINO ACID CONCEPT. JAMES
TERM: CHEBI:16670
peptide
obsolete_polypeptide
James Malone
Peptides containing ten or more amino acid residues
Philippe Rocca-Serra
Susanna Sansone
TEMP FOR NOW FOR STRUCTURE - MAY NEED TO REMOVE THIS. JAMES
HAS MADE_UP_OF RELATION WITH PEPTIDE CONCEPT. JAMES
TERM: CHEBI:15841
polypeptide
obsolete_protein (obsolete)
James Malone
Melanie Courtot
Naturally occurring polypeptides synthesized at the ribosome.(CHEBI)
Proteins are large organic compounds made of amino acids arranged in a linear chain and joined together by peptide bonds between the carboxyl and amino groups of adjacent amino acid residues.
Philippe Rocca-Serra
Susanna Sansone
TEMP FOR NOW FOR STRUCTURE - MAY NEED TO REMOVE THIS. JAMES
HAS MADE_UP_OF RELATION WITH POLYPEPTIDE CONCEPT. JAMES
TERM: CHEBI:16541
WEB: http://en.wikipedia.org/wiki/Protein
hemoglobin
protein
data transformation
A protocol application which has the objective to produce output data from input data
Philippe Rocca-Serra
A data transformation is a protocol application which produces output data from input data - e.g. the application of a clustering protocol to microarray data or the application of a statistical testing method on a primary data set to determine a p-value.
Branch editors
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Richard Scheuermann
Ryan Brinkman
Tina Hernandez-Boussard
a protocol application which has the objective to produce output data from input data
data analysis
data processing
data transformation
logistic-log curve fitting
A logistic-log curve fitting is a curve fitting where a curve of the form y=d+((a-d)/(1+(x/c)^b)) is obtained, where a, b, c, and d are determined so to optimize its fit to the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n).
ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448
Elisabetta Manduchi
James Malone
Melanie Courtot
Ryan Brinkman
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case a and d correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively; c is the dilution associated with the point of symmetry of the sigmoid and is located at the midpoint of the assay found at the inflection point of the curve; b is a curvature parameter and is related to the slope of the curve.
logistic-log curve fitting
logit-log curve fitting
A logit-log curve fitting is a curve fitting where first the limits y_0 an y_infty of y when x->0 and x->infinity, respectively, are estimated from the input data points (x_1, y_1), (x_2,y_2), ..., (x_n, y_n). Then a curve with equation log((y-y_0)/(y_infty-y))=a+b log(x) is obtained, where a and b are determined to optimize its fit to the input data points.
ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1448
Elisabetta Manduchi
James Malone
Melanie Courtot
Ryan Brinkman
The above definition refers to the 'fully specified' logit-log model. The reduced form of this, when it is assumed that y_0=0, is named 'partially specified' logit-log model.
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution. In this case OD_0 (also referred to OD_min) and OD_infty (also referred to OD_max) correspond to the theoretical OD of the assay at zero and infinite concentrations, respectively.
logit-log curve fitting
log-log curve fitting
A log-log curve fitting is a curve fitting where first a logarithmic transformation is applied both to the x and the y coordinates of the input data points (x_1, y_1), (x_2, y_2), ..., (x_n, y_n), and then coefficients a and b are determined to optimize the fit of log(y)=a+b*log(x) to these input data points.
ARTICLE: Plikaytis B.D. et al. (1991), J. Clin. Microbiol. 29(7): 1439-1446
Elisabetta Manduchi
James Malone
Melanie Courtot
Ryan Brinkman
Typically used in an enzyme-linked immunosorbent assay (ELISA) to model the relationship between optical density (OD) and dilution.
log-log curve fitting
feature extraction objective
Elisabetta Manduchi
A feature extraction objective is a data transformation objective where the aim of the data transformation is to generate quantified values from a scanned image.
James Malone
TERM: http://mged.sourceforge.net/ontologies/MGEDOntology.owl#feature_extraction
feature extraction objective
biexponential transformation
A biexponential transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation B(y)-x=0, where B denotes a b transformation.
Elisabetta Manduchi
Joseph Spliden
Ryan Brinkman
This type of transformation is typically used in flow cytometry.
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
biexponential transformation
box-cox transformation
A box-cox transformation is a data transformation according to the methods of Box and Cox as described in the article Box, G. E. P. and Cox, D.R. (1964) An analysis of transformations. Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246.
ARTICLE: Box, G. E. P. and Cox, D.R. (1964), "An analysis of transformations", Journal of Royal Statistical Society, Series B, vol. 26, pp. 211-246.
Ryan Brinkman
box-cox transformation
hyperlog transformation
A hyperlog transformation ia a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation EH(y)-x=0, where EH denotes an eh transformation.
ARTICLE: Bagwell C.B. (2006), "Hyperlog - a flexible log-like transform for negative, zero, and positive valued data", Cytometry A 64, 34-42."
Elisabetta Manduchi
Joseph Spliden
Ryan Brinkman
This type of transformation is typically used in flow cytometry
http://flowcyt.sourceforge.net/gating/latest.pdf
hyperlog transformation
obsolete_background correction
Obsolete as now replaced with objective background correction
A background correction is a data transformation where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation.
Elisabetta Manduchi
James Malone
Melanie Courtot
PERSON: Elisabetta Manduchi
loess scale group transformation one-channel
A loess scale group transformation one-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation one-channel, to render the M group variances similar.
Elisabetta Manduchi
Loess scale group normalization applied to data from two one-channel expression microarray assays.
OTHER: Editor's adjustment based on MGED Ontology term
loess scale group transformation one-channel
logicle transformation
A logicle transformation is a data transformation that, for each (one dimensional) real number input x, outputs an approximation (found, e.g. with the Newton's method) to a solution y of the equation S(y)-x=0, where S denotes an s transformation.
Elisabetta Manduchi
Joseph Spliden
Ryan Brinkman
This type of transformation is typically used in flow cytometry.
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
logicle transformation
loess scale group transformation two-channel
A loess scale group transformation two-channel is a loess scale group transformation consisting in the application of a scale adjustment following a loess group transformation two-channel, to render the M group variances similar.
Elisabetta Manduchi
Loess scale group normalization applied to data from a two-channel expression microarray assay.
OTHER: Adjusted from MGED Ontology
loess scale group transformation two-channel
loess global transformation one-channel
A loess global transformation one-channel is a loess global transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
Elisabetta Manduchi
Loess global normalization applied to data from two one-channel expression microarray assays, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases.
OTHER: Editor's generalization based on MGED Ontology term
loess global transformation one-channel
split-scale transformation
A split-scale transformation is a data transformation which is an application of a function f described as follows to a (one dimensional) real number input. f(x)=a*x+b if x=for x>t; where log denotes a logarithmic transformation and a, b, c, d, r, t are real constants, with a, c, d, r, t positive, chosen so that f is continuos with a continuous derivative at the transition point t.
Elisabetta Manduchi
Joseph Spliden
Ryan Brinkman
This type of transformation is typically used in flow cytometry
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
split-scale transformation
loess global transformation two-channel
A loess global transformation two-channel is a loess global transformation in the special case where the input the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
Elisabetta Manduchi
Loess global normalization applied to data from a two-channel expression microarray assay, where the curve is obtained using all reporters. The goal is to remove intensity-dependent biases.
OTHER: Editor's generalization based on MGED Ontology term
loess global transformation two-channel
sine transformation
A sine transformation is a data transformation which consists in applying the sine function to a (one dimensional) real number input. The sine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Sine.html.
Elisabetta Manduchi
WEB: http://mathworld.wolfram.com/Sine.html
sine transformation
sine(0)=0, sine(pi/2)=1, sine(pi)=0, sine(3*pi/2)=-1, sine(pi/6)=1/2, sine(x+2*k*pi)=sine(x) where k is any integer, etc.
cosine transformation
A cosine transformation is a data transformation which consists in applying the cosine function to a (one dimensional) real number input. The cosine function is one of the basic trigonometric functions and a definition is provided, e.g., at http://mathworld.wolfram.com/Cosine.html.
Elisabetta Manduchi
WEB: http://mathworld.wolfram.com/Cosine.html
cosine transformation
cosine(0)=1, cosine(pi/2)=0, cosine(pi)=-1, cosine(3*pi/2)=0, cosine(pi/3)=1/2, cosine(x+2*k*pi)=cosine(x) where k is any integer, etc.
loess group transformation one-channel
A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
A loess group transformation one-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from two related one-channel assays.
Elisabetta Manduchi
OTHER: Editor's generalization based on MGED Ontology term
loess group transformation one-channel
loess group transformation two-channel
A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
A loess group transformation two-channel is a loess group transformation in the special case where the input is the result of an MA transformation applied to intensities from the two channels of a two-channel assay.
Elisabetta Manduchi
OTHER: Editor's generalization based on MGED Ontology term
loess group transformation two-channel
homogeneous polynomial transformation
A homogeneous polynomial transformation is a polynomial transformation where all the term of the polynomial have the same degree.
Elisabetta Manduchi
WEB: http://mathworld.wolfram.com/HomogeneousPolynomial.html
a*x, with a non-zero, is a homogeneous polynomial of degree 1 in 1 variable, a*x^2, with a non-zero, is a homogeneous polynomial of degree 2 in 1 variable; a_1*x_1+...+a_n*x_n, with at least one of the a_i's non-zero, is a homogeneous polynomial of degree one in n variables; a*x_n^3+b*x_1*x_2*x_3, with at least one of a and b non-zero, is a homogeneous polynomial of degree 3 in n variables.
homogeneous polynomial transformation
linlog transformation
A linlog transformation is a data transformation, described in PMID 16646782, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (9) of this paper, where values below an appropriately determined threshold (dependent on the row i) are transformed via a polynomial of degree 1, and values above this threshold are transformed via a logarithm.
Elisabetta Manduchi
PMID: 16646782
This can be used for microarray normalization, e.g. to normalize the data from a two-channel expression microarray assay, as described in PMID 16646782.
linlog transformation
variance stabilizing transformation
A variance stabilizing transformationi is a data transformation, described in PMID 12169536, whose input is a matrix [y_ik] and whose output is a matrix obtained by applying formula (6) in this paper. One of the goals is to obtain an output matrix whose rows have equal variances. The method relies on various assumptions described in the paper.
Elisabetta Manduchi
James Malone
Melanie Courtot
PMID: 12169536
This can be used for expression microarray assay normalization and it is referred to as "variance stabilizing normalization", according to the procedure described e.g. in PMID 12169536.
variance stabilising transformation
variance stabilizing transformation
loess global transformation
A loess global transformation is a loess transformation where only one loess fitting is performed, utilizing one subset of (or possiby all of) the data points in the input so that there is only one resulting loess curve y=f(x) which is used for the transformation.
Elisabetta Manduchi
James Malone
Melanie Courtot
OTHER: Editor's generalization based on MGED Ontology term
loess global transformation
loess group transformation
A loess group transformation is a loess transformation where the input is partitioned into groups and for each group a loess fitting is performed, utilizing a subset of (or possibly all of) the data points in that group. Thus, a collection of loess curves y=f_i(x) is generated, one per group. Each (x, y) in the input is transformed into (x, y-f_i(x)), where f_i(x) is the curve corresponding to the group to which that data point belongs.
Elisabetta Manduchi
James Malone
Melanie Courtot
OTHER: Editor's generalization based on MGED Ontology term
loess group transformation
loess scale group transformation
A loess scale group transformation is a data transformation consisting in the application of a scale adjustment following a loess group transformation, to render the group variances for the second variable (y) similar. Has objective scaling.
Elisabetta Manduchi
James Malone
Melanie Courtot
OTHER: Editor's generalization based on MGED Ontology term
loess scale group transformation
total intensity transformation single
A total intensity transformation single is a data transformation that takes as input an n-dimensional (real) vector and multiplies each component of this vector by a coefficient, where the coefficient is obtained by taking the sum of the input components or of a subset of these, multiplied by a constant of choice.
Elisabetta Manduchi
Helen Parkinson
James Malone
Melanie Courtot
Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent.
OTHER: Adjusted from MGED Ontology
This can be used as a simple normalization method for expression microarray assays. For example, each intensity from a one-channel microarray assay is multiplied by a constant so that the output mean intensity over the microarray equals a desired target T (the multiplicative constant in this case is the T/(mean intensity)).
total intensity transformation single
total intensity transformation paired
A total intensity transformation paired is a data transformation that takes as input two n-dimensional (real) vectors and multiplies each component of the first vector by a coefficient, where the coefficient is obtained by taking the ratio of the sum of the second input components or of a subset of these by the sum of the first input components or of a subset of these (the same subset is used for the two vectors).
Elisabetta Manduchi
Note that if the word "sum" is replaced by the word "mean" in the definition, the resulting definition is equivalent.
OTHER: Adjusted from MGED Ontology
This can be used as a simple normalization method for the two channels from a two-channel expression microarray assay or from two related one-channel expression microarray assays.
total intensity transformation paired
quantile transformation
A quantile transformation is a data transformation that takes as input a collection of data sets, where each can be thought as an n-dimensional (real) vector, and which transforms each data set so that the resulting output data sets have equal quantiles.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
This can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
quantile transformation
mean centering
A mean centering is a data transformation that takes as input an n-dimensional (real) vector, performs a mean calculation on its components, and subtracts the resulting mean from each component of the input.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be mean-centered.
mean centering
mean centring
median centering
A median centering is a data transformation that takes as input an n-dimensional (real) vector, performs a median calculation on its components, and subtracts the resulting median from each component of the input.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
This can be used as a normalization method in expression microarray assays. For example, given a two-channel microarray assay, the log ratios of the two channels (M values) can be median-centered.
median centering
median centring
differential expression analysis objective
A differential expression analysis objective is a data transformation objective whose input consists of expression levels of entities (such as transcripts or proteins), or of sets of such expression levels, under two or more conditions and whose output reflects which of these are likely to have different expression across such conditions.
Analyses implemented by the SAM (http://www-stat.stanford.edu/~tibs/SAM), PaGE (www.cbil.upenn.edu/PaGE) or GSEA (www.broad.mit.edu/gsea/) algorithms and software
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
differential expression analysis objective
K-fold cross validation method
K-fold cross validation method
leave one out cross validation method
leave one out cross validation method
jackknifing method
jackknifing method
boostrapping
Bootstrapping is a statistical method for estimating the sampling distribution of a statistic by sampling with replacement from the original data, most often with the purpose of deriving robust estimates of standard errors and confidence intervals of a population parameter like a mean, median, proportion, odds ratio, correlation coefficient or regression coefficient
boostrapping
Benjamini and Hochberg false discovery rate correction method
Benjamini and Hochberg false discovery rate correction method
pareto scaling
A pareto scaling is a data transformation that divides all measurements of a variable by the square root of the standard deviation of that variable.
Community submitted term (MSI)
Elisabetta Manduchi
PMID:16762068
Philippe Rocca-Serra
pareto scaling
obsolete_clustering method
Clustering is the partitioning of a data set into related subsets (clusters), the input is a single cluster of data and the output is partitioned data or information on cluster labels
James Malone
clustering method
editor
modular decomposition
Molecular decompostion is the partition of a network into distinct subgraphs for the purpose of identifying functional clusters. The network data is run through any of several existing algorithms designed to partition a network into distinct subgraphs for the purpose of isolating groups of functionally linked biological elements such as proteins.
Tina Hernandez-Boussard
editor
modular decomposition
k-means clustering
Elisabetta Manduchi
A k-means clustering is a data transformation, typically with a class discovery objective, which takes as input a collection of objects (represented as points in multidimensional space) and which partitions them into a specified number k of clusters. The algorithm attempts to find the centers of natural clusters in the data. The most common form of the algorithm starts by partitioning the input points into k initial sets, either at random or using some heuristic data. It then calculates the mean point, or centroid, of each set. It constructs a new partition by associating each point with the closest centroid. Then the centroids are recalculated for the new clusters, and the algorithm repeated by alternate applications of these two steps until convergence, which is obtained when the points no longer switch clusters (or alternatively centroids are no longer changed).
James Malone
WEB: http://en.wikipedia.org/wiki/K-means
k-means clustering
hierarchical clustering
A hierarchical clustering is a data transformation, typically with a class discovery objective, which takes as input a collection of objects and builds a hierarchy of clusters. The traditional representation of this hierarchy is a tree (visualized by a dendrogram), with the individual input objects at one end (leaves) and a single cluster containing every object at the other (root).
James Malone
WEB: http://en.wikipedia.org/wiki/Data_clustering#Hierarchical_clustering
hierarchical clustering
average linkage hierarchical clustering
An average linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the average distance between objects from the first cluster and objects from the second cluster.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
average linkage hierarchical clustering
complete linkage hierarchical clustering
A complete linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the maximum distance between objects from the first cluster and objects from the second cluster.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
complete linkage hierarchical clustering
single linkage hierarchical clustering
Elisabetta Manduchi
A single linkage hierarchical clustering is an agglomerative hierarchical clustering which generates successive clusters based on a distance measure, where the distance between two clusters is calculated as the minimum distance between objects from the first cluster and objects from the second cluster.
PERSON: Elisabetta Manduchi
single linkage hierarchical clustering
obsolete_projection
A projection is a dimensionality reduction where the transformation is a simple projection into a subset of the components, i.e. (x_1, x_2, ..., x_m) is transformed into (x_i1, x_i2, ..., x_in) for some 1<=i1... <=m and n<m.
Elisabetta Manduchi
Exclude all x_i's which do not fulfill a pre-formulated condition.
James Malone
Melanie Courtot
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
projection
Benjamini and Yekutieli false discovery rate correction method
Benjamini and Yekutieli false discovery rate correction method
dimensionality reduction
data projection
A dimensionality reduction is data partitioning which transforms each input m-dimensional vector (x_1, x_2, …, x_m) into an output n-dimensional vector (y_1, y_2, …, y_n), where n is smaller than m.
Elisabetta Manduchi
James Malone
Melanie Courtot
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
dimensionality reduction
principal components analysis dimensionality reduction
A principal components analysis dimensionality reduction is a dimensionality reduction achieved by applying principal components analysis and by keeping low-order principal components and excluding higher-order ones.
Elisabetta Manduchi
James Malone
Melanie Courtot
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
pca data reduction
principal components analysis dimensionality reduction
probabilistic algorithm
A probabilistic algorithm is one which involves an element of probability or randomness in the transformation of the data.
James Malone
PERSON: James Malone
probabilistic algorithm
expectation maximization
EM is a probabilistic algorithm used to estimate the maximum likelihood of parameters from existing data where the model involves unobserved latent variables. The input to this method is the data model for which the estimation is performed over and the output is an approximateed probability function.
James Malone
PERSON: James Malone
expectation maximization
global modularity calculation
A network graph quality calculation in which an input data set of subgraph modules and their indegree and outdegree qualities is used to calculate the average modularity of subgraphs within the network.
PERSON: Richard Scheuermann
Richard Scheuermann
global modularity calculation
dye swap merge
A dye swap merge is a replicate analysis which takes as input data from paired two-channel microarray assays where the sample labeled with one dye in the first assay is labeled with the other dye in the second assay and viceversa. The output for each reporter is obtained by combining its (raw or possibly pre-processed) M values in the two assays, where the M value in an assay is defined as the difference of the log intensities in the two channels. This can be used as a normalization step, when appropriate assumptions are met.
Elisabetta Manduchi
James Malone
PERSON: Elisabetta Manduchi
PERSON: James Malone
dye swap merge
moving average
A moving average is a data transformation in which center calculations, usually mean calculations, are performed on values within a sliding window across the input data set.
Elisabetta Manduchi
Helen Parkinson
PERSON: Elisabetta Manduchi
PERSON: Helen Parkinson
The moving average is often used to handle data from tiling arrays.
moving average
replicate analysis
A replicate analysis is a data transformation in which data from replicates are combined, e.g. through descriptive statistics calculations, and the results might be utilized for a variety of purposes, like assessing reproducibility, identifying outliers, normalizing, etc.
Elisabetta Manduchi
Helen Parkinson
PERSON: Helen Parkinson
PERSON:Elisabetta Manduchi
Replicate analysis can be used in microarray analysis to identify and potentially exclude low quality data.
replicate analysis
b cell epitope prediction
A B cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a B Cell Epitope.
Helen Parkinson
PERSON: Helen Parkinson
b cell epitope prediction
mhc binding prediction
An MHC binding prediction takes an input of a biomaterial sequence and through an analysis of this sequence, produces as output a prediction of the likelihood that the biomaterial will bind to an MHC molecule.
Helen Parkinson
PERSON: Helen Parkinson
mhc binding prediction
t cell epitope prediction
A T cell epitope prediction takes as input an antigen sequence, and through an analysis of this sequence, produces as output a prediction of the likelihood the biomaterial is a T cell epitope.
Helen Parkinson
PERSON: Helen Parkinson
t cell epitope prediction
data imputation
ARTICLE: Little, RJA and Rubin, DB (2002). Statistical Analysis with Missing Data, Second Edition. John Wiley: Hoboken New Jersey, pp. 59-60.
Imputation is a means of filling in missing data values from a predictive distribution of the missing values. The predictive distribution can be created either based on a formal statistical model (i,e, a multivariate normal distribution) or an algorithm.
Monnie McGee
data imputation
continuum mass spectrum
A continuum mass spectrum is a data transformation that contains the full profile of the detected signals for a given ion.
Tina Hernandez-Boussard
continuum mass spectrum
editor
example to be added
characteristic path length calculation
Quantifying subgraph navigability based on shortest-path length averaged over all pairs of subgraph vertices
Tina Hernandez-Boussard
characteristic path length calculation
editor
example to be added
centroid mass spectrun
A centroid mass spectrum is a data transformation that is generated by drawing a line from the tip of each peak to the base of the graph. Centroid mass spectra contain discrete peaks of zero width.
Tina Hernandez-Boussard
centroid mass spectrun
editor
example to be added
Holm false discovery rate correction method
Holm false discovery rate correction method
_unclassified
All classes yet to be suitably placed in a hierarchy
James Malone
_unclassified
editor
this class should be removed
edge weighting
Edge weighting is the substitution or transformation of edge length using numerical data. Data input include a symmetric adjacency matrix for a network and a second data set, for example a list of interactor pairs and a confidence score associated with the experimental detection of each pair's interaction. Each element in the adjacency matrix is transformed or replaced with the corresponding number in the second data set. Output data are a modified adjacency matrix reflecting the transformed state of the network.
Tina Hernandez-Boussard
edge weighting
editor
was classified under algorithm class which is not acceptable super-class
TO BE DEALT WITH STILL BY RICHARD. JAMES
loess transformation
A loess transformation is a data transformation that takes as input a collection of real number pairs (x, y) and, after performing (one or more) loess fittings, utilizes the resulting curves to transform each (x, y) in the input into (x, y-f(x)) where f(x) is one of the fitted curves.
Elisabetta Manduchi
James Malone
Melanie Courtot
OTHER: Editor's generalization based on MGED Ontology term
loess transformation
curve fitting data transformation
A curve fitting is a data transformation that has objective curve fitting and that consists of finding a curve which matches a series of data points and possibly other constraints.
Elisabetta Manduchi
James Malone
Melanie Courtot
WEB: http://en.wikipedia.org/wiki/Curve_fitting
curve fitting data transformation
family wise error rate correction method
A family wise error rate correction method is a multiple testing procedure that controls the probability of at least one false positive.
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
Monnie McGee
FWER correction
family wise error rate correction method
submatrix extraction
A submatrix extraction is a projection whose input is a matrix and whose output is a matrix obtained by selecting certain rows and columns from the input. (Note that, if one represents the input matrix as a vector obtained by concatenating its rows, then extracting a submatrix is equivalent to projecting this vector into that composed by the entries belonging to the rows and columns of interest from the input matrix.)
Elisabetta Manduchi
James Malone
Melanie Courtot
Note that this can be considered as a special case of projection if one represents the input matrix as a vector obtained by concatenating its rows. Then extracting a submatrix is equivalent to projecting this vector into the entries belonging to the rows and columns of interest from the input matrix.
WEB: http://en.wikipedia.org/wiki/Submatrix
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes and/or some of the samples out, the resulting data set corresponds to a submatrix of the original set.
submatrix extraction
row submatrix extraction
A row submatrix extraction is a submatrix extraction where all the columns of the input matrix are retained and selection only occurs on the rows.
Elisabetta Manduchi
James Malone
Melanie Courtot
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the genes out, the resulting data set corresponds to a row submatrix of the original set.
row submatrix extraction
column submatrix extraction
A column submatrix extraction is a submatrix extraction where all the rows of the input matrix are retained and selection only occurs on the columns.
Elisabetta Manduchi
James Malone
Melanie Courtot
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
When presented with the data from an expression microarray experiment in the form of a matrix, whose rows correspond to genes and whose columns correspond to samples, if one filters some of the samples out, the resulting data set corresponds to a column submatrix of the original set.
column submatrix extraction
gating
Gating is a property-based vector selection with the objective of partitioning a data vector set into vector subsets based on dimension values of individual vectors (events), in which vectors represent individual physical particles (often cells) of a sample and dimension values represent light intensity qualities as measured by flow cytometry.
James Malone
Josef Spidlen
Melanie Courtot
PERSON: James Malone
PERSON: Josef Spidlen
PERSON: Richard Scheuermann
PERSON: Ryan Brinkman
PERSON:Melanie Courtot
Richard Scheuermann
Ryan Brinkman
gating
descriptive statistical calculation objective
A descriptive statistical calculation objective is a data transformation objective which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
Elisabetta Manduchi
James Malone
Melanie Courtot
Monnie McGee
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
PERSON: Monnie McGee
descriptive statistical calculation objective
mean calculation
A mean calulcation is a descriptive statistics calculation in which the mean is calculated by taking the sum of all of the observations in a data set divided by the total number of observations. It gives a measure of the “center of gravity” for the data set. It is also known as the first moment.
From Monnie's file comments - need to add moment_calculation and center_calculation roles but they don't exist yet - (editor note added by James Jan 2008)
James Malone
Monnie McGee
PERSON: James Malone
PERSON: Monnie McGee
mean calculation
network analysis
network topology analysis
A data transformation that takes as input data that describes biological networks in terms of the node (a.k.a. vertex) and edge graph elements and their characteristics and generates as output properties of the constituent nodes and edges, the sub-graphs, and the entire network.
PERSON: Richard Scheuermann
Richard Scheuermann
network analysis
sequence analysis objective
A sequence analysis objective is a data transformation objective which aims to analyse some ordered biological data for sequential patterns.
