Relation
Recommended best practice is to reference the resource by means
of a string or number conforming to a formal identification
system.
A reference to a related resource.
Description
An account of the content of the resource.
Description may include but is not limited to: an abstract,
table of contents, reference to a graphical representation
of content or a free-text account of the content.
Contributor
An entity responsible for making contributions to the
content of the resource.
Examples of a Contributor include a person, an
organisation, or a service. Typically, the name of a
Contributor should be used to indicate the entity.
Language
A language of the intellectual content of the resource.
Recommended best practice is to use RFC 3066 [RFC3066],
which, in conjunction with ISO 639 [ISO639], defines two-
and three-letter primary language tags with optional
subtags. Examples include "en" or "eng" for English,
"akk" for Akkadian, and "en-GB" for English used in the
United Kingdom.
Resource Type
The nature or genre of the content of the resource.
Type includes terms describing general categories, functions,
genres, or aggregation levels for content. Recommended best
practice is to select a value from a controlled vocabulary
(for example, the DCMI Type Vocabulary [DCMITYPE]). To
describe the physical or digital manifestation of the
resource, use the Format element.
Source
A reference to a resource from which the present resource
is derived.
The present resource may be derived from the Source resource
in whole or in part. Recommended best practice is to reference
the resource by means of a string or number conforming to a
formal identification system.
Creator
An entity primarily responsible for making the content
of the resource.
Examples of a Creator include a person, an organisation,
or a service. Typically, the name of a Creator should
be used to indicate the entity.
Publisher
An entity responsible for making the resource available
Examples of a Publisher include a person, an organisation,
or a service.
Typically, the name of a Publisher should be used to
indicate the entity.
Subject and Keywords
The topic of the content of the resource.
Typically, a Subject will be expressed as keywords,
key phrases or classification codes that describe a topic
of the resource. Recommended best practice is to select
a value from a controlled vocabulary or formal
classification scheme.
Coverage
Coverage will typically include spatial location (a place name
or geographic coordinates), temporal period (a period label,
date, or date range) or jurisdiction (such as a named
administrative entity).
Recommended best practice is to select a value from a
controlled vocabulary (for example, the Thesaurus of Geographic
Names [TGN]) and that, where appropriate, named places or time
periods be used in preference to numeric identifiers such as
sets of coordinates or date ranges.
The extent or scope of the content of the resource.
Resource Identifier
An unambiguous reference to the resource within a given context.
Recommended best practice is to identify the resource by means
of a string or number conforming to a formal identification
system.
Example formal identification systems include the Uniform
Resource Identifier (URI) (including the Uniform Resource
Locator (URL)), the Digital Object Identifier (DOI) and the
International Standard Book Number (ISBN).
Date
A date associated with an event in the life cycle of the
resource.
Typically, Date will be associated with the creation or
availability of the resource. Recommended best practice
for encoding the date value is defined in a profile of
ISO 8601 [W3CDTF] and follows the YYYY-MM-DD format.
Format
The physical or digital manifestation of the resource.
Typically, Format may include the media-type or dimensions of
the resource. Format may be used to determine the software,
hardware or other equipment needed to display or operate the
resource. Examples of dimensions include size and duration.
Recommended best practice is to select a value from a
controlled vocabulary (for example, the list of Internet Media
Types [MIME] defining computer media formats).
Title
Typically, a Title will be a name by which the resource is
formally known.
A name given to the resource.
Rights Management
Typically, a Rights element will contain a rights
management statement for the resource, or reference
a service providing such information. Rights information
often encompasses Intellectual Property Rights (IPR),
Copyright, and various Property Rights.
If the Rights element is absent, no assumptions can be made
about the status of these and other rights with respect to
the resource.
Information about rights held in and over the resource.
part_of
mao.obo
is_annotation
mao.obo
is_attribute
mao.obo
is_name
mao.obo
Generic property that links a concept to another concept it is a constituent of. The property is a synonym of part_of.
The property links a Node to one of the edges that are incident on such node.
The property links a Node to the Edge it belongs to in the child position.
The property links a Node to one of the Edges where the node appears in the parent position (i.e., closer to the root).
This property relates a character-state datum to its TU.
Generic 'has' property.
This property relates an amino acid character (a column in a protein sequence alignment) to a state datum for the character (an individual cell in the alignment column).
This property associates a amino acid character-state instance with a state value from the domain of amino acid states.
The property links a node to any of the other nodes that are its ancestors in a rooted tree.
This property relates a transformation to the components that compose it.
This property associates a character data matrix with a character (a column) represented in the matrix.
The property links a node to a node that is an immediate descendant in the tree.
