data part of
type: ObjectProperty
type: TransitiveProperty
comment: This specialization of the 'part-of' relation is to relate immaterial continuants (as defined in 'Relations in biomedical ontologies', Barry Smith et. al.). [Satya & Will 03/02/06]
domain: data
range: data
sub property of: part of

generated by proteolytic enzyme
type: ObjectProperty
comment: associates the peptide with the enzyme that released it. [Dr. York & Satya: 06/28/05]
sub property of: is effect of
domain: peptide
range: proteolytic enzyme

generates ms-ms peak list
type: ObjectProperty
comment: Peak list produced from tandem ms experiments. [James & Satya: 03/27/05]
sub property of: generates processed data
range: ms-ms peak list
domain: tandem mass spectrometer

generates ms peak list
type: ObjectProperty
comment: All mass spectrometers can produce peak lists containing masses and intensities. Different types of mass spectrometers can produce different formats of ms peak lists. [James & Satya: 03/27/05]
sub property of: generates processed data
domain: mass spectrometer

has SemURI concept ID
type: ObjectProperty
type: FunctionalProperty
type: InverseFunctionalProperty
comment: This property enables mapping of each concept in ProPreO to a concept in the SemURI framework. [will & satya 03/03/06]
range: SemURI concept ID
sub property of: has provenance property
domain: Class
  union of: data
  union of: material continuant
  union of: task

has agent
type: ObjectProperty
comment: This object property is subsumed by "has_agent" object property as defined in Barry Smith et. al. "Relations in biomedical ontologies", Genome Biology, Vol 6, Article R46.
range: agent
domain: task

has biological source
type: ObjectProperty
comment: Associates a biomolecule with its biological source. [Dr. York & Satya: 06/28/05]
range: biological continuant
domain: Class
  union of: biochemical sample
  union of: molecule

has input data
type: ObjectProperty
comment: This object property is subsumed by "has_participant" object property as defined in Barry Smith et. al. "Relations in biomedical ontologies", Genome Biology, Vol 6, Article R46.
range: data collection
sub property of: has participant
domain: task

has output data
type: ObjectProperty
comment: This object property is subsumed by "has_participant" object property as defined in Barry Smith et. al. "Relations in biomedical ontologies", Genome Biology, Vol 6, Article R46.
range: experimentally measured data collection
sub property of: is cause of
domain: Class
  union of: analytical instrument
  union of: task

has parent protein
type: ObjectProperty
comment: Defines the protein from which the peptide was cleaved. The peptide is a specific entity and not a generic sequence. [Dr. York & Satya: 06/10/05]
domain: peptide
range: polypeptide

has part
type: ObjectProperty
type: TransitiveProperty
comment: This object property describes the canonical composition of all data collection - they are made up of either parameters or data collection itself. [Satya - 02/23/06]

has provenance property
type: ObjectProperty
comment: An abstract object property subsuming object properties that map to an objectified and classified parameter. The objectified parameter wraps a datum value associated with it. For example, has_mass maps to objects of the class "mass", which have the data property "has_value". Then, "has_value" is restricted to float values (amu) for the class "mass"

is cause of
type: ObjectProperty
comment: This is an 'abstract' property that subsumes properties that denote causality in the active voice. [Will & Satya: 01/19/06]

is described by
type: ObjectProperty
comment: This property describes the chemical entity in terms of either a collection of parameters (substance_associated_data_collection) or an individual parameter (substance_parameter). [Dr. York & Satya: 04/11/06]
domain: chemical entity
range: Class
  union of: substance associated data collection
  union of: substance parameter

is effect of
type: ObjectProperty
comment: This is an 'abstract' property that subsumes properties that denote causality in the passive voice. [Will & Satya: 01/19/06]

material part of
type: ObjectProperty
type: TransitiveProperty
comment: This specialization of the 'part-of' relation is to relate material continuants (as defined in 'Relations in biomedical ontologies', Barry Smith et. al.). [Satya & Will 03/02/06]
range: material continuant
domain: material continuant
sub property of: part of

part of
type: ObjectProperty
type: TransitiveProperty
comment: One of the top level relations, as defined in the 'Relations in biomedical ontologies', Barry Smith et. al. Genome Biology 2005, 6:R46. Thsi relation has been defined for all the top level classes in ProPreO (through subsumption from owl:Thing) i.e. all classes in ProPreO have a or are a 'part-of' another ProPreO class. [Satya & Will 03/01/2006]
inverse of: has part

refers to material continuant
type: ObjectProperty
type: FunctionalProperty
comment: A parameter may describe a chemical entity such as a HPLC solvent or a MALDI matrix. This property relates such a parameterto a specific chemical entity which is not a parameter but a continuant. [will & satya 04/10/06]
range: material continuant
domain: parameter

task part of
type: ObjectProperty
type: TransitiveProperty
comment: This specialization of the 'part-of' relation is to relate immaterial continuants (as defined in 'Relations in biomedical ontologies', Barry Smith et. al.). [Satya & Will 03/02/06]
sub property of: part of
range: task
domain: task

has value
type: DatatypeProperty
type: FunctionalProperty
comment: Defines the general concept of the value of a class of data. The explicit restrictions of this value (i.e., its primitive data type, cardinality, etc) are separately defined for each class in the domain. [Dr. York & Satya: 06/13/05]
domain: parameter

ABI 4700 TOF TOF mass spectrometer
type: Class
subclass of: tandem time of flight mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: ABI 4700 TOF TOF ms raw data
comment: Defines type of tandem mass spectrometer. Tandem time-of-flight spectrometer can perform ms and ms/ms type of analysis. [James & Satya: 01/31/05]

ABI 4700 TOF TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this instrument. [James & Satya: 03/22/05]

ABI Voyager DE Pro MALDI TOF mass spectrometer
type: Class
subclass of: MALDI-TOF mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: ABI Voyager DE Pro MALDI TOF ms raw data
comment: A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05]

ABI Voyager DE Pro MALDI TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this instrument. [James & Satya: 03/22/05]

Agilent HPLC
type: Class
subclass of: high performance liquid chromatograph
comment: A High Performance Liquid Chromatograph manufactured by Agilent Technologies. [James & Satya: 01/31/05]

Agilent HPLC data processing application
type: Class
subclass of: HPLC data processing application
comment: The family of application software developed by Agilent for processing HPLC data. [James & Satya: 03/27/05]

Agilent mass spectrometer data processing application
type: Class
subclass of: MS data processing application
comment: Application software developed by Agilent for processing mass spectrometer data. [James & Satya: 03/27/05]

Applied Bio Systems mass spectrometer data processing application
type: Class
subclass of: MS data processing application
comment: Application software developed by Applied Bio Systems for processing mass spectrometer data. [James & Satya: 03/27/05]

Bruker APEX IV mass spectrometer
type: Class
subclass of: fourier transform mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker APEX IV ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Bruker APEX IV ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this instrument. [James & Satya: 03/27/05]

Bruker APEX Q FT mass spectrometer
type: Class
subclass of: hybrid tandem mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker APEX Q FT ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Bruker APEX Q FT ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/27/05]

Bruker BioTOF Q quadrupole time of flight mass spectrometer
type: Class
subclass of: quadrupole time of flight mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker BioTOF Q quadrupole time of flight ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Bruker BioTOF Q quadrupole time of flight ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Bruker Daltomics mass spectrometer data processing application
type: Class
subclass of: MS data processing application
comment: Application software developed by Bruker Daltonics for processing mass spectrometer data. [James & Satya: 03/27/05]

Bruker HCT ion trap mass spectrometer
type: Class
subclass of: ion trap mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker HCT ion trap ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Bruker HCT ion trap ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Bruker HCTplus ion trap mass spectrometer
type: Class
subclass of: ion trap mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker HCTplus ion trap ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Bruker HCTplus ion trap ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Bruker autoflex MALDI TOF mass spectrometer
type: Class
subclass of: MALDI-TOF mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker autoflex MALDI TOF ms raw data
comment: A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05]

Bruker autoflex MALDI TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Bruker autoflex TOF TOF mass spectrometer
type: Class
subclass of: tandem time of flight mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker autoflex TOF TOF ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Bruker autoflex TOF TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Bruker esquire4000 ion trap mass spectrometer
type: Class
subclass of: ion trap mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker esquire4000 ion trap ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Bruker esquire4000 ion trap ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Bruker esquire6000 ion trap mass spectrometer
type: Class
subclass of: ion trap mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker esquire6000 ion trap ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Bruker esquire6000 ion trap ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Bruker microQTOF quadrupole time of flight mass spectrometer
type: Class
subclass of: quadrupole time of flight mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker microQTOF quadrupole time of flight ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Bruker microQTOF quadrupole time of flight ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Bruker microflex MALDI TOF mass spectrometer
type: Class
subclass of: MALDI-TOF mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker microflex MALDI TOF ms raw data
comment: A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05]

Bruker microflex MALDI TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Bruker omniflex MALDI TOF mass spectrometer
type: Class
subclass of: MALDI-TOF mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker omniflex MALDI TOF ms raw data
comment: A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05]

Bruker omniflex MALDI TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Bruker ultraflex MALDI TOF mass spectrometer
type: Class
subclass of: MALDI-TOF mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker ultraflex MALDI TOF ms raw data
comment: A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05]

Bruker ultraflex MALDI TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Bruker ultraflex TOF TOF mass spectrometer
type: Class
subclass of: tandem time of flight mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Bruker ultraflex TOF TOF ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Bruker ultraflex TOF TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

CARBANK ID
type: Class
subclass of: glycan accession number
comment: A parameter that specifies the identifier for a glycan record in the CARBANK database. URL: ftp://ncbi.nlm.nih.gov/repository/carbbank/ [Dr. York & Satya: 06/14/05]

CCSD ID
type: Class
subclass of: glycan accession number
comment: A parameter that specifies the unique identifier for a glycan structure in the CARBANK database. URL: http://bssv01.lancs.ac.uk/gig/pages/gag/carbbank.htm#ccsd [Dr. York & Satya: 06/14/05]

CHEBI ID
type: Class
subclass of: substance accession number
comment: A parameter that corresponds to the CHEBI ID from the ChEBI Ontology http://www.ebi.ac.uk/chebi/

DNA nucleotide sequence
type: Class
subclass of: molecular sequence
comment: A parameter describing the sequence of deoxynucleotides in a DNA molecule. Nucleotides are listed from the 5' end to the 3' end.