James Malone
PERSON: James Malone
sequence analysis objective
longitudinal data analysis
graph_position_temporary
longitudinal data analysis
survival analysis
should become DT objective
survival analysis
obsolete_time series analysis
Remove from data transformation in order to avoid multiple inheritance. A time series analysis is a generic term to encompass analyses whose input are time series, but the analysis could be one of many different types, e.g. differential expression (e.g. EDGE algorithm), or forecasting etc. On the other hand an analysis of a given type (e.g. differential expression) is not necessarily taking in time series data, i.e. is not necessarily a time series analysis. The different data types should be dealt by DENRIE (see Comment), but in DT we should have only concepts describing specific types of algorithms and their description could specify whether or not the input can be a time series.
time series analysis
mass spectrometry analysis
mass spectrometry analysis
spread calculation data transformation
A spread calculation is a data transformation that has objective spread calculation.
James Malone
spread calculation data transformation
Kaplan Meier
Kaplan Meier
multiple testing correction method
A multiple testing correction method is a hypothesis test performed simultaneously on M > 1 hypotheses. Multiple testing procedures produce a set of rejected hypotheses that is an estimate for the set of false null hypotheses while controlling for a suitably define Type I error rate
Monnie McGee
PAPER: Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 9-10.
multiple testing procedure
multiple comparison adjustments
multiple comparison adjustments
inter-rater agreement
inter-rater agreement
Westfall and Young family wise error rate correction
Westfall and Young family wise error rate correction
Westfall_and_Young_FWER_correction
polynomial transformation
A polynommial transformation is a data transformation that is obtained through a polynomial, where a polynomial is a mathematical expression involving a sum of powers in one or more variables multiplied by coefficients (e.g. see http://mathworld.wolfram.com/Polynomial.html). The number of variables and the degree are properties of a polynomial. The degree of a polynomial is the highest power of its terms, where the terms of a polynomial are the individual summands with the coefficients omitted.
Elisabetta Manduchi
WEB: http://mathworld.wolfram.com/Polynomial.html
a*x+b, with a non-zero, is a polynomial of degree one in one variable; a*x^2+b*x+c, with a nonzero, is a polynomial of degree 2 in 1
variable; a*x*y+b*y+c, with a non-zero, is a polynomial of degree 2 in 2 variables (x and y); a_1*x_1+...+a_n*x_n+b, with at least one of the a_i's non-zero, is a polynomial of degree one in n variables
polynomial transformation
logarithmic transformation
A logarithmic transformation is a data transformation consisting in the application of the logarithm function with a given base a (where a>0 and a is not equal to 1) to a (one dimensional) positive real number input. The logarithm function with base a can be defined as the inverse of the exponential function with the same base. See e.g. http://en.wikipedia.org/wiki/Logarithm.
Elisabetta Manduchi
WEB: http://en.wikipedia.org/wiki/Logarithm
logarithmic transformation
exponential transformation
An exponential transformation is a data transformation consisting in the application of the exponential function with a given base a (where a>0 and a is typically not equal to 1) to a (one dimensional) real number input. For alternative definitions and properties of this function see, e.g., http://en.wikipedia.org/wiki/Exponential_function and http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function.
Elisabetta Manduchi
WEB: http://en.wikipedia.org/wiki/Characterizations_of_the_exponential_function
WEB: http://en.wikipedia.org/wiki/Exponential_function
exponential transformation
spectral integration with user-controlled baseline correction
non-negative matrix factorization
soft independent modeling of class analogy analysis
SIMCA
SIMCA
Soft independent modelling by class analogy (SIMCA) is a descriptive statistics method for supervised classification of data. The method requires a training data set consisting of samples (or objects) with a set of attributes and their class membership. The term soft refers to the fact the classifier can identify samples as belonging to multiple classes and not necessarily producing a classification of samples into non-overlapping classes.
Tina Hernandez-Boussard
WEB: http://en.wikipedia.org/wiki/Soft_independent_modelling_of_class_analogies
discriminant function analysis
Discriminant function analysis is a form of discriminant analysis used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome.
Tina Hernandez-Boussard
WEB: http://www.statsoft.com/textbook/stdiscan.html
discriminant function analysis
canonical variate analysis
CVA
Tina Hernandez-Boussard
WEB: http://en.wikipedia.org/wiki/Canonical_analysis
canonical variate analysis
canonical variate analysis is a form of discriminant analysis that takes several continuous predictor variables and uses the entire set to predict several criterion variables, each of which is also continuous. CVA simultaneously calculates a linear composite of all x variables and a linear composite of all y variables. Unlike other multivariate techniques, these weighted composites are derived in pairs. Each linear combination is called a canonical variate and takes the general linear form.
linear discriminant functional analysis
Linear discriminant functional analysis (LDFA) is a multivariate technique used in special applications where there are several intact groups (random assignment may be impossible) and they have been measured on several independent measures. Thus, you will want to describe how these groups differ on the basis of these measures. In this case, classification and prediction is the main objective.
PERSON: Tina Hernandez-Boussard
Tina Hernandez-Boussard
linear discriminant functional analysis
regression analysis method
BOOK: Richard A. Berk, Regression Analysis: A Constructive Critique, Sage Publications (2004) 978-0761929048
Regression analysis is a descriptive statistics technique that examines the relation of a dependent variable (response variable) to specified independent variables (explanatory variables). Regression analysis can be used as a descriptive method of data analysis (such as curve fitting) without relying on any assumptions about underlying processes generating the data.
Tina Hernandez-Boussard
regression analysis method
multiple linear regression analysis
Tina Hernandez-Boussard
WEB:http://en.wikipedia.org/wiki/Linear_regression
multiple linear regression analysis
multiple linear regression is a regression method that models the relationship between a dependent variable Y, independent variables Xi, i = 1, ..., p, and a random term ε. The model can be written as
Y = \beta_0 + \beta_1 X_1 + \beta_2 X_2 + \cdots +\beta_p X_p + \varepsilon
where β0 is the intercept ("constant" term), the βis are the respective parameters of independent variables, and p is the number of parameters to be estimated in the linear regression.
principal component regression
The Principal Component Regression method is a regression analysis method that combines the Principal Component Analysis (PCA)spectral decomposition with an Inverse Least Squares (ILS) regression method to create a quantitative model for complex samples. Unlike quantitation methods based directly on Beer's Law which attempt to calculate the absorbtivity coefficients for the constituents of interest from a direct regression of the constituent concentrations onto the spectroscopic responses, the PCR method regresses the concentrations on the PCA scores.
Tina Hernandez-Boussard
WEB: : http://www.thermo.com/com/cda/resources/resources_detail/1,2166,13414,00.html
principal component regression
partial least square regression analysis
ARTICLE: de Jong, S. (1993). SIMPLS: An alternative approach to partial least squares regression. Chemometrics and Intelligent Laboratory Systems, 18: 251-263.
PLS-RA
Partial least squares regression is an extension of the multiple linear regression model (see, e.g., Multiple Regression or General Stepwise Regression). In its simplest form, a linear model specifies the (linear) relationship between a dependent (response) variable Y, and a set of predictor variables, the X's, so that
Y = b0 + b1X1 + b2X2 + ... + bpXp
In this equation b0 is the regression coefficient for the intercept and the bi values are the regression coefficients (for variables 1 through p) computed from the data.
Tina Hernandez-Boussard
partial least square regression analysis
discriminant analysis
Discriminant function analysis is used to determine which variables discriminate between two or more naturally occurring groups. Analysis is used to determine which variable(s) are the best predictors of a particular outcome.
Tina Hernandez-Boussard
WEB: http://www.statsoft.com/textbook/stdiscan.html
discriminant analysis
partial least square discriminant analysis
PLS Discriminant Analysis (PLS-DA) is a discriminant analysis performed in order to sharpen the separation between groups of observations, by hopefully rotating PCA (Principal Components Analysis) components such that a maximum separation among classes is obtained, and to understand which variables carry the class separating information.
WEB: http://www.camo.com/rt/Resources/pls-da.html
James Malone
PLS-DA
partial least square discriminant analysis
eh transformation
An eh transformation is a data transformation obtained by applying the function EH described in what follows to a (one dimensional) real number input. EH(x)=exp(x*d/r)+b*(d/r)*x-1, if x>=0, and EH(x)=-exp(-x*d/r)+b*(d/r)*x+1, otherwise. Here exp denotes an exponential transformation and b, d, r are positive real constants with the objective of normalization.
Elisabetta Manduchi
Joseph Spliden
Ryan Brinkman
This type of transformation is typically used in flow cytometry.
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
eh transformation
b transformation
A b transformation is a data transformation obtained by applying the function B described in what follows to a (one dimensional) real number input. B(x)= a*exp(b*x)-c*exp(-d*x)+f, where exp denotes an exponential transformation and a, b, c, d, f are real constants with a, b, c, d positive with the objective of normalization.
Elisabetta Manduchi
Joseph Spliden
Ryan Brinkman
This type of transformation is typically used in flow cytometry.
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
b transformation
s transformation
An s transformation is a data transformation obtained by applying the function S described in what follows to a (one dimensional) real number input. S(x)=T*exp(w-m)*(exp(x-w)-(p^2)*exp((w-x)/p)+p^2-1) if x>=w, S(x)=-S(w-x) otherwise; where exp denotes an exponential_transformations, 'p^' denotes the exponential transformation with base p; T, w, m, p are real constants with T, m, and p positive and w non-negative, and where w and p are related by w=2p*ln(p)(p+1) with the objective of normalization.
Elisabetta Manduchi
Joseph Spliden
Ryan Brinkman
This type of transformation is typically used in flow cytometry.
WEB: http://flowcyt.sourceforge.net/gating/latest.pdf
s transformation
obsolete_visualization
Elisabetta Manduchi
James Malone
Melanie Courtot
PERSON: Elisabetta Manduchi
PERSON: James Malone
PERSON: Melanie Courtot
PERSON: Tina Boussard
Tina Boussard
Visualization is a data transformation that creates images, diagrams or animations from the input.
visualisation
visualization
obsolete_MA plotting
Elisabetta Manduchi
MA plots are typically used in microarray data analyses to visualize intensity-dependent ratio of raw data. In this context the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2.
MA plotting
MA plotting is a visualization whose input is a collection of data points (g_1, r_1), (g_2, r_2), …, (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is a scatterplot of M (y-axis) versus A (x-axis) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M=log(r_i)-log(g_i). Here log denotes a logarithmic transformation.
PERSON: Elisabetta Manduchi
similarity calculation
A similarity calculation is a data transformation that attaches to each pair of objects in the input a number that is meant to reflect how 'close' or 'similar' those objects are.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
similarity calculation
euclidean distance calculation
An euclidean distance calculation is a similarity calculation that attaches to each pair of real number vectors of the same dimension n the square root of the sum of the square differences between corresponding components. The smaller this number, the more similar the two vectors are considered.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
euclidean distance calculation
pearson correlation coefficient calculation
A pearson correlation coefficient calculation is a similarity calculation which attaches to each pair of random variables X and Y the ratio of their covariance by the product of their standard deviations. Given a series of n measurements of X and Y written as x_i and y_i where i = 1, 2, ..., n, then their Pearson correlation coefficient refers to the "sample correlation coefficient" and is written as the sum over i of the ratios (x_i-xbar)*(y_i-ybar)/((n-1)*s_x*s_y) where xbar and ybar are the sample means of X and Y , s_x and s_y are the sample standard deviations of X and Y. The closer the pearson correlation coefficient is to 1, the more similar the inputs are considered.
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
WEB: http://en.wikipedia.org/wiki/Correlation
pearson correlation coefficient calculation
loess fitting
A loess fitting is a curve fitting obtained by localized regression. The latter refers to fitting a polynomial (straight line, quadratic, cubic, etc) to data values within a window covering a fraction of the total number of observations. As the window slides along the axis, a new polynomial is fit to the observations falling within the window. This continues until all points are fit with a local polynomial. The results are then smoothed together to form a curve. The smoothness of loess fits is controlled by a smoothing parameter (often denoted as alpha, usually between ¼ and 1) and the degree of the polynomial that is fitted by the method (usually denoted by lambda).
ARTICLE: Mathematical details of loess fits are given in Cleveland, William (1993) Visualizing Data. Hobart Press, Summit, New Jersey, pp. 94-101.
Monnie McGee
loess fitting
mode calculation
A mode calulcation is a descriptive statistics calculation in which the mode is calculated which is the most common value in a data set. It is most often used as a measure of center for discrete data.
From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008)
James Malone
Monnie McGee
PERSON: James Malone
PERSON: Monnie McGee
mode calculation
quantile calculation
A quantile calculation is a descriptive statistics calculation in which the kth quantile is the data value for which an approximate k fraction of the data is less than or equal to that value. See http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html for details.
Monnie McGee
WEB: http://www.stat.wvu.edu/SRS/Modules/Quantiles/quantiles.html
quantile calculation
median calculation
A median calculation is a descriptive statistics calculation in which the midpoint of the data set (the 0.5 quantile) is calculated. First, the observations are sorted in increasing order. For an odd number of observations, the median is the middle value of the sorted data. For an even number of observations, the median is the average of the two middle values.
From Monnie's file comments - need to add center_calculation role but it doesn't exist yet - (editor note added by James Jan 2008)
James Malone
Monnie McGee
PERSON: James Malone
PERSON: Monnie McGee
median calculation
variance calculation
A variance calculation is a descriptive statistics calculation in which the variance is defined as the average squared distance of each observation in the data set to the mean of the data set. It is also known as the second central moment.
From Monnie's file comments - need to add spread_calculation and moment_calculation roles but they don't exist yet - (editor note added by James Jan 2008)
Monnie McGee
PERSON: Monnie McGee
variance calculation
standard deviation calculation
A standard deviation calculation is a descriptive statistics calculation defined as the square root of the variance. Also thought of as the average distance of each value to the mean.
From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008)
Monnie McGee
PERSON: Monnie McGee
standard deviation calculation
interquartile-range calculation
From Monnie's file comments - need to add spread calculation role but they doesn't exist yet - (editor note added by James Jan 2008)
Monnie McGee
PERSON: Monnie McGee
The interquartile range is a descriptive statistics calculation defined as the difference between the 0.75 quantile and the 0.25 quantile for a set of data.
interquartile-range calculation
skewness calculation
A skewness calculation is a descriptive statistics calculation defined as a parameter that describes how much a distribution (or a data set) varies from a bell-shaped curve. See http://www.riskglossary.com/link/skewness.htm for details. It is also known as the third central moment
From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008)
Monnie McGee
WEB: http://www.riskglossary.com/link/skewness.htm
skewness calculation
kurtosis calculation
A kurtosis calculation is a descriptive statistics calculation defined as a parameter that measures how large or small the tails of a distribution are relative to the mean. For details, see http://davidmlane.com/hyperstat/A53638.html
From Monnie's file comments - need to add moment calculation role but they doesn't exist yet - (editor note added by James Jan 2008)
Monnie McGee
WEB: http://davidmlane.com/hyperstat/A53638.html
kurtosis calculation
data pooling
A data transformation in which individual input data elements and values are merged together into a output set of data elements and values.
Richard Scheuermann
data pooling
editor
network graph construction
A network analysis in which an input data set describing objects and relationships between objects is transformed into an output representation of these objects as nodes and the relationships as edges of a network graph.
PERSON: Richard Scheuermann
Richard Scheuermann
network graph construction
weighted network graph construction
A network graph construction in which an input data set describing objects and quantitative relationships between objects is transformed into and output representation of these objects as nodes and the quantitative relationships as weighted edges of a network graph.
PERSON: Richard Scheuermann
Richard Scheuermann
weighted network graph construction
directed network graph construction
A network graph construction in which an input data set describing objects and directional relationships between objects is transformed into and output representation of these objects as nodes and the directional relationships as directed edges of a network graph.
PERSON: Richard Scheuermann
Richard Scheuermann
directed network graph construction
node quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the node objects in the network.
PERSON: Richard Scheuermann
Richard Scheuermann
node quality calculation
node degree calculation
A node quality calculation in which an input data set describing object nodes and relationship edges between object nodes is used to enumerate the number of unique relationships of an individual object node.
PERSON: Richard Scheuermann
Richard Scheuermann
node degree calculation
quantitative node degree calculation
A node quality calculation in which an input data set describing object nodes and quantitative relationship edges between object nodes is used to sum all of the quantitative relationships of an individual object node.
PERSON: Richard Scheuermann
Richard Scheuermann
quantitative node degree calculation
node indegree calculation
A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing into an individual object node.
PERSON: Richard Scheuermann
Richard Scheuermann
node indegree calculation
node outdegree calculation
A node quality calculation in which an input data set describing object nodes and directional relationship edges between object nodes is used to enumerate the number of unique relationships pointing out of an individual object node.
PERSON: Richard Scheuermann
Richard Scheuermann
node outdegree calculation
node shortest path identification
A node quality calculation in which a path describing the shortest path needed to transverse through connected nodes and edges to arive at a specific target node in the network.
PERSON: Richard Scheuermann
Richard Scheuermann
node shortest path identification
edge quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of one of the edge relationships in the network.
PERSON: Richard Scheuermann
Richard Scheuermann
edge quality calculation
edge betweenness calculation
An edge quality calculation in which the input is a data sets of shortest paths between all pairs of node in the network and the output is the sum of all shortest paths that traverse the specific edge.
PERSON: Richard Scheuermann
Richard Scheuermann
edge betweenness calculation
network subgraph quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of a subgraph partition of the network.
PERSON: Richard Scheuermann
Richard Scheuermann
network subgraph quality calculation
subgraph degree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships of an individual subgraph.
PERSON: Richard Scheuermann
Richard Scheuermann
subgraph degree calculation
quantitative subgraph degree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and quantitative relationship edges between subgraphs and other network objects is used to sum the quantitative relationships of an individual subgraph.
PERSON: Richard Scheuermann
Richard Scheuermann
quantitative subgraph degree calculation
mathematical feature
PERSON: James Malone
mathematical feature
James Malone
This class is temporary and will be placed outside of data transformation ultaimtely (if it still remains at all after review)
feature is a (parent_class) that describes a characteristic, trait or quality of a data transformation
log base
Elisabetta Manduchi
The log base is a feature of a logarithmic function which is defined in http://en.wikipedia.org/wiki/Logarithm. Its value can be any positive real number different from 1.
WEB: http://en.wikipedia.org/wiki/Logarithm
log base
logarithm base
logarithmic base
subgraph indegree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and directional relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing into an individual subgraph.
PERSON: Richard Scheuermann
Richard Scheuermann
subgraph indegree calculation
subgraph outdegree calculation
A network subgraph quality calculation in which an input data set describing subgraphs and relationship edges between subgraphs and other network objects is used to enumerate the number of unique relationships pointing out of an individual subgraph.
PERSON: Richard Scheuermann
Richard Scheuermann
subgraph outdegree calculation
intra subgraph connectivity calculation
A network subgraph quality calculation in which an input data set describing internal nodes, edges and node degrees is used to determine the average node degree within the subgraph.
PERSON: Richard Scheuermann
Richard Scheuermann
intra subgraph connectivity calculation
subgraph modularity calculation
A network subgraph quality calculation in which an input data set of subgraph indegree and outdegree qualities is used to calculate the ratio of indegree to outdegree as a measure of modularity.
PERSON: Richard Scheuermann
Richard Scheuermann
subgraph modularity calculation
network graph quality calculation
A network analysis in which an input data set describing node objects and edge relationships between node objects is used to determine the output quality of the network as a whole.
PERSON: Richard Scheuermann
Richard Scheuermann
network graph quality calculation
unit-variance scaling
A unit-variance scaling is a data transformation that divides all measurements of a variable by the standard deviation of that variable.
Community submitted term (MSI)
Elisabetta Manduchi
PMID:16762068
Philippe Rocca-Serra
autoscaling
unit-variance scaling
MA transformation
An MA transformation is a data transformation which takes as input a collection of data points (g_1, r_1), (g_2, r_2), ..., (g_n, r_n) with the r_i and g_i positive real numbers, and whose output is the collection of data points (A_1, M_1), (A_2, M_2), ..., (A_n, M_n) where, for each i, A_i=(log(g_i)+log(r_i))/2 and M_i=log(r_i)-log(g_i). Here log denotes a logarithmic transformation.
Elisabetta Manduchi
MA transformation
MA transformations are typically used in microarray data analyses. In this context, the g_i and r_i represent the reporter intensities in the two channels of a 2-channel assay or the reporter intensities in two related one-channel assays. Typically the base used for the logarithm is 2.
PERSON: Elisabetta Manduchi
exponential base
Elisabetta Manduchi
The exponential base is a feature of an exponential function which is defined in http://en.wikipedia.org/wiki/Exponential_function. Its value can be any positive real number (typically different from 1).
WEB: http://en.wikipedia.org/wiki/Exponential_function
exponential base
polynomial degree
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
The polynomial degree is a feature of a polynomial function defined as the highest power of the polynomial's terms, where the terms of a polynomial are the individual summands with the coefficients omitted.
polynomial degree
number of variables
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
The number of variables is a feature of any function (including polynomial functions) with domain contained in an n-dimensional vector space and is defined as n, the dimension of such space.
number of variables
agglomerative hierarchical clustering
Elisabetta Manduchi
bottom-up hierarchical clustering
An agglomerative hierarchical clustering is a hierarchical clustering which starts with each object as a separate cluster and then successively combines these clusters until there is only one cluster remaining.
James Malone
PERSON: Elisabetta Manduchi
agglomerative hierarchical clustering
divisive hierarchical clustering
Elisabetta Manduchi
top-down hierarchical clustering
A divisive hierarchical clustering is a hierarchical clustering which starts with a single cluster containing all objects, and then successively splits resulting clusters until only clusters of individual objects remain.
James Malone
PERSON: Elisabetta Manduchi
divisive hierarchical clustering
data partioning
Data partitioning is a data transformation with the objective of partitioning or separating input data into output subsets.
James Malone
PERSON: Melanie Courtot
PERSON: Richard Scheuermann
PERSON: Ryan Brinkman
data partioning
data vector reduction objective
James Malone
Data vector reduction is a data transformation objective in which k m-dimensional input vectors are reduced to j m-dimensional output vectors, where j is smaller than k.
PERSON: Richard H. Scheuermann
Richard H. Scheuermann
data vector reduction objective
obsolete_random vector selection
no longer required as gating has been dealt with using objectives data vector reduction and partioning
Elisabetta Manduchi
James Malone
Melanie Courtot
PERSON: Elisabetta Manduchi
obsolete_property-based vector selection
no longer required as gating has been dealt with using objectives data vector reduction and partioning
Elisabetta Manduchi
James Malone
Melanie Courtot
PERSON: Elisabetta Manduchi
generalized family wise error rate correction method
A generalized FWER correction method is a multiple testing procedure that controls the probability of at least k+1 false positives, where k is a user-supplied integer.
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
Monnie McGee
gFWER correction
generalized family wise error rate correction method
quantile number of false positives correction method
A quantile number of false positives correction method is a MTP that controls for the pth quantile of the distribution of the number of false positives out of the total number of tests performed'
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 19
Monnie McGee
QNFP
quantile number of false positives correction method
tail probability for the proportion of false positives correction method
A TPPFP correction method is a MTP that controls the probability that the proportion of false positives among all rejected hypotheses is no greater than a constant q, where q is between 0 and 1.
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 20
Monnie McGee
TPPFP correction method
tail probability for the proportion of false positives correction method
false discovery rate correction method
A false discovery rate correction method is a multiple testing procedure that controls for the expected value of the proportion of false positives among the rejected hypotheses.
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21
Monnie McGee
FDR correction method
false discovery rate correction method
proportion of expected false positives correction method
A proprotion of expected false positives correction method is a multiple testing procedure that controls the ratio of the expected value of the numbers of false positives to the expected value of the numbers of rejected hypotheses.
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21
Monnie McGee
PEFP correction method
proportion of expected false positives correction method
quantile proportion of false positives correction method
A quantile proportion of false positives correction method is a multiple testing procedure that controls the pth quantile of the distriubition of the proportion of false positives among the rejected hypothesis (false discovery rate).
Dudoit, Sandrine and van der Laan, Mark J. (2008) Multiple Testing Procedures with Applications to Genomics. New York: Springer , p. 21
Monnie McGee
QPFP correction method
quantile proportion of false positives correction method
data transformation objective
A data transformation objective is an objective specification that a data transformation may have towards which the realization of that transformation is directed.
James Malone
PERSON: James Malone
data transformation objective
normalize objective
normalization objective
Elisabetta Manduchi
Helen Parkinson
PERSON: Elisabetta Manduchi
PERSON: Helen Parkinson
A normalization objective is a data transformation objective where the aim is to remove
systematic sources of variation to put the data on equal footing in order
to create a common base for comparisons.
James Malone
PERSON: James Malone
Quantile transformation which has normalization objective can be used for expression microarray assay normalization and it is referred to as "quantile normalization", according to the procedure described e.g. in PMID 12538238.
normalization objective
correction objective
PERSON: James Malone
PERSON: Melanie Courtot
A correction objective is a data transformation objective where the aim is to correct for error, noise or other impairments to the input of the data transformation.
James Malone
Type I error correction
correction objective
normalization data transformation
James Malone
A normalization data transformation is a data transformation that has objective normalization.
PERSON: James Malone
normalization data transformation
averaging data transformation
James Malone
An averaging data transformation is a data transformation that has objective averaging.
PERSON: James Malone
averaging data transformation
partitioning data transformation
James Malone
A partitioning data transformation is a data transformation that has objective partitioning.
PERSON: James Malone
partitioning data transformation
partitioning objective
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
A k-means clustering which has partitioning objective is a data transformation in which the input data is partitioned into k output sets.
A partitioning objective is a data transformation objective where the aim is to generate a collection of disjoint non-empty subsets whose union equals a non-empty input set.
James Malone
partitioning objective
background correction objective
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
A background correction objective is a data transformation objective where the aim is to remove irrelevant contributions from the measured signal, e.g. those due to instrument noise or sample preparation.
James Malone
background correction objective
curve fitting objective
Elisabetta Manduchi
PERSON: Elisabetta Manduchi
A curve fitting objective is a data transformation objective in which the aim is to find a curve which matches a series of data points and possibly other constraints.
James Malone
curve fitting objective
class discovery data transformation
James Malone
discriminant analysis data transformation
A class discovery data transformation (sometimes called unsupervised classification) is a data transformation that has objective class discovery.
PERSON: James Malone
class discovery data transformation
Fisher's exact test
Fisher's exact test
Fisher's exact test is a data transformation used to determine if there are nonrandom associations between two categorical variables.
James Malone
WEB:http://mathworld.wolfram.com/FishersExactTest.html
center calculation objective
PERSON: James Malone
A center calculation objective is a data transformation objective where the aim is to calculate the center of an input data set.
A mean calculation which has center calculation objective is a data transformation in which the center of the input data is discovered through the calculation of a mean average.