The property associates to a Directed Edge the Node that is in the child position in the edge, i.e., the node touched by the edge and closer to the leaves of the tree.
This property relates a compound character (a character with some states that are subdividable) to a state datum for the character.
This property associates a compound character-state instance with its compound state value.
This property relates a continuous character to a state datum for the character.
This property associates a character-state instance with a state value on a continuous numeric scale.
This property links a coordinate to the coordinate system it references.
This property relates a character to a state datum for the character.
A property that links a node to any of its descendants in a rooted tree.
Associates a TU to some external taxonomy reference.
The property that relates a coordinate list to the first item in the list.
This property relates a transformation to a 'left' node (the node that has the 'left' state).
This property relates a transformation to a 'left' state (the state associated with the 'left' node).
Property that associates to each Edge the Nodes it connects.
This property relates a nucleotide character (a column in a nucleotide alignment) to a state datum for the character (an individual cell in the alignment column).
This property associates a nucleotide character-state instance with a state value from the domain of nucleotide states.
The property that links a node to its unique parent in a rooted tree.
Associates to a Directed Edge the Node that is in the parent position in the edge (i.e., the node touched by the edge and closer to the root of the tree)
The property that relates a coordinate list to the item in the list beyond the first item.
This property relates a transformation to a 'right' node (the node that has the 'right' state).
This property relates a transformation to a 'right' state (the state associated with the 'right' node).
The property links a rooted tree to the specific node that represents the unique root of the tree.
This property associates a character-state instance with its state value, e.g., a state value expressed in terms of an imported domain ontology.
This property associates a character data matrix with a TU (a row) represented in the matrix.
This property relates a type of evolutionary change (an Edge_Transformation) to the character that undergoes the change. The change is a transformation_of the affected character.
This propery relates different instances of the same character, including the case when the states of the character differ (e.g., large_beak of beak_size_character of TU A is homologous_to small_beak of beak_size_character of TU B).
This property relates a TU to a node that represents it in a network.
This property relates a TU or taxonomic unit (typically associated with character data) to a phylogenetic history (Tree).
This property links two networks where the latter is a substructure of the former
This should carry the full body of the input message (e.g. the SOAP payload). It does not contain individual parameter-values, but rather carrys the entire invocation message.
This is a link to an executable version of the service. This will normally be represented by a workflow containing just the service
describes preconfigured values for input parameters
describes whether an input parameter is required or optional to execute the service
value should be the full XML body of the output message (i.e. the SOAP Payload) which can be used canonically (using xmldiff) to validate the output from the service given the input of the associated unit test.
value is a regular expression that should match the output from the service given the associated input from the unit test
value is an XPath statement that can be used to validate the output of a service given the associated input in the unit test
multiple_sequence_alignment
mao.obo
msa
A representation of a set of sequences, in which structurally or functionally equivalent residues are aligned together. The rows of the multiple alignment represent the different sequences, while the columns represent equivalent residues. Insertions/deletions in the sequences are represented by one or more gap characters.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
structural_location
mao.obo
The location of the residue in the 3D structure.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
residue_function
mao.obo
Function of the residue, such as catalysis, binding or post-translational modification. A residue may exhibit zero, one or more activities.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
column_conservation_level
mao.obo
The level of conservation associated with a given column. This may be specified by either a qualitative score or a quantitative score.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
conserved_residue_list
mao.obo
A user specified list of conserved residues.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
biological_process
mao.obo
GeneOntology interface
GO:0008150
http://purl.org/obo/owl/GO#GO_0008150
cellular_component
mao.obo
GeneOntology interface
GO:0005575
http://purl.org/obo/owl/GO#GO_0005575
molecular_function
mao.obo
GeneOntology interface
GO:0003674
http://purl.org/obo/owl/GO#GO_0003674
conserved_small_residue
mao.obo
A conserved small residue e.g. PAGST
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
conserved_negatively_charged_residue
mao.obo
A conserved negatively charged residue e.g. DE
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
conserved_hydrophobic_residue
mao.obo
A conserved hydrophobic residue e.g. ACFGLIMVWY
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
conserved_hydrophilic_residue
mao.obo
A conserved hydrophilic residue e.g. DEHKNQRST
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
quantitative_conservation_level
mao.obo
A quantitative score for the conservation associated with a given column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
qualitative_conservation_level
mao.obo
A qualitative description of the level of conservation associated with a given column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
low_conservation
mao.obo
A low level of conservation associated with a given column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
medium_conservation
mao.obo
A medium level of conservation associated with a given column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
high_conservation
mao.obo