ESI source
type: Class
subclass of: MS source
comment: For for > microlitre/min flow rates. [James & Satya: 02/24/05]

Finnigan ASC ms-ms peak list
type: Class
subclass of: ms-ms peak list
comment: A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. Files in this format are created by the LIST command on the ICIS data system. The header block for each MS/MS dataset begins with a "LIST:" field. The text in this field is used by Mascot to identify the query, equivalent to an embedded TITLE parameter. The ASC file header does not specify a charge state for the precursor peptide. This can be specified (globally) on the search form, or by an embedded CHARGE parameter at the head of the data file. The precursor peptide m/z value is parsed from the "Mode:" field. Mascot uses the prevailing CHARGE value to calculate Mr from the observed m/z. A blank line to delimit MS/MS datasets is optional. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05]

Finnigan LCQ classic mass spectrometer
type: Class
subclass of: ion trap mass spectrometer
subclass of: Restriction
  on property: generates ms-ms peak list
  all values from: Class
    union of: Finnigan ASC ms-ms peak list
    union of: Finnigan Sequest DTA ms-ms peak list
subclass of: Restriction
  on property: generates raw data
  all values from: Finnigan LCQ classic ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Finnigan LCQ classic ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Finnigan LTQ FT mass spectrometer
type: Class
subclass of: hybrid tandem mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Finnigan LTQ FT ms raw data
subclass of: Restriction
  on property: generates ms-ms peak list
  all values from: Class
    union of: Finnigan ASC ms-ms peak list
    union of: Finnigan Sequest DTA ms-ms peak list
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Finnigan LTQ FT ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/27/05]

Finnigan LTQ linear ion trap mass spectrometer
type: Class
subclass of: ion trap mass spectrometer
subclass of: Restriction
  on property: generates ms-ms peak list
  all values from: Class
    union of: Finnigan ASC ms-ms peak list
    union of: Finnigan Sequest DTA ms-ms peak list
subclass of: Restriction
  on property: generates raw data
  all values from: Finnigan LTQ linear ion trap ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Finnigan LTQ linear ion trap ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Finnigan Sequest DTA ms-ms peak list
type: Class
subclass of: ms-ms peak list
comment: A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. The DTA format is very simple. The first line contains the singly protonated peptide mass (MH+) and the peptide charge state as a pair of space separated values. Subsequent lines contain space separated pairs of fragment ion m/z and intensity values. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05]

GPS Explorer application
type: Class
subclass of: Applied Bio Systems mass spectrometer data processing application
comment: Application software developed by Applied Bio Systems for processing mass spectrometer data. [James & Satya: 03/27/05]

GycO ID
type: Class
subclass of: glycan accession number
comment: A parameter that specifies the unique identifier for a glycan instance in glycan domain ontology: GlycO. URL: http://lsdis.cs.uga.edu/projects/glycomics/glyco/ [Dr. York & Satya: 06/13/05]

HPLC analytical scale fraction collector
type: Class
subclass of: HPLC fraction collector
comment: An HPLC fraction collector that directs the eluant from an analytical scale HPLC experiment. [James & Satya: 01/31/05]

HPLC autosampler
type: Class
subclass of: HPLC component
comment: An HPLC component that is programmed to automatically inject samples into the HPLC column. [James & Satya: 01/31/05]

HPLC buffer
type: Class
subclass of: HPLC instrumental operating parameter
subclass of: substance identifier
subclass of: Restriction
  on property: has units
  cardinality: 0
subclass of: Restriction
  on property: refers to material continuant
  all values from: Class
    union of: solution
    union of: solvent
comment: A parameter that identifies the elution buffer used in HPLC. A mixture of buffers is often prepared in a mixing device to form a time-dependent elution gradient. The HPLC_buffer parameter is a substance identifier, which points to an instance of "solution". A "solution" is_described_by one or more mixture_component_descriptor(s), each of which has two parts: the component_amount and a substance_identifier that specifies the identity of the component. This is a flexible way of describing solutions. For example, a solution can be described as a mixture of two other solutions (e.g., buffer A and buffer B), in which case the mixture_component_descriptor(s) each specify the identity and amount of each of these buffers. Alternatively, a solution can be described according to the concentrations of its solutes (molecules), each of which is specified by a mixture_component_descriptor. In this case, complete description of the solution requires that the solvent be specified using the property has_solvent, which points to an instance of the class "solvent". [James & Satya: 01/31/05]

HPLC chromatogram
type: Class
equivalent class: Restriction
  on property: has data part
  all values from: HPLC time signal pair
subclass of: HPLC experimental data collection
comment: A data collection (chromatogram) generated by an HPLC experiment -This typically consists of a collection of time/signal intensity pairs [James & Satya: 03/29/05]

HPLC chromatogram XML format data
type: Class
subclass of: HPLC chromatogram
comment: A data collection (chromatogram) generated by an HPLC experiment - This describes, two-column data which are signal vs time. The data columns are in XML. [James & Satya: 03/29/05]

HPLC chromatogram text format data
type: Class
subclass of: HPLC chromatogram
comment: A data collection (chromatogram) generated by an HPLC experiment - This describes, two-column data which are signal vs time. The data columns are generally tab, space or comma separated. [James & Satya: 03/29/05]

HPLC column
type: Class
subclass of: HPLC component
comment: A matrix-containing tube that is used for high-performance liquid chromatography. The sample is separated into its components by injecting it into the column and elutimng with a solvent or buffer.

HPLC component
type: Class
subclass of: instrument component
comment: A component of a hgh-performance liquid chromatograph

HPLC data collection
type: Class
subclass of: process associated data collection
comment: A data collection used or generated by a high performance liquid chromatography experiment

HPLC data processing application
type: Class
subclass of: data processing application
comment: Application software used in processing/manipulating HPLC data. [James & Satya: 03/27/05]

HPLC detection wavelength
type: Class
subclass of: HPLC instrumental operating parameter
subclass of: Restriction
  on property: has units
  all values from: length units
subclass of: Restriction
  on property: has value
  all values from: float
comment: A parameter that describes the detection wavelength of the HPLC detector, which may be either an absorbance detector or a fluorescence detector. [James & Satya: 01/31/05]

HPLC detector
type: Class
subclass of: HPLC component
comment: An HPLC instrument component that detects molecules that are eluted from the HPLC column. [James & Satya: 01/31/05]

HPLC detector signal
type: Class
subclass of: HPLC experimentally measured parameter
comment: A parameter that describes the detector signal measured at a particular time of an HPLC experiment.

HPLC diode array detector
type: Class
subclass of: HPLC detector
comment: A type of HPLC detector. [James & Satya: 01/31/05]

HPLC excitation wavelength
type: Class
subclass of: HPLC instrumental operating parameter
subclass of: Restriction
  on property: has units
  all values from: length units
subclass of: Restriction
  on property: has value
  all values from: float
comment: A parameter that describes the excitation wavelength of a fluorescence HPLC detector. [James & Satya: 01/31/05]

HPLC experimental data collection
type: Class
equivalent class: Class
  intersection of: HPLC data collection
  intersection of: experimentally measured data collection
comment: c

HPLC experimentally measured parameter
type: Class
subclass of: HPLC parameter
subclass of: experimentally measured parameter
comment: A parameter that is measured during an HPLC experiment - E.G. the detector signal intensity at a particular time.

HPLC flowrate
type: Class
subclass of: HPLC instrumental operating parameter
subclass of: Restriction
  on property: has units
  all values from: flowrate units
comment: A parameter that describes the eluant flow rate for an HPLC experiment. [James & Satya: 01/31/05]

HPLC fluorenscence detector
type: Class
subclass of: HPLC detector
comment: A type of HPLC detector. [James & Satya: 01/31/05]

HPLC fraction collector
type: Class
subclass of: HPLC component
comment: An HPLC instrument component that directs the eluant from the HPLC column to a series of separate vessels (tubes of wells). The collector may direct the eluant to different vessels based on elution time, detector response, or some other criterion.

HPLC gradient program
type: Class
subclass of: HPLC operating parameter collection
subclass of: Restriction
  on property: has data part
  all values from: HPLC gradient time point
comment: A collection of parameters that describe the solvent gradient for an HPLC run [Dr. York & Satya: 05/17/05]

HPLC gradient time point
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has data part
    some values from: HPLC time parameter
  intersection of: Restriction
    on property: has data part
    some values from: mixture component descriptor
subclass of: HPLC operating parameter collection
comment: A collection of parameters that defines a HPLC run time and the associated buffer mixture that comprises the eluent at that time. It can have multiple values of component portion for that time value. [Dr. York & Satya: 06/28/05]

HPLC injection loop volume
type: Class
subclass of: HPLC instrumental operating parameter
subclass of: Restriction
  on property: has units
  all values from: volume units
subclass of: Restriction
  on property: has value
  all values from: float
comment: A parameter that describes the injuection loop volume for an HPLC experiment.

HPLC instrumental operating parameter
type: Class
subclass of: HPLC parameter
subclass of: operating parameter
comment: A parameter that defines the operating state of the chromatograph during data collection

HPLC manual injector
type: Class
subclass of: HPLC component
comment: An HPLC component that is used for manual injection of the sample onto the column. [James & Satya: 01/31/05]

HPLC micro autosampler
type: Class
subclass of: HPLC autosampler
comment: A type of HPLC autosampler. [James & Satya: 01/31/05]

HPLC micro well plate autosampler
type: Class
subclass of: HPLC autosampler
comment: A type of HPLC autosampler. [James & Satya: 01/31/05]

HPLC microscale MALDI spotter
type: Class
subclass of: HPLC fraction collector
comment: An HPLC fraction collector that directs the eluant from an micro scale HPLC experiment onto specific locatons on a MALDI target for subsequent MALDI MS analysis.

HPLC microscale fraction collector
type: Class
subclass of: HPLC fraction collector
comment: An HPLC fraction collector that directs the eluant from an microscale HPLC experiment. [James & Satya: 01/31/05]

HPLC multiwavelength detector
type: Class
subclass of: HPLC detector
comment: A type of HPLC detector. [James & Satya: 01/31/05]

HPLC operating parameter collection
type: Class
equivalent class: Class
  intersection of: HPLC data collection
  intersection of: operating parameter collection
subclass of: Restriction
  on property: has data part
  all values from: Class
    union of: HPLC gradient program
    union of: HPLC gradient time point
    union of: HPLC parameter
comment: A collection of parameters required to perform or analyze an HPLC run. [Dr. York & Satya: 05/17/05]

HPLC parameter
type: Class
subclass of: process associated parameter
comment: A parameter that is used/created/generated during the acquisition or processing of HPLC data

HPLC pump
type: Class
subclass of: HPLC component
comment: An HPLC component that pumps the eluant through the HPLC column, usually at high pressure and at a tightly controlled flow rate.

HPLC refractive index detector
type: Class
subclass of: HPLC detector
comment: A type of HPLC detector. [James & Satya: 01/31/05]

HPLC standard autosampler
type: Class
subclass of: HPLC autosampler
comment: A type of HPLC autosampler. [James & Satya: 01/31/05]

HPLC standard well plate autosampler
type: Class
subclass of: HPLC autosampler
comment: A type of HPLC autosampler.

HPLC time parameter
type: Class
subclass of: HPLC experimentally measured parameter
subclass of: HPLC instrumental operating parameter
subclass of: process time parameter
comment: A parameter that describes the time (measured from the start of the experiment) within a HPLC experiment that an event occurs. This time parameter can be associated, for example, with a signal intensity or a buffer gradient condition.

HPLC time signal pair
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has data part
    some values from: HPLC detector signal
  intersection of: Restriction
    on property: has data part
    some values from: HPLC time parameter
subclass of: HPLC experimental data collection
comment: A single time-point generated by an HPLC experiment - This corresponds to a pair of parameters, the internal HPLC time and the detector signal at that time.