James Malone
center calculation objective
class discovery objective
PERSON: Elisabetta Manduchi
PERSON: James Malone
discriminant analysis objective
unsupervised classification objective
A class discovery objective (sometimes called unsupervised classification) is a data transformation objective where the aim is to organize input objects (typically vectors of attributes) into classes, where the number of classes and their specifications are not known a priori. Depending on usage, the class assignment can be definite or probabilistic.
James Malone
class discovery objective
class prediction objective
PERSON: Elisabetta Manduchi
PERSON: James Malone
supervised classification objective
A class prediction objective (sometimes called supervised classification) is a data transformation objective where the aim is to create a predictor from training data through a machine learning techique. The training data consist of pairs of objects (typically vectors of attributes) and
class labels for these objects. The resulting predictor can be used to attach class labels to any valid novel input object. Depending on usage, the prediction can be definite or probabilistic. A classification is learned from the training data and can then be tested on test data.
James Malone
class prediction objective
spread calculation objective
Awaiting English definition from Monnie McGee
James Malone
spread calculation objective
center calculation data transformation
James Malone
A center calculation data transformation is a data transformation that has objective of center calculation.
PERSON: James Malone
center calculation data transformation
data vector reduction data transformation
A data vector reduction is a data transformation that has objective data vector reduction and that consists of reducing the input vectors k to a smaller number of outpu vectors j, where j<k.
James Malone
PERSON: James Malone
data vector reduction data transformation
scaling objective
Awaiting English definition from Monnie McGee
James Malone
scaling objective
descriptive statistical calculation data transformation
A descriptive statistical calculation data transformation is a data transformation that has objective descriptive statistical calculation and which concerns any calculation intended to describe a feature of a data set, for example, its center or its variability.
James Malone
PERSON: James Malone
descriptive statistical calculation data transformation
scaling data transformation
A scaling data transformation is a data transformation that has objective scaling.
James Malone
PERSON: James Malone
scaling data transformation
error correction objective
PERSON: James Malone
An error correction objective is a data transformation objective where the aim is to remove (correct for) erroneous contributions from the input to the data workshop.
James Malone
error correction objective
sequence analysis data transformation
A sequence analysis data transformation is a data transformation that has objective sequence analysis and has the aim of analysing ordered biological data for sequential patterns.
James Malone
sequence analysis data transformation
cross validation objective
A cross validation objective is a data transformation objective in which the aim is to partition a sample of data into subsets such that the analysis is initially performed on a single subset, while the other subset(s) are retained for subsequent use in confirming and validating the initial analysis.
WEB: http://en.wikipedia.org/wiki/Cross_validation
rotation estimation objective
James Malone
cross validation objective
merging objective
A merging objective is a data transformation objective in which the data transformation has the aim of performing a union of two or more sets.
PERSON: Data Transformation Branch
combining objective
merging objective
merging of columns from two different data sets
James Malone
sequential design
Any design in which the decision as to whether to enroll the next patient, pair of patients, or block of patients is determined by whether the cumulative treatment difference for all previous patients is within specified limits. Enrollment is continued if the difference does not exceed the limits. It is terminated if it does
MUSC
PMID: 17710740.Pharm Stat. 2007 Aug 20.Sequential design approaches for bioequivalence studies with crossover designs.
Philippe Rocca-Serra
Provenance: OCI
sequential design
observation design
OBI branch derived
PMID: 12387964.Lancet. 2002 Oct 12;360(9340):1144-9.Deficiency of antibacterial peptides in patients with morbus Kostmann: an observation study.
Philippe Rocca-Serra
observation design
observation design is a study design in which subjects are monitored in the absence of any active intervention by experimentalists.
obsolete__move to protocol application
obsolete__move to information_content_entity
obsolete__a defined class is needed
Placeholder class, for all children,more work is required
OBI Biomaterial derived
Philippe Rocca-Serra
obsolete__move_to_site
OBI Biomaterial derived
Philppe Rocca-Serra
placeholder, possibility of deprecation
collection (of entities of organismal origin)
Susanna Sansone
PERSON: Philippe Rocca-Serra
PMID: 18037794. Magn Reson Med Sci. 2007;6(3):139-46. Imaging of a large collection of human embryo using a super-parallel MR microscope.[the Orsay Museum has a nice collection of Impressionnist paintings]
PRS: How can we distinguish with 'collection' as the process of collecting entities, (eg. data collection, urine collection)
Philippe Rocca-Serra
a collection is a bfo:aggregate object, that is a set of material object of the same kind
added during 22-02-2008 biomaterial call to distinguish library and population
set, group, ensemble
pool of specimens
CEBS
Jennifer Fostel
A pool of specimens is a sample population that is a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish.
PRS:22-02-2008: does not feel right, definition is unclear. a pool is in this is case understood as a process of mixing to homogeneity but NOT the creation of a population of individuals which retain the capability of being singled out.
check with advisors as to how to represent multiple instances of any class? a set of specimens which have been gathered from one or more sample_populations, obtained by the physical process of mixing individual specimens, e.g. mixing the DNA collected from the individual fish
obsolete_test synthetic peptide
OBI Biomaterial derived
Philippe Rocca-Serra
Placeholder for testing
maybe will be moved to placeholder _defined class
to be added
obsolete_?all kind ofl lavage
PRS:22-02-2008: see bronchial alveolar lavage under experimental biomaterial entity
obsolete_histologic preparation
PRS 22-02-2008
obsolete_multi-tissue structure
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
CARO
PRS:22022008:possible import from CARO dbxref=CARO:0000055
Philippe Rocca-Serra
organ
obsolete_portion of tissue
PMID: 18173349. J Neurosurg Spine. 2008 Jan;8(1):67-73..OBJECT: Hydrogels are nontoxic, chemically inert synthetic polymers with a high water content and large surface area that provide mechanical support for cells and axons when implanted into spinal cord tissue.
PRS22022008: possible import from CARO dbxref=0000043
Philippe Rocca-Serra
a tissue is a multicellular entity of organismal origin with is made a one or more cell type which has recognisable morphological and functional characteristics
CARO Definition: Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships.
adapted from OED and possible import from CARO
chemical entities in solution
Bjoern Peters
OBI Biomaterial derived
PMID: 18289311.Anesth Analg. 2008 Apr;106(4):1078-86.Less impairment of hemostasis and reduced blood loss in pigs after resuscitation from hemorrhagic shock using the small-volume concept with hypertonic saline/hydroxyethyl starch as compared to administration of 4% gelatin or 6% hydroxyethyl starch solution.
Philippe Rocca-Serra
a solution of chemicals is a material which is made up of at least 2 chemical entities, one chemical entity playing the role of solvent and the other one playing the role of solute.
liquid chemical solution
buffer role
OBI
Philippe Rocca-Serra
buffer
solvent role
PMID: 18373502.Transfusion. 2008 Mar 25. Solvent/detergent treatment of platelet concentrates enhances the release of growth factors.
Philippe Rocca-Serra
adpated from wikipedia (http://en.wikipedia.org/wiki/Solvatation)
solvent role is a role played by a chemical entity capable of ensuring the dissolution of another chemical entity, thereby exhibiting solvatation properties
solute role
PMID: 18380397.Pharmazie. 2008 Feb;63(2):113-21.Deviations of drug solubility in water-cosolvent mixtures from the Jouyban-Acree model--effect of solute structure.
Philippe Rocca-Serra
adapted from wikipedia (http://en.wikipedia.org/wiki/Solute)
solute role is a role played by a chemical entity which is dissolved by another chemical entity (the solvent) when creating a solution
comet assay
PMID: 18326531.Mutagenesis. 2008 Mar 6.Recommendations for design of the rat comet assay.
PMID:7686265 .Mutat Res. 1993 Jul;288(1):47-63.The single cell gel electrophoresis assay (comet assay): a European review.
Philippe Rocca-Serra
SCGE assay
a comet assay is an assay which utilizes gel electropheris on cell exposed to a challenge with the objective to assess DNA damage (DNA breakage) by determining the size and shape of DNA migration in cell placed in an electric field in specific conditions.
comet assay
single cell gel electrophoresis assay
PCR-SSCP assay
has_input should be "DNA molecules" or something similar - as of 9/4/08 "ChEBI ontology" was the best choice
PCR-SSCP assay
PMID: 17334176.Hum Exp Toxicol. 2007 Jan;26(1):9-18.Is there a role for PCR-SSCP among the methods for missense mutation detection of TP53 gene?
PMID: 18219595.Mol Biotechnol. 2008 Feb;38(2):155-63.PCR-SSCP: a method for the molecular analysis of genetic diseases.
Philippe Rocca-Serra
a PCR-SSCP assay is an assay which aims at the identification of DNA sequence variation (mutation,deletion, insertions) using gel electrophoresis technique and denaturating conditions on target DNA sequences amplified using polymerase chain reaction procedure.
polymerase chain reaction-single strand conformation polymorphism assay
liver
OBI Biomaterial Branch
PMID: 2104732. Caudate lobe of the liver: anatomy, embryology, and pathology.
AJR Am J Roentgenol. 1990 Jan;154(1):87-93.
PRS: Test. added for evaluation and validation of possible imports from CARO (or other anatomical resources)
Philippe Rocca-Serra
liver is an anatomical entity which consituant are mainly hepatocytes, which has a function of detoxification,hemotapoeietic center, glucose and fat metabolism management. liver is only found in animals , all Vertebrates and some families of invertebrates
obsolete_epithelium
PMID: 18431835. Alteration of medial-edge epithelium cell adhesion in two Tgf-beta3 null mouse strains. Differentiation. 2008 Apr;76.4.417-30
Philippe Rocca-Serra
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina (From CARO:) OR epithelium is a tissue composed of layers of cells that line the cavities and surfaces of structures throughout the body (adapted from Wikipedia).
Wikipedia and possible import from CARO:0000066
adipose tissue
OBI Biomaterial derived
PMID: 18435934.Fatty acid composition of adipose tissue and blood in humans and its use as a biomarker of dietary intake.Prog Lipid Res. 2008 Apr 4.
PRS: this class has been added during major biomaterial.owl cleanup for evaluation and testing of imports from CARO
Philippe Rocca-Serra
adipose tissue is a tissue which main constituants are adipocytes. adipose tissue can be classified base on its location (site) but also based on adipocyte subtypes (brown or white) which reflect functional differences and is only found in animals, Vertebrates or invertebrates.
cross-linked
Degradable Disulfide Core-Cross-Linked Micelles as a Drug Delivery System Prepared from Vinyl Functionalized Nucleosides via the RAFT Process.
Biomacromolecules. 2008 Oct 9.PMID: 18842025
OBI Biomaterial
Philippe Rocca-Serra
cross linked is a conferred qualify which inheres in material resulting from an cross linking process
denatured
Philippe Rocca-Serra
denatured is a conferred qualify which inheres in material resulting from an denaturation process
acclimatized
Philippe Rocca-Serra
decapitated
OBI Biomaterial
Ovarian development induced in decapitated female Culex pipiens pallens mosquitoes by infusion of physiological quantities of 20-hydroxyecdysone together with amino acids.
J Insect Physiol. 1998 May;44(5-6):525-528. PMID: 12770172
Philippe Rocca-Serra
decapitated is a conferred qualify which inheres in material resulting from an decapitation process
validated
Philippe Rocca-Serra
validated is a conferred qualify which inheres in material resulting from an validation process
transplanted
OBI Biomaterial
Philippe Rocca-Serra
Self-renewal and expansion of single transplanted muscle stem cells.
Nature. 2008 Sep 17. PMID: 18806774
transplanted is a conferred qualify which inheres in material resulting from an transplantation process
curated
Philippe Rocca-Serra
centrifuged
Philippe Rocca-Serra
has_been_treated
Philippe Rocca-Serra
renamed this from treated, to distinguish from "treated" a role, versus the case where we remember that the organism was treated but it is not longer under treatment.
aliquoted
Philippe Rocca-Serra
filtered
Detrimental effects of prenatal exposure to filtered diesel exhaust on mouse spermatogenesis.
Arch Toxicol. 2008 May 1.PMID: 18449530
OBI Biomaterial
Philippe Rocca-Serra
filtered is a conferred qualify which inheres in material resulting from an filtration process
stored
Philippe Rocca-Serra
randomized
Philippe Rocca-Serra
methylated
Binding and penetration of methylated DNA into primary and transformed human cells.
Ann N Y Acad Sci. 2008 Aug;1137:36-40. PMID: 18837922
OBI Biomaterial
Philippe Rocca-Serra
methylated is a conferred qualify which inheres in material resulting from an methylation process
irradiated
OBI Biomaterial
Philippe Rocca-Serra
Thrombomodulin exerts cytoprotective effect on low-dose UVB-irradiated HaCaT cells.
Biochem Biophys Res Commun. 2008 Oct 18. PMID: 18940182
irradiated is a conferred qualify which inheres in material resulting from an irradiation process
cloned
OBI Biomaterial
Philippe Rocca-Serra
Trichostatin A improved epigenetic modifications of transfected cells but did not improve subsequent cloned embryo development. Anim Biotechnol. 2008;19(4):211-24. PMID: 18855246
cloned is a conferred qualify which inheres in material resulting from an cloning process
immobilized
Carboxylic multi-walled carbon nanotubes as immobilized stationary phase in capillary electrochromatography. Electrophoresis. 2008 Sep;29(18):3850-7. PMID: 18850654
OBI Biomaterial
Philippe Rocca-Serra
immobilized is a conferred qualify which inheres in material resulting from an immobilization process
fixed
Gene Expression in Fixed Tissues and Outcome in Hepatocellular Carcinoma.
N Engl J Med. 2008 Oct 15. PMID: 18923165
OBI Biomaterial
Philippe Rocca-Serra
fixed is a conferred qualify which inheres in material resulting from an fixation process
precipitated
OBI Biomaterial
Philippe Rocca-Serra
precipitated is a conferred qualify which inheres in material resulting from an precipitation process
trypsinized
Because OBI will probably be used by text-mining tools so the context is different. Having such terms related to the processes causing them to appear is probably something useful - Philippe
Carbohydrate-induced modulation of cell membrane. VIII. Agglutination with mammalian lectin galectin-1 increases osmofragility and membrane fluidity of trypsinized erythrocytes.
FEBS Lett. 2006 Mar 6;580(6):1691-5. PMID: 16497300
Philippe Rocca-Serra
Why do we need this? There is always the actual record of the specific type of digestion that was done. - Alan
trypsinized is a conferred qualify which inheres in material resulting from an trypsination process
enrolled
Characteristics and outcome of pediatric patients enrolled in phase I oncology trials.
Oncologist. 2008 Jun;13(6):679-89. PMID: 18586923
OBI Biomaterial
Philippe Rocca-Serra
enrolled is a conferred qualify which inheres in material resulting from an enrollment process
purified
Gene expression analysis of RNA purified from embryonic stem cells and embryoid body-derived cells using a high-throughput microarray platform. Curr Protoc Stem Cell Biol. 2007 Sep;Chapter 1:Unit 1B.2. PMID: 18785160
OBI Biomaterial
Philippe Rocca-Serra
purified is a conferred qualify which inheres in material resulting from an purification process
polymerized
Biodegradable and radically polymerized elastomers with enhanced processing capabilities.
Biomed Mater. 2008 Sep;3(3):034104. PMID: 18689916
OBI Biomaterial
Philippe Rocca-Serra
polymerized is a conferred qualify which inheres in material resulting from an polymerization process
electrocuted
Philippe Rocca-Serra
ligated
Identification of zinc-ligated cysteine residues based on 13Calpha and 13Cbeta chemical shift data.
J Biomol NMR. 2006 Apr;34(4):259-69. PMID: 16645816
OBI Biomaterial
Philippe Rocca-Serra
ligated is a conferred qualify which inheres in material resulting from an ligation process
genetically modified
A protocol for removal of antibiotic resistance cassettes from human embryonic stem cells genetically modified by homologous recombination or transgenesis.
Nat Protoc. 2008;3(10):1550-8. PMID: 18802436
OBI Biomaterial
Philippe Rocca-Serra
genetically modified is a conferred qualify which inheres in material resulting from an genetic modification process
subtracted
Identification of candidate molecular markers of nasopharyngeal carcinoma by microarray analysis of subtracted cDNA libraries constructed by suppression subtractive hybridization.
Eur J Cancer Prev. 2008 Nov;17(6):561-71. PMID: 18941378
OBI Biomaterial
Philippe Rocca-Serra
substracted is a conferred qualify which inheres in material resulting from an substraction process
resuspended
Assessment of the risk of phosphorus loading due to resuspended sediment.
J Environ Qual. 2001 May-Jun;30(3):960-6. PMID: 11401287
OBI Biomaterial
Philippe Rocca-Serra
resuspended is a conferred qualify which inheres in material resulting from an resuspension process
renatured
Philippe Rocca-Serra
amplified
Macroarray Detection of Plant RNA Viruses Using Randomly Primed and Amplified Complementary DNAs from Infected Plants. Phytopathology. 2007 Jan;97(1):119-127. PMID: 18942945
OBI Biomaterial
Philippe Rocca-Serra
amplified is a conferred qualify which inheres in material resulting from an amplification process
lysed
OBI Biomaterial
Philippe Rocca-Serra
Variation of pH in lysed platelet concentrates influence proliferation and alkaline phosphatase activity in human osteoblast-like cells. Platelets. 2007 Mar;18(2):113-8. PMID: 17365859
lyzed is a conferred qualify which inheres in material resulting from an lysis process
stained
Different assessments of immunohistochemically stained Ki-67 and hTERT in glioblastoma multiforme yield variable results: a study with reference to survival prognosis.
Clin Neuropathol. 2008 Jul-Aug;27(4):224-33. PMID: 18666438
OBI Biomaterial
Philippe Rocca-Serra
stained is a conferred qualify which inheres in material resulting from an staining/dyeing process
activated
OBI Biomaterial
Philippe Rocca-Serra
Reduction of Nuclear Peroxisome Proliferator-Activated Receptor gamma Expression in Methamphetamine-Induced Neurotoxicity and Neuroprotective Effects of Ibuprofen.
Neurochem Res. 2008 Oct 23. PMID: 18946735
activated is a conferred qualify which inheres in material resulting from an activation process
predicted
Philippe Rocca-Serra
predicted is a
mean-centered
Philippe Rocca-Serra
reverse transcribed
Fully-spliced HIV-1 RNAs are reverse transcribed with similar efficiencies as the genomic RNA in virions and cells, but more efficiently in AZT-treated cells. Retrovirology. 2007 May 2;4:30. PMID: 17474982
OBI Biomaterial
Philippe Rocca-Serra
reverse transcribed is a conferred qualify which inheres in material resulting from a reverse transcription process
blocked
Philippe Rocca-Serra
digested
Cellobiose is extensively digested in the small intestine by beta-galactosidase in rats.
Nutrition. 2008 Nov-Dec;24(11-12):1199-204. PMID: 18752931
OBI Biomaterial
Philippe Rocca-Serra
digested is a conferred qualify which inheres in material resulting from an digestion process
pooled
OBI Biomaterial
Philippe Rocca-Serra
SNP frequency estimation using massively parallel sequencing of pooled DNA.
Eur J Hum Genet. 2008 Oct 15. PMID: 18854868
pooled is a conferred qualify which inheres in material resulting from an material pooling process
labeled
Analysis of the Spatial Distribution of Identical and Two Distinct Virus Populations Differently Labeled with Cyan and Yellow Fluorescent Proteins in Coinfected Plants.
Phytopathology. 2007 Oct;97(10):1200-1206. PMID: 18943677
OBI Biomaterial
Philippe Rocca-Serra
labeled is a conferred qualify which inheres in material resulting from an labeling process
use role
edited
Philippe Rocca-Serra
excised
Glioma-like proliferation within tissues excised as tubers in patients with tuberous sclerosis complex. Acta Neuropathol. 2008 Jul;116(1):67-77. PMID: 1858112
OBI Biomaterial
Philippe Rocca-Serra
excised is a conferred qualify which inheres in material resulting from an excision process
dissolved
Philippe Rocca-Serra
blotted
Philippe Rocca-Serra
hybridized
Multi-stringency wash of partially hybridized 60-mer probes reveals that the stringency along the probe decreases with distance from the microarray surface. Nucleic Acids Res. 2008 Sep 19. PMID: 18805905
OBI Biomaterial
Philippe Rocca-Serra
hybridized is a conferred qualify which inheres in material resulting from an hybridization process
extracted
Antiproliferative Effects of Carotenoids Extracted from Chlorella ellipsoidea and Chlorella vulgaris on Human Colon Cancer Cells. J Agric Food Chem. 2008 Oct 23. PMID: 18942838
OBI Biomaterial
Philippe Rocca-Serra
extracted is a conferred qualify which inheres in material resulting from an extraction process
washed
Effect of extraction conditions on the yield and purity of apple pomace pectin precipitated but not washed by alcohol. J Food Sci. 2007 Jan;72(1):C001-9. PMID: 17995865
OBI Biomaterial
Philippe Rocca-Serra
washed is a conferred qualify which inheres in material resulting from an washing process
normalized
Philippe Rocca-Serra
would have to inhere in data - nono. Is this related to the objective
eluted
OBI Biomaterial
Philippe Rocca-Serra
Vaccinia peptides eluted from HLA-DR1 isolated from virus-infected cells are recognized by CD4+ T cells from a vaccinated donor. J Proteome Res. 2008 Jul;7(7):2703-11. PMID: 18507432
eluted is a conferred qualify which inheres in material resulting from an elution process
electroporated
Modified whole-mount in situ hybridization protocol for the detection of transgene expression in electroporated chick embryos. PLoS ONE. 2008 Jul 9;3(7):e2638. PMID: 18612382
OBI Biomaterial
Philippe Rocca-Serra
electroporated is a conferred qualify which inheres in material resulting from an electroporation process
extraction
Philippe Rocca-Serra
filtration
OBI-Branch: adapted from wikipedia and wordnet
PMID: 18524968.Filtration of CSF improves isolation of Mycobacteria.J Clin Microbiol. 2008 Jun 4.
Philippe Rocca-Serra
filtration is a process which separates components suspended in a fluid based on granularity properties relying on a filter device
centrifugation
PMID: 18428461.Purification of oligodendrocytes and their progenitors using immunomagnetic separation and Percoll gradient centrifugation. Curr Protoc Neurosci. 2001 May;Chapter 3:Unit 3.12.
Philippe Rocca-Serra
adapted from http://www.fao.org/DOCREP/003/X3910E/X3910E06.htm
centrifugation is a process separating molecules by size or density using centrifugal forces generated by a spinning rotor. G-forces of several hundred thousand times gravity are generated in ultracentrifugation
staining
PMID: 18540298. Role of modified bleach method in staining of acid-fast bacilli in lymph node aspirates. Acta Cytol. 2008 May-Jun;52(3):325-8.
Philippe Rocca-Serra
Staining is a process which results in the addition a class-specific (DNA, proteins, lipids, carbohydrates) dye to a substrate to qualify or quantify the presence of a specific compound.
adapted from Wikipedia: http://en.wikipedia.org/wiki/Staining
washing
OBI-Branch
PMID: 6874122. Dialysis leucopenia--no correction after prolonged washing of the membrane. Int J Artif Organs. 1983 May;6(3):113-4.
Philippe Rocca-Serra
washing is a process by which a material entity acting as contaminant (e.g. excess staining reagent) is removed by application of one or more cycles of solution in flow.
irradiation
PMID: 18563778.Histological and modeling study of skin thermal injury to 2.0 mum laser irradiation.Lasers Surg Med. 2008 Jun 18;40(5):358-370.
Philippe Rocca-Serra
adapted from wikipedia (http://en.wikipedia.org/wiki/Irradiation)
irradiation is a process by which a material entity is exposed to radiative energy, which could be ionizing radiation (such as gamma rays or X-rays) or not such as UV light or microwaves
polymerization
OBI-Branch
PMID: 18517209. The electronic role of DNA-functionalized carbon nanotubes: efficacy for in situ polymerization of conducting polymer nanocomposites. J Am Chem Soc. 2008 Jun 25;130(25):7921-8. Epub 2008 Jun 3.
PRS:22102008: need to import catalyst from CHEBI 35223
Philippe Rocca-Serra
polymerization is process by which molecular entity of small mass are aggregated in motifs over the course of a chemical reaction catalyzed by enzymes or other molecular entities acting as catalyst. ploymerization results in molecular entity of high molecular weight
trypsination
OBI PA
Philippe Rocca-Serra
The use of mild trypsinization conditions in the detachment of endothelial cells to promote subsequent endothelialization on synthetic surfaces. Biomaterials. 2007 Sep;28(27):3928-35. PMID: 17570483
trypsination is a protease cleavage which uses enzyme trypsin to act on proteins present in an input material entity
enzymatic ligation
OBI-Branch
PMID: 17853876. Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat Protoc. 2007;2(9):2198-202.
Philippe Rocca-Serra
enzymatic ligation is a process which fragments of molecule can be united or or open molecules can be circularized by covalent bond through the action of enzyme or other agent with ligase activity
storage
OBI-Branch
PMID: 18550121.Total Prostate Specific Antigen Stability Confirmed After Long-Term Storage of Serum at -80C. J Urol. 2008 Jun 10.
Philippe Rocca-Serra
storage is a process by which material entities are placed in well identified location and possibly under controlled environment in ad-hoc devices/structures in order to preserve and protect them from decay/alteration and maintain availability
cell lysis
PMID: 18484276.Cell lysis with dimethyl sulphoxide produces stable homogeneous solutions in the dichlorofluorescein oxidative stress assay. Free Radic Res. 2008 May;42(5):435-41.
Philippe Rocca-Serra
adapted from wikipedia [http://en.wikipedia.org/wiki/Lysis]
cell lysis is a process by which cell membrane integrity of live cells is compromised and leads to cell death. Cell lysis may be achieved by means of viral action or osmotic shock.
electrocution
OBI branch
PMID: 9587208. Electrocution of horses and cattle. Vet Rec. 1998 Apr 4;142(14):376.
Philippe Rocca-Serra
electrocution is process by which electric current is applied to a material with quality alive and result the termination of life process.
cervical dislocation
OBI branch
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-3
PRS:21102008: Input must be restricted to Vertebrates (requires import from NCBI tax)
Philippe Rocca-Serra
cervical dislocation is a process by which a Vertebrate organism has its life terminated by rupturing spinal cord between cervical vertebrae induced by excessive mechanical torsion
asphyxiation
OBI branch
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
Philippe Rocca-Serra
asphyxiation is a process by which oxygen supplies are restricted (by mechanical, e.g obstructing airways or chemical means, e.g. increasing CO2 partial pressure) resulting in termination of life in oxygen reliant organisms.
intentional overdosing
In vivo measurement of tumor blood oxygenation by near-infrared spectroscopy: immediate effects of pentobarbital overdose or carmustine treatment.