A high level of conservation associated with a given column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
catalytic_site
mao.obo
A residue that is directly involved in some aspect of the reaction catalysed by the enzyme.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
domain
mao.obo
A discrete portion of a protein assumed to fold independently of the rest of the protein and possessing its own function. [NCBI Bioinformatics] A region of a proteins amino acid sequence that has evolutionary, structural, or functional significance. The amino acid sequence of a domain determines a proteins 3D structure. [CHI Structural proteomics report]
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
post translational modification
mao.obo
A sequence modification that occurs after synthesis of the protein on the ribosome. e.g. cleavage (thus eliminating signal sequences, transit or pro- peptides and initiator methionines) or addition of simple chemical groups or more complex molecules, such as sugars and lipids. (Human Proteomics Initiative) http://www.expasy.ch/sprot/hpi/ n
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
ptm
psi_mutation
mao.obo
PSI interface
MI:0118
http://purl.org/obo/owl/MI#MI_0118
msa_construction_method
mao.obo
The method used to construct the multiple sequence alignment.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
surface_accessibility
mao.obo
Surface area accessible to solvent
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
N_terminal
mao.obo
A residue in a protein chain that has a free amino group.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
amino_terminus
C_terminal
mao.obo
A residue in a protein chain that has a free carboxyl group.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
carboxyl_terminus
in_domain
mao.obo
A residue in a domain i.e. in a discrete portion of a protein assumed to fold independently of the rest of the protein and possessing its own function. [NCBI Bioinformatics]
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
in_hinge_region
mao.obo
A residue in a hinge region i.e. a flexible region of the protein between two globular domains.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
in_transmembrane_region
mao.obo
A residue in a transmembrane region i.e. in a domain in a amphipathic membrane protein where the hydrophobic regions traverse the lipid bilayers of the membranes, while the hydrophilic regions extend on either side of the membrane and interact with water.[Folding@home glossary, Stanford Univ].
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
in_helix
mao.obo
A residue in a helical portion of a protein structure i.e. in a frequently highly stable protein chain conformation stabilised by hydrogen bonding between peptide groups and having side chains projecting outwards in a spiral (3.6 residues per turn). [The Biochemical Society Glossary].
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
in_strand
mao.obo
in_beta_strand
A residue in a beta_strand i.e. a stable "zig-zag" conformation of protein chain which can align with sections of chain in same conformation and cross-link efficiently via hydrogen bonds between the peptide linkages. [The Biochemical Society Glossary].
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
in_loop
mao.obo
A residue in a loop i.e. a section of the protein chain connecting classical secondary structures like helix and sheet. [The Biochemical Society Glossary].
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
sub_alignment
mao.obo
cluster
group
sub_group
A subset of sequences in the msa. e.g. a phylogenetic subgroup such as 'mammals', or a sequence cluster calculated by an automatic method such as secator/dpc or any other subset.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
residue
mao.obo
The part of a single sugar that appears in a polysaccharide; of a single amino acid in a protein; of a single nucleotide in a nucleic acid, etc.; usually the monomer minus the elements of water.Glossary of Biochemistry and Molecular Biology, David M. Glick.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
gap_character
mao.obo
The character used to represent an insertion/deletion.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
unknown_residue_function
mao.obo
unknown_structural_location
mao.obo
kegg_id
mao.obo
KEGG interface
KEGG:xref
http://purl.org/obo/owl/KEGG#KEGG_xref
alignment_sequence
mao.obo
The order of residues and insertions/deletions represented by gap characters in a single sequence. For proteins, this is known as the primary structure.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
sequence_name
mao.obo
The name given to the sequence.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
column_score
mao.obo
A score associated with a given column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
column_conservation_type
mao.obo
The type of residue conserved in a given column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
organism
mao.obo
The organism that was the source of the sequence.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
sequence_feature
mao.obo
A region of the sequence, defined by a start and stop residue, that has a specific property.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
fitem
feature_start_residue
mao.obo
The residue at the beginning of the feature.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
feature_stop_residue
mao.obo
The residue at the end of the feature.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
consensus_sequence
mao.obo
A pseudo-sequence that summarises the residue information contained in an aligned set of sequences.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
column_weight
mao.obo
A weight associated with a given column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
sequence_weight
mao.obo
A weight assigned to a sequence.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
feature_description
mao.obo
A general text description of the feature.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
protein:protein interactions
mao.obo
PSI interface
MI:0000
http://purl.org/obo/owl/MI#MI_0000
msa_name
mao.obo
The name given to the multiple sequence alignment.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
ec_number
mao.obo
Enzyme Commission interface
EC:xref
http://purl.org/obo/owl/EC#EC_xref
hydrophobicity
mao.obo
A measure of how insoluble a given molecule is when in water or other polar liquids.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
feature_name
mao.obo
The name given to the feature.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