HPLC vacuum degasser
type: Class
subclass of: HPLC component
comment: An HPLC instrument component that uses a vacuum to remove dissolved gas from a sample or eluant before it is pumped through the HPLC column.

HPLC variable wavelength detector
type: Class
subclass of: HPLC detector
comment: A type of HPLC detector. [James & Satya: 01/31/05]

KEGG ID
type: Class
subclass of: glycan accession number
comment: A parameter that specifies the unique glycan identifier in the KEGG database. URL: http://www.genome.jp/kegg/ [Dr. York & Satya: 06/14/05]

LINUCS ID
type: Class
subclass of: glycan accession number
comment: A parameter that specifies the unique glycan identifier in SWEETDB. URL: http://www.glycosciences.de/sweetdb/index.php [Dr. York & Satya: 06/13/05]

MALDI-TOF mass spectrometer
type: Class
subclass of: mass spectrometer
subclass of: Restriction
  on property: has material part
  all values from: Class
    union of: MALDI source
    union of: MS detector
    union of: TOF analyzer
comment: A Matrix-Assisted-Laser-Desorption-Time-of-Flight mass spectrometer. Such a spectrometer contains a MALDI source and a TOF analyzer. [James & Satya: 03/27/05]

MALDI matrix
type: Class
subclass of: molecular aggregate
subclass of: Restriction
  on property: has material part
  all values from: small molecule
comment: A molecular aggragate that is used in a MALDI source. The MALDI matrix absorbs energy from the laser, and this energy promotes transfer to the gas phase and ionizaton of the analyte.

MALDI source
type: Class
subclass of: MS source
comment: Defines the type of source. [James & Satya: 02/24/05]

MS analyzer
type: Class
subclass of: MS component
comment: A mass spectromete component that separates ions according to their mass to charge ratio. Ions are produced in the ion source.

MS analyzer TOF type
type: Class
subclass of: MS analyzer parameter
subclass of: Restriction
  on property: refers to material continuant
  all values from: TOF analyzer
subclass of: Restriction
  on property: has units
  cardinality: 0
comment: A parameter that defines the type of TOF analyzer. It may either be: a) Reflectron or b) Linear [James & Satya: 02/24/05]

MS analyzer focus mass
type: Class
subclass of: MS analyzer parameter
subclass of: Restriction
  on property: has value
  all values from: float
subclass of: Restriction
  on property: has units
  all values from: mass units
comment: A parameter that defines the center of the mass range or the center of the calibration curve for the given mass range. [James & Satya: 02/24/05]

MS analyzer interscan delay
type: Class
subclass of: MS analyzer parameter
comment: A parameter that defines the time period between MS and MS-MS scans. [James & Satya: 02/24/05]

MS analyzer mass range max
type: Class
subclass of: MS analyzer parameter
subclass of: Restriction
  on property: has units
  all values from: mass units
comment: A parameter that defines the maximum mass range associated with a MS experiment. Mass range is determined by the user and the instrument. It typically has a value from 0 to 500,000. [James & Satya: 02/24/05]

MS analyzer mass range min
type: Class
subclass of: MS analyzer parameter
subclass of: Restriction
  on property: has units
  all values from: mass units
comment: A parameter that defines the minimum mass range associated with a MS experiment.

MS analyzer mode
type: Class
subclass of: MS analyzer parameter
comment: A parameter that defines the analyzer mode associated with a MS experiment. This parameter can have values of positive or negative. It describes the charge of the ions that are detected. [James & Satya: 02/24/05]

MS analyzer parameter
type: Class
subclass of: MS instrumental operating parameter
comment: A parameter that defines the operating state of the mass spectrometer analyzer during data collection [Will & Satya 02/15/06]

MS analyzer parameter collection
type: Class
subclass of: MS instrument setup parameter collection
subclass of: Restriction
  on property: has data part
  all values from: MS analyzer parameter
comment: A collection of parameters controlling the operation of the analyzer of a mass spectrometer [James & Satya: 02/24/05]

MS analyzer scan time
type: Class
subclass of: MS analyzer parameter
comment: A parameter that defines the length of time for an MS or MS-MS scan. [James & Satya: 02/24/05]

MS component
type: Class
subclass of: instrument component
comment: A component of a mass spectrometer

MS data collection
type: Class
subclass of: process associated data collection
comment: A data collection used or generated by a mass spectrometry experiment

MS data processing application
type: Class
subclass of: data processing application
comment: Application software used in processing/manipulating ms or ms-ms data. [James & Satya: 03/27/05]

MS data processing parameter
type: Class
subclass of: MS parameter
subclass of: data processing parameter
comment: A parameter that is used by an application that processes mass spectral data

MS data processing parameter collection
type: Class
subclass of: MS operating parameter collection
comment: A collection of computational parameters required to process ms or ms-ms data [James & Satya: 03/27/05]

MS detector
type: Class
subclass of: MS component
comment: This is for self-manufactured or modified that are not found under the mass spectrometer instruments. [James & Satya: 02/24/05]

MS experimentally measured parameter
type: Class
subclass of: MS parameter
subclass of: experimentally measured parameter
comment: A parameter that is measured during an MS experiment - E.G. the abundance of an ion having a particular m/z value.

MS instrument setup parameter collection
type: Class
subclass of: MS operating parameter collection
subclass of: Restriction
  on property: has data part
  all values from: MS instrumental operating parameter
comment: A collection of instrumental parameters required to record mass spectral data [James & Satya: 03/27/05]

MS instrumental operating parameter
type: Class
subclass of: MS parameter
subclass of: operating parameter
comment: A parameter that defines the operating state of the mass spectrometer during data collection

MS operating parameter collection
type: Class
equivalent class: Class
  intersection of: MS data collection
  intersection of: operating parameter collection
subclass of: Restriction
  on property: has data part
  all values from: Class
    union of: MS operating parameter collection
    union of: MS parameter
comment: A collection of parameters required to perform a task that generates or processes mass spectral data

MS parameter
type: Class
subclass of: process associated parameter
comment: A parameter that is used/created/generated during the acquisition or processing of MS data [Will & Satya: 01/19/06]

MS raw data converted format
type: Class
subclass of: ms raw data
comment: A collection of mass spectral data that has NOT been computationally processed, except that its digital format has been modified

MS raw data native format
type: Class
subclass of: ms raw data
comment: A collection of mass spectral data that has NOT been computationally processed in any way. That is, the raw output from the mass spectrometer. These may be of multiple formats [James & Satya: 03/22/05]

MS source ESI capillary voltage
type: Class
equivalent class: Restriction
  on property: has value
  all values from: float
subclass of: MS source ESI parameter
subclass of: Restriction
  on property: has units
  all values from: electrical potential units
comment: A parameter that defines the voltage applied to the ESI capillary. [James & Satya: 02/24/05]

MS source ESI parameter
type: Class
subclass of: MS source parameter
comment: A parameter associated with an electrospray ionization source.

MS source ESI parameter collection
type: Class
equivalent class: Class
  intersection of: MS source parameter collection
  intersection of: Restriction
    on property: has data part
    all values from: MS source ESI parameter
comment: A collection of parameters controlling the operation of an electrospray ionization source of a mass spectrometer [Will & Satya 02/15/06]

MS source MALDI laser intensity
type: Class
equivalent class: Restriction
  on property: has value
  all values from: float
subclass of: MS source MALDI parameter
subclass of: Restriction
  on property: has units
  all values from: laser pulse intensity units
comment: A parameter that defines the intensity of the laser used in the MS experiment. [James & Satya: 02/24/05]

MS source MALDI matrix
type: Class
equivalent class: Class
  intersection of: MS source MALDI parameter
  intersection of: substance identifier
subclass of: Restriction
  on property: refers to material continuant
  all values from: MALDI matrix
comment: A parameter that defines the matrix used in the MALDI analysis. It may be of multiple types like: a) DHB b) Alpha-Cyano [James & Satya: 02/24/05]

MS source MALDI number of laser shots
type: Class
equivalent class: Restriction
  on property: has value
  all values from: int
subclass of: MS source MALDI parameter
subclass of: Restriction
  on property: has units
  cardinality: 0
comment: A parameter that defines the number of laser shots in a MALDI experiment. This is a pure integer (no units). [James & Satya: 02/24/05]

MS source MALDI parameter
type: Class
subclass of: MS source parameter
comment: A parameter associated with a matrix assisted laser induced ionization source. [James & Satya: 02/24/05]

MS source MALDI parameter collection
type: Class
equivalent class: Class
  intersection of: MS source parameter collection
  intersection of: Restriction
    on property: has data part
    all values from: MS source MALDI parameter
comment: A collection of parameters controlling the operation of a matrix-assisted laser-desorption ionization source of a mass spectrometer [Will & Satya 02/15/06]

MS source cone voltage
type: Class
equivalent class: Restriction
  on property: has value
  all values from: float
subclass of: MS source ESI parameter
subclass of: Restriction
  on property: has units
  all values from: electrical potential units
comment: A parameter that defines the voltage applied to the inlet cone. [James & Satya: 02/24/05]

MS source parameter
type: Class
subclass of: MS instrumental operating parameter
comment: A parameter that defines the operating state of the mass spectrometer ion source during data collection [Will & Satya 02/15/06]

MS source parameter collection
type: Class
subclass of: MS instrument setup parameter collection
subclass of: Restriction
  on property: has data part
  all values from: MS source parameter
comment: A collection of parameters controlling the operation of the ion source of a mass spectrometer [James & Satya: 02/24/05]

MS time parameter
type: Class
subclass of: MS parameter
subclass of: process time parameter
comment: A parameter that describes the time within a mass spectrometry that an event occurs. E.G., the time (measured from the start of the experiment) that a particular mass spectrum was recorded.