J Neurooncol. 1994;22(3):209-20. PMID: 7760097
OBI Biomaterial
Philippe Rocca-Serra
intentional overdosing is a process by which an excess dose of a chemical compound is given with the intent of causing death
lethal injection
decapitation
OBI-Branch
PMID: 18246869. Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation. Comp Med. 2007 Dec;57(6):570-
Philippe Rocca-Serra
decapitation is a process by which the head of a living organism is physically removed from the body, usually resulting in rapid death (in the case of Rhodnius prolixus, it might take a bit longer..)
randomization
PMID: 18349405. Randomization reveals unexpected acute leukemias in Southwest Oncology Group prostate cancer trial. J Clin Oncol. 2008 Mar 20;26(9):1532-6.
Philippe Rocca-Serra
adapted from wikipedia [http://en.wikipedia.org/wiki/Randomization]
randomization is a group assignemnt which relies on chance to assign materials to a group of materials in order to avoid biais in experimental set up.
activation
OBI-Branch
PMID: 18566411.Activation of the JAK/STAT-1 Signaling Pathway by IFN-{gamma} Can Down-Regulate Functional Expression of the MHC Class I-Related Neonatal Fc Receptor for IgG.J Immunol. 2008 Jul 1;181(1):449-63.
Philippe Rocca-Serra
activation is a process by which a material entity status is modified and confered a capability of reacting
(this sounds like a circular definition , hugh!)
immobilization
OBI-Branch
PMID: 18562258. The immobilization of proteins on biodegradable fibers via biotin-streptavidin bridges.Acta Biomater. 2008 May 23.
Philippe Rocca-Serra
immbolization is a process by which material entity become (possibly covalently but not necessarily) attached to the surface of another material entity used a substratum.
nucleic acid hybridization
PMID: 18555787.Quantitative analysis of DNA hybridization in a flowthrough microarray for molecular testing. Anal Biochem. 2008 May 27.
Philippe Rocca-Serra
adapted from wikipedia [http://en.wikipedia.org/wiki/Nucleic_acid_hybridization]
hybridization of nucleic acid is process by which totally or partially complementary, single-stranded nucleic acids can be combined into a single molecule called heteroduplex or homoduplex depending on the quality of the complementation.
elution
PMID: 18549238.Theory and Application of the Two-Mode Gradient Elution in Liquid Chromatography Involving Simultaneous Changes in Temperature and Mobile-Phase Composition.Anal Chem. 2008 Jun 13.
Philippe Rocca-Serra
the process of extracting one material from another by washing with a solvent to remove adsorbed material from an adsorbent (as in washing of loaded ion-exchange resins to remove captured ions)
wordnet.princeton.edu/perl/webwn
substraction
DNA subtraction is a material separation process by which repetitive genomic DNA is removed during the construction of cDNA library.
OBI-Branch
PMID: 10718422. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope. 2000 Mar;110(3 Pt 1):374-81
Philippe Rocca-Serra
document editing
Philippe Rocca-Serra
Wax DB, Beilin Y, Hossain S, Lin HM, Reich DL.
Manual editing of automatically recorded data in an anesthesia information management system. Anesthesiology. 2008 Nov;109(5):811-5. PMID: 18946292
adapted from wikipedia
curation, proofreading
editing is a process which checks for and corrects errors in spelling, punctuation, capitalization, grammar, and usage;
prediction
OBI
Philippe Rocca-Serra
Prediction of TF target sites based on atomistic models of protein-DNA complexes. BMC Bioinformatics. 2008 Oct 16;9(1):436. PMID: 18922190
a process by which an event or an entity is described before it actually happens or is being discovered and identified.
validation
PMID: 18557814 . Chemical and genetic validation of dihydrofolate reductase-thymidylate synthase as a drug target in African trypanosomes. Mol Microbiol. 2008 Jun 16.
Philippe Rocca-Serra
adapted from wordnet (wkipedia)
validation is a process by which the accuracy or the quality of a claim or prediction satisfies criteria and is assessed by comparing with independent results
electroporation
Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by an externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance into a cell, such as loading it with a molecular probe, a drug that can change the cell's function, or a piece of coding DNA
PMID: 18551712. Microfluidic electroporation for selective release of intracellular molecules at the single-cell level. Electrophoresis. 2008 Jun 13.
Philippe Rocca-Serra
wikipedia
http://en.wikipedia.org/wiki/Electroporation
digital curation
Digital curation is the process of establishing and developing long term repositories of digital assets for current and future reference by researchers, scientists, and historians, and scholars generally.
PMID: 16901087. Supporting the curation of biological databases with reusable text mining.Genome Inform. 2005;16(2):32-44.
Philippe Rocca-Serra
wikipedia
device
A device can be any instrument such as a mass spectrometer or lab ware such as a petri dish
A device is a material that is manufactured by an organization or person, designed with the intent to perform a specific function or functions.
Instrument branch
Instrument branch
device
hardware
instrument
An example of an instrument is a mass spectrometer or a flow cytometer
An instrument is a device which provides a mechanical or electronic function.
was:
An instrument is a device which provides a mechanical or electronic advantage as a participant in a process
OBI InstrumentBranch
OBI InstrumentBranch
instrument
rem1: At the meeting in Philly I wrote that BS said that it should be a count term, such as a set of instruments. By allowing connected devices we avoid the problem of things like LCMS being considered separate items, since we have a number of discrete functions like separation, making things fly, monitoring the charge and mass of what flies etc that are all part of a single machine.
FG: Get rid of it and make it a defined class under device
obsolete_labware
An example of labware are test tubes, petri dishes, glass beakers.
Daniel Schober
Labware is a device that has low overall complexity and usually facilitates less process steps than other devices. Its low complexity is signified through the fact that it is often regarded as passive (not active). Labware needs a proactive agent (human or computer) to facilitate a process (its intended use).
OBI
The class labware is here as a place holder class to accout for entities such as test tubes, beakers, centrifuge tubes etc. It is expected as we identify subclasses we will be in a better position to identify the hierarchy, the definition and possibly the label for this class.
labware
A10-Analyzer
A A10 is a flow_cytometer_analyser manufactured by Apogee. It uses an arc lamp as a light source, with choices of 75W Xe, 75W Xe/Hg or 100W Hg arc lamps. It has filters and collectors for up to three fluorescent parameters and two scatter parameters. It uses analog electronics. The A10 can be used for measuring the properties of individual cells.
A10-Analyzer
John Quinn
http://www.apogeeflow.com/flow_cytometry_products.htm
A40-MiniFCM
A A40-MiniFCM is a flow_cytometer_analyser that allows for the choise of one of four lasers (375nm, 405nm,488nm, 532nm, 635nm), and PMTs and filters for collecting up to four parameters. It uses digital electronics. A military version of this cytometer is available as well. The A40-MiniFCM is geared towards the most demanding applications such as archaea, bacteria and large virus.
A40-MiniFCM
John Quinn
http://www.apogeeflow.com/flow_cytometry_products.htm
analog-to-digital converter
A-D
A2D
An analog-to-digital_converter is an instrument that converts an infinite resolution analog signal to a finite resolution digital signal.
John Quinn
Melanie Courtot
The analog to digital converter transformed the analog output from the photomultiplier tube to a digital signal for collection.
analog-to-digital converter
http://en.wiktionary.org/wiki/Analog-to-Digital_Converter
original definition says "part of the electronic subsystem"
flow cytometer analyzer
An analyser is a flow_cytometer that is used to measure properties of particles (whole cells, nuclei, chromosomes, diatoms, plankton, bacteria, viruses) by moving these particles through a detection chamber. An analyser is used to collect data for anaylsis.
FACS Calibur, Luminex 100
John Quinn
The definitions for leaf node instruments do not currently follow OBO Foundry. They are preliminary solutions and definitions will not get placed on the Modell level.
flow cytometer analyzer
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
arc lamp
Arc lamp is a light source that produces light by an electric arc (or voltaic arc). The lamp consists of two electrodes typically made of tungsten which are separated by a gas. The type of lamp is often named by the gas contained in the bulb; including neon, argon, xenon, krypton, sodium, metal halide, and mercury. The electric arc in an arc lamp consists of gas which is initially ionized by a voltage and is therefore electrically conductive. To start an arc lamp, usually a very high voltage is needed to ignite or strike the arc. This requires an electrical circuit sometimes called an igniter, which is part of a larger circuit called the ballast. The ballast supplies a suitable voltage and current to the lamp as its electrical characteristics change with temperature and time. Older cytometers may use arc lamps to irradiate particles at the interogation point.
John Quinn
The Jablochkoff Candle
arc lamp
http://en.wikipedia.org/wiki/Arc_lamp
argon ion laser
http://en.wikipedia.org/wiki/Laser#Gas_lasers
An argon-ion laser is an ion laser that uses argon ions as the lasing medium. These lasers are used primarily to emit light at wave lengths of 458 nm, 488 nm or 514.5 nm, though it is possible to use them to emit several wavelengths of blue and green light. Argon-ion lasers can emit light at many different wave lenghts, and excite a number of different flourochromes.
Daniel Schober
John Quinn
argon ion laser
argon ion laser in a cytometer
avalanche photodiode
An avalanche photodiode is typically used to collect photons emmitted by forward scatter because it is far less sensitive, and less likely o be burned out, than a PMT. A photodiode wih high quantom efficiency and a mechanism for producing gains as high as a few thousand.
C30644E - InGaAs Avalanche Photodiode
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
avalanche photodiode
Bactiflow
A Bactiflow is a flow_cytometer_analyser manufactured by Chemunex SA. It is a cell counter for bacteria and other micro organisms. Bacteria are stained with a fluorochrome and the number of particles that fluoresce are counted. The system uses digital electronics, a single laser and a single detector. An ALS version is available as well - Automatic Labeling System. The Bactiflow is specialized cytometer used exclusively for counting microbes.
Bactiflow
John Quinn
http://www.chemunex.com/products/chemframe.htm
band pass filter
530/30 BP filter, 585/42 BP filter
A band pass filter is an optical filter that passes wavelengths of light within a certain range and rejects (attenuates) frequencies outside that range. The passed wavelengths are indicated in the specifications of the filter and its name. A 480/20 bandpass filter pass light with at wavelengths of 460 to 500 nm and attenuates all others.
John Quinn
band_pass_filter
http://en.wikipedia.org/wiki/Band_pass_filter
BioSorter1000
A BioSorter1000 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 1000 is an instrument for analyzing and sorting objects from 200-600 microns in diameter.
BioSorter 1000 at TSRI Flow Cytometry Core Facility
BioSorter1000
John Quinn
http://www.unionbio.com/products/BioSorter.html
BioSorter2000
A BioSorter2000 is a sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 fluorescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 2000 is an instrument for analyzing and sorting objects from 500 microns to 1.5 millimeters in diameter.
BioSorter 2000 at TSRI Flow Cytometry Core Facility
BioSorter2000
John Quinn
http://www.unionbio.com/products/BioSorter.html
BioSorter250
A BioSorter250 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 flourescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 250 is an instrument for analyzing and sorting objects from 40-200 microns in diameter.
BioSorter 250 at TSRI Flow Cytometry Core Facility
BioSorter250
John Quinn
http://www.unionbio.com/products/BioSorter.html
BioSorter500
A BioSorter500 is a flow_cytometer_sorter manufactured by Union Biometrica. It includes analog electronics, 488/514 nm multi-line Argon-ion laser for fluorescence and a light stabilized 670 nm forward scatter laser for extinction and time-of-flight. It has filters and PMTs for 3 flourescent parameters and photodiodes for scatter, time of flight, and extinction. The flow cell is quartz cuvette. The BioSorterTM 500 is an instrument for analyzing and sorting objects from 100-250 microns in diameter and less than 2mm in length.
BioSorter 500 at TSRI Flow Cytometry Core Facility
BioSorter500
John Quinn
http://www.unionbio.com/products/BioSorter.html
Cell Lab Quanta SC
A Cell Lab Quanta SC is a flow_cytometer_analyser manufactured by Becman Coulter. It features a mercury arc lamp optimized at 366, 405, and 435 nm, and a 488 nm laser diode. It has filters and PMTs to collect up to 3 flourescent parameters, and a photodiode for side scatter detection. This cytometer uses Couter-Volume for cell size measurements. The Cell Lab Quanta SC can be used for measuring the properties of inividal cells.
Cell Lab Quanta SC
John Quinn
http://www.beckmancoulter.com/cell-lab
charge plate
John Quinn
LSR2 charge plate
Part of the fluidics subsystem. Charge plates are used or sorters. They create an charged electric field when particles deemed to be desired for further analysis are shaken form the piexo electric crystal. The charged particles are drawn toward the charged plate, and the altered drop location causes the particles to fall into a collection tube. Charge plates enable sorting.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
charge plate
collection tube
DS: a collection tube is no instrument. This is yet another example of distorted is_a and part_of hierarchy...
part_of fluidic_subsystem
John Quinn
LSR2 collection tube
Part of the fluidics subsystem. The collection tube is a vessel for capturing cells of interest that have been identified by a sorter. The collection tube is the end location of sorted cells.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
collection tube
Cyan
A Cyan is a flow_cytometer_analyser manufactured by Dako Cytomation. It features include digital electronics, three lasers: 488 nm, 635 nm, and 405 nm, and filters and collectors for nine flourescent parameters and two scatter parameters. The Cyan can be used for measuring the properties of inividal cells.
Cyan
John Quinn
http://www.dakousa.com/prod_productrelatedinformation?url=gprod_cyan_index.htm
CYFlow ML
A CyFlow_ML is a flow_cytometer_analyser manufactured by Partec. It is a digital machine which uses 4 light sources: triple laser configurations including new powerful 200mW@488nm blue solid state laser + 100W UV lamp for highest resolution DNA analysis, and can collect 16 optical parameters: FSC1, FSC2, SSC, FL1-FL13. Ultracompact high end desktop multilaser Flow Cytometer for all applications in cell analysis and absolute counting.
CYFlow ML
John Quinn
http://www.partec.de/products/cyflow-ml.html
CyFlow SL
A CyFlow_Sl is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37, highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser , other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for realtime data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing Compact mobile Flow Cytometer for any kind of cell analysis and absolute volumetric counting. The CyFlow_SL allows to analyze forward and side scatter signals in combination with up to 3 fluorescence channels.
CYFlow SL
John Quinn
http://www.partec.de/products/cyflow.html
CyFlow SL3
A CyFlow_Sl3 is a flow_cytometer_analyser manufactured by Partec. Its specs are: ultracompact and fully equipped mobile/portable instrument, dimensions [cm]: L 43 x H 16 x D 37 , highest stability/robustness and highest precision, 5 optical parameters: FSC, SSC, FL-1, FL-2, FL-3, 20mW@488nm blue solid state laser, other laser light sources optional (UV, violet, green, red), WindowsTM XP FloMax (software for realtime data acquisition, data display, and data evaluation), parallel 16 bit digital pulse processing. The CyFlow SL3 is a compact and dedicated portable Flow Cytometer for accurate and affordable cell analysis and true volumetric absolute counting in HIV Monitoring and AIDS patient follow-up by precise and direct CD4 and CD4% measurement.
CyFlow SL3
John Quinn
http://www.partec.de/products/cyflowsl3.html
CyFlow Space
A CyFlow_Space is a flow_cytometer_sorter manufactured by Partec. Its specs are: 8optical parameters, 6 colours:FSC, SSC, FL1-FL6 , 3laser light sources: 200mW@488nm blue solid state laser 25mW@635nm red diode laser 50mW@405nm violet or 8mW@375nm ultraviolet diode laser _ultracompact desktop high end instrument. Parallel 16bit digital pulse processing. The CyFlow Space is a 6-Colour FCM System and Cell Sorter for Clinical Routine and Research.
CyFlow Space
CyFlow Space at TSRI Flow Cytometry Core Facility
John Quinn
http://www.partec.de/products/cyflowspace.html
CytoBuoy
A CytoBuoy is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are the buoy mounted version of the CytoSense, equipped with wireless transmission of control and data files.They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters.
CytoBuoy
CytoBuoy can be used to conduct extended and/or high frequency time series of phytoplankton distribution and abundance on fixed locations
John Quinn, Melanie Courtot
http://www.cytobuoy.com/
CytoSence
A CytoSense is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSense is the basic instrument, which can be used for normal laboratory applications, as well as for autonomous monitoring with internal data logging or direct data transmission. The special instrument design and its splashproof housing allow operation on moving platforms and outdoor sites.
CytoSence
John Quinn
http://www.cytobuoy.com/
CytoSub
A CytoSub is a flow_cytometer_analyser manufactured by Cyto Buoy Inc. They are a single laser, multi parameter instrument. Various types of micro-laser are offered; available measuring parameters are forward light scatter, side scatter, and fluorescence (max. 9 colour bands). The current series have 5 parameters. The CytoSub is the submersible version equipped with a high pressure sample inlet loop and a high pressure housing to allow underwater operation down to 200 m, lowered on a cable or mounted on a flooded underwater vehicle.
CytoSub
John Quinn
http://www.cytobuoy.com/
dichroic filter
A dichroic filter is an optical filter which is used to selectively pass light of a small range of colors while reflecting other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light.
Cy3 Dichroic Filter
John Quinn
dichroic filter
http://en.wikipedia.org/wiki/Dichroic_filter
dichroic mirror
A dichroic mirror is an optical filter which is used to selectively reflect light of a small range of colors while passing other colors. A dichroic filter passes the specified range of light whereas a dichroic mirror reflects the specified range of light.
John Quinn
ViewLux Alexa 594 dichroic mirror
dichroic mirror
http://en.wikipedia.org/wiki/Dichroic_mirror
differential pressure gauge
John Quinn
LSR2 differential pressure gauge
Part of the fluidics subsystem. The differential pressure gauge monitors the difference between sample and sheath fluid pressures in systems where pressure is used to force the sample fluid to flow in the center of the sheath fluid. A differential pressure gauge can be used by the operator to make sure that the sample fluid is at a greater pressure than the sheath fluid, which maintains a core of sample fluid.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
differential pressure gauge
diode laser
A diode laser is a laser in which the active medium is a p-n junction semiconductor laser diode, similar to that found in a light-emitting diode. Laser diodes emit at wavelengths from 375 nm to 1800 nm, and wavelengths of over 3 micrometer have been demonstrated. A diode laser can by used to irradiate cells in a flow cytometer.
Daniel Schober
FAX-RS3-H0 diode laser manufactured by Diode Laser Concepts, Inc.
John Quinn
diode laser
dye laser
A dye laser is a laser in which the lasing medium is a flourescent dye, usually disolved in an organic solvent such as ethanol or ethylene glycol. The particular dye used determines the wavelengths the laser can emit. The laser medium is places between two parallel mirrors for light emmission amplification.
Daniel Schober
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
Rhodamine 101 dye laser used to irradiate cells in a flow cytometer.
dye laser
FACS Calibur
"FACS Calibur at TFL, BCCRC, Vancouver"
"http://www.bdbiosciences.com/immunocytometry_systems/products/display_product.php?keyID=45, 2007-05-11"
FACS Calibur
John Quinn
The FACS Calibur is one of the most popular cytometers in use for research.
editor_note pending
FACS Canto
A FACS_Canto is a flow_cytometer_analyser manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm, and a HeNe 633 nm lasers, and filters and PMTs for collecting up to 6 flourescent parameters. The FACS_Canto is an analyser usually used in clinical applications.
FACS Canto
John Quinn
http://www.bdbiosciences.com/pdfs/brochures/23-8742-00.pdf
FACS Canto2
A FACS_Canto2 is a flow_cytometer_analyser manufactured by BD. It features digital electronics, two solid state lasers at 488 and 633 nm with the option for a third 405 nm laser, and filters and collectors for measuring up to 8 flourescent paramters with either the 2 or 3 laser option. The FACS_Canto2 is an analyser usually used in clinical aplications.
FACS Canto2
John Quinn
http://www.bdbiosciences.com/cgi-bin/literature/view?part_num=23-8786-01
FACS Scan
A FACS_Scan is a flow_cytometer_analyser manufactured by Becton Dickinson. IT features analog electronics, one 488 nm solid state laser, and the filters and PMTs to collect up to three flourescent parameters The FACS_Scan is usually used for research applications.
FACS Scan
John Quinn
http://www.brc.ubc.ca/brc/facs.html
FACSAria
A FASCSAria is a flow_cytometer_sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser, a solid state 407 nm violet laser, and a HeNe (633 nm) ion laser. The Aria has the filters and PMTs to collect side scatter and 9 flourescent parameters. The Aria has a photodiode detector for forward scatter collector. The flow cell is Quartz cuvette. The FACSAria is a sorter used to collect and analyse cells using up to 11 parameters.
FACSAria
FACSAria at TSRI Flow Cytometry Core Facility
John Quinn
http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/SJ-0003-00Aria.pdf
FACSvantage
FACSvantage
FACSvantage at TSRI Flow Cytometry Core Facility
John Quinn
The FACSvantage is a flow_cytometer_sorter manufactured by Becton Dickinson. It has analog electronics, three lasers (several options are available), and the filters and PMTs to collect 6 fluorescent parametersand side scatter, and a photodiode to collect forward scatter. The FACSvantage can be used to analyse, sort and collect cells.
http://www.bdbiosciences.com/features/products/display_product.php?keyID=42
FC 500
A FC_500 is a flow_cytometer_analyser manufactured by Beckman Coulter. It features digital electronics, 488 nm and 635 nm lasers, filters and PMTs for 5 flourescent parameters, a diode for collecting side scatter and a solid state detector for forward scatter. The FC 500 is an analyser usually used for either research or clinical applications.
FC 500
John Quinn
http://www.beckmancoulter.com/products/instrument/flowcytometry/fc500series.asp
flow cell
Aparatus in the fluidic subsystem where the sheath and sample meet. Can be one of several types; jet-in-air, quartz cuvette, or a hybrid of the two. The sample flows through the center of a fluid column of sheath fluid in the flow cell.
Biofilm Flow Cell
John Quinn
flow_cell
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
flow cytometer
A flow_cytometer is an instrument for counting, examining and sorting microscopic particles in suspension. It allows simultaneous multiparametric analysis of the physical and/or chemical characteristics of single cells flowing through an optical and/or electronic detection apparatus. A flow cytometer is an instrument that can be used to quantitatively measure the properties of individual cells in a flowing medium.
DS: Is this class justified? (has currently only one subclass), ask Ryan and Function Branch for differrentiae...
FACS Calibur
John Quinn
flow cytometer
http://en.wikipedia.org/wiki/Flow_cytometer
fluid pressure regulator
John Quinn
LSR2 fluid pressure regulator
Part of the fluidic subsystem. The fluid pressure regulator maintains constant pressure within the sheath and or sample lines by filling the lines with enough gas to push the fluid at the desired rate. The gas is usually air, and less freqeuntly nitorgen. In the sheath line, the gas is pushed into the sheath tank. In the sample line the gas is pushed into the collection tube. Fluid pressure regulators maintain great enough pressure to push sample fluid out of the tube and sheath fluid out of the sheath tank.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
fluid_pressure_regulator
gas laser
http://en.wikipedia.org/wiki/Gas_laser
A gas laser is a laser in which the lasing medium is a gas. The laser medium is places between two parallel mirrors for light emmission amplification. The gas is excited to emit light via an external light source or an electric current dischargeing through the gas.
Daniel Schober
John Quinn
gas_ aser
helium-neon gas laser used to erradiate cells in a flow cytometer.
Guava EasyCyte Mini
A Guava_EasyCyte_Mini is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 3 flourescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The mini accepts tubes only for inputing cells or beads. The Guava_EasyCyte_Mini cytometer is a small portable cytometer particularly useful for field measurement.
Guava EasyCyte Mini
John Quinn
http://www.guavatechnologies.com/main/products/easyCyteMini.cfm
Guava EasyCyte Plus
A Guava_EasyCyte_Plus System is a flow_cytometer_analyser that includes a single 488 nm laser, and filters and PMTs to collect up to 4 fluorescent parameters. It includes a photodiode forward scatter collector and an optional photodiode for side scatter collection.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The EasyCyte plus accepts 96 well plates as well as tubes. The Guava_EasyCyte_Plus cytometer is a small portable cytometer particularly useful for field measurement.
Guava EasyCyte Plus
John Quinn
http://www.guavatechnologies.com/main/products/easycyte-new.cfm
Guava Personal Cell Analysis
A Guava_Personal_Cell_Analysis System is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 fluorescent parameters. It includes a photodiode forward scatter collector. Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses only tubes to introduce specimen. The Guava PCA cytometer is a small portable cytometer particularly useful for field measurement.
Guava Personal Cell Analysis
Guava_PCA
John Quinn
http://www.guavatechnologies.com/main/products/PCA-new.cfm
Guava Personal Cell Analysis-96
Guava Personal Cell Analysis-96
Guava_PCA-96
John Quinn
The Guava_Personal_Cell_Analysis-96 Systems is a flow_cytometer_analyser that includes a single 532 nm laser, and filters and PMTs to collect up to 2 flourescent parameters. It includes a photodiode forward scatter collector.Guava cytometers use aspiration instead of fluid systems to transport cells within the machine. The PCA96 uses either tubes or 96 well plates to introduce specimen. The Guava PCA -96 cytometer is a small portable cytometer particularly useful for field measurement.
http://www.guavatechnologies.com/main/products/PCA-96new.cfm
helium cadmium ion laser
A helium-cadmium laser is a metal vapor laser that emits wavelengths of 442, 325 and 354 nms. This laser is a metal vapor laser. A helium-cadmium laser can by used to irradiate cells in a flow cytometer.
John Quinn
KIMMON HeCd 325nm laser
helium cadmium ion laser
http://en.wikipedia.org/wiki/Laser#Gas_lasers
helium neon ion laser
http://en.wikipedia.org/wiki/Laser#Gas_lasers
A helium neon laser can by used to irradiate cells in a flow cytometer.
A helium-neon laser (HeNe) is an ion laser that uses helium and neon gas-ions as lasing medium. HeNe lasers emit at 543 nm and 633 nm most commonly and can also be used at 543, 594, and 611 nm.
Daniel Schober
John Quinn
helium neon ion laser
image stream
ImageStream
It has both components, an Image cytometer and a flow cytometer.
John Quinn
Melanie Courtot
The ImageStream is a multispectral_imaging_flow_cytometer manufactured by Amnis. Its has digital electronics, a single standard 488 nm solid state laser. In addition an optional 658 nm and your choice of either a 405 nm or 375 nm solid state laser can be added. Information is collected using cameras. The ImageStream system CCD camera produces six images of each cell, including darkfield, brightfield, and up to four fluorescent colors. Each image is used to calculate over 40 features, so a six-image assay results in ~250 morphometric and photometric features per cell. The ImageStream is a flow cytometer that takes pictures of the cells in flow.