sequence_feature_type
mao.obo
The type of the sequence feature.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
interpro_domain
mao.obo
Interpro interface
IPR:xref
http://purl.org/obo/owl/IPR#IPR_xref
transmembrane_helix
mao.obo
tm
coiled_coil
mao.obo
msa_core_block
mao.obo
A conserved region in the sub_alignment.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
helix
mao.obo
A frequently highly stable protein chain conformation stabilised by hydrogen bonding between peptide groups and having side chains projecting outwards in a spiral (3.6 residues per turn). The Biochemical Society Glossary.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
alpha_helix
strand
mao.obo
Stable "zig-zag" conformation of protein chain which can align with sections of chain in same conformation and cross-link efficiently via hydrogen bonds between the peptide linkages. The Biochemical Society Glossary.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
beta_strand
accession_number
mao.obo
accession
A unique identifier in the sequence databases.Accession numbers should remain static between database updates.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
sequence_description
mao.obo
A general description of the sequence.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
taxid
mao.obo
NCBI taxonomy database interface
taxid:xref
http://purl.org/obo/owl/taxid#taxid_xref
sequence_repeat
mao.obo
A region which has multiple copies in the sequence. Repeats range from short stretches of adjacent, similar residues to multiple copies of complete domains.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
signal
mao.obo
Extent of a signal sequence (prepeptide).
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
sequence_variant
mao.obo
varsplic
A region where an alternative sequence has been observed.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
low_complexity_region
mao.obo
A region of biased residue composition, e.g. homopolymeric runs, short repeats, and more subtle overrepresentations of one or a few residues. Low-complexity regions in amino acid sequences typically assume non-globular structure in proteins. [NCBI sef.glossary).
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
site
mao.obo
A generic term for the extent of a user-specified site.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
sequence_keyword_list
mao.obo
A list of keywords that provide information that can be used to generate indexes of the sequence entries based on functional, structural, or other categories.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
buried
mao.obo
A residue in the core of the protein that has no surface area accessible to solvent.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
core_residue
residue_hydrogen_bond
mao.obo
A type of attractive intermolecular force that exists between two partial electric charges of opposite polarity.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
conserved_aliphatic_residue
mao.obo
A conserved aliphatic residue e.g. AGLIV
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
conserved_aromatic_residue
mao.obo
A conserved aromatic residue e.g. YWFH
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
conserved_basic_residue
mao.obo
A conserved basic residue e.g. HKR
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
conserved_hydroxyl_residue
mao.obo
A conserved hydroxyl residue e.g. STY
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
dna_binding_site
mao.obo
A residue that is directly involved in binding to dna.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
column_conservation
mao.obo
The conservation associated with a given column in the msa.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
residue_function_detection_method
mao.obo
The method used to detect the activity or function of the residue.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
column_conservation_construction_method
mao.obo
The method used to construct the conservation score associated with a given column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
user_conservation_value
mao.obo
A user defined conservation term e.g. mixed conservation from different methods
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
strict_conservation
mao.obo
A strictly conserved column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
no_conservation
mao.obo
An unconserved column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
in_cavity
mao.obo
in_pocket
The residue is touching a cavity.
MAO:pk
http://purl.org/obo/owl/MAO#MAO_pk
alignment_column
mao.obo
The alignment_column contains one residue (or a gap character) from each sequence. The residues in the column are considered to be equivalent. If no equivalent residue exists for a given sequence, a gap character is inserted.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
sub_alignment_construction_method
mao.obo
sub_group_construction_method
The method used to determine the sub_alignment or sub_families.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
cluster_construction_method
group_construction_method
loop
mao.obo
A section of the protein chain connecting classical secondary structures like helix and sheet. Often of irregular structure, surface exposed and containing hydrophilic residues. The Biochemical Society Glossary.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
interresidue_contact_list
mao.obo
residue_contact_list
List of spatial contacts between two residues
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
contact_residue1
mao.obo
First residue involved in contact
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
interresidue_contact
mao.obo
residue_contact
Spatial contact between two residues
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
differential_conservation
mao.obo
A column that is conserved differently in the different sub_families. e.g. a residue that is conserved in mammals, but is divergent in the other organisms.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
conserved_gap_character
mao.obo
A conserved insertion/deletion.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
structural_location_detection_method
mao.obo
The method used to determine the location of the residue in the 3d structure.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
3d_atomic_coordinates
mao.obo
The coordinates of the atom in 3-dimensional space.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
atom
mao.obo
The fundamental building blocks of chemistry, which cannot be broken by