Masslynx Micromass application
type: Class
subclass of: Micromass mass spectrometer data processing application
comment: Application software developed by Micromass for processing mass spectrometer data. [James & Satya: 03/27/05]

Masslynx proteinlynx denovo sequencing results data
type: Class
subclass of: denovo sequencing output data collection
comment: A data collection produced by performing Proteinlynx denovo sequecing. [James & Satya: 03/29/05]

Micromass MALDI micro MX MALDI TOF mass spectrometer
type: Class
subclass of: MALDI-TOF mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Micromass MALDI micro MX MALDI TOF ms raw data
comment: A type of MALDI-TOF mass spectrometer. [James & Satya: 03/27/05]

Micromass MALDI micro MX MALDI TOF ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Micromass QTOF 2 quadrupole time of flight mass spectrometer
type: Class
subclass of: quadrupole time of flight mass spectrometer
subclass of: Restriction
  on property: generates ms-ms peak list
  all values from: Class
    union of: Finnigan Sequest DTA ms-ms peak list
    union of: micromass pkl ms-ms peak list
subclass of: Restriction
  on property: generates raw data
  all values from: Micromass QTOF 2 quadrupole time of flight ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Micromass QTOF 2 quadrupole time of flight ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Micromass Q TOF micro quadrupole time of flight mass spectrometer
type: Class
subclass of: quadrupole time of flight mass spectrometer
subclass of: Restriction
  on property: generates ms-ms peak list
  all values from: Class
    union of: Finnigan Sequest DTA ms-ms peak list
    union of: micromass pkl ms-ms peak list
subclass of: Restriction
  on property: generates raw data
  all values from: Micromass Q TOF micro quadrupole time of flight ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Micromass Q TOF micro quadrupole time of flight ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Micromass Q TOF ultima quadrupole time of flight mass spectrometer
type: Class
subclass of: quadrupole time of flight mass spectrometer
subclass of: Restriction
  on property: generates ms-ms peak list
  all values from: Class
    union of: Finnigan Sequest DTA ms-ms peak list
    union of: micromass pkl ms-ms peak list
subclass of: Restriction
  on property: generates raw data
  all values from: Micromass Q TOF ultima quadrupole time of flight ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Micromass Q TOF ultima quadrupole time of flight ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Micromass Quatro micro triple quadrupole mass spectrometer
type: Class
subclass of: triple quadrupole mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Micromass Quatro micro triple quadrupole ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Micromass Quatro micro triple quadrupole ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Micromass Quatro premier triple quadrupole mass spectrometer
type: Class
subclass of: triple quadrupole mass spectrometer
subclass of: Restriction
  on property: generates raw data
  all values from: Micromass Quatro premier triple quadrupole ms raw data
comment: A type of tandem mass spectrometer. [James & Satya: 03/27/05]

Micromass Quatro premier triple quadrupole ms raw data
type: Class
subclass of: MS raw data native format
comment: The raw data output from this intrument. [James & Satya: 03/22/05]

Micromass mass spectrometer data processing application
type: Class
subclass of: MS data processing application
comment: Application software developed by Micromass for processing mass spectrometer data. [James & Satya: 03/27/05]

N-glycosylation consensus presence
type: Class
subclass of: molecular parameter
subclass of: Restriction
  on property: has value
  all values from: boolean
comment: A boolean parameter that describes whether a N-glycosylation consensus sequence is present in a peptide or protein. [will & satya 04/25/06]

Nano ESI source
type: Class
subclass of: ESI source
comment: Electrospray source for flow rates < 3 microlitres/min. [James & Satya: 02/24/05]

PDB accession number
type: Class
subclass of: protein accession number
comment: A parameter that specifies the unique identifier for a particular protein in the PDB database. URL: http://www.rcsb.org/pdb/ [Dr. York & Satya: 06/14/05]

PEAKS denovo sequencing results data
type: Class
subclass of: denovo sequencing output data collection
comment: A data collection produced by performing PEAKKS denovo sequecing. [James & Satya: 03/29/05]

PerSeptive PKS 51 ms-ms peak list
type: Class
subclass of: ms-ms peak list
comment: A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. PSD peak lists exported from Grams as .PKS files contain data from a single PSD spectrum. Since the .PKS format does not include details of the precursor peptide m/z, this information must be entered manually into the PRECURSOR and CHARGE form fields. This limitation also means that multiple spectra cannot be merged into a single data file. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05]

Proteinlynx micromass MALDI data processing parameters collection
type: Class
subclass of: MS data processing parameter collection
comment: The collection of processing parameters used by Proteinlynx when converting a MALDI '.raw' file into a '.pkl' or a '.dta' file, when using Proteinlynx. [James & Satya: 04/01/05]

Proteinlynx micromass electrospray data processing parameters collection
type: Class
subclass of: MS data processing parameter collection
comment: The collection of processing parameters used by Proteinlynx when converting a electrospray '.raw' file into a '.pkl' or a '.dta' file, when using Proteinlynx. [James & Satya: 04/01/05]

Proteinlynx micromass ms-ms survey data processing parameters collection
type: Class
subclass of: MS data processing parameter collection
comment: The collection of processing parameters used by Proteinlynx when converting a ms/ms survey '.raw' file into a '.pkl' or a '.dta' file, when using Proteinlynx. [James & Satya: 04/01/05]

REFSEQ polynucleotide accession number
type: Class
subclass of: polynucleotide accession number
comment: A parameter that specifies the unique identifier that refers to a particular gene or other nucleotide sequence in the RefSeq system. URL: www.ncbi.nlm.nih.gov/RefSeq/key.html [Dr. York & Satya: 06/23/05]

REFSEQ protein accession number
type: Class
subclass of: protein accession number
comment: A parameter that specifies the unique identifier for a particular protein in the RefSeq system. URL: www.ncbi.nlm.nih.gov/RefSeq/ [Dr. York & Satya: 06/14/05]

RNA nucleotide sequence
type: Class
subclass of: molecular sequence
comment: A parameter describing the sequence of nucleotides in an RNA molecule. Nucleotides are listed from the 5' end to the 3' end.

Sciex API III ms-ms peak list
type: Class
subclass of: ms-ms peak list
comment: A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. Peak lists exported from PE Sciex API III contain data from a single MS/MS spectrum. Since the file format does not include details of the precursor peptide m/z, this information must be entered manually into the PRECURSOR and CHARGE form fields. This limitation also means that multiple spectra cannot be merged into a single data file. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05]

SemURI
type: Class
subclass of: SemURI parameter
subclass of: Restriction
  on property: has value
  all values from: string
comment: The semantic Universal Resource Identifier (semURI) for a specific instance defined in ProPreO or other aligned ontology. By semantic URI we mean an URI that lexically incorporates semantic description by succinctly representing a chronologically ordered list of concepts that are defined in ProPreO or other ontologies. These concepts can include both (physical and computational) tasks and the (physical and digital) objects that these tasks use and generate. Thus, each task or object class is assigned a SemURI_concept_ID, which is appended (along with a SemURI_instance_ID) to the SemURI of the the object's predecessor to generate a new SemURI that identifies the new task or object. Thus, the SemURI constitutes a very succinct representation of the entire provenance of an object, including all of the tasks and intermediate objects in its history.

SemURI concept ID
type: Class
subclass of: SemURI parameter
subclass of: Restriction
  on property: has value
  all values from: string
subclass of: Restriction
  on property: has SemURI concept ID
  cardinality: 0
comment: The first component of a semantic Universal Resource Identifier (semURI) module. Each instance of this parameter maps the module to a specific concept in ProPreO. [will & satya 03/03/06]

SemURI instance ID
type: Class
subclass of: SemURI parameter
subclass of: Restriction
  on property: has value
  all values from: string
subclass of: Restriction
  on property: has SemURI concept ID
  cardinality: 0
comment: The second component of a semantic Universal Resource Identifier (semURI) module. This identifies a specific instance (within the context of a provenance chain) of a SemURI concept. It is important to note that the same SemURI_instance_ID can be used for two distinct instances of the same concept, as long as the two instances are not present at the same location of a single provenance chain. This allows the SemURI_instance_ID to be short and still insures that the SemURI as a whole is unique. Uniqueness stems from the entire SemURI, which consists of several SemURI modules. That is, two SemURIs can be unique even if they share a common SemURI module, just as two words can be unique even if they share a common letter of series of letters. [will & satya 03/03/06]

SemURI module
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has data part
    some values from: SemURI concept ID
  intersection of: Restriction
    on property: has data part
    some values from: SemURI instance ID
  intersection of: Restriction
    on property: has data part
    cardinality: 2
subclass of: annotation associated data collection
comment: This describes the two-component, basic building block of the Semantic URI provenance scheme. The two components are: 1- SemURI_concept_ID 2- SemURI_instance_ID [will & satya 03/03/06]

SemURI parameter
type: Class
subclass of: annotation parameter
comment: By semantic URI (SemURI) we mean an URI that lexically incorporates semantic description by succinctly representing a chronologically ordered list of concepts that are defined in ProPreO or other ontologies. These concepts can include both (physical and computational) tasks and the (physical and digital) objects that these tasks use and generate. Thus, each task or object class is assigned a SemURI_concept_ID, which is appended (along with a SemURI_instance_ID) to the SemURI of the the object's predecessor to generate a new SemURI that identifies the new task or object. Thus, the SemURI constitutes a very succinct representation of the entire provenance of an object, including all of the tasks and intermediate objects in its history.

Spectrum mill application
type: Class
subclass of: Agilent mass spectrometer data processing application
comment: Application software developed by Agilent for processing mass spectrometer data. [James & Satya: 03/27/05]

TOF analyzer
type: Class
subclass of: MS analyzer
comment: A type of MS analyzer

ThermoElectron mass spectrometer data processing application
type: Class
subclass of: MS data processing application
comment: Application software developed by ThermoElectron for processing mass spectrometer data. [James & Satya: 03/27/05]

Turbo Sequest application
type: Class
subclass of: ThermoElectron mass spectrometer data processing application
comment: Application software developed by ThermoElectron for processing mass spectrometer data. [James & Satya: 03/27/05]

UNIPROT accession number
type: Class
subclass of: protein accession number
comment: A parameter that specifies the unique identifier for a particular protein in the UNIPROT (formerly SWISSPROT) database. URL: www.uniprot.org/ [Dr. York & Satya: 06/14/05]

URL parameter
type: Class
subclass of: annotation parameter
comment: A string parameter that specifies the location of a resource (such as a data file) on the internet - I.e., a Universal Resource Locator

UV spectrometer
type: Class
subclass of: analytical instrument
comment: An instrument that measures the transmittance of ultraviolet light through a sample (usually a liquid).

absolute amount
type: Class
subclass of: substance amount
comment: A parameter describing the amount of a substance in absolute terms (total mass, total volume, total number of moles, as appropriate). [will & satya 04/13/06]

absolute mass
type: Class
subclass of: absolute amount
comment: A parameter describing the total mass of a particular substance (e.g., 5 grams of NaCl) in a molecular aggregate

absolute volume
type: Class
subclass of: absolute amount
comment: A parameter describing the total volume of a particular substance (e.g., 5 Liters of water) in a molecular aggregate

agent
type: Class
subclass of: material continuant
comment: An agent is a real world object that causes something to happen, i.e., it initiates or implements a process. Examples are human operators, analytical instruments, enzymes, and software applications

amino acid sequence
type: Class
subclass of: molecular sequence
comment: A parameter describing the sequence of amino acid residues of a peptide or protein. Amino acids are listed starting at the N-terminus and continuing to the C-terminus using standard one-letter amino acid nomenclature. The name of the amino acid sequence is same as the sequence string. [Dr. York & Satya: 06/10/05]

analytical instrument
type: Class
equivalent class: Class
  intersection of: hardware
  intersection of: Restriction
    on property: has material part
    all values from: instrument component
comment: An analytical instrument is a piece of hardware designed to measure a parameter or analyze a sample.

annotation associated data collection
type: Class
subclass of: data collection
comment: a data collection that is used to annotate other data

annotation parameter
type: Class
subclass of: parameter
comment: A parameter used in the annotation of data

antibody affinity HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

archaea
type: Class
subclass of: procaryotic organism
comment: Organisms, including the Crenarchaeota, Euryarchaeota and Korarchaeota, with a cell structure that is similar to other prokaryotes, but with some biochemical features that are similar to eukaryotes, some similar to bacteria, and some unique to archaea.