It has both components, an Image cytometer and a flow cytometer.
http://www.amnis.com/
inFlux Analyzer
John Quinn
The inFlux Analyzer is a flow_cytometer_analyser manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. FIlters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx analyser can be used to measure the properties of individual cells.
http://www.cytopeia.com/analyzer.htm
inFlux Analyzer
Influx Cell Sorter
A Influx Cell Sorter is a flow_cytometer_sorter manufactured by Cytopeia. It is a digital machine, with these laser options: Coherent 70, 90, 300 series water cooled lasers, solid state UV 355nm, Violet 408nm, Violet-Blue 479nm, Blue-488nm, Green-531nm, Red-635nm, Red-647nm. The sorting is multi-way, index, and proportional sorting. FIlters and PMTs are used for all parameters (including forward light scatter), and up to 12 PMTs can be included. The Influx cell sorter can be used to measure, sort, and collect ndividual cells.
Influx Cell Sorter
Influx Cell Sorter at TSRI Flow Cytometry Core Facility
John Quinn
http://www.cytopeia.com/sorter.htm
interrogation_point
DS: Spatial entity?
AI: Ryan goes back to John Quinn and saks for usage example of this term.
Interrogation point in BD FACS Calibur
John Quinn
Point within the fluidic subsystem at which the laser intersects the stream, illuminating the cells where they emit their fluorescence and scatter the light. The laser irratidates the cell at the interogation point.
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm, 2007-05-11
interrogation_point
ion laser
http://en.wikipedia.org/wiki/Ion_laser
2 Watt Lexel 88 Argon Ion laser
An ion laser is a gas laser which uses an ionized gas as its lasing medium.
Daniel Schober
John Quinn
ion laser
jet_in_air_flow_chamber
A flow cell in which the cells are pinched off as droplets and allowed to drop through the air. The laser intersects with the cell in mid-air. A jet in air flow chamber allows the laser to intersect with the cells without any intermitent media other than air.
DS: a chamber is not an instrument, its a spatial entity...
AI: Ryan goes back to John Quinn and saks for usage example of this term.
Jet-in-air flow chamber in DakoCytomation MoFlo high-speed cell sorter
John Quinn
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
jet_in_air_flow_chamber
krypton ion laser
A krypton-ion laser is an ion laser that uses krypton as the lasing medium. These lasers can emit at 468, 476, 482, 520, 531, 568, 647 (the most powerfull line), and 676 nm all at once. They have much lower gain than argon lasers however.
Daniel Schober
John Quinn
Lexel 95L krypton laser
krypton ion laser
LactoScope C4
A LactoScope_C4 is a spectrophotometer with which the composition of milk and milk products is analysed via infrared technology. The LactoScope determines the amount of the constituents fat, protein, lactose and the total solids content with extreme accuracy.
Josef Spidlen
LactoScope C4
LactoScope C4 Automatic Economical
Melanie Courtot
http://www.aicompanies.com/DeltaCD/lacto_ftir_auto.htm
laser
http://en.wikipedia.org/wiki/Laser
A laser (acronym for light amplification by the stimulated emission of radiation) is a light source that emits photons of the same characteristics in a coherent beam. A laser uses a solid, liquid or gaseous lasing medium, that conmtains molecules, of which some atoms have electrons that emit photons of the same frequency when falling back to their normal orbital after excitation (pumping) by external means A laser is the most common way to irradiate a cell in a flow cytometer.
A laser is the most common way to irradiate a cell in a flow cytometer.
Daniel Schober
John Quinn
laser
light amplification by the stimulated emission of radiation
light source
A light source is an optical subsystem that provides light for use in a distant area using a delivery system (e.g., fiberoptics). Light sources may include one of a variety of lamps (e.g., xenon, halogen, mercury). Most light sources are operated from line power, but some may be powered from batteries. They are mostly used in endoscopic, microscopic, and other examination and/or in surgical procedures. The light source is part of the optical subsystem. In a flow cytometer the light source directs high intensity light at particles at the interogation point. The light source in a flow cytometer is usually a laser.
DS: this is a role I guess, not an instrument.
Elizabeth M. Goralczyk
John Quinn
Olga Tchuvatkina
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
light source
logarithmic voltage amplifier
A logarithmic voltage amplifier is an analog electronic circuit that puts out a voltage or current proportioal o the voltage or current at its input, with logarithmic proportionality. In an analog system, the logarithmic voltage amplifier is used to present parameters with a high dynamic range on a more useful scale.
HLVA-100 logarithmic voltage amplifier developed by FEMTO Messtechnik, GmbH
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
logarithmic voltage amplifier
long pass filter
750 LP filter
A long pass filter is an optical filter that passes high wavelengths of light but attenuates (or reduces) wavelengths lower than the cutoff frequency. A long pass filter with a cutoff of 500 nm would pass all wavelengths greater than 500 nm.
John Quinn
http://en.wikipedia.org/wiki/high-pass_filter
long pass filter
LSR2
A LSR2 is a sorter manufactured by Becton Dickinson. It features digital electronics, a solid state 488 nm blue laser and optionally can also have any combination of solid state UV (355 nm) and violet (405 nm) lasers and the a HeNe (633 nm) ion laser. The LSR2 has the filters and PMTs to work with 13 flourescent parameters. The LSR II is one of the most common sorters in use.
John Quinn
LSR2
LSR2 at TSRI Flow Cytometry Core Facility
http://www.bdbiosciences.com/external_files/is/doc/mkt_lit/brochures/live/web_enabled/SJ-0142-00LSR2.pdf
Luminex 100
John Quinn
Luminex 100
The Luminex 100 is a flow_cytometer_analyser manufactured by Luminex. It is a single laser system (575 nm) with avalanche photodiodes in red and infrared and a single PMT for fluorescnce. The flow chamber is a square quartz cuvette.
http://www.luminexcorp.com/products/luminex_100IS.html
Luminex 200
A Luminex_200 is a flow_cytometer_analyser manufactured by Luminex. The optical specifications are: Reporter laser: 532 nm, nominal output 10 - 15 mW, maximum 500 mW, frequency-doubled diode; mode of operation, continuous wave (CW). Classification laser: 635 nm, 9.1 __ 6%, maximum output 25 mW, diode; mode of operation, continuous wave (CW) Reporter detector: Photomultiplier tube, detection bandwidth of 565 - 585 nm Classification detector and doublet discriminator: Avalanche photo diodes with temperature compensation
John Quinn
Luminex 200
http://www.luminexcorp.com/support/faqs.html
MACS Quant
A MACS Quant is a flow_cytometer_analyser manufactured by Miltenyi. It uses digital electronics, and has three lasers of wavelengths 405 nm, 488 nm, and 635 nm. It has filters and dectors to collect 7 flourescent parameters and 2 scatter parameters. The MACS Quant is an analyser usually used in research applications.
John Quinn
MACS Quant
http://www.miltenyi.com
metal vapor laser
A metal vapor laser is a gas laser in which the lasing medium is metal vapor. A metal vapor laser can by used to irradiate cells in a flow cytometer.
Gold vapor laser, Helium-cadmium metal-vapor laser
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
metal vapor laser
mixed argon-krypton gas laser
A mixed argon krypton gas laser is an ion laser in which the lasing medium is a mixture of argon and krypton. A mixed argon-krypton laser can by used to irradiate cells in a flow cytometer.
John Quinn
argon-krypton laser in a cytometer
http://www.eio.com/repairfaq/sam/laserarg.htm
mixed argon-krypton gas laser
MoFlo
A MoFlo is a flow_cytometer_sorter manufactured by Dako Cytomation. It features digital electronics, the option to include several lasers (solid state 488 nm, 635 nm, and a 351 nm diode laser), and has the filtering and colelction capacity for up to 10 flouresecent parameters. The MoFlo is an instrument that can be used to both analyze quantitatively and collect cells in a flowing medium.
John Quinn
MoFlo
MoFlo at TSRI Flow Cytometry Core Facility
http://www.dakousa.com/index/prod_search/prod_groups.htm?productareaid=16
multi-well plate
FG this is synonymous with microtitre plate
96 well plate, 48 multiwell plate
A partical deliver vessel. A multi-well plate is a vessel that can deliver multiple samples to a flow cytometer in a specified order. It must be used with a plate loader.
John Quinn
http://www.nuncbrand.com/page.aspx?ID=301
multi-well plate
neodymium-YAG laser
A Neodymium-YAG (yttrium aluminum garnet) laser is a solid state laser in which the lasing medium is a solid rod of crystaline material pumped by a flashlamp or a diode laser. Typical output wavelengths are 355, 532, and 1064 nm. A neodymium-YAG laser can by used to irradiate cells in a flow cytometer.
Daniel Schober
John Quinn
Neodymium-YAG Laser in DURIP99 System
neodymium-YAG laser
obscuration bar
Flow Cytometry: First Principles, by Alice Longobardi Givan, ISBN-10: 0471382248, ISBN-13: 978-0471382249
An obscuration bar is a an optical subsystem which is a strip of metal or other material that serves to block out direct light from the illuminating beam. The obscuration bar prevents the bright light scattered in the forward directions from burning out the collection device.
Daniel Schober
John Quinn
obscuration bar
obscuration bar in a flow cytometer
optical filter
720 LP filter, 580/30 BP filter
An optical filter is an optical subsystem that selectively transmits light having certain properties (often, a particular range of wavelengths, that is, range of colours of light), while blocking the remainder. They are commonly used in photography, in many optical instruments, and to colour stage lighting Optical filters can be arranged to segregate and collect light by wave length.
John Quinn
http://en.wikipedia.org/wiki/Optical_filter
optical filter
optical subsystem
An optical subsystem is an instrument or part of an instrument that deals with the behavior and properties of light and the interaction of light with matter. Commonly optical subsystems consist of an excitation optics and collection optics. The excitation optics of a flow cytometer optical subsystem consist of the laser and lenses that are used to shape and focus the laser beam. The collections optics consist of a collection lens to collect light emitted from the particle laser beam interaction and a system of optical mirrors and filters to route specified wavelengths of the collected light to designated optical detectors. The optical subsystem in a flow cytometer consists of the equipment used to irradiate particles, and collect the light either emmitted or scattered by those particles.
DS: Is 'subsytem' necessary or is 'optical_system' enough. Not sure its graph position since an optical subsystem is not necessarily an instrument, but more likely part of one.
Daniel Schober
John Quinn
optical subsystem of a cytometer
optical_subsystem
particle delivery vessel
FG: this should be delted - particle delivery is a role that an object can play
FC 500 particle delivery vessel
John Quinn
Part of the fluidics subsystem. A particle delivery vessel is used to introcue either a single sample or multiple samples to a flow cytometer. The most common particle delivery vessel is a sample tube.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
particle_delivery_vessel
photodetector
A photodetector is a device used to detect and measure the intensity of radiant energy through photoelectric action. In a cytometer, photodetectors measure either the number of photons of laser light scattered on inpact with a cell (for example), or the flourescence emmited by excitation of a lourescent dye.
A photomultiplier tube, a photo diode
John Quinn
http://einstein.stanford.edu/content/glossary/glossary.html
photodetector
photodiode
A photodiode is a semiconductor photodector used to detect light and generate an electrical current. Typically used in forward scatter (FSC) detection. The photodiode collects the forward light scatter in a cytometer.
Avalanche photodiode
John Quinn
http://cyto.mednet.ucla.edu/Protocols/flow.htm
photodiode
photomultiplier tube
A photomultiplier is a device that is normally in the form of a tube, that uses a photocathode to convert photons into photoelectrons which are then amplified. PMTs are typically used to detect SSC and flourescent parameters. Cytometers have a PMT for each color they can collect.
John Quinn
R9647 by manufactured by Hamamatsu
http://cyto.mednet.ucla.edu/Protocols/flow.htm
photomultiplier tube
piezo electric crystal
Apparatus in the fluidic subsystem of sorters that vibrates to break up the stream coming out of the flow chamber into droplets for sorting. The peizo electric crystal vibrates in a manner that breaks off droplets at regular intervals. Not all droplets contain a cell.
John Quinn
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
piezo_electric_crystal
quartz piezoelectric crystal, topaz piezoelectric crystal, piezoelectric crystal in a sonar
plate loader
FC 500 plate loader
John Quinn
Part of the fluidics system. A plate loader positions the wells of a multi-well plate under the aspiration tube is a preset order. A plate loader is used for high throughput applications.
http://www.beckmancoulter.com/literature/Bioresearch/P-10202A.pdf
plate loader
preamplifier
A preamplifier is part of the electronics subsystem. It converts the current output from its associated detecor to a voltage. The preamplifier is the first stage in alalog electronics signal processing.
Built in preamplifier in a Hamamatsu H9656 PMT
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
preamplifier
quartz cuvette flow chamber
A flow cell in which the laser irradiates the cell as it passes through a quartz cuvette. A quartz cuvette flow chamber can be used to allow the laser to irradiate cells.
CVF-Q-10 flow chamber, CV-Q-10 flow chamber
John Quinn
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
quartz cuvette flow chamber
Reflection
A Reflection is a sorter manufactured by iCyte. It uses digital signal processing, and can be configured with lasers of the users choice from among these excitation wavelengths: 355, 405,488, 532, 635nm. It accommodates up to 48 traditional PMTs. Options include an acousto-optical tunable filter (AOTF) and 16 channel spectrometer (370 to 730 nm). The various detection components can be uniquely configured across multiple Highly Automated Parallel Sorting (HAPS) modules. The Reflection can be used to analyse, sort, and collect cells.
John Quinn
Reflection
Reflection at TSRI Flow Cytometry Core Facility
http://www.i-cyt.com/reflection.htm
sample tube
A partical delivery vessel. The sample tube is a vessel in which the sample is introduced to the cytometer. Frequently the tube is placed on the cytometer in such a manner that a seal is formed between the tube and cytometer, and gas is used to create enough pressure to push the sample out of the tube and into the cytometer.
John Quinn
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
sample tube
sample tube in a cytometer
sheath tank
John Quinn
LSR2 sheath tank
Part of the fluidics system. The sheath tank is the vessel that holds the sheath fluid at a constant pressure, allowing for it to be pushed into the flow chamber at a constant rate. The sheath tank holds the pressurized sheath fluid.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
sheath tank
short pass filter
620 SP filter
A short pass filter is an optical filter that passes low wavelengths of light but attenuates (or reduces) wavelengths higher than the cutoff frequency. A short pass filter with a cutoff of 500 nm would pass all wavelengths less than 500 nm.
John Quinn
http://en.wikipedia.org/wiki/Low-pass_filter
short pass filter
solid state laser
A solid-state laser is a laser that uses a lasing medium that is a solid, rather than a liquid such as dye lasers or a gas such as gas lasers. Semiconductor-based diode lasers are also in the solid state, but are generally considered separately from solid-state lasers. The first laser developed was an optical pumped ruby cristal solid state laser.
Daniel Schober
Solid State Heat Capacity Laser developed at DOE's Lawrence Livermore National Laboratory for the USA Army's Space and Missile Defense Command
http://en.wikipedia.org/wiki/Solid-state_laser
solid state laser
Somacount
A Somacount is a flow_cytometer_analyser manufactured by Bently Instruments. It is a specialized tool for counting somatic cells in milk by specifically staining them with Ethidium Bromide and counting the cells that flouresce. It has one laser, and the filters and a PMT for the single parameter. There are three sizes availalbe, the 150, 300, and 500 with the number indicating the maximum number of cells tthat can be analysed per hour. The Somacount is an example of a very specific use cytometer; it exclusively counts somatic cells in milk.
John Quinn
Somacount
http://www.bentleyinstruments.com/somacount.html#Anchor-Bentley-49575
SomaScope
"http://www.aicompanies.com/DeltaCD/soma_auto_adv.htm, 2007-05-10"
Josef Spidlen
SomaScope
SomaScope Mark II Automatic Economical
The SomaScope is an instrument to quantify somatic cells in milk.
editor_note pending
flow cytometer sorter
A flow_cytometer_sorter is a flow_cytometer that analyzes and separates or sorts particles passing through (based on properties measured during anlysis) to collect cells of interest.
BioSorter2000, LSR2
John Quinn
Melanie Courtot
flow cytometer sorter
http://www.flocyte.com/FRTP/Resources/flow_cytometry_glossary.htm
syringe pump
John Quinn
NE-1000 Single Syringe Pump
Part of the fluidics system. A syringe pump can be used to inject the sample fluid and cells into the sheath fluid in the flow chamber. Syringe pumps are useful for creating stable flow rates.
http://www.answers.com/topic/syringe, 2007-05-11
syringe_pump
voltage amplifier
Frank Gibson
A voltage amplifier is a device that amplifies the voltage signal.
John Quinn
Linear amplifier, log amplifier, microwave amplifier
http://en.wiktionary.org/wiki/amplifier
voltage amplifier
waste tank
John Quinn
LSR2 waste tank
Part of the fluidics systems. In analyzers the sheath and sample fluid, once analyzed is dumped into a waste tank. The waste tank is where the fluids passing through the cytometer end up after the analysis is finished.
Practical Flow Cytometry 4th Edition, Howard Shapiro, ISBN-10: 0471411256, ISBN-13: 978-0471411253
waste_tank
DNA sequencer
A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
ABI 377 DNA Sequencer, ABI 310 DNA Sequencer
DNA sequencer
FG: Definition normalised from raw import. AL: Typo fixed in definition.
MO
Trish Whetzel
array scanner
An array scanner is an instrument which acquires visual images of microarray chips by measuring fluorescence (induced with lasers) from labeled molecules on the surface of the microarray chip and converts the information into digital data.
FG: definition normalised from raw import
GenePix 4200A, GenePix4000B
MO
Trish Whetzel
array scanner
arrayer
An arrayer is an instrument which deposits biological material onto a substrate in a defined pattern.
BioRobotics Microgrid II TAS, Affymetrix GMS 417
FG: definition normalised from raw import
MO
Trish Whetzel
arrayer
centrifuge
A centrifuge is an instrument, generally driven by a motor, that puts an object in rotation around a fixed axis, applying force perpendicular to the axis. The centrifuge works using the sedimentation principle, where the centripetal acceleration is used to separate substances of greater and lesser density.
Eppendorf Multipurpose Centrifuge
Melanie Courtot
Trish Whetzel
centrifuge
http://en.wikipedia.org/wiki/Centrifuge
computer
A computer is an instrument which manipulates (stores, retrieves, and processes) data according to a list of instructions.
Apple PowerBook, Dell OptiPlex
Melanie Courtot
Trish Whetzel
computer
http://en.wikipedia.org/wiki/Computer
heating block
A heating block is an instrument or part of an instrument which raises or maintains the temperature of a sample to a defined constant temperature during certain parts of an assay
An instrument used to heat and/or maintain material at a set temperature.
Daniel Schober
MO
heating block
homogenizer
A homogenizer is an instrument for the homogenization of various types of material, such as tissue, plant, food, soil, and many others.
Melanie Courtot
Trish Whetzel
homogenizer
http://en.wikipedia.org/wiki/Homogenizer
mortar, blender
hybridization chamber
A container which is used to maintain constant contact of a liquid on an array. This can be either a glass vial or slide.
Glass Array Hybridization Cassette
MC: should be chamber with role hybridization?
MO
Trish Whetzel
hybridization chamber
hybridization station
An instrument which is used to maintain the temperature of one or more hybridization_chamber(s) at a defined, constant temperature.
Labnet Problot12
MC: should be a station with role hybridization?
MO
Trish Whetzel
hybridization station
liquid handler
A liquid_handler is an instrument used for automated liquid transfer and handling.
Beckman BioMek 2000
DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses.
TW: This is required by MO.
FG & DS: Capture as function.
All: Needs to be reviewed, according to query use case. If we keep it its kept as unnamed owl class.
The liquid handling class remains but as an undefined class with are unlikely to have children. It is expected that the reasoner would classifiy appropriate classes under this class that meet the have the liquid_handling function relation.
DS: Is this class justified? Its a unnamed class. If so, put a fluidic_system and the fluidic_subsystem as subclasses.
TW: This is required by MO.
FG: Or as function.
MO
liquid handler
liquid_handling_instrument
oligonucleotide synthesizer
An instrument used to chemically synthesize oligonucleotides.
Automated Multiplex Oligonucleotide Synthesizer
MO
Trish Whetzel
oligonucleotide synthesizer
sonicator
An instrument that converts a variable electrical current to mechanical vibration of a metalic probe. The instrument is used for the lysis of cells, the mixing of compounds or solutions, or to create emulsions.
MO
Sonicator 3000
Trish Whetzel
sonicator
spectrophotometer
A spectrophotometer is an instrument that measures the intensity of light as a function of the color, or more specifically, the wavelength of light, transmitted by a substance.
Helios Gamma Spectrophotometer
MO
Melanie Courtot
Trish Whetzel
spectrophotometer
thermal cycler
An instrument that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time.
DNA_amplifier
MO
Melanie Courtot
PCR_machine
Piko™ 96-well Thermal Cycler
Polymerase_Chain_Reaction_ machine
Trish Whetzel
thermal cycler
thermocycler
vacuum dryer
An instrument which removes liquid by the application of negative pressure, i.e. vacuum.
MO
Model 777 Microarray Oven
Trish Whetzel
vacuum dryer
vortexer
A vortexer is an instrument that mixes small vials of liquid by creating a rotation of the liquid around its own center. It consists of an electric motor with the drive shaft oriented vertically and attached to a cupped rubber piece mounted slightly off-center. As the motor runs the rubber piece oscillates rapidly in a circular motion. When a test tube or other appropriate container is pressed into the rubber cup (or touched to its edge) the motion is transmitted to the liquid inside and a vortex is created.
Melanie Courtot
Trish Whetzel
VWR Genie 2
http://en.wikipedia.org/wiki/Vortex_mixer
vortex_mixer
vortexer
microarray wash station
A microarray wash station is an instrument used to wash Affymetrix-type arrays.
AL: definition normalised from raw import
ArrayIt® Microarray Wash Station
MO
Trish Whetzel
microarray wash station
temperature control bath
A temperature_control_bath is a device that has the function to regulate the temperature of a material, the function to contain fluid and the function to vary and maintain the temperature of the contained fluid. Heat exchange (energy transfer) between the material and the heating element is facilitated via the contained fluid. A temperature_control_bath is composed of a container, a heating element and/or a cooling element and a means to adjust the needed temperature. In most cases also a timer and a means to stir the fluid is provided as well.
Alan Ruttenburg
DS: This was heated_bath. It was renamed to reflect the possability that the same bath can be used for cooling. We can now define the temperature variables and based on that infer if it is a cooling device or a heating device (also quite relative to surrounding temperature).
Daniel Schober
Frank Gibson
OBI Instrument branch
VWR Signature Deep-Chamber Heated Water Bath. A water bath is used for temperatures up to 100 °C. An oil bath is employed for temperatures over 100 °C.
temperature control bath
molecular crosslinker
A molecular crosslinker is an instrument that is able to chemically join two or more molecules.
AL: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other "crosslinkers" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly.
MO
MO
Stratalinker
Trish Whetzel
molecular crosslinker
molecular crosslinker
image cytometer
An image_cytometer is an instrument for image-based study or measurement of cells.
Melanie Courtot
The most common current application of image cytometry is for DNA analysis, followed by quantitation of immunohistochemical staining.
http://web.mit.edu/solab/Research/ImageCytometry.html
image cytometer
cytometer
A cytometer is an instrument for counting and measuring cells.
Melanie Courtot
cytometer
http://medical.merriam-webster.com/medical/cytometer
gel tank
Frank Gibson
electrophoresis box
electrophoresis unit
A gel tank is a device which holds a gel and running buffers to allow electrophoresis to be performed. A gel tank has the function to contain and to control the contained environment and transfer energy from an energy supply through the running buffers to the gel matrix and the material with charged molecules in an electric field across a porous matrix or medium with the objective to separate the charged molecules.
CHEF gel box, slab gel box, capillary electrophoresis
Kevin Clancy
gel_tank
sep:00095
power supply
Frank Gibson
PSU
electrical power supply
power pack
power supply unit
sep:00093
was power_pack, maps to SEP electrical_power_supply
A AC/DC transformer that generates the reqired power for an electrophoresis apparatus
A power supply is an device or part of a device that permits the required application of a defined electrical charge to an instrument. The power supply may permit the defined application of a given amount of current for a defined length of time.
Daniel Schober
PERSON: Daniel Schober
power supply
fluorometer
A fluorometer is an instrument for the detection and measurement of parameters of fluoresence, which in turn are used to identify the presence and amount of specific molecules in the sample.
AL: Original definition_editor was Kevin Clancy, and then I (Allyson Lister) added to it. I changed the editor to OBI, but am not sure if I should have put both our names in.
Allyson Lister
Kevin Lister
OBI
fluorometer
laser/detector in capillary electrophoresis apparatus, NanoDrop ND-3300
multispectral imaging flow cytometer
A multispectral_imaging_flow_cytometer is an instrument which combines quantitative image analysis and flow cytometry in a single platform. It measures the amount, location and movement of molecules on, in, or between cells, and the location and co-localization of multiple markers on or in cells. It can also quantitate morphologically distinct cell subpopulations.
MIFC
Melanie Courtot
http://www.amnis.com/
multispectral imaging flow cytometer
microarray
PERSON: Daniel Schober
microarray
A microarray is a device that is used as physical 2D immobilisation matrix for defined biomolecule sequences in ordered spatial position. The array-bound DNA fragments, antibodies, or proteins are used as targets for a hybridising probes form a sample to be investigated. The array typically consists of a glass, filter, or silicon wafer (chip).
DS: The subclasses might be thought of as XPS like: microarray has_probe any biomolecule
Daniel Schober
DNA microarray
Affymetrix users
DNA Chip
DNA microarray
DS: DNA-Microarray can't be an exact alternative term. Its more a specification/subclass of it.
Moran G, Stokes C, Thewes S, Hube B, Coleman DC, Sullivan D (2004). "Comparative genomics using Candida albicans DNA microarrays reveals absence and divergence of virulence-associated genes in Candida dubliniensis". Microbiology 150: 3363–3382. doi:10.1099/mic.0.27221-0. PMID 15470115
PERSON: Frank Gibson
Web:<http://en.wikipedia.org/wiki/DNA_microarray>@2008/03/03
instrument-branch
A DNA-microarray is a microarray that is used as a physical 2D immobilisation matrix for DNA sequences. DNA microarray-bound DNA fragments are used as targets for a hybridising probed sample.