bacteria
type: Class
subclass of: procaryotic organism
comment: A diverse group of prokaryotic organisms, distinct from the Archaea.

binary HPLC pump
type: Class
subclass of: HPLC pump
comment: A type of HPLC pump. [James & Satya: 01/31/05]

biochemical sample
type: Class
subclass of: molecular aggregate
subclass of: Restriction
  on property: is described by
  all values from: substance parameter
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: Class
      union of: ion parameter
      union of: molecular parameter
comment: A molecular aggregate that has been prepared in the laboratory from a biological continuant.

biological continuant
type: Class
subclass of: material continuant
comment: This class includes organisms at various stages of development or life-cycle (e.g., spore, seed, blastula, embryo, adult, epimastigote) and parts of these organisms (e.g., organs, tissues and cells). It also includes cultured cells and tissues (e.g., cultured embryonic stem cells). The ProPreO is not meant to explicitly describe all of these objects. Rather, it is meant to provide access to ontological descriptions of these objects by defining broad classes that are more fully modeled in other ontologies.

biological source parameter
type: Class
subclass of: parameter
subclass of: Restriction
  on property: refers to material continuant
  all values from: biological continuant
comment: A parameter that describes some aspect of part of an organism that was used as the source of a biological_sample or biomolecule. A biological source parameter refers to, for example, a species, organ, cell type, life-cycle stage, develomental stage, etc. Within the context of ProPreO, biological source parameters are meant to describe laboratory samples that are analyzed by or used in proteomics or glycoproteomics methods.

capillary HPLC pump
type: Class
subclass of: HPLC pump
comment: A type of HPLC pump. [James & Satya: 01/31/05]

cell
type: Class
subclass of: biological continuant
comment: A cell, such as a neutrophil or a stem cell. These are more fully modeled in the cell ontology http://obo.sourceforge.net/cgi-bin/detail.cgi?cell

chemical abstracts accession number
type: Class
subclass of: substance accession number
subclass of: Restriction
  on property: has units
  cardinality: 0
comment: A parameter that corresponds to the Chemical Abstrracts Accession number of a molecule.

chemical agent
type: Class
subclass of: agent
comment: A chemical agent is a chemical or molecule (such as an enzyme) that implements or initiates a molecular process.

chemical entity
type: Class
subclass of: material continuant
comment: A material continuant that is described chiefly with respect to its chemical composition.

classify data
type: Class
subclass of: process data
comment: The computational processing in which data elements are matched to a spcific group to which they belong. This includes: a) identifying molecules associated with experimental data features such as ion masses (e.g., MASCOT analysis) b) categorize features in data using a set of parameters. For example, distinguish peptides from glycopeptides [Dr. York & Satya: 11/21/05]

component amount
type: Class
subclass of: substance amount
subclass of: Restriction
  on property: has value
  all values from: float
comment: A parameter describing the amount of a substance in a mixture. This is expressed as some sort of fractional amount, such as weight percent, molarity, etc.

computational task
type: Class
subclass of: task
comment: A task involved in the processing of data by a computational application. [Dr. York & Satya: 11/21/05]

concentration units
type: Class
subclass of: physical units
comment: A parameter defining the physical units of concentration

cyclotron analyzer
type: Class
subclass of: MS analyzer
comment: A type of MS analyzer

data
type: Class
comment: Data constitute the basic units of information. Data can include collections of information or individual units of information. Data can be experimental (measured) or theoretical (calculated). [satya 02/15/06]

data collection
type: Class
equivalent class: Restriction
  on property: has data part
  min cardinality: 0
subclass of: data
comment: This defines a broad class that includes any collection of data. It can hold other data collections, it can hold parameters, which are defined as atomic objects in ProPreO (i.e., parameters cannot be further subdivided.) [Will & Satya 02/15/06]

data file URL
type: Class
subclass of: URL parameter
comment: A string parameter that contains the URL of a data file.

data processing application
type: Class
subclass of: agent
comment: Application software used in processing/manipulating data. [James & Satya: 03/27/05]

data processing parameter
type: Class
subclass of: operating parameter
comment: A parameter that is used by a data processing application

database search data collection
type: Class
subclass of: process associated data collection
comment: A data collection that is used or generated by a database search with ms, ms-ms data

database search output data collection
type: Class
equivalent class: Class
  intersection of: database search data collection
  intersection of: experimentally measured data collection
comment: A data collection that is generated by a database search with ms, ms-ms data [James & Satya: 03/27/05]

database search processing parameter collection
type: Class
equivalent class: Class
  intersection of: database search data collection
  intersection of: operating parameter collection
comment: A collection of parameters required to perform a database search with ms, ms-ms data. [James & Satya: 03/27/05]

database search result Mascot HTML dataset
type: Class
subclass of: database search results Mascot data
comment: Following a Mascot db search, the data is saved in a HTML format. The results may further be converted into other representation formats. [James & Satya: 03/29/05]

database search result Mascot dat dataset
type: Class
subclass of: database search results Mascot data
comment: This is a Mascot specific result file, produced from a database search - it is in text format. The sections of the file are delimited by a unique ID string and a Content-Type specification. [James & Satya: 03/29/05]

database search result Mascot peptide summary dataset
type: Class
subclass of: database search result Mascot HTML dataset
comment: The body of the Peptide Summary report contains a tabular listing of the proteins, sorted by descending protein score. [Dr. York & Satya: 07/19/05]

database search result Mascot protein summary dataset
type: Class
subclass of: database search result Mascot HTML dataset
comment: The body of the report contains a tabular summary of the best matching proteins. [Dr. York & Satya: 07/19/05]

database search results Mascot data
type: Class
subclass of: database search output data collection
comment: A data collection that is generated by a Matrix Science Mascot database search with ms, ms-ms data

database search results Sequest data
type: Class
subclass of: database search output data collection
comment: A data collection that is generated by a Sequest database search with ms, ms-ms data [James & Satya: 03/29/05]

database search results Spectrum Mill data
type: Class
subclass of: database search output data collection
comment: A data collection that is generated by a Spectrum Mill database search with ms, ms-ms data [James & Satya: 03/29/05]

denovo sequencing data collection
type: Class
subclass of: process associated data collection
comment: A data collection used or generated by a denovo sequencing process with ms-ms data.

denovo sequencing output data collection
type: Class
equivalent class: Class
  intersection of: denovo sequencing data collection
  intersection of: experimentally measured data collection
comment: A data collection generated by a denovo sequencing process with ms-ms data. [James & Satya: 03/27/05]

denovo sequencing processing parameter collection
type: Class
equivalent class: Class
  intersection of: denovo sequencing data collection
  intersection of: operating parameter collection
comment: A collection of parameters required to perform a denovo sequencing with ms-ms data. [James & Satya: 03/27/05]

electric sector analyzer
type: Class
subclass of: MS analyzer
comment: A type of MS analyzer

electrical potential units
type: Class
subclass of: potential units
comment: A parameter describing the units of electrical potential

elemental composition
type: Class
subclass of: molecular parameter
subclass of: Restriction
  on property: has units
  cardinality: 0
comment: A parameter describing the identities of chemical elements and the number of atoms of each element that constitute a molecule. [Dr. York & Satya: 11/21/05]

enzyme
type: Class
subclass of: chemical agent
subclass of: polypeptide
comment: An enzyme is a protein or protein complex that catalyzes a specific set of chemical reactions.

enzyme HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

eucaryotic organism
type: Class
subclass of: organism
comment: An organism whose cells contain a nucleus and internal membranes. [Dr. York & Satya: 06/28/05]

experimental chemical mass
type: Class
subclass of: experimental mass
comment: A parameter describing the measured chemical mass of a particularmolecule or ion. [Dr. York & Satya: 06/13/05]

experimental ion abundance
type: Class
subclass of: MS experimentally measured parameter
subclass of: ion abundance
comment: A parameter describing the measured abundance of a particular ion.

experimental ion charge
type: Class
subclass of: MS experimentally measured parameter
subclass of: ion charge
comment: A parameter describing the measured charge of a particular ion.

experimental isoelectric point
type: Class
subclass of: isoelectric point
comment: Measured from an experiment. [Dr. York & Satya: 06/28/05]

experimental mass
type: Class
subclass of: mass
comment: A parameter describing the measured mass of a particular molecule or ion. [Dr. York & Satya: 06/28/05]

experimental mass to charge ratio
type: Class
subclass of: MS experimentally measured parameter
subclass of: mass to charge ratio
comment: A parameter describing the measured mass to charge ratio (m/z) of a particular ion.

experimental monoisotopic mass
type: Class
subclass of: experimental mass
comment: A parameter describing the measured monoisotopic mass of a particularmolecule or ion. [Dr. York & Satya: 06/13/05]

experimentally measured data collection
type: Class
subclass of: data collection
comment: This describes collections of experimental (measured) data, either raw or processed. Such data can serve as the input to a data processing task or the output of an experimental measurement or computational task.

experimentally measured parameter
type: Class
subclass of: parameter
comment: An experimentally measured parameter, either raw or processed. (E.G., signal intensity) A collection of such parameters can serve as the input to a data processing task or the output of an experimental measurement or computational task.

flourescence spectrometer
type: Class
subclass of: analytical instrument
comment: A fluorescence spectrometer measures the intensity of light that is re-emitted by a fluorescent molecule.

fluorescence activated cell sorter
type: Class
subclass of: analytical instrument
comment: An instrument that performs a type of flow cytometry (cell counting), sorting cells in a suspension according to their fluorescence properties.

fourier transform mass spectrometer
type: Class
subclass of: tandem mass spectrometer
comment: The type of tandem_mass_spectrometer. [James & Satya: 03/27/05]

fragment peptide C terminus index
type: Class
subclass of: molecular parameter
comment: A parameter describing the index (within the parent protein) of the C- terminus of a fragment peptide. [will & satya 04/25/06]

fragment peptide N terminus index
type: Class
subclass of: molecular parameter
comment: A parameter describing the index (within the parent protein) of the N- terminus of a fragment peptide. [will & satya 04/25/06]

gel electrophoresis data collection
type: Class
subclass of: process associated data collection
comment: A data collection used or generated by gel electrophoresis experiments

gel electrophoresis experimental data collection
type: Class
subclass of: experimentally measured data collection
subclass of: gel electrophoresis data collection
comment: A data collection generated by a gel electrophoresis experiment

gel electrophoresis processing parameter collection
type: Class
equivalent class: Class
  intersection of: gel electrophoresis data collection
  intersection of: operating parameter collection
comment: A collection of parameters required to perform a gel electrophoresis experiment. [James & Satya: 03/27/05]

glycan
type: Class
subclass of: molecule
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: polynucleotide accession number
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: molecular sequence
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: protein accession number
comment: A biomolecule composed of glycosyl residues. A glycan is a type of carbohydrate molecule. [Dr. York & Satya: 06/10/05]

glycan accession number
type: Class
subclass of: substance accession number
comment: A parameter that specifies the unique identifierfor a glycan. [Dr. York & Satya: 06/13/05]

hardware
type: Class
subclass of: agent
comment: An object manufactured to perform a specfic task. Examples are bolts (which hold other objects together), computers (which execute software), and mass spectrometers (which separate and count ions based on their mass to charge ratios).

high performance liquid chromatograph
type: Class
subclass of: analytical instrument
subclass of: Restriction
  on property: has material part
  all values from: HPLC component
comment: An instrument that separates molecules by passing a solution of the molecules through a column containing a solid matrix that differentially interacts with the molecules.

hybrid tandem mass spectrometer
type: Class
subclass of: tandem mass spectrometer
comment: A type of tandem_mass_spectrometer. [James & Satya: 03/27/05]

hybrid task
type: Class
subclass of: task
comment: A task that combines both physical and computational tasks. [Dr. York & Satya: 11/21/05]

identify components
type: Class
subclass of: hybrid task
comment: The complex task of identifhying the components of a mixture. This may involve, for example, HPLC of the mixture (i.e. separate_by_HPLC) followed by computational peak picking and peak matching (i.e., classify_data).

inorganic solvent molecule
type: Class
subclass of: solvent molecule
comment: A solvent molecule that does not contain carbon, e.g., water.

instrument component
type: Class
subclass of: hardware
comment: A part of a scientific instrument. Many instruments are modular, assembled by combining several interacting components.

ion
type: Class
subclass of: chemical entity
subclass of: Restriction
  on property: is described by
  all values from: ion parameter
comment: An electrically charged chemical species, which may be a single atom (e.g., Na+), or many atoms (e.g., NH4+).

ion abundance
type: Class
subclass of: ion parameter
subclass of: Restriction
  on property: has value
  all values from: float
comment: A parameter describing the (measured or theoretical) abundance of a particular ion.

ion charge
type: Class
subclass of: ion parameter
subclass of: Restriction
  on property: has units
  all values from: electrical charge units
subclass of: Restriction
  on property: has value
  all values from: int
comment: A parameter describing the (measured or theoretical) charge of a particular ion.

ion parameter
type: Class
subclass of: substance parameter
comment: A parameter describing the properties of an ion.

ion trap mass spectrometer
type: Class
subclass of: tandem mass spectrometer
comment: A type of tandem_mass_spectrometer. [James & Satya: 03/27/05]

isocratic HPLC pump
type: Class
subclass of: HPLC pump
comment: A type of HPLC pump. [James & Satya: 01/31/05]

isoelectric point
type: Class
subclass of: molecular parameter
comment: Describes the pH at which a zwitter ionic molecule has no charge also called pI. [Dr. York & Satya: 06/28/05]

laser pulse intensity units
type: Class
subclass of: physical units
comment: A parameter that defines the units used to describe the intensity of a laser pulse

lectin affinity HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

length units
type: Class
subclass of: physical units
comment: A parameter defining the physical units of length

life-cycle form
type: Class
subclass of: biological continuant
comment: An organism in the form it adopts at a specific stage in its life-cycle. For example, an epimastigote is a life-cycle form of a Trypanosome. Ontologies that more fully model life-cycle stages are in development, for example, http://obo.sourceforge.net/cgi-bin/detail.cgi?plasmodium_life_cycle

magnetic sector analyzer
type: Class
subclass of: MS analyzer
comment: A type of MS analyzer

manufacturer
type: Class
subclass of: agent
comment: The person or company that manufactures an instrument, reagent or other product.

mass
type: Class
subclass of: ion parameter
subclass of: molecular parameter
subclass of: Restriction
  on property: has value
  cardinality: 1
subclass of: Restriction
  on property: has value
  all values from: float
comment: Describes the molecular mass of a molecule or ion . [Dr. York & Satya: 06/13/05]

mass percent
type: Class
subclass of: component amount
comment: A parameter describing the amount of a particular substance in a mixture. The mass percent of the substance is its percent contribution to the total mass of the mixture. Sometimes mass percent is called weight/weight percent, and abbreviated %w/w.

mass spectrometer
type: Class
subclass of: analytical instrument
subclass of: Restriction
  on property: has material part
  all values from: MS component
subclass of: Restriction
  on property: generates raw data
  all values from: MS raw data native format
comment: A mass spectrometer separates and counts ions based on their mass to charge ratios. [James & Satya: 03/27/05]

mass to charge ratio
type: Class
subclass of: ion parameter
subclass of: Restriction
  on property: has value
  all values from: float
comment: A parameter describing the (measured or theoretical) mass-to-charge ratio (m/z) of a particular ion.

mass units
type: Class
subclass of: physical units
comment: A parameter defining the physical units of mass

mass volume percent
type: Class
subclass of: component amount
comment: A parameter describing the amount of a particular substance in a solution. The mass-volume percent of the substance is usually expressed as the number of grams of the substance divided by the number of milliliters of the solution, all divided by 100. Sometimes the mass-volume percent is abbreviated %w/v.

material continuant
type: Class
comment: A material continuant is a real-world object.

meta data file URL
type: Class
subclass of: URL parameter
comment: A string parameter that contains the URL of a meta-data file.

micromass pkl ms-ms peak list
type: Class
subclass of: ms-ms peak list
comment: A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. QTof users can export peak list data in either DTA or PKL format using the Micromass ProteinLynx package. The PKL format is similar to the DTA file format, but supports multiple MS/MS datasets in a single file. The first line of a PKL dataset contains the observed m/z, intensity, and charge state of the precursor peptide as a triplet of space separated values. Subsequent lines contain space separated pairs of fragment ion m/z and intensity values. Multiple MS/MS datasets are delimited by at least one blank line. (Reference: http://www.matrixscience.com/help/data_file_help.html#QTOF) [James & Satya: 03/27/05]

mixture
type: Class
subclass of: molecular aggregate
subclass of: Restriction
  on property: is described by
  all values from: mixture component descriptor
comment: A molecular aggregate composed of more than one type of molecule. A mixture is_described_by one or more mixture_component_descriptor(s), each of which has two parts: the component_amount and a substance_identifier that specifies the component itself.

mixture component descriptor
type: Class
subclass of: substance associated data collection
subclass of: Restriction
  on property: has data part
  cardinality: 2
subclass of: Restriction
  on property: has data part
  some values from: component amount
subclass of: Restriction
  on property: has data part
  some values from: substance identifier
comment: A pair of parameters that describes the amount of a particular component of a mixture. For example "0.5 M NaCl" describes the amount of sodium chloride in a solution - there are two parts to this description - 0.5 M specifies the amount (half molar) - NaCl identifies the component that is present at that concentration.

molarity
type: Class
subclass of: component amount
comment: A parameter describing the amount of a substance in a solution. The molarity is the number of moles of the substance that is dissolved in one Liter of the solution.

mole fraction
type: Class
subclass of: component amount
comment: A parameter describing the amount of a substance in a solution. The mole fraction is the number of moles of a particular solute divided by the total number of moles of in the solution.

molecular aggregate
type: Class
subclass of: chemical entity
comment: An aggregate of molecules, which may or may not be homogeneous. E.G.: a liter of water (homogeneous) a pound of wheat flour (heterogeneous) a milligram of extracted protein (heterogeneous) [will & satya 03/02/06]

molecular description
type: Class
subclass of: molecular parameter
subclass of: Restriction
  on property: has value
  all values from: string
subclass of: Restriction
  on property: has value
  cardinality: 1
comment: Describes the molecule, its properties, origin etc. [Dr. York & Satya: 06/13/05]

molecular parameter
type: Class
subclass of: substance parameter
comment: A parameter describing the identity or a physical property of a molecule. [James & Satya: 04/01/05]

molecular sequence
type: Class
subclass of: molecular parameter
comment: A parameter describing the sequence of residues in a biopolymer. [Dr. York & Satya: 06/28/05]

molecule
type: Class
equivalent class: Restriction
  on property: material part of
  all values from: molecular aggregate
subclass of: chemical entity
subclass of: Restriction
  on property: is described by
  all values from: Class
    union of: molecular parameter
    union of: substance accession number
comment: An individual molecule, categorized according to a few broadly defined classes. [Dr. York & Satya: 06/10/05]

ms-ms peak list
type: Class
subclass of: ms processed data
comment: A data collection consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment. Often, the abundance of the ion is included in the peak list. The ms/ms peak list can be used to perform database searching or denovo sequencing. [James & Satya: 03/27/05]

ms output data collection
type: Class
equivalent class: Class
  intersection of: MS data collection
  intersection of: experimentally measured data collection
comment: A data collection generated by a mass spectrometer or mass spectral data processing application

ms processed data
type: Class
subclass of: ms output data collection
comment: A collection of mass spectral data that has been computationally processed - E.G. a peak list [James & Satya: 03/22/05]

ms raw data
type: Class
subclass of: ms output data collection
comment: A collection of mass spectral data that has NOT been computationally processed other than to change its digital format

mzXML ms raw data
type: Class
equivalent class: Restriction
  on property: has SemURI concept ID
  has value: mzXML ms raw data tsuka
subclass of: MS raw data converted format
comment: A collection of mass spectral data that has NOT been computationally processed, except that it has been converted to mzXML format

mz abundance pair
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has data part
    some values from: ion abundance
  intersection of: Restriction
    on property: has data part
    some values from: mass to charge ratio
subclass of: ms output data collection
comment: A typical mass spectral data pair consisting of a mass-to-charge (m/z) ratio and the abundance associated with that ratio

nanoflow HPLC pump
type: Class
subclass of: HPLC pump
comment: A type of HPLC pump. [James & Satya: 01/31/05]

normal-phase HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

peptide
type: Class
subclass of: molecule
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: Class
      union of: DNA nucleotide sequence
      union of: RNA nucleotide sequence
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: polynucleotide accession number
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: glycan accession number
comment: A biomolecule composed of amino acids connected by amide bonds. A peptide can be generated by fragmentation of a protein by a protease (e.g. trypsin). In ProPreO, peptides are distinguished from proteins mainly by size (oligopeptides are smaller, and thereby distinct from polypeptides). [Dr. York & Satya: 06/10/05]

operating parameter
type: Class
subclass of: parameter
comment: A parameter that is used to control the execution of a task, such as a physical parameter required for recording a mass spectrum or a computational parameter for processing a data set.

operating parameter collection
type: Class
subclass of: data collection
comment: A data collection that is used to control the execution of a task, such as the physical parameters required for recording a mass spectrum or the computational parameters for processing a data set.

organ
type: Class
subclass of: biological continuant
comment: A specific biological organ, such as heart or leaf. Several OBO ontologies model anatomical features of organsims, including their organs, tissues, cells, etc. and additional semantic information can be specified by cross reference to these other ontologies.

organic solvent molecule
type: Class
subclass of: small organic molecule
subclass of: solvent molecule
comment: A solvent molecule that contains carbon, e.g., methanol.