DNA-array
PERSON: Daniel Schober
protein microarray
PERSON: Daniel Schober
protein microarray
A protein-microarray is a microarray, ususlly a piece of glass, on which different molecules of protein have been affixed at separate locations in an ordered manner. These are used to identify protein-protein or protein-small molecule interactions.
Daniel Schober
The most common protein microarray is the antibody microarray, where antibodies are spotted onto the protein chip and are used as capture molecules to detect proteins from cell lysate solutions.
obsolete_software
droplet sorter
A droplet sorter is part_of a flow cytometer sorter that converts the carrier fluid stream into individual droplets, and these droplets are directed into separate locations for recovery (enriching the original
sample for particles of interest based on qualities determined by gating) or disposal.
OBI Instrument branch
OBI Instrument branch
The instrument branch needs to identify parts of instruments. The above def is needed to disambiguate between flow cytometer and flow cytometer sorter.
The part between () is optional. A flow cytometer sorter has all the parts a flow cytometer has and is also has a "droplet sorter"
droplet sorter
water bath
A water bath is a temperature control bath in which a water acts as contact medium enabeling temperature transfer from the heating element or cooling element to the sample. The temperature can be controlled in the 0 to 100 degree centigrade range (under normal pressure).
A water bath was used to allow for cell incubation at 38 degree centigrade for 8 hours.
Daniel Schober
PERSON: Daniel Schober
water bath
oil bath
An oil bath is a temperature control bath in which oil acts as contact medium for the temperature transfer (from heating or cooling elements to the sample).
An oil bath was used to allow for fast reaction of two chemical compounds during a 2 hour period.
Daniel Schober
PERSON: Daniel Schober
oil bath
digital-to-analog converter
A digital-to-analog_converter is an instrument that converts a finite resolution digital signal into an infinite resolution analog signal.
A digital-to-analog_converter is used to convert a computergenerated discrete signal into a continuous analog one, e.g. a sound.
Daniel Schober
PERSON: Daniel Schober
digital-to-analog converter
device function
A device function is a function inhering in a device enabling it to participate in a critical process in the context of a specific investigation plan.
Daniel Schober: Bill, please check ID and definition
PERSON:Daniel Schober
Schober: Bill, please check ID and definition.
device function
microtome
A microtome is a mechanical instrument used to cut biological specimens into very thin segments for further treatment (e.g. ISH) and ultimately microscopic or histologic examination. Most microtomes provide cooling facilities (cryo-microtome) and use a steel blade to cut a slice of defined thickness. Some are automatic, and some are driven by hand.
PERSON: Daniel Schober
PERSON: Phillippe Rocca-Serra
PMID: 9974145.Serial sectioning of thick tissue with a novel vibrating blade microtome. Brain Res Brain Res Protoc. 1999 Jan;3(3):302-7.
microtome
microscope
A microscope is an instrument which magnifies the view on objects (too small to be viewed by the naked eye) under increased resolution. A microscope can be an optical instrument but also and electronic instrument. There are various kind of optical microscopes, e.g confocal microscope, epifluoresence microscope)
PERSON: Phillippe Rocca-Serra
PMID:18466942. A light and transmission electron microscope study of hepatic portal tracts in the rhesus monkey (Macacus rhesus). Tissue Cell. 2008 May 6
microscope
wikipedia
microscope slide
OBI biomaterial branch
PERSON: Phillippe Rocca-Serra
PMID: 9668975.Microscope slide for enhanced analysis of DNA damage using the comet assay.
a microscope slide is a device usually made of glass which is used as a solid matrix for (biological) material deposited on its surface and which is compatible for use with a microscope instrument
microscope slide
animal cage
OBI biomaterial branch
PERSON: Phillippe Rocca-Serra
PMID: 18246864.Barthold SW.Effects of cage density on behavior in young adult mice.
a laboratory cage is a device which defines an bounded habitat which is amenable to breeding and keeping laboratory animals during experimentation. cages may be made in various material and serve specific purpose (e.g metabolic cages). cages maybe equiped with additional devices such as water and food dispenser, weighing device
animal cage
laboratory cage
microarray function
DS: This and its subclasses are experimantal classes added purely for experimentation and implementation of a simple use case.
microarray function
RNA microarray function
RNA microarray function
transcription analysis function
transcription analysis function
NMR spectroscopy function
NMR spectroscopy function
metabolic profiling function
metabolic profiling function
microscope function
microscope function
polystyrene tube function
polystyrene tube function
study design
A formal description of the constraints on the possible configurations of an experiment which is subject to given conditions. A design is sometimes called an experimental design. source:http://mathworld.wolfram.com/Design.html\nEditor Note: Philippe Rocca-Serra added this; Description of how an experiment is performed. Experiments are designed by applying applications to biomaterials in an ordered fashion. Applications define protocols which are used to moving biomaterial through a series of manipulations to generate one or more desired products. methods describe the particulars of the manipulation, reagents and associated materials used in the manipulation of the biomaterial.
From Kevin Clancy not yet discussed
KPC
KPC
TODO:
experimental design
study design
clinical study design
Clinical Research Glossary Version 4.0 CDICS glossary group
MSI
PMID: 17655677.J Cardiovasc Electrophysiol. 2007 Aug;18(9):965-71.Biventricular versus right ventricular pacing in patients with AV block (BLOCK HF): clinical study design and rationale.
Plan for the precise procedure to be followed in a clinical trial, including planned and actual timing of events, choice of control group, method of allocating treatments, blinding methods; assigns a subject to pass through one or more epochs in the course of a trial. Specific design elements, e.g., crossover, parallel; dose-escalation [Modified from Pocock, Clinical Trials: A Practical Approach]
PlanAndPlannedProcess Branch
The definition needs to be extended to other things than simply patients
clinical study design
repeated measure design
A repeated measure design is a study design which use the same individuals and exposure them to a set of conditions. The effect of order and practice can be confounding factor in such designs
MSI
PMID: 10959922.J Biopharm Stat. 2000 Aug;10(3):433-45.Equivalence in test assay method comparisons for the repeated-measure, matched-pair design in medical device studies: statistical considerations.
PlanAndPlannedProcess Branch
http://www.holah.karoo.net/experimentaldesigns.htm
repeated measure design
cross over design
(source: http://www.sbu.se/Filer/Content0/publikationer/1/literaturesearching_1993/glossary.html)
MSI
PMID: 17601993-Objective: HIV-infected patients with lipodystrophy (HIV-lipodystrophy) are insulin resistant and have elevated plasma free fatty acid (FFA) concentrations. We aimed to explore the mechanisms underlying FFA-induced insulin resistance in patients with HIV-lipodystrophy. Research Design and Methods: Using a randomized placebo-controlled cross-over design, we studied the effects of an overnight acipimox-induced suppression of FFA on glucose and FFA metabolism by using stable isotope labelled tracer techniques during basal conditions and a two-stage euglycemic, hyperinsulinemic clamp (20 mU insulin/m(2)/min; 50 mU insulin/m(2)/min) in nine patients with nondiabetic HIV-lipodystrophy. All patients received antiretroviral therapy. Biopsies from the vastus lateralis muscle were obtained during each stage of the clamp. Results: Acipimox treatment reduced basal FFA rate of appearance by 68.9% (52.6%-79.5%) and decreased plasma FFA concentration by 51.6 % (42.0%-58.9%), (both, P < 0.0001). Endogenous glucose production was not influenced by acipimox. During the clamp the increase in glucose-uptake was significantly greater after acipimox treatment compared to placebo (acipimox: 26.85 (18.09-39.86) vs placebo: 20.30 (13.67-30.13) mumol/kg/min; P < 0.01). Insulin increased phosphorylation of Akt (Thr(308)) and GSK-3beta (Ser(9)), decreased phosphorylation of glycogen synthase (GS) site 3a+b and increased GS-activity (I-form) in skeletal muscle (P < 0.01). Acipimox decreased phosphorylation of GS (site 3a+b) (P < 0.02) and increased GS-activity (P < 0.01) in muscle. Conclusion: The present study provides direct evidence that suppression of lipolysis in patients with HIV-lipodystrophy improves insulin-stimulated peripheral glucose-uptake. The increased glucose-uptake may in part be explained by increased dephosphorylation of GS (site 3a+b) resulting in increased GS activity.
Philippe Rocca-Serra
Replace patient or subject (keep track of this in the definition): DONE
a cross-over design is a study design which ensures that experimental units receive, in sequence, the treatment (or the control), and then, after a specified time interval (aka *wash-out periods*), switch to the control (or treatment). In this design, subjects (patients in human context) serve as their own controls, and randomization may be used to determine the ordering which a subject receives the treatment and control
cross over design
n-to-1 design
Adapted from http://www.childrens-mercy.org/stats/definitions/crossover.htm and source:http://symptomresearch.nih.gov/chapter_6/sec1/csss1pg1.htm)
MSI
N-of-1 design is a cross-over design in which the same patient is repeatedly randomised to receive either the experimental treatment or its control (Senn, 1993).
Philippe Rocca-Serra
example to be added
n-to-1 design
matched pairs design
A matched pair design is a study design which use groups of individuals associated (hence matched) to each other based on a set of criteria, one member going to one treatment, the other member receiving the other treatment.
MSI
PMID: 17288613-BSTRACT: BACKGROUND: Physicians in Canadian emergency departments (EDs) annually treat 185,000 alert and stable trauma victims who are at risk for cervical spine (C-spine) injury. However, only 0.9% of these patients have suffered a cervical spine fracture. Current use of radiography is not efficient. The Canadian C-Spine Rule is designed to allow physicians to be more selective and accurate in ordering C-spine radiography, and to rapidly clear the C-spine without the need for radiography in many patients. The goal of this phase III study is to evaluate the effectiveness of an active strategy to implement the Canadian C-Spine Rule into physician practice. Specific objectives are to: 1) determine clinical impact, 2) determine sustainability, 3) evaluate performance, and 4) conduct an economic evaluation. METHODS: We propose a matched-pair cluster design study that compares outcomes during three consecutive 12-months before, after, and decay periods at six pairs of intervention and control sites. These 12 hospital ED sites will be stratified as teaching or community hospitals, matched according to baseline C-spine radiography ordering rates, and then allocated within each pair to either intervention or control groups. During the after period at the intervention sites, simple and inexpensive strategies will be employed to actively implement the Canadian C-Spine Rule. The following outcomes will be assessed: 1) measures of clinical impact, 2) performance of the Canadian C-Spine Rule, and 3) economic measures. During the 12-month decay period, implementation strategies will continue, allowing us to evaluate the sustainability of the effect. We estimate a sample size of 4,800 patients in each period in order to have adequate power to evaluate the main outcomes. DISCUSSION: Phase I successfully derived the Canadian C-Spine Rule and phase II confirmed the accuracy and safety of the rule, hence, the potential for physicians to improve care. What remains unknown is the actual change in clinical behaviors that can be affected by implementation of the Canadian C-Spine Rule, and whether implementation can be achieved with simple and inexpensive measures. We believe that the Canadian C-Spine Rule has the potential to significantly reduce health care costs and improve the efficiency of patient flow in busy Canadian EDs.
Philippe Rocca-Serra
http://www.holah.karoo.net/experimentaldesigns.htm
matched pairs design
parallel group design
A parallel group design or independent measure design is a study design which uses unique experimental unit each experimental group, in other word no two individuals are shared between experimental groups, hence also known as parallel group design. Subjects of a treatment group receive a unique combination of independent variable values making up a treatment
MSI
PMID: 17408389-Purpose: Proliferative vitreoretinopathy (PVR) is the most important reason for blindness following retinal detachment. Presently, vitreous tamponades such as gas or silicone oil cannot contact the lower part of the retina. A heavier-than-water tamponade displaces the inflammatory and PVR-stimulating environment from the inferior area of the retina. The Heavy Silicone Oil versus Standard Silicone Oil Study (HSO Study) is designed to answer the question of whether a heavier-than-water tamponade improves the prognosis of eyes with PVR of the lower retina. Methods: The HSO Study is a multicentre, randomized, prospective controlled clinical trial comparing two endotamponades within a two-arm parallel group design. Patients with inferiorly and posteriorly located PVR are randomized to either heavy silicone oil or standard silicone oil as a tamponading agent. Three hundred and fifty consecutive patients are recruited per group. After intraoperative re-attachment, patients are randomized to either standard silicone oil (1000 cSt or 5000 cSt) or Densiron((R)) as a tamponading agent. The main endpoint criteria are complete retinal attachment at 12 months and change of visual acuity (VA) 12 months postoperatively compared with the preoperative VA. Secondary endpoints include complete retinal attachment before endotamponade removal, quality of life analysis and the number of retina affecting re-operation within 1 year of follow-up. Results: The design and early recruitment phase of the study are described. Conclusions: The results of this study will uncover whether or not heavy silicone oil improves the prognosis of eyes with PVR.
Philippe Rocca-Serra
http://www.holah.karoo.net/experimentaldesigns.htm
independent measure design
parallel group design
randomized complete block design
A randomized complete block design is_a study design which assigns randomly treatments to block. The number of units per block equals the number of treatment so each block receives each treatment exactly once (hence the qualifier 'complete'). The design was originally devised from field trials used in agronomy and agriculture. The analysis assumes that there is no interaction between block and treatment. The method was then used in other settings So The randomised complete block design is a design in which the subjects are matched according to a variable which the experimenter wishes to control. The subjects are put into groups (blocks) of the same size as the number of treatments. The members of each block are then randomly assigned to different treatment groups.
MSI
Philippe Rocca-Serra
http://www.stats.gla.ac.uk/steps/glossary/anova.html,(A researcher is carrying out a study of the effectiveness of four different skin creams for the treatment of a certain skin disease. He has eighty subjects and plans to divide them into 4 treatment groups of twenty subjects each. Using a randomised blocks& design, the subjects are assessed and put in blocks of four according to how severe their skin condition is; the four most severe cases are the first block, the next four most severe cases are the second block, and so on to the twentieth block. The four &members of each block are then randomly assigned, one to each of the four treatment groups. http://www.stats.gla.ac.uk/steps/glossary/anova.html#rbd))
http://www.tufts.edu/~gdallal/ranblock.htm
randomized complete block design
balanced incomplete block design
MSI
PMID: 7622388.Health Educ Q. 1995 May;22(2):201-10.Balanced incomplete block design: description, case study, and implications for practice.
Philippe Rocca-Serra
balanced incomplete block design
balanced incomplete block design is a kind of factorial design where all treatment pairs occur together within a block an equal number ?? times. ??ii' is the number of times treatment i occurs with i'
http://en.wikipedia.org/wiki/Block_design and http://www.stat.psu.edu/~jglenn/stat503/05_factorial/02_factorial_IBD.html
loop design
A loop experiment design is where labeled extracts are compared in consecutive pairs. synonym: circular design
MO
MO_912
PMID: 12933549
Philippe Rocca-Serra on behalf of MO
loop design
reference design
A reference experiment design type is where all samples are compared to a common reference.
MO
MO_699
PMID: 12933549
Philippe Rocca-Serra on behalf of MO
reference design
latin square design
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
Latin square design is_a study design which allows in its simpler form controlling 2 levels of nuisance variables (also known as blocking variables).he 2 nuisance factors are divided into a tabular grid with the property that each row and each column receive each treatment exactly once.
MSI
PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
Philippe Rocca-Serra
latin square design
graeco latin square design
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
Greco-Latin square design is a study design which relates to Latin square design
MSI
PMID: 6846242-Beaton et al (Am J Clin Nutr 1979;32:2546-59) reported on the partitioning of variance in 1-day dietary data for the intake of energy, protein, total carbohydrate, total fat, classes of fatty acids, cholesterol, and alcohol. Using the same food intake data and the expanded National Heart, Lung and Blood Institute food composition data base, these analyses of sources of variance have been expanded to include classes of carbohydrate, vitamin A, vitamin C, thiamin, riboflavin, niacin, calcium, iron, total ash, caffeine, and crude fiber. The analyses relate to observed intakes (replicated six times) of 30 adult males and 30 adult females obtained under a paired Graeco-Latin square design with sequence of interview, interviewer, and day of the week as determinants. Neither sequence nor interviewer made consistent contribution to variance. In females, day of the week had a significant effect for several nutrients. The major partitioning of variance was between interindividual variation (between subjects) and intraindividual variation (within subjects) which included both true day-to-day variation in intake and methodological variation. For all except caffeine, the intraindividual variability of 1-day data was larger than the interindividual variability. For vitamin A, almost all of the variance was associated with day-to-day variability. One day data provide a very inadequate estimate of usual intake of individuals. In the design of nutrition studies it is critical that the intended use of dietary data be a major consideration in deciding on methodology. There is no ideal dietary method. There may be preferred methods for particular purposes.
Philippe Rocca-Serra
graeco latin square design
only 2 articles in pubmed ->probably irrelevant
hyper graeco latin square design
Adapted from: http://www.itl.nist.gov/div898/handbook/pri/section3/pri3321.htm and
MSI
PRS to do
Philippe Rocca-Serra
example to be added
hyper graeco latin square design
no example found in pubmed->not in use in the community
factorial design
MSI
PMID: 17582121-Our objective was to examine the effects of dietary cation-anion difference (DCAD) with different concentrations of dietary crude protein (CP) on performance and acid-base status in early lactation cows. Six lactating Holstein cows averaging 44 d in milk were used in a 6 x 6 Latin square design with a 2 x 3 factorial arrangement of treatments: DCAD of -3, 22, or 47 milliequivalents (Na + K - Cl - S)/100 g of dry matter (DM), and 16 or 19% CP on a DM basis. Linear increases with DCAD occurred in DM intake, milk fat percentage, 4% fat-corrected milk production, milk true protein, milk lactose, and milk solids-not-fat. Milk production itself was unaffected by DCAD. Jugular venous blood pH, base excess and HCO3(-) concentration, and urine pH increased, but jugular venous blood Cl- concentration, urine titratable acidity, and net acid excretion decreased linearly with increasing DCAD. An elevated ratio of coccygeal venous plasma essential AA to nonessential AA with increasing DCAD indicated that N metabolism in the rumen was affected, probably resulting in more microbial protein flowing to the small intestine. Cows fed 16% CP had lower urea N in milk than cows fed 19% CP; the same was true for urea N in coccygeal venous plasma and urine. Dry matter intake, milk production, milk composition, and acid-base status did not differ between the 16 and 19% CP treatments. It was concluded that DCAD affected DM intake and performance of dairy cows in early lactation. Feeding 16% dietary CP to cows in early lactation, compared with 19% CP, maintained lactation performance while reducing urea N excretion in milk and urine.
Philippe Rocca-Serra
factorial design
factorial design is_a study design which is used to evaluate two or more factors simultaneously. The treatments are combinations of levels of the factors. The advantages of factorial designs over one-factor-at-a-time experiments is that they are more efficient and they allow interactions to be detected. In statistics, a factorial design experiment is an experiment whose design consists of two or more factors, each with discrete possible values or levels, and whose experimental units take on all possible combinations of these levels across all such factors. Such an experiment allows studying the effect of each factor on the response variable, as well as the effects of interactions between factors on the response variable.
http://www.stats.gla.ac.uk/steps/glossary/anova.html#facdes And from wikipedia (01/03/2007): http://en.wikipedia.org/wiki/Factorial_experiment)
2x2 factorial design
2x2 factorial design
2x2 factorial design is factorial design which has 2 experimental factors (aka independent variables) and 2 factor levels per experimental factors
MSI
PMID: 17561240
PMID: 17561240-The present experiment evaluates the effects of intermittent exposure to a social stimulus on ethanol and water drinking in rats. Four groups of rats were arranged in a 2x2 factorial design with 2 levels of Social procedure (Intermittent Social vs Continuous Social) and 2 levels of sipper Liquid (Ethanol vs Water). Intermittent Social groups received 35 trials per session. Each trial consisted of the insertion of the sipper tube for 10 s followed by lifting of the guillotine door for 15 s. The guillotine door separated the experimental rat from the conspecific rat in the wire mesh cage during the 60 s inter-trial interval. The Continuous Social groups received similar procedures except that the guillotine door was raised during the entire duration of the session. For the Ethanol groups, the concentrations of ethanol in the sipper [3, 4, 6, 8, 10, 12, 14, and 16% (vol/vol)] increased across sessions, while the Water groups received 0% ethanol (water) in the sipper throughout the experiment. Both Social procedures induced more intake of ethanol than water. The Intermittent Social procedure induced more ethanol intake at the two highest ethanol concentration blocks (10-12% and 14-16%) than the Continuous Social procedure, but this effect was not observed with water. Effects of social stimulation on ethanol drinking are discussed.
Philippe Rocca-Serra
fractional factorial design
A fractional factorial design is_a study design in which only an adequately chosen fraction of the treatment combinations required for the complete factorial experiment is selected to be run
MSI
Philippe Rocca-Serra
example to be added
fractional factorial design
http://www.itl.nist.gov/div898/handbook/pri/section3/pri334.htm From ASQC (1983) Glossary & Tables for Statistical Quality Control
dye swap design
An experiment design type where the label orientations are reversed. exact synonym: flip dye, dye flip
MO
MO_858
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
Philippe Rocca-Serra on behalf of MO
dye swap design
replicate design
A replicate experimental design type is where a series of replicates are performed to evaluate reproducibility or as a pilot study to determine the appropriate number of replicates for a subsequent experiments.
MO
MO_885
Philippe Rocca-Serra on behalf of MO
example to be added
replicate design
self vs self design
A self vs. self experiment design investigates variance and error estimates in the experimental system, and is where the same extract is compared.
MO
MO_490
PMID: 17411393-Dye-specific bias effects, commonly observed in the two-color microarray platform, are normally corrected using the dye swap design. This design, however, is relatively expensive and labor-intensive. We propose a self-self hybridization design as an alternative to the dye swap design. In this design, the treated and control samples are labeled with Cy5 and Cy3 (or Cy3 and Cy5), respectively, without dye swap, along with a set of self-self hybridizations on the control sample. We compare this design with the dye swap design through investigation of mouse primary hepatocytes treated with three peroxisome proliferator-activated receptor-alpha (PPARalpha) agonists at three dose levels. Using Agilent's Whole Mouse Genome microarray, differentially expressed genes (DEG) were determined for both the self-self hybridization and dye swap designs. The DEG concordance between the two designs was over 80% across each dose treatment and chemical. Furthermore, 90% of DEG-associated biological pathways were in common between the designs, indicating that biological interpretations would be consistent. The reduced labor and expense for the self-self hybridization design make it an efficient substitute for the dye swap design. For example, in larger toxicogenomic studies, only about half the chips are required for the self-self hybridization design compared to that needed in the dye swap design.
Philippe Rocca-Serra on behalf of MO
self vs self design
time series design
Groups of assays that are related as part of a time series.
MO
MO_887
PMID: 14744830-Microarrays are powerful tools for surveying the expression levels of many thousands of genes simultaneously. They belong to the new genomics technologies which have important applications in the biological, agricultural and pharmaceutical sciences. There are myriad sources of uncertainty in microarray experiments, and rigorous experimental design is essential for fully realizing the potential of these valuable resources. Two questions frequently asked by biologists on the brink of conducting cDNA or two-colour, spotted microarray experiments are 'Which mRNA samples should be competitively hybridized together on the same slide?' and 'How many times should each slide be replicated?' Early experience has shown that whilst the field of classical experimental design has much to offer this emerging multi-disciplinary area, new approaches which accommodate features specific to the microarray context are needed. In this paper, we propose optimal designs for factorial and time course experiments, which are special designs arising quite frequently in microarray experimentation. Our criterion for optimality is statistical efficiency based on a new notion of admissible designs; our approach enables efficient designs to be selected subject to the information available on the effects of most interest to biologists, the number of arrays available for the experiment, and other resource or practical constraints, including limitations on the amount of mRNA probe. We show that our designs are superior to both the popular reference designs, which are highly inefficient, and to designs incorporating all possible direct pairwise comparisons. Moreover, our proposed designs represent a substantial practical improvement over classical experimental designs which work in terms of standard interactions and main effects. The latter do not provide a basis for meaningful inference on the effects of most interest to biologists, nor make the most efficient use of valuable and limited resources.
Philippe Rocca-Serra on behalf of MO
time series design
obsolete_rule
MSI
PRS
PRS
a rule is an executable which guides, defines, restricts actions
example to be added
replaced by IAO_0000055
rule
stopping rule
MSI
PMID: 17591081-BACKGROUND/AIMS: To investigate the viral kinetics of Chinese CHC patients received pegylated interferon plus ribavirin and examine the impact of HCV genotypes and severity of liver disease. METHODOLOGY: 65 treatment-naove CHC patients who finished a 24-week therapy with peginterferon (alpha-2b (1.5 mcg/kg/week) plus ribavirin (1000-1200 mg /day) and 24 weeks of follow-up were enrolled. Hepatic fibrosis was graded by the METAVIR scoring system. Serum quantitative HCV RNA was determined by Versant HCV RNA 3.0 assay (Bayer Inc.). RESULTS: Genotype non-1 patients responded quickly and a higher percentage of them achieved undetectable HCV RNA (< 615 IU/mL) at week 4 compared with genotype 1 patients (93% vs. 69%, p = 0.018). Degree of hepatic fibrosis significantly affected end-of-treatment and sustained response (SVR). For patients who did not achieve early virological response (EVR), the negative predictive value for SVR was 100%. In genotype 1 patients, undetectable HCV RNA by week 4 was a good marker to predict treatment response, with a positive predictive value of 84% and a negative predictive value of 82%. CONCLUSIONS: EVR can be applied to Chinese patients as an early stopping rule. A 24-week duration of pegylated IFN/ribavirin might be adequate for genotype 1 patients who rapidly responded to therapy.
PRS
PRS
a stopping rule (criterion) is_a *rule* which causes a *stopping process* to happen
stopping rule
compliance rule
MSI
PRS
PRS
a compliance rule is a rule which ensures a compliance process occurs
compliance rule
example to be added
standard compliance rule
MSI
PRS
PRS
a standard compliance rule is a compliance rule which defines conformity to a representation standard
example to be added
standard compliance rule
ethical standard compliance rule
MSI
PRS
PRS
an ethical standard compliance rule is_a *compliance rule* which enable a *ethical compliance process* to occur
ethical standard compliance rule
example to be added
eligibility rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
MSI
PMID: 17579629 -Eligibility criteria included: untreated ED-SCLC; age >/=70 and performance status 0-2, or age <70 and PS 3.
PRS
an eligibility rule (criterion) is_a *rule* which defines the positive and negative criteria decide an entity to enter a study and that will define the population of the study
eligibility rule
inclusion rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
MSI
PMID: 17599746-RESULTS: Fifteen trials met our inclusion criteria. The summary effect size was 0.35 (95% confidence interval 0.14, 0.56). I(2) was 0.80.
PRS
an inclusion rule (criterion) is_ rule* in a protocol that prospective subjects must meet to be eligible for participation in a study
inclusion rule
exclusion rule
Adapted from Clinical Research Glossary Version 4.0 CDICS glossary group
MSI
PMID: 17600285-Exclusion criteria included the use of any topical ophthalmic or topical oral medication and/or history of ocular or oral surgery within the past six months.
PRS
an exclusion rule (criterion) is_a *eligibility rule* prospective subjects should not meet to be eligible for participation in a study
exclusion rule
administering substance to cell culture
Bjoern Peters
IEDB
adding fetal calf serum to a 96 well plate containing a cell culture derived from a blood sample of a patient
administering substance to cell culture
material combination where one of the input materials is a cell culture and another material is not a cell culture
tumor grading
Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
Determination of the grade (severity/stage) of a tumor sample, used in cancer biology to describe abnormalities/qualities of tumor cells or tissues.Values can be described by terms from NCI Thesaurus.
OBI branch derived; submitted by MO
grading of tumor
tumor grading
clinical diagnosis
(maybe CIO)
OBI branch derived
PlanAndPlannedProcess Branch
a protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition.
clinical diagnosis
human subject enrollment
Bjoern Peters
IEDB
criteria come from plan / clinical trial branch
enlisting familiy members of HIV patients into a study
enrollment of humans based on eligibility criteria for an investigation
human subject enrollment
taking sample from organism
Bjoern Peters
IEDB
is a protocol application in which material that is part of an organism is separated from the organism
taking a sputum sample from a cancer patient, taking the spleen from a killed mouse
taking sample from organism
killing
Philippe Rocca-Serra
euthanisia
life termination
sacrifice
A protocol application in which an organism is intentionally put to death
CEBS, Biomaterial_branch
Jennifer Fostel
Terminal sacrifice of animals by cervical dislocation at the end of an investigation.
death status type
difficult to place this properly - JG. Death process (e.g. unscheduled death) is out of scope but should be added somewhere. All killings have death process as a part, but not all death processes are part of a killing.
killing
administering substance in vivo
Bjoern Peters
Different routes and means of administration should go as children underneath this
IEDB
a substance is intentionally given to an organism through a specified route of administration
administering substance in vivo
injecting mice with 10 ug morphine intranasally, a patient taking two pills of 1 mg aspirin orally
needs roles such as perturber and perturbee (children of input role). Perturb is too strong. Host might be the name for one role. Others considered: Doner, Donated, Acceptor.
acquisition
This needs to be fleshed out and logical definitions added that will allow to place the children terms automatically under acquisition
Bjoern Peters
IEDB
acquisition
the process of obtaining a continuant from a source.
exposure of material to environment
Alan says there will be problmes, e.g. with selection by survival
Bjoern Peters
IEDB
Putting cells in a freezer at -80C. Cy5-labeled DNA is irradiated with a laser to excite the fluorophore. Inducing a phase transition in a material by putting it in an environment with a specific temperature. Oxygen deprivation in a chamber.
an input material is exposed to a defined set of conditions in a controlled environment. The environment is an input of the protocol.
exposure of material to environment
object acquisition
Acquiring 50 C57BL/6 mice in the investigators animal facilities. Purchasing 1 mg of peptides synthesized by Mimotopes at 80% purity. Getting a gift of purified CD4+ specific antibodies presented by Stephen Schoenberger at LIAI.
Bjoern Peters, Alan Ruttenberg
Bjoern is concerned that information such as model number and serial number are to be associated with the process. Others contend that these are associated, perhaps as labels, to the instances that are the participants.
IEDB
an object acquisition is an acquisition of an object from an investigator, institution or vendor. Participant roles include source, destination, carrier, container, transaction record, payer...
object acquisition
acclimatization
A protocol application in which an object is left in an environment for some period of time, until some qualities of interest are in equilibrium with that environment.
CEBS, Biomaterial_branch
Jennifer Fostel
acclimatization
placing mice in animal facility for 2 weeks prior to an experiment to accustom them to their environment, reducing stress
environmental material collection
Bjoern Peters, Alan Ruttenberg
IEDB
Taking 1 liter of surface ocean water from the San Diego Mission Bay Jetty. Capturing mice living in rural Arkansas
environmental material collection
environmental_material_collection is an acquisition where an object is taken from an environment and put into a storage container. Roles include, environment, thing collected, container, acquirer.
the researcher is very interested in the location
data collection
Bjoern Peters
Gathering all influenza HA sequences from GenBank, Retrieveing HLA allele frequencies in the North American populations from dbMHC
Is an aquisition of information from an organization that provides information. This is not an assay. It consists of specifiying a query what information is desired, putting this query to an organization, and retrieveing the requested information from the organization.
OBI branch derived
data collection
material separation
purification
Bjoern Peters
IEDB
Using a cell sorter to separate a mixture of T cells into two fractions; one with surface receptor CD8 and the other lacking the receptor
a protocol application in which one input material is separated (in space) into two or more output materials
material separation
group assignment
2
OBI Plan
Philippe Rocca-Serra
group assignment
group assignment is a process which results in the creation of at least 2 sub population from the starting population, also understood as assigning objects/subject to groups
splitting an enrolled population into a treated and controlled sub-group; randomized group assignment
material pooling
2
OBI branch derived
PlanAndPlannedProcess Branch
http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=104564; Combining spleens of 20 mice, Combining supernatant from a cell culture obtained at different time points
like' is one of the things that you should be controling for in a well-designed experiment. The instances of material need to have the same class.
material pooling
physical combination of several instances of like material
sample pooling
detection of label
Determination of the amount of phycoerytherin label present in a cell population stained with anti-CD8-PE in order to determine the percentage of CD8+ T cells present
OBI branch derived
PERSON:Bjoern Peters
detection of label
the detection of the amount of a label which is a proxy for the detection of the labeled biomaterial
material portioning
A material separtion in which the input substance is partitioned into a number of portions that are similar in composition.
OBI branch derived
PERSON:Bjoern Peters
aliquoting
apportioning
material portioning
pouring 50 mL aliquots of fetal calf serum into conical tubes from a 500 mL stock
non-specific labeling
OBI branch derived
PlanAndPlannedProcess Branch
The addition of a reagent labeling the entire input biomaterial enabling future detection of the output biomaterial
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies.
definition blessed by Allyson, Bjoern, Jay & Randi
non-specific labeling
histology
OBI branch derived
PERSON:Compiled by Helen Parkinson for Transcriptomics thanks to Adam Witney
histology
need to incorporate parts\n---\nThis is a very vague term, it should be in the same place as transcriptomics, proteomics metaboloimcs. It is the 'study' of tissues, not the process of studying tissues\n
the counting of the number of cells with fluorescent label at their surface to determine the percentage of the population which was activated
the visual examination of cells or tissue (or images of them) with an assessment regarding a quality of the cells or tissue. Parts are: staining, imaging, judgement
cell fixation
OBI branch derived
PERSON:Bjoern Peters
a protocol application to preserve defined qualities of cells or tissues (sample) which may otherwise change over time
cell fixation
http://www.tissuearray.org/CellLinesProtocolforTMA112.pdf; the treatment of CD8+ cells with methanol at -20oC; http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=16080188&dopt=AbstractPlus
should include capturing what qualities are being preserved
we could generalize this for other input materials
excision
Alan Ruttenberg, Kevin Clancy
BP: duplicate rdfs:label entry, en
Cutting out the portion of a gel which contains a DNA fragment
excision
the use physical means to remove a portion of a substance from the rest
www.crohnsresource.com/glossary.jsp (via google define:resection)
non specific enzymatic cleavage
OBI branch derived
PERSON:Kevin Clancy
The use of agarase to digest an agar gel
a protocol application to digest the fraction of input material that is susceptible to that enzyme
non specific enzymatic cleavage
maintaining cell culture
OBI branch derived
PlanAndPlannedProcess Branch
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the maintaining_cell_culture step comprises all steps after the initial dilution and plating of the cells into culture, e.g. placing the culture into an incubator, changing or adding media, and splitting a cell culture
a protocol application in which cells are kept alive in a defined environment outside of an organism. part of cell_culturing
maintaining cell culture
substance detection
OBI branch derived
PERSON:Kevin Clancy
any protocol which results in the detection of a specified substance
substance detection
the detection of phycoerytherin by means of flow cytometry
weight assessment
Alan says something is funny\n---\nThis is a description of what you did as opposed to the description of the assay. This should be more generic. something like 'mass_assay'\n
OBI branch derived
PlanAndPlannedProcess Branch
The comparison of the weight of vaccinated and non-vaccinated mice after infection with influenza A over 6 weeks post-infection
an assay in which the weight of an organism is measured over time
weight assessment
artifically induced cell membrane lysis
---\nThere is a more general 'membrane lysis', which could apply to artificial membranes etc. For this general membrane encapsulated objects would need to be defined.
OBI branch derived
PlanAndPlannedProcess Branch
a material transformation to break the membranes of cells, releasing the cells contents; input=>cells; output=>cell_lysate
artifically induced cell membrane lysis
http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=16080188&dopt=AbstractPlus; The destruction of cell membranes with detergent.
artificially induced reverse transcription
We need to indicate the relationship between the cDNA generated and the RNA that was used as a template. This may be outside of the OBI scope
multiple reagents including dNTPs are utilized in therprocess. Need to be added
OBI branch derived
PERSON:Kevin Clancy
The use of M-MLV reverse transcriptase from the Moloney murine leukemia virus to transcribe an RNA sample into cDNA
a protocol with the objective to transcribe single-stranded RNA into complementary DNA (cDNA)
artifically induced reverse transcription
isolation of cell culture supernatant
OBI branch derived
PlanAndPlannedProcess Branch
Pouring out a portion of the fluid part of an adherant cell culture growing in a flask.; The centrifugation of a T cell culture followed by aspiration of the supernatant while the cellular pellet remains in the centrifuge tube.
This does not apply to the case where the cells are lysed
a protocol which results in the separation of supernatant material from a cell culture
isolation of cell culture supernatant
experimental disease induction
OBI branch derived
PlanAndPlannedProcess Branch
a protocol application to induce a specific disease in an organism
could be defined class
experimental disease induction
the injection of mice with LCM virus iv to establish an LCMV infection. Witholding food from animals to induce starvation syndrome.
ELISPOT assay
Determination of the frequency of cells producing IFN-gamma in response to viral peptides
ELISPOT
OBI branch derived
PlanAndPlannedProcess Branch
\n---\nThis term conflates several things. Everytime you stain a population of cells and count them this is NOT an ELISPOT assay. We need assay terms to describe the staining of things that are cells, and a counting of things that are cells. We need to work out what make an ELISPOT assay different from staining and counting cells\n
an assay in which the number of cells producing a biomaterial in a larger cell population are stained and counted
artifically induced DNA repair
---\nis this really a protocol?\n--> This as several other protocol applications is also a natural process. The fact that it is induced experimetnally by following a protocol makes it a protocol application. Need to make sure that labels don't conflict wi
OBI branch derived
PlanAndPlannedProcess Branch
a protocol application to repair damaged DNA molecules
artifically induced DNA repair
the use of DNA repair enzymes uracil DNA glycosylase and 3-methyladenine DNA glycosylase to repair DNA strands
cell permeabilization
need to add output cell has_quality permeable
A protocol application to permeabilize cell membranes, allowing molecules to more easily pass through the membrane than was possible prior to the protocol application
Electroporation of HeLa cells to allow transfection with pUC19.
OBI branch derived
PERSON:Bjoern Peters
cell permeabilization
definition blessed by Jay, Alan, Randi
precipitation
OBI branch derived
PERSON:Kevin Clancy
The use of ethanol to precipitate DNA molecules from a solution containing DNA
a protocol application to cause a material to precipitate (becoming a solid) out of solution. Input is a solution, ouput is a solution plus a solid component (the precipitate)
precipitation
establishing cell culture
Effects of establishing cell cultures and cell culture conditions on the proliferative life span of human fibroblasts isolated from different tissues and donors of different ages.
Exp Cell Res. 2002 Apr 1;274(2):275-87. PMID: 11900488
When harvesting blood from a human, isolating T cells, and then limited dilution cloning of the cells, the establishing_cell_culture step comprises preparing the cells at a certain dilution and plating them in a container with growth medium.
OBI branch derived
PlanAndPlannedProcess Branch
establishing a cell culture is a process which results in creating an in vitro environment in which cells are sustained from input material containing cells. input: cell-containing material, output cell culture, part of cell culturing. Cells are originally plated at a certain concentration referred to as seeding density.
establishing cell culture
cell culture splitting
OBI branch derived
PlanAndPlannedProcess Branch
The act of taking a cell culture of high density, counting the cells, removing part of the cells, and re-seeding a select number of the cells into new flasks with fresh tissue culture media.
The act of taking part of a homogeneous cell culture and creating one or more additional separate cultures of similar qualities. input: cell_culture, output cell_culture min cardinality 2. part of cell culturing
cell culture splitting
labeling
OBI branch derived
PERSON:Kevin Clancy
The addition of phycoerytherin label to an anti-CD8 antibody, to label all antibodies. The addition of anti-CD8-PE to a population of cells, to label the subpopulation cells that are CD8+.
definition blessed by Allyson, Bjoern, Jay & Randi
labeling
the addition of a labeling reagent to an input biomaterial in order to detect the labeled material in the future
artifically induced methylation
Long format, assuming GO will have the process methylation defined, methylation_induction is realization of a protocol to induce the natural process of methylation
OBI branch derived
PERSON:Kevin Clancy
a protocol application to add methyl groups to molecules
artifically induced methylation
the use of enzymes to add methyl groups to DNA molecules
synthesis
OBI branch derived
PERSON:Kevin Clancy
This probably needs breaking down into more specific applications. The example given is already covered in reverse_transcription
making cDNA from nucleotides using RNA as a template
synthesize
the construction of a biomaterial from simpler biomaterials
concentrate
Evaporation of the solution containing DNA to increase the concentration of the DNA molecules
OBI branch derived
PERSON:Kevin Clancy
a protocol application to create an output material with an increased density of a material of interest that is part of the input material by separating other parts of the input material
concentrate
recombinant plasmid cloning
OBI branch derived
PERSON:Kevin Clancy
The DNA fragment encoding the p35 gene from Mycobacterium avium complex was inserted into pcDNAII and expressed in E coli in order to study p35.
recombinant plasmid cloning
the insertion of a particular DNA fragment into a plasmid in order to make copies of a biomaterial
genetic transformation
OBI branch derived
PERSON:Kevin Clancy
The transduction of E. coli through the introduction of a plasmid encoding for M. avium p35
genetic transformation
the introduction and integration of genetic material into a cell or organism in order to alter its genetic make-up
lavage
OBI branch derived
PlanAndPlannedProcess Branch
This is not washing, in which case the material of interest is not the resulting fluid
a protocol application to separate cells and/or cellular secretions from an anatomical space by the introduction and removal of fluid
lavage
the collection of bronchoalveolar lavage fluid (BAL) from the lungs of mice in order to study the cytokines present
structure assay
OBI branch derived
PERSON:Kevin Clancy
The use of NMR Spectroscopy to determine the 3D-Structure of the binding of an epitope to an MHC molecule
any protocol resulting in information on the 3-dimensional qualities of a biomaterial
structure assay
chromatography
Jay/Bjoern think this is problematic. There are so many different types of chromatography. This term may be overloaded. May be best to define each type separately underneath material_separation. Also, example seems to be an assay.
OBI branch derived
PERSON:Kevin Clancy
The use of gas chromatography in order to identify the presence of pesticides in a sample of eggs
chromatography
the use of a biomaterial's preferential affinity for either the mobile phase or the stationary phase to separate it from other materials of differing affinity
sequencing
has_output should be sequence of input; we don't have sequence well defined yet
OBI branch derived
PlanAndPlannedProcess Branch
The use of the Sanger method of DNA sequencing to determine the order of the nucleotides in a DNA template
sequencing
the use of a chemical or biochemical means to infer the sequence of a biomaterial
amplification of a clone
E coli expressing the gene for M avium p35 were cultured in order to produce p35.
OBI branch derived
PERSON:Kevin Clancy
amplification of a clone
the use of a clonal cell line to produce a biomaterial
DNA polymerase amplification
Philippe Rocca-Serra
DNA polymerase amplification
DNA polymerase amplification is an enzymatic amplification which uses DNA polymerase enzyme to make copies of a DNA conainted in biomaterial used as input
OBI branch derived
PERSON:Kevin Clancy
The use of taq polymerase to amplify a DNA fragment during a PCR.
specific enzymatic cleavage
OBI branch derived
PERSON:Kevin Clancy
The use of a protease to digest a protein into peptides
a protocol application to digest the fraction of input material that is susceptible to that enzyme
specific enzymatic cleavage
gradient separation
OBI branch derived
PERSON:Kevin Clancy
a protocol application that uses different concentrations of materials in a defined order to create a gradient to facilitate the separation of an input material into its components with specific qualities
gradient separation
the use of a sucrose gradient to isolate mitochondria
dialysis
OBI branch derived
PERSON:Kevin Clancy
a protocol application that uses diffusiton through a semi-permeable membrane to separate an input material into two fractions of different composition
dialysis
the use of a dialysis bag of select pore size to remove salt from collagen isolated from mouse cartilage
electrophoresis
Loading a mixture of proteins into a polyacrylamide gel and the application of an electrical current to the gel to separate the proteins by size and change.
Need to define more terms like gel_separation, matrix,centrifugation, and the connection between the force used to separate materials and the medium or barriers.
OBI branch derived
PERSON:Kevin Clancy
a protocol application that uses an electrical potential to move material through a defined matrix in order to separate it by its resistance to movement and its charge
electrophoresis
selection by survival
OBI branch derived
PERSON:Kevin Clancy
The insertion of a gene for antibiotic resistance into a cell population and subsequent growth in the presence of the antibiotic to select for those cells which were successfully transfected
selection by survival
the use of environmental conditions to select for the organism or cells that have a certain trait
DNA cleavage, restriction analysis
restriction enzyme assay
DNA cleavage, restriction analysis
PERSON:Kevin Clancy
the use of enzymes to cut DNA molecules, the study of DNA through cleavage, mapping, and analysis of the fragments
the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
the use of the restriction enzymes SalPI and PstI to cleave DNA into fragments, assay made up of components
protease cleavage
OBI branch derived
PlanAndPlannedProcess Branch
enzymatic digestion
protease cleavage
protease cleavage is an enzymatic cleavage which relies on enzyme with protease activity to act on proteins and produce polypeptides (protein fragments).
the use of trypsin to cleave pepsin into peptide fragments
enzymatic DNA replication
OBI branch derived
PERSON:Kevin Clancy
enzymatic DNA replication
the use of enzymes to duplicate DNA moleculeany process used to make additional copies of a biomaterial
the use of enzymes to duplicate DNA molecules
enzymatic amplification
OBI branch derived
PERSON:Kevin Clancy
enzymatic amplification
the use of a polymerase chain reaction to amplify a fragment of DNA
the use of enzymes to increase the number of molecules of a biomaterial
DNA transduction
DNA transduction
DNA transduction is a genetic transformation which relies on the use of lysogenic infection to transfer DNA sequences into an organism
OBI branch derived
PERSON:Kevin Clancy
The transfer of a recombinant bacterial plasmid into E.coli to facilitate amplification of a specific protein
DNA transfection
DNA transfection
DNA transfection is a genetic transformation which relies on the use of physical, electrical and chemical phenomena to introduce DNA into a cell
OBI branch derived
PERSON:Kevin Clancy
The use of electroporation to permeabilize a cell membrane in order to introduce a plasmid encoding for a labeled protein of interest
planned process
OBI branch derived
PlanAndPlannedProcess Branch
is a process that is the realization of some plan
planned process
several roles are implied in this: There must be one or more actors that realizes the plan, potentially a planner that devised the plan, potentially a supervisor monitoring the plan.
cell growth mediated amplification
OBI branch derived
PlanAndPlannedProcess Branch
cell growth mediated amplification
is the generation of copies of biomaterial by in a cell_culture modified for this purpose by insertion of an expression vectors
needs defined relationship to cell culture
recombinant vector cloning
OBI branch derived
insertion of a DNA fragment into a cloning vector which creates. Has input vectors + DNA fragments. Has output: recombinant vectors
pa_branch (Alan, Randi, Kevin, Jay, Bjoern)
recombinant vector cloning
specific labeling
OBI branch derived
PlanAndPlannedProcess Branch
The addition of anti-CD8 antibody for an ICCS assay in order to selectively stain the CD8+ cells
a labeling in which the labeling reagent used has a specificity to bind only certain components of the input material
definition blessed by Allyson, Bjoern, Jay & Randi
specific labeling
RNA extraction
A RNA extraction is a nucleic acid extration where the desired output material is RNA
OBI branch derived
PlanAndPlannedProcess Branch
RNA extraction
requested by Helen Parkinson for MO
nucleic acid extraction
OBI branch derived
Phenol / chlorophorm extraction disolvation of protein content folllowed by ethanol precipitation of the nucleic acid fraction over night in the fridge followed by centrifugation to obtain a nucleic acid pellet.
PlanAndPlannedProcess Branch
a material separation to recover the nuceic acid fraction of an input material
nucleic acid extraction
requested by Helen Parkinson for MO. Could be defined class
obsolete_obi_function
Daniel Schober: I think obi_function should be trashed.
A function inhering in an biomedical investigation-related entity where the necessary material continuants, processes, roles, and biophysical qualities have been identitified and there interelations in this functional context have been specified.
Bill Bug
E.g. reagent function, instrument function, instrument part function, etc.
PERSON:William Bug@2007/07/10
Still debating whether Assay_function, Assessment_function (sub-class of Assay_function), and Algorithm_function have any meaning in a BFO context, where function appears to be intended to inhere only in independent material continuants (BB:2007-07-10).
obi_function
obsolete_reagent function
A function inhering a molecule, set of molecules, cell, collection of cells, or tissue enabling it to participate in critical material transformation in the context of a specific investigation plan.
Bill Bug
E.g. the function of Cy5 coupled-ligands to enable separation of cells in a Fluorescence-Activated Cell Sorter (FACS) by virtue of cells possessing specific receptors with an specific affinity to bind the coupled ligand thereby causing only those cells to fluoresce when illuminated with laser light frequency that specifically excites Cy5, triggering relays and redirecting the solution flow to a separate effluent container.
PERSON:William Bug@2007/07/10
reagent function
obsolete_instrument platform function
A function inhering an instrument_platform enabling it to participate in critical process in the context of a specific investigation plan.
Bill Bug
E.g. the function of a high pressure liquid chromatagraphic (HPLC) system to separate molecules based on their solubility properties
PERSON:William Bug@2007/07/10
instrument platform function
obsolete_instrument part function
A function inhering the cardinal part of an instrument necessary for that instrument to participate in critical process in the context of a specific investigation plan.
Bill Bug
E.g. the function of the electromagnetic lenses in an electron microscope to direct the incident electron beam trajectory so as to systematically raster across a specimen when constructing the overall image; the function of Nomarksi optics to enhance the constrast of specimens viewed in a light microscope based on their ability to refract visible wavelengths of light.
PERSON:William Bug@2007/07/10
instrument part function
obsolete_labware function
A function inhering in a type of labware enabling it to participate in critical process in the context of a specific investigation plan.
Bill Bug
E.g. the function of semi-permeable dialysis tubing to separate solutes based on size by virtue of restricted diffusion and osmosis; the function of a plastic 25 ml centrifuge tube to act as an inert storage vessel for a material sample.
How does this relate to an object such as the enzyme-coated plate used in an ELISA protocol application? The plate itself is a type of labware, but the enzyme is a reagent.(BB:2007-07-10).
PERSON:William Bug@2007/07/10
labware function
obsolete_analytical instrument function
An instrument function where the process in which the instrument participates results in a quality measurement of the material under examination which is critical in the context of a specific investigation plan.
Bill Bug
E.g. the function of a spectrophotometer to provide a measure of the relative absorbance of a liquid sample for a particular wavelength (or set of wavelengths) of light.
PERSON:William Bug@2007/07/10
analytical instrument function
obsolete_dialysis tubing function
PERSON:William Bug@2007/07/10
dialysis tubing function
obsolete_homogenous substance
PRS: homogeneous and heterogeneous will be submitted to PATO following BM140308 call
Any form of matter (material) that is homogeneous throughout, i.e. solid, liquid, gas
DS: Create alternative terms material or matter then, and move up in hierarchy...
Susanna Sansone
homogenous substance
none
cell culture supernatant
Bjoern Peters
IEDB
PRS:22022008. result from protocol_application where input=cell culture and output=supernatant
PRS:22022008: moved from _unclassified to _a defined class is needed following BM call
Supernatant of a cell culture is a material entity which contains media, supplements, and secreted products of the cells and becomes the environment of cultivated cell.
cell culture supernatant
solution containing RPMI, fetal calf sera, antibiotics, and monoclonal antibody UCHT1.
Isolation of proliferation factor of immature T-cell clone in concanavalin A-stimulated splenocyte culture supernatant. Immunology. 2003 Jun;109(2):209-16. PMID: 12757615
cell pellet
Philippe Rocca-Serra
A cell pellet is a entity of organismal origin which results from the aggegration of cells produced by the application of centrifugal force to a liquid containing cells in suspension
CEBS and OBI Biomaterial
Detection of fetal DNA in a cell pellet after centrifugation of mountant. J Forensic Sci. 2003 Jan;48(1):135-6. PMID: 12570214
Helen Parkinson
cell pellet
phage display library
Bjoern Peters
PMID: 15905471.Nucleic Acids Res. 2005 May 19;33(9):e81.Oligonucleotide-assisted cleavage and ligation: a novel directional DNA cloning technology to capture cDNAs. Application in the construction of a human immune antibody phage-display library. [Phage display library encoding fragments of human antibodies. m-rna library encoding for 9-mer peptides]
PRS: 22022008. class moved under population,
modification of definition and replacement of biomaterials in previous definition with 'material'
addition of has_role restriction
Philippe Rocca-Serra
WEB: http://www.immuneepitope.org/home.do
a display library is a collection of materials in which a mixture of genes or gene fragments is expressed and can be individually selected and amplified.
display_library
phage display library
cell lysate
The effect of vaccination with the lysate of heat-shocked tumor cells on nitric oxide production in BALB/c mice with fibrosarcoma tumor. Cell Biol Int. 2008 Jul;32(7):835-40. PMID: 18455932
lysed material
PRS:22-02-2008: is a material which has output_role during lysis protocol-application.
old defintion: A mixture (collection) of cell components created by rupturing of the cell wall resulting from a lysis process
PSI
Susanna Sansone
a cell lysate is a material entity which is output of a cell lysis process
lysate
peptide construct
Bjoern Peters
IEDB
Multiple Antigenic Peptide (MAP) construct containing T and B cell epitopes from p. falciparum congugated to a central glycin
A novel multivalent human CTL peptide construct elicits robust cellular immune responses in HLA-A*0201 transgenic mice: implications for HTLV-1 vaccine design. Vaccine. 2003 Jun 20;21(21-22):2767-81. PMID: 12798617
PRS:22-02-2008: is a chemical entity which has output_role during conjugation protocol-application AND derives_from Peptide
a peptide construct is entity of organismal origin which contains a number of peptides derived from naturally occuring proteins conjugated together in a non-linear fashion
peptide construct
transgenic organism
Philippe Rocca-Serra
Bjoern Peters
HLA-A*0201 transgenic mice, Vaccinia virus expressing the LCMV gp protein
Possible ecological risks of transgenic organism release when transgenes affect mating success: sexual selection and the Trojan gene hypothesis. Proc Natl Acad Sci U S A. 1999 Nov 23;96(24):13853-6. PMID: 10570162
IEDB
PRS:22-02-2008: is a organism which has output_role during genetic modification of type (KO) protocol-application
a transgenic organism is material entity which derives from an organism which has been modified to express a gene not normally part of it
transgenic organism
whole mount tissue
Philippe Rocca-Serra
A whole_mount tissue is an entity of organismal origin resulting from a histological preparation known as whole mount preparation where the whole specimen is mounted or spread on the microscope (glass) slide
Helen Parkinson
OBI
PRS:22-02-2008: indicates the need to create a protocol application and distinguish it from this entity
PRS:22-02-2008: is a material which has output_role during whole mount preparation protocol-application
whole mount sample
whole mount tissue
bead
A globular or round particle of defined physicochemical properties and size which can be exploited as either the primary substance for detection or as a secondary solid platform for the attachment of bioactive molecules.
DS: Probably better modeled as a role.
Dynabeads are commercially available magnetic beads which are precoated with antibodies specific for select cellular receptors and are used to separate cell populations.
OBI
bead
source pending
obsolete_dye
A substance capable of staining or coloring defined targets.
Acridine orange is a nucleic acid selective dye.
OBI
REALLY NOT SURE IF THIS IS A ROLE OR BIOMATERIAL. JAMES
dye
source pending
chromium release assay
An assay in which radioactive chromium is absorbed by cells and released into supernatant when the cells die. The amount of radioactivity measured in the supernatant is a proxy for the number of cells that have died.
OBI branch derived
PlanAndPlannedProcess Branch
chromium release assay
from http://cvi.asm.org/cgi/content/full/11/2/255 (and slightly simplified)\nAutologous EBV-transformed B-LCL were used as target cells for the influenza virus-specific CTL assays. Equal volumes of target (5 x 10E4 cells/ml) and effector cells were added to triplicate wells of 96-well tissue culture plates, and 1:2 serial dilutions of effectors were made, producing effector-to-target (E:T) ratios of 100:1, 50:1, 25:1, and 12.5:1 (9). Spontaneous release of 51Cr was assessed by the incubation of target cells in medium alone, and maximum release of 51Cr was determined by the incubation of target cells in 0.1% Triton X-100 (Sigma-Aldrich).\nAfter a 4-h incubation of the effector cells with the target cells at 37?é??C in 6% CO2, supernatants were collected following brief centrifugation. The supernatant was collected into filters of supernatant collection system harvesting frames (Molecular Devices Skatron, Sunnyvale, Calif.) and transferred to polystyrene tubes to be counted with the LKB 1272 Clinigamma counter (Wallac).\nPercent specific was determined with the following equation: (experimental 51Cr release - spontaneous 51Cr release)/(maximum 51Cr release - spontaneous 51Cr release) x 100.
obsolete_chromium_release_assay_target_role
obsolete_chromium_release_assay_effector_role
obsolete_label_role
Portion of tissue
portion of tissue
Portion of tissue
Anatomical structure, that consists of similar cells and intercellular matrix, aggregated according to genetically determined spatial relationships.
portion of tissue
multi-tissue structure
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
multi-tissue structure
epithelium
Portion of tissue, that consists of one or more layers of epithelial cells connected to each other by cell junctions and which is underlain by a basal lamina.
epithelium
polypeptides
A peptide containing ten or more amino acid residues.
polypeptides
peptides
Amides derived from two or more amino carboxylic acid molecules (the same or different) by formation of a covalent bond from the carbonyl carbon of one to the nitrogen atom of another with formal loss of water. The term is usually applied to structures formed from alpha-amino acids, but it includes those derived from any amino carboxylic acid.
peptides
deoxyribonucleic acids
High molecular weight, linear polymers, composed of nucleotides containing deoxyribose and linked by phosphodiester bonds; DNA contain the genetic information of organisms.
deoxyribonucleic acids
glucose
glucose
Molecular entity
molecular entities
Molecular entity
A molecular entity is any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity.
molecular entities
acrylamide
acrylamide
ribonucleic acids
Naturally occurring polyribonucleotides.
ribonucleic acids
amino acids
Carboxylic acids containing one or more amino groups.
amino acids
double-stranded DNA
double-stranded DNA
chromium-51
A synthetic radioactive isotope of chromium having a half-life of 27.7 days and decaying by electron capture with emission of gamma rays (0.32 MeV); it is used to label red blood cells for measurement of mass or volume, survival time, and sequestration studies, for the diagnosis of gastrointestinal bleeding, and to label platelets to study their survival.
chromium-51
tris
A compound widely used as a biological buffer substance in the pH range 7--9; pKa = 8.3 at 20 degreeC; pKa = 7.82 at 37 degreeC.
tris
cell
Anatomical structure that has as its parts a maximally connected cell compartment surrounded by a plasma membrane.
PMID:18089833.Cancer Res. 2007 Dec 15;67(24):12018-25. "...Epithelial cells were harvested from histologically confirmed adenocarcinomas .."
cell
B cell
A type of lymphocyte whose defining characteristic is the expression of an immunoglobulin complex.
B cell
CD8-positive, alpha-beta cytotoxic T cell
A CD8-positive, alpha-beta T cell capable of killing target cells in an antigen specific manner.
CD8-positive, alpha-beta cytotoxic T cell
soil
Any material within 2 m from the Earth's surface that is in contact with the atmosphere, with the exclusion of living organisms, areas with continuous ice not covered by other material, and water bodies deeper than 2 m.
soil
podzol
Podzols are soils with a typically ash-grey upper subsurface horizon, bleached by loss of organic matter and iron oxides, on top of a dark accumulation horizon with brown, reddish or black illuviated humus and/or reddish Fe compounds. Podzols occur in humid areas in the boreal and temperate zones and locally also in the tropics.
podzol
Body substance
Body substance
Material anatomical entity in a gaseous, liquid, semisolid or solid state, with or without the admixture of cells and biological macromolecules; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. Examples: saliva, semen, cerebrospinal fluid, inhaled air, urine, feces, blood, plasma, lymph.
Blood
Blood
Body substance which consists of plasma and blood cells
molecular_function
Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
molecular_function
Catalytic activity (disposition)
catalytic activity
Catalytic activity (disposition)
Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
catalytic activity
RNA-directed DNA polymerase activity
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
RNA-directed DNA polymerase activity
cellular_component
The part of a cell or its extracellular environment in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
cellular_component
gene expression
The process by which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
gene expression
DNA polymerase activity
Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a nucleic acid template and primer.
DNA polymerase activity
DNA polymerase complex
A protein complex that possesses DNA polymerase activity and is involved in template directed synthesis of DNA.
DNA polymerase complex
membrane-bounded organelle
Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
membrane-bounded organelle
protein complex
Any macromolecular complex composed of two or more polypeptide subunits, which may or may not be identical. Protein complexes may have other associated non-protein prosthetic groups, such as nucleotides, metal ions or carbohydrate groups.
protein complex
Viruses
Viruses
Bacteria
Bacteria
Archaea
Archaea
Eukaryota
Eukaryota
diluted
A concentration which relative low.
diluted
damaged
A quality inhering in a bearer by virtue of being harmed or injured or spoiled.
damaged
lateral to
A relational spatial quality where on entity is located toward the side relative to another entity.
lateral to
ventral to
A relational spatial quality where on entity is located toward the abdomen of an organism relative to another entity.
ventral to
dorsal to
A relational spatial quality where on entity is located toward the back or upper surface of an organism relative to another entity.
dorsal to
monadic quality of continuant
A quality of continuant which inheres in a single-bearer.
monadic quality of continuant
relational quality of continuant
A quality of continuant which inheres in multiplicity of bearers.
relational quality of continuant
alive
A viability quality inhering in a bearer by virtue of its condition of before death.
alive
dead
A viability quality inhering in a bearer by virtue of the cessation of its life.
dead
quality of a solid
A physical quality inhering in an entity exhibiting the physical characteristics of a solid.
quality of a solid
quality of a gas
A physical quality inhering in an entity exhibiting the physical characteristics of a gas.
quality of a gas
quality of a liquid
A physical quality inhering in an entity exhibiting the physical characteristics of a liquid.
quality of a liquid
relational spatial quality
A monadic quality of continuant inhering in a bearer by virtue of its pertaining to or involving or having the nature of space in relation to another entity.
relational spatial quality
anterior to
frontal
A relational spatial quality where on entity is located toward the front of an organism relative to another entity.
anterior to
radioactive
A radiation quality inhering in bearer vy virtue of its exhibiting or being caused by radioactivity.
move to dependent.owl
radioactive
left side of
A relational spatial quality where on entity is located on left side of from the a another entity.
left side of
right side of
A relational spatial quality where on entity is located on right side of a another entity.
right side of
frozen
A quality inhering in a bearer by virtue of being kept below its freezing point.
frozen
protein
A biological macromolecule that is composed of amino acids linked in a linear sequence (a polypeptide chain) and is genetically encoded. Proteins descended from a common ancestor can be classified into families and superfamilies composed of products of evolutionarily-related genes. The domain architecture of a protein is described by the order of its constituent domains. Proteins with the same domains in the same order are defined as homeomorphic.
protein
circular
A quality of a nucleotide polymer that has no terminal nucleotide residues.
circular
entity
continuant
Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts.
Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building
Synonyms: endurant
dependent_continuant
Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities.
disposition
Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C.
Examples: the disposition of vegetables to decay when not refrigerated, the disposition of a vase to brake if dropped, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease, the disposition of metal to conduct electricity.
fiat_object_part
Definition: An independent continuant [snap:IndependentContinuant] that is part of an object [snap:Object] but is not demarcated by any physical discontinuities.
Examples: upper and lower lobes of the left lung, the dorsal and ventral surfaces of the body, the east side of Saarbruecken, the lower right portion of a human torso
Synonyms: fiat substance part
function
Definition: A realizable entity [snap:RealizableEntity] the manifestation of which is an essentially end-directed activity of a continuant [snap:Continuant] entity in virtue of that continuant [snap:Continuant] entity being a specific kind of entity in the kind or kinds of contexts that it is made for.
Examples: the function of a birth canal to enable transport, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc., the function of reproduction in the transmission of genetic material, the digestive function of the stomach to nutriate the body, the function of a hammer to drive in nails, the function of a computer program to compute mathematical equations, the function of an automobile to provide transportation, the function of a judge in a court of law
generically_dependent_continuant
Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time.
Examples: a certain PDF file that exists in different and in several hard drives
independent_continuant
Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything.
Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building
Synonyms: substantial entity
object
Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended, maximally self-connected and self-contained (the parts of a substance are not separated from each other by spatial gaps) and possesses an internal unity. The identity of substantial object [snap:Object] entities is independent of that of other entities and can be maintained through time.
Examples: an organism, a heart, a chair, a lung, an apple
Synonyms: substance
object_aggregate
Definition: An independent continuant [snap:IndependentContinuant] that is a mereological sum of separate object [snap:Object] entities and possesses non-connected boundaries.
Examples: a heap of stones, a group of commuters on the subway, a collection of random bacteria, a flock of geese, the patients in a hospital
Synonyms: substance aggregate
object_boundary
Comment: Boundaries are theoretically difficult entities to account for, however the intuitive notion of a physical boundary as a surface of some sort (whether inside or outside of a thing) will generally serve as a good guide for the use of this universal.
Definition: An independent continuant [snap:IndependentContinuant] that is a lower dimensional part of a spatial entity, normally a closed two-dimensional surface. Boundaries are those privileged parts of object [snap:Object] entities that exist at exactly the point where the object [snap:Object] is separated off from the rest of the existing entities in the world.
Examples: the surface of the skin, the surface of the earth, the surface of the interior of the stomach, the outer surface of a cell or cell wall
Synonyms: substance boundary
one_dimensional_region
Definition: A spatial region [snap:SpatialRegion] with one dimension.
Examples: the part of space that is a line stretching from one end of absolute space to the other, an edge of a cube-shaped part of space
quality
Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that is exhibited if it inheres in an entity or entities at all (a categorical property).
Examples: the color of a tomato, the ambient temperature of air, the circumference of a waist, the shape of a nose, the mass of a piece of gold, the weight of a chimpanzee
realizable_entity
Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized.
Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances.
Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity
role
Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts.
Examples: the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university
site
Comment: An instance of Site [snap:Site] is a mixture of independent continuant [snap:IndependentContinuant] entities which act as surrounding environments for other independent continuant [snap:IndependentContinuant] entities, most importantly for instances of object [snap:Object]. A site [snap:Site] is typically made of object [snap:Object] or fiat object part [snap:FiatObjectPart] entities and a surrounding medium in which is found an object [snap:Object] occupying the site [snap:Site]. Independent continuant [snap:IndependentContinuant] entities may be associated with others (which, then, are sites) through a relation of "occupation". That relation is connected to, but distinct from, the relation of spatial location. Site [snap:Site] entities are not to be confused with spatial region [snap:SpatialRegion] entities. In BFO, site [snap:Site] allows for a so-called relational view of space which is different from the view corresponding to the class spatial region [snap:SpatialRegion] (see the comment on this class).
Definition: An independent continuant [snap:IndependentContinuant] consisting of a characteristic spatial shape in relation to some arrangement of other continuant [snap:Continuant] entities and of the medium which is enclosed in whole or in part by this characteristic spatial shape. Site [snap:Site] entities are entities that can be occupied by other continuant [snap:Continuant] entities.
Examples: a particular room in a particular hospital, Maria's nostril or her intestines for a variety of bacteria.
spatial_region
Comment: All instances of continuant [snap:Continuant] are spatial entities, that is, they enter in the relation of (spatial) location with spatial region [snap:SpatialRegion] entities. As a particular case, the exact spatial location of a spatial region [snap:SpatialRegion] is this region itself.
Comment: An instance of spatial region [snap:SpatialRegion] is a part of space. All parts of space are spatial region [snap:SpatialRegion] entities and only spatial region [snap:SpatialRegion] entities are parts of space. Space is the entire extent of the spatial universe, a designated individual, which is thus itself a spatial region [snap:SpatialRegion].
Comment: Space and spatial region [snap:SpatialRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of space is sometimes called "absolutist" or "the container view". In BFO, the class site [snap:Site] allows for a so-called relational view of space, that is to say, a view according to which spatiality is a matter of relative location between entities and not a matter of being tied to space. The bridge between these two views is secured through the fact that while instances of site [snap:Site] are not spatial region [snap:SpatialRegion] entities, they are nevertheless spatial entities.
Definition: A continuant [snap:Continuant] that is neither bearer of quality [snap:Quality] entities nor inheres in any other entities.
Examples: the sum total of all space in the universe, parts of the sum total of all space in the universe
specifically_dependent_continuant
Definition: A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same.
Examples: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc.
Synonyms: property, trope, mode
three_dimensional_region
Definition: A spatial region [snap:SpatialRegion] with three dimensions.
Examples: a cube-shaped part of space, a sphere-shaped part of space
two_dimensional_region
Definition: A spatial region [snap:SpatialRegion] with two dimensions.
Examples: the surface of a cube-shaped part of space, the surface of a sphere-shaped part of space, the surface of a rectilinear planar figure-shaped part of space
zero_dimensional_region
Definition: A spatial region [snap:SpatialRegion] with no dimensions.
Examples: a point
connected_spatiotemporal_region
Definition: A space time region [span:SpaceTimeRegion] that has temporal and spatial dimensions such that all points within the spatiotemporal region are mediately or immediately connected to all other points within the same space time region [span:SpaceTimeRegion].
Examples: the spatial and temporal location of an individual organism's life, the spatial and temporal location of the development of a fetus
connected_temporal_region
Definition: A temporal region [span:TemporalRegion] every point of which is mediately or immediately connected with every other point of which.
Examples: the 1970s years, the time from the beginning to the end of a heart attack, the time taken up by cellular meiosis
fiat_process_part
Definition: A processual entity [span:ProcessualEntity] that is part of a process but that does not have bona fide beginnings and endings corresponding to real discontinuities.
Examples: chewing during a meal, the middle part of a rainstorm, the worst part of a heart-attack, the most interesting part of Van Gogh's life
occurrent
Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants.
Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor
Synonyms: perdurant
process
Definition: A processual entity [span:ProcessualEntity] that is a maximally connected spatiotemporal whole and has bona fide beginnings and endings corresponding to real discontinuities.
Examples: the life of an organism, the process of sleeping, the process of cell-division
process_aggregate
Definition: A processual entity [span:ProcessualEntity] that is a mereological sum of process [span:Process] entities and possesses non-connected boundaries.
Examples: the beating of the hearts of each of seven individuals in the room, the playing of each of the members of an orchestra, a process of digestion and a process of thinking taken together
process_boundary
Definition: A processual entity [span:ProcessualEntity] that is the fiat or bona fide instantaneous temporal process boundary.
Examples: birth, death, the forming of a synapse, the onset of REM sleep, the detaching of a finger in an industrial accident, the final separation of two cells at the end of cell-division, the incision at the beginning of a surgery
processual_context
Comment: An instance of a processual context [span:ProcessualContext] is a mixture of processual entity [span:ProcessualEntity] which stand as surrounding environments for other processual entity [span:ProcessualEntity] entities. The class processual context [span:ProcessualContext] is the analogous among occurrent [span:Occurrent] entities to the class site [snap:Site] among continuant [snap:Continuant] entities.
Definition: An occurrent [span:Occurrent] consisting of a characteristic spatial shape inhering in some arrangement of other occurrent [span:Occurrent] entities. processual context [span:ProcessualContext] entities are characteristically entities at or in which other occurrent [span:Occurrent] entities can be located or occur.
Examples: The processual context for a given manipulation occurring as part of an experiment is made of processual entities which occur in parallel, are not necessarily all parts of the experiment themselves and may involve continuant [snap:Continuant] entities which are in the spatial vicinity of the participants in the experiment.
processual_entity
Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity.
Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird
scattered_spatiotemporal_region
Definition: A space time region [span:SpaceTimeRegion] that has spatial and temporal dimensions and every spatial and temporal point of which is not connected with every other spatial and temporal point of which.
Examples: the space and time occupied by the individual games of the World Cup, the space and time occupied by the individual liaisons in a romantic affair
scattered_temporal_region
Definition: A temporal region [span:TemporalRegion] every point of which is not mediately or immediately connected with every other point of which.
Examples: the time occupied by the individual games of the World Cup, the time occupied by the individual liaisons in a romantic affair
spatiotemporal_instant
Definition: A connected space time region [span:ConnectedSpaceTimeRegion] at a specific moment.
Examples: the space time region occupied by a single instantaneous temporal slice (part) of a process
spatiotemporal_interval
Definition: A connected space time region [span:ConnectedSpaceTimeRegion] that endures for more than a single moment of time.
Examples: the space time region occupied by a process or by a fiat processual part
spatiotemporal_region
Comment: All instances of occurrent [span:Occurrent] are spatiotemporal entities, that is, they enter in the relation of (spatiotemporal) location with spatiotemporal region [span:SpatiotemporalRegion] entities. As a particular case, the exact spatiotemporal location of a spatiotemporal region [span:SpatiotemporalRegion] is this region itself.
Comment: An instance of the spatiotemporal region [span:SpatiotemporalRegion] is a part of spacetime. All parts of spacetime are spatiotemporal region [span:SpatiotemporalRegion] entities and only spatiotemporal region [span:SpatiotemporalRegion] entities are parts of spacetime. In particular, neither spatial region [snap:SpatialRegion] entities nor temporal region [span:TemporalRegion] entities are in BFO parts of spacetime. Spacetime is the entire extent of the spatiotemporal universe, a designated individual, which is thus itself a spatiotemporal region [span:SpatiotemporalRegion]. Spacetime is among occurrents the analogous of space among continuant [snap:Continuant] entities.
Comment: Spacetime and spatiotemporal region [span:SpatiotemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of spacetime can be called "absolutist" or "the container view". In BFO, the class processual context [span:ProcessualContext] allows for a so-called relational view of spacetime, that is to say, a view according to which spatiotemporality is a matter of relative location between entities and not a matter of being tied to spacetime. In BFO, the bridge between these two views is secured through the fact that instances of processual context [span:ProcessualContext] are too spatiotemporal entities.
Definition: An occurrent [span:Occurrent] at or in which processual entity [span:ProcessualEntity] entities can be located.
Examples: the spatiotemporal region occupied by a human life, the spatiotemporal region occupied by the development of a cancer tumor, the spatiotemporal context occupied by a process of cellular meiosis
temporal_instant
Definition: A connected temporal region [span:ConnectedTemporalRegion] comprising a single moment of time.
Examples: right now, the moment at which a finger is detached in an industrial accident, the moment at which a child is born, the moment of death
temporal_interval
Definition: A connected temporal region [span:ConnectedTemporalRegion] lasting for more than a single moment of time.
Examples: any continuous temporal duration during which a process occurs
temporal_region
Comment: All instances of occurrent [span:Occurrent] are temporal entities, that is, they enter in the relation of (temporal) location with temporal region [span:TemporalRegion] entities. As a particular case, the exact spatiotemporal location of a temporal region [span:TemporalRegion] is this region itself. Continuant [snap:Continuant] entities are not temporal entities in the technical sense just explained; they are related to time in a different way, not through temporal location but through a relation of existence at a time or during a period of time (see continuant [snap:Continuant].
Comment: An instance of temporal region [span:TemporalRegion] is a part of time. All parts of time are temporal region [span:TemporalRegion] entities and only temporal region [span:TemporalRegion] entities are parts of time. Time is the entire extent of the temporal universe, a designated individual, which is thus a temporal region itself.
Comment: Time and temporal region [span:TemporalRegion] entities are entities in their own rights which exist independently of any entities which can be located at them. This view of time can be called "absolutist" or "the container view" in analogy to what is traditionally the case with space (see spatial region [snap:SpatialRegion].
Definition: An occurrent [span:Occurrent] that is part of time.
Examples: the time it takes to run a marathon, the duration of a surgical procedure, the moment of death
example to be eventually removed
metadata complete
Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete.
placeholder
PERSON:Alan Ruttenberg
This isn't a class that OBI will keep - it's a placeholder for edits that are underway. The class name should start with an underscore
ready for release
Class has undergone final review, is ready for use, and will be included in the next OBI release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release."
metadata incomplete
Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors.
uncurated
Nothing done yet beyond assigning a unique class ID and proposing a preferred term.
pending final vetting
All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the definition editor.
Transformation-ML
Transformation-ML
web-page:http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf
Transformation-ML file describing parameter transformations used in a GvHD experiment.
Transformation-ML is a format standard of a digital entity that is conformant with the Transformation-ML standard.(http://wiki.ficcs.org/ficcs/Transformation-ML?action=AttachFile&do=get&target=Transformation-ML_v1.0.26.pdf)
XML_file
person:Jennifer Fostel
ACS
web-page:http://www.isac-net.org/content/view/607/150/
ACS
ACS is a format standard of a digital entity that is conformant with the Analytical Cytometry Standard. (http://www.isac-net.org/content/view/607/150/)
analytical_cytology_data_file
d06.acs, ACS1.0 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
person:Jennifer Fostel
XML
web-page:http://www.w3.org/XML/
RDF/XML file, OWL file, Compensation-ML file, WSDL document, SVG document
XML
XML is a format standard of a digital entity that is conformant with the W3C Extensible Markup Language Recommendation.(http://www.w3.org/XML/)
person:Jennifer Fostel
text_based_digital_entity
RDF
A FOAF file, a SKOS file, an OWL file.
person:Jennifer Fostel
web-page:http://www.w3.org/RDF/
RDF
RDF is a format standard of a digital entity that is conformant with the W3C Resource Description Framework RDF/XML Syntax specification.(http://www.w3.org/RDF/)
XML_file
zip
web-page:http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/
MagicDraw MDZIP archive, Java JAR file.
binary_digital_entity
person:Jennifer Fostel
zip
zip is a format standard of a digital entity that is conformant with the PKWARE .ZIP file format specification (http://www.pkware.com/index.php?option=com_content&task=view&id=59&Itemid=103/)
tar
web-page:http://www.gnu.org/software/tar/manual/
Example.tar file.
binary_digital_entity
person:Jennifer Fostel
tar
tar is a format standard of a digital entity that is conformant with the tape archive file format as standardized by POSIX.1-1998, POSIX.1-2001, or any other tar format compliant with the GNU tar specification. (http://www.gnu.org/software/tar/manual/)
FCS
web-page:http://www.fcspress.com/
FCS
FCS is a format standard of a digital entity that is conformant with the Flow Cytometry Data File Standard.(http://www.fcspress.com/)
analytical_cytology_data_file
d01.fcs, FCS3 data file of well D06 of plate 2 of part 1 of a GvHD experiment.
person:Jennifer Fostel
Compensation-ML
Compensation-ML
web-page:http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf
Compensation-ML is a format standard of a digital entity that is conformant with the Compensation-ML standard. (http://wiki.ficcs.org/ficcs/Compensation-ML?action=AttachFile&do=get&target=Compensation-ML_v1.0.24.pdf)
XML_file
compfoo.xml, Compensation-ML file describing compensation used in a GvHD experiment
person:Jennifer Fostel
Gating-ML
Gating-ML is a format standard of a digital entity that is conformant with the Gating-ML standard. (http://www.flowcyt.org/gating/)
XML_file
foogate.xml, Gating-ML file describing gates used in a GvHD experiment.
person:Jennifer Fostel
web-page:http://www.flowcyt.org/gating/
Gating-ML
OWL
web-page:http://www.w3.org/2004/OWL/
OBI ontology file, Basic Formal Ontology file, BIRNLex file, BioPAX file.
OWL
OWL is a format standard of a digital entity that is conformant with the W3C Web Ontology Language specification.(http://www.w3.org/2004/OWL/)
XML_file
person:Jennifer Fostel