organism
type: Class
subclass of: biological continuant
comment: A biological species, such as Homo sapiens or Arabidopsis thaliana. The taxonomic classification of a biological species are modeled in other ontologies. http://obo.sourceforge.net/cgi-bin/detail.cgi?ncbi_taxonomy http://obo.sourceforge.net/cgi-bin/detail.cgi?newt Instances of specific organisms may be specified iwithin ProPreO, but their complete systematic taxonomy should be found in these other ontologies. [Dr. York & Satya: 06/28/05]

parameter
type: Class
equivalent class: Restriction
  on property: has data part
  cardinality: 0
subclass of: data
comment: In ProPreO, a parameter is a single, indivisible datum (i.e., parameters cannot be further subdivided.) Collections of parameters are called data_collections in ProPreO. Note that in ProPreO, a parameter (such as a substance_identifier or biological_source_parameter) may refer to a specific object (such as an organism or a molecule), but the parameter and the object that it refers to are separate. In these cases, the parameter is piece of information that may be found, for example, in a data file and the object it points to is a real world object of class of objects. These two entities are related by the property "refers_to_material_continuant". [satya 02/15/06]

parent ion
type: Class
subclass of: ion
comment: An ion, generated in a mass spectrometer, that is subsequently dissociated into fragment ions in an MS/MS experiment

person
type: Class
subclass of: agent
comment: A human who initiates or implementes a task.

physical task
type: Class
subclass of: task
comment: A task that is performed by a human or physical instrument working on a physical sample.

physical units
type: Class
subclass of: parameter
subclass of: Restriction
  on property: has units
  cardinality: 0
subclass of: Restriction
  on property: has value
  all values from: string
comment: A parameter defining the physical units of a parameter (measurement of setting) [will &satya 04/14/06]

polynucleotide accession number
type: Class
subclass of: substance accession number
comment: A parameter that specifies the unique identifier in a database that refers to a particular gene or other nucleotide sequence. [Dr. York & Satya: 06/24/05]

potential units
type: Class
subclass of: physical units
comment: A parameter defining the physical units of potential, such as electrical potential, gravitational potential, etc. Potentials generally have units "energy per amount", for example volts are Joules per Coulomb

power units
type: Class
subclass of: physical units
comment: A parameter defining the physical units of power

procaryotic organism
type: Class
subclass of: organism
comment: An organism whose cells do not have a nucleus or internal membranes. [Dr. York & Satya: 06/28/05]

process associated data collection
type: Class
subclass of: data collection
comment: A data collection that is classified according to the process that uses/creates/generates it.

process associated parameter
type: Class
subclass of: parameter
comment: A parameter that is classified according to the process that uses/creates/generates it. [will & satya 02/17/06]

process data
type: Class
subclass of: computational task
comment: The task of processing data using computational applications. [Dr. York & Satya: 11/21/05]

process time parameter
type: Class
subclass of: process associated parameter
comment: A parameter that describes the time within a process that an event occured. E.G., a "retention time" in HPLC or a "scan acquisition time" in mass spectrometry.

processed gel electrophoresis data
type: Class
subclass of: gel electrophoresis experimental data collection
comment: A data collection generated by a processing raw gel electrophoresis data. This data will include, for example 1. Spot location 2. Spot Intensity 3. Spot Identity [Dr. York & Satya: 06/28/05]
version info: TODO: Find out the various formats, softwares used...

polypeptide
type: Class
subclass of: molecule
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: glycan accession number
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: Class
      union of: DNA nucleotide sequence
      union of: RNA nucleotide sequence
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: polynucleotide accession number
comment: A biomolecule composed of amino acids connected by amide bonds. In ProPreO, a protein is distinguished from an oligopeptide mainly by its size (proteins are larger, and so are polypeptides rather than oligopeptides) . [Dr. York & Satya: 06/10/05]

protein accession number
type: Class
subclass of: substance accession number
comment: A parameter that specifies the unique identifier for a particular protein in a database. [Dr. York & Satya: 06/13/05]

proteolytic enzyme
type: Class
subclass of: enzyme
comment: A protein that catalyzes the cleavage of peptide bonds in proteins to generate peptides. [Dr. York & Satya: 06/28/05]

pure substance
type: Class
subclass of: molecular aggregate
subclass of: Restriction
  on property: has material part
  all values from: molecule
comment: A molecular aggregate composed of many copies of same molecule. [will & satya 03/02/06]

quadrupole analyzer
type: Class
subclass of: MS analyzer
comment: A type of MS analyzer

quadrupole time of flight mass spectrometer
type: Class
subclass of: tandem mass spectrometer
comment: A type of tandem_mass_spectrometer. [James & Satya: 03/27/05]

quantify components
type: Class
subclass of: hybrid task
comment: The complex task of quantifying the components of a mixture. This may involve, for example, HPLC of the mixture (i.e. separate_by_HPLC) followed by computational peak picking and signal integration (i.e., quantify_data).

quantify data
type: Class
subclass of: process data
comment: The computational processing in which a quantity (e.g. amount) is associated with various data elements.

quaternary HPLC pump
type: Class
subclass of: HPLC pump
comment: A type of HPLC pump. [James & Satya: 01/31/05]

raw2mzXML transformation
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: has input experimental data collection
    all values from: ms raw data
  intersection of: Restriction
    on property: has output data
    all values from: mzXML ms raw data
  intersection of: Restriction
    on property: has SemURI concept ID
    has value: raw2mzXML transformation tsuka
subclass of: tranform encoding format
comment: This task converts a raw mass spec data file into the mzXML format.

raw gel image electrophoresis data
type: Class
subclass of: gel electrophoresis experimental data collection
comment: A data collection generated by a gel electrophoresis experiment - this corresponds to an image of the gel, stored in a file format. [James & Satya: 03/29/05]

record ms data
type: Class
subclass of: record raw data
subclass of: Restriction
  on property: generates raw data
  all values from: MS raw data native format
comment: Tthe physical task of running a mass spectrometer on a specific sample and recording the resulting spectra. [Dr. York & Satya: 11/21/05]

record raw data
type: Class
subclass of: physical task
comment: The task of recording raw data using an analytical instrument. [Dr. York & Satya: 11/21/05]

reversed-phase HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

salt
type: Class
subclass of: molecule
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: substance accession number
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: isoelectric point
subclass of: Restriction
  on property: has material part
  all values from: ion
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: molecular sequence
comment: A chemical compound composed of at least one cation (positive ion) and at least one anion (negative ion).

search and replace
type: Class
subclass of: transform data
comment: A computational task involving the identification of specific data elements and their replacement by another data element.

separate by HPLC
type: Class
subclass of: separate by chromatography
comment: The process of separating components by high-performance liquid chromatography.

separate by chromatography
type: Class
subclass of: separate components
comment: The process of separating components by chromatography. [Dr. York & Satya: 11/21/05]

separate by dialysis
type: Class
subclass of: separate components
comment: Separate components of a mixture by dialysis. The dialysis membrane allows some components to pass through while retaining other components.

separate by filtration
type: Class
subclass of: separate components
comment: Separate components of a mixture by filtration. The filter allows some components to pass through while retaining other components.

separate by lectin affinity chromatography
type: Class
subclass of: separate by chromatography
comment: The process of separating components by lectin-affinity chromatography.

separate by size exclusion chromatography
type: Class
subclass of: separate by chromatography
comment: The process of separating components by size-exclusion chromatography.

separate components
type: Class
subclass of: physical task
comment: The task of physcially spearating the components of a mixture.

simulate analytical data
type: Class
subclass of: simulate data
comment: The simulation of the output of an analytical instrument like NMR, ms or chromatography. It is computed based on a set of input parametres. [Dr. York & Satya: 11/21/05]

simulate data
type: Class
subclass of: computational task
comment: The simulation of data from input data. For example, simulation of a theoretical spectrum from a chemical composition. [Dr. York & Satya: 11/21/05]

simulate molecular data
type: Class
subclass of: simulate data
comment: The computational simulation of the structure, physical properties or behavior of a molecule, such as conformational trajectory or reaction kinetics. [Dr. York & Satya: 11/21/05]

simulate ms data
type: Class
subclass of: simulate analytical data
subclass of: Restriction
  on property: has input data
  all values from: Class
    union of: elemental composition
    union of: mass
    union of: molecular sequence
comment: Tthe simulation of mass spectra. For example, calculation of an isotopic distribution based on elemental composition and subsequent simulation of a mass spectum based on the calculated isotopic distribution. [Dr. York & Satya: 11/21/05]

size exclusion HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

small molecule
type: Class
subclass of: molecule
comment: A molecule that is very generally classified by its small size. This class is intended to allow the classification of molecules that are encountered in proteomics analysis (such as a solvent molecule or a MALDI matrix component), but are not classified as a major type of biomolecule.

small organic molecule
type: Class
subclass of: small molecule
comment: A small molecule that contains the element carbon.

solid mixture
type: Class
subclass of: mixture
comment: A mixture that is in the solid state, for example, dry baking powder, composed of solid NaHCO3 and tartaric acid. [Satya & Will 03/02/06]

solution
type: Class
subclass of: mixture
comment: A mixture in the form of a homogeneous liquid contaning a solvent and at least one solute. A "solution" is_described_by one or more mixture_component_descriptor(s), each of which has two parts: the component_amount and a substance_identifier that specifies the identity of the component. This is a flexible way of describing solutions. For example, a solution can be described as a mixture of two other solutions (e.g., buffer A and buffer B), in which case the mixture_component_descriptor(s) each specify the identity and amount of each of these buffers. Alternatively, a solution can be described according to the concentrations of its solutes (dissolved molecules), each of which is specified by a mixture_component_descriptor. In this case, complete description of the solution requires that the solvent be specified using the property has_solvent, which points to an instance of the class "solvent". [Satya & Will 03/02/06]

solvent
type: Class
subclass of: pure substance
comment: The solvent of a solution, consisting of many copies of the solvent molecule.

solvent molecule
type: Class
subclass of: small molecule
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: substance accession number
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: isoelectric point
subclass of: Restriction
  on property: is described by
  all values from: Class
    complement of: molecular sequence
comment: A molecule that exists as a liquid in the laboratory, and that can dissolve other molecules. E.G. water, methanol.

sort data
type: Class
subclass of: transform data
comment: A computational task involving the reordering of data elements according to a specific set of criteria.

source cell
type: Class
subclass of: biological source parameter
subclass of: Restriction
  on property: refers to material continuant
  all values from: cell
comment: A parameter that specifies the cell type from which the biological sample is taken.

source organ
type: Class
subclass of: biological source parameter
subclass of: Restriction
  on property: refers to material continuant
  all values from: organ
comment: A parameter that specifies the organ from which the biological sample is taken.

source organism
type: Class
subclass of: biological source parameter
subclass of: Restriction
  on property: refers to material continuant
  all values from: organism
comment: A parameter that specifies the organism from which the biological sample is taken.

strong anion exchange HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

strong cation exchange HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

substance accession number
type: Class
subclass of: substance identifier
subclass of: Restriction
  on property: has value
  all values from: string
subclass of: Restriction
  on property: refers to material continuant
  all values from: chemical entity
comment: A parameter that specifies the unique identifier in a database that refers to a particular molecule or gene. The name of each accession number instance should contain the accession number itself. [Dr. York & Satya: 06/13/05]

substance amount
type: Class
subclass of: substance parameter
comment: A parameter describing the amount of a substance.

substance associated data collection
type: Class
subclass of: data collection
comment: a data collection that describes the physical substances such as buffers, gases etc.

substance identifier
type: Class
subclass of: substance parameter
comment: A parameter that identifies a molecule or molecular aggergate.

substance parameter
type: Class
subclass of: parameter
comment: A parameter that describes a physical substance such as a buffer, gas etc.

tandem mass spectrometer
type: Class
subclass of: mass spectrometer
comment: A mass spectrometer that can perform both MS and MS/MS analysis. [James & Satya: 03/27/05]

tandem time of flight mass spectrometer
type: Class
subclass of: tandem mass spectrometer
comment: A type of tandem_mass_spectrometer. [James & Satya: 03/27/05]

task
type: Class
comment: A process that is initiated or implemented by an agent.

theoretical chemical mass
type: Class
subclass of: theoretical mass
comment: A parameter describing the theoretical (calculated) chemical mass of a particular molecule or ion. [Dr. York & Satya: 06/28/05]

theoretical ion abundance
type: Class
subclass of: ion abundance
comment: A parameter describing the theoretical abundance of a particular ion.

theoretical ion charge
type: Class
subclass of: ion charge
comment: A parameter describing the theoretical charge of a particular ion.

theoretical isoelectric point
type: Class
subclass of: isoelectric point
comment: Calculated from the molecular structure. [Dr. York & Satya: 06/28/05]

theoretical mass
type: Class
subclass of: mass
comment: A parameter describing the theoretical (calculated) mass of a particular molecule or ion. [Dr. York & Satya: 06/28/05]

theoretical mass to charge ratio
type: Class
subclass of: mass to charge ratio
comment: A parameter describing the theoretical mass-to-charge ratio (m/z) of a particular ion. [will & satya 03/02/06]

theoretical monoisotopic mass
type: Class
subclass of: theoretical mass
comment: A parameter describing the theoretical (calculated) monoisotopic mass of a particular molecule or ion. [Dr. York & Satya: 06/13/05]

time units
type: Class
subclass of: physical units
comment: A parameter defining the physical units of time

tranform encoding format
type: Class
subclass of: transform data format
comment: The task of transforming one encoding type into another. For example, binary to ascii. [Dr. York & Satya: 11/21/05]

tranform representation format
type: Class
subclass of: transform data format
comment: The transformation of the representational format of data. For example, FASTA format to GCG format. [Dr. York & Satya: 11/21/05]

transform data
type: Class
subclass of: process data
comment: One of a diverse collection of computational processing tasks including: a) Changing the format b) Search and Replace (e.g., modification of DataBase) c) Sort [Dr. York & Satya: 11/21/05]

transform data format
type: Class
subclass of: transform data
comment: The task of transforming the format of data, usually creating a new data file with either new file format or data encoding. [Dr. York & Satya: 11/21/05]

transform glycan structure format
type: Class
subclass of: tranform representation format
comment: This describes the task of transforming a given glycan structure from one representation format into another. For example from LINUCS to GLYDE. [Dr. York & Satya: 11/21/05]

transform peptide sequence format
type: Class
subclass of: tranform representation format
comment: This describes the tranformation of a given peptide sequence from one format into another. [Dr. York & Satya: 11/21/05]

triple quadrupole mass spectrometer
type: Class
subclass of: tandem mass spectrometer
comment: A type of tandem_mass_spectrometer. [James & Satya: 03/27/05]

trypsin
type: Class
subclass of: proteolytic enzyme
comment: Class of related proteolytic enzymes that cleave after basic amino acids K & R except when followed by P. [Dr. York & Satya: 06/28/05]

tryptic peptide
type: Class
subclass of: peptide
subclass of: Restriction
  on property: generated by proteolytic enzyme
  all values from: trypsin
comment: A peptide that is generated by treatment of a protein with the proteolytic enzyme trypsin . [Dr. York & Satya: 06/28/05]

volume percent
type: Class
subclass of: component amount
comment: A parameter describing the amount of a particular substance in a mixture. The volume percent of the substance is its percent contribution to the total volume of the mixture. Sometimes volume percent is called volume/volume percent, and abbreviated %v/v.

volume units
type: Class
subclass of: physical units
comment: A parameter defining the physical units of time

weak anion exchange HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

weak cation exchange HPLC column
type: Class
subclass of: HPLC column
comment: A type of HPLC column

xml ms-ms peak list
type: Class
subclass of: ms-ms peak list
comment: A data collection (in XML format) consisting of a list of precursor ion masses and associated fragment ion masses from an ms/ms experiment.

CAS 28166-41-8
type: NamedIndividual
type: chemical abstracts accession number
has value: 28166-41-8
comment: The CAS number of alpha-cyano-4-hydroxycinnamic acid
refers to material continuant: alpha-cyano-4-hydroxycinnamic acid

CAS 490-79-9
type: NamedIndividual
type: chemical abstracts accession number
has value: 490-79-9
comment: The CAS number of 2,5-dihydroxybenzoic acid
refers to material continuant: 2-5-dihydroxybenzoic acid

CAS 7732-18-5
type: NamedIndividual
type: chemical abstracts accession number
has value: 7732-18-5
comment: The CAS number of water
refers to material continuant: water

CHEBI_15377
type: NamedIndividual
type: CHEBI ID
has value: CHEBI:15377
comment: The ChEBI ID for water
refers to material continuant: water

C
type: NamedIndividual
type: electrical charge units
comment: The units of electrical charge defined as coulombs, which can also be expresses as Amperes seconds. One coulomb is equivalent to the charge of 6.24151E18 electrons.
has value: coulombs

DHB MALDI matrix
type: NamedIndividual
type: MALDI matrix
comment: Defines a matrix composed of 2,5-dihydroxybenzoic acid, used for MALDI MS
has material part: 2-5-dihydroxybenzoic acid

DHB
type: NamedIndividual
type: MS source MALDI matrix
comment: A MALDI matrix composed of dihydroxybenzoic acid
has value: DHB
refers to material continuant: DHB MALDI matrix

Homo sapiens
type: NamedIndividual
type: eucaryotic organism
label: Man
comment: Man [Dr. York & Satya: 06/28/05]

N-glycosylation consensus presence false
type: NamedIndividual
type: N-glycosylation consensus presence
has value: false

N-glycosylation consensus presence true
type: NamedIndividual
type: N-glycosylation consensus presence
has value: true

2-5-dihydroxybenzoic acid
type: NamedIndividual
type: small organic molecule
comment: An aromatic molecule (2-5-dihydroxybenzoic_acid) used as a MALDI matrix
is described by: CAS 490-79-9

alpha-cyano-4-hydroxycinnamic acid
type: NamedIndividual
type: small organic molecule
comment: An aromatic molecule (alpha-cyano-4-hydroxycinnamic acid) used as a MALDI matrix
is described by: CAS 28166-41-8

alpha-cyano-4-hydroxycinnamic acid MALDI matrix
type: NamedIndividual
type: MALDI matrix
comment: Defines a matrix composed of alpha-Cyano-4-hydxoxycinnamic_acid, used for MALDI MS
has material part: alpha-cyano-4-hydroxycinnamic acid

alpha-cyano-4-hydroxycinnamic acid
type: NamedIndividual
type: MS source MALDI matrix
comment: A MALDI matrix composed of alpha-cyano-4-hydroxycinnamic acid
has value: alpha-cyano-4-hydroxycinnamic acid
refers to material continuant: alpha-cyano-4-hydroxycinnamic acid MALDI matrix

amu
type: NamedIndividual
type: mass units
comment: 1 amu ≈ 1.66053886 × 10E-27 kg
has value: amu

e
type: NamedIndividual
type: electrical charge units
label: q
comment: The elementary electrical charge is the charge of a single electron
has value: e

g
type: NamedIndividual
type: mass units
has value: grams
comment: the physical units of mass in grams

hours
type: NamedIndividual
type: time units
has value: hours
comment: the physical units of time in hours

Homo sapiens
type: NamedIndividual
type: source organism
label: Man
has value: Homo sapiens
refers to material continuant: Homo sapiens

kg
type: NamedIndividual
type: mass units
has value: kilograms
comment: the physical units of mass in kilograms

linear TOF MS analyzer
type: NamedIndividual
type: MS analyzer TOF type
has value: linear TOF analyzer

liters
type: NamedIndividual
type: volume units
has value: liters
comment: the physical units of volume in liters

micrograms
type: NamedIndividual
type: mass units
has value: micrograms
comment: the physical units of mass in micrograms

microliters
type: NamedIndividual
type: volume units
has value: microliters
comment: the physical units of volume in microliters

microliters per minute
type: NamedIndividual
type: flowrate units
has value: microliters per minute
comment: the physical units of flowrate in microliters per minute

micrometers
type: NamedIndividual
type: length units
has value: micrometers
comment: the physical units of length in micrometers, or 0.000001 meters

mg
type: NamedIndividual
type: mass units
has value: milligrams
comment: the physical units of mass in milligrams

milliliters
type: NamedIndividual
type: volume units
has value: milliliters
comment: the physical units of volume in milliliters

milliliters per minute
type: NamedIndividual
type: flowrate units
has value: milliliters per minute
comment: the physical units of flowrate in milliliters per minute

millimeters
type: NamedIndividual
type: length units
has value: millimeters
comment: the physical units of length in millimeters, or 0.001 meters

milliseconds
type: NamedIndividual
type: time units
has value: milliseconds
comment: the physical units of time in milliseconds

millivolts
type: NamedIndividual
type: electrical potential units
comment: The units of electrical potential defined as millivolts, or thousandths of a volt.
has value: millivolts

minutes
type: NamedIndividual
type: time units
has value: minutes
comment: the physical units of time in minutes

molarity units
type: NamedIndividual
type: concentration units
has value: moles per liter
comment: the physical units of concentration in moles per liter

ng
type: NamedIndividual
type: mass units
has value: nanograms
comment: the physical units of mass in nanograms

nanoliters per minute
type: NamedIndividual
type: flowrate units
has value: nanoliters per minute
comment: the physical units of flowrate in nanoliters per minute

nanometers
type: NamedIndividual
type: length units
has value: nanometers
comment: the physical units of length in nanometers, or 0.000000001 meters

negative MS mode
type: NamedIndividual
type: MS analyzer mode
has value: negative mode

reflectron TOF MS analyzer
type: NamedIndividual
type: MS analyzer TOF type
has value: reflectron TOF analyzer

seconds
type: NamedIndividual
type: time units
has value: seconds
comment: the physical units of time in seconds

volts
type: NamedIndividual
type: electrical potential units
comment: The units of electrical potential defined as volts, which can also be expressed as Joules per coulomb
has value: volts

water
type: NamedIndividual
type: inorganic solvent molecule
comment: A molecule of water, the most common solvent for HPLC
is described by: CAS 7732-18-5
is described by: CHEBI_15377

water solvent
type: NamedIndividual
type: solvent
comment: A collection of water molecules, acting as a solvent
has material part: water

deleted
comment: The ChEBI ID of alpha-cyano-4-hydroxycinnamic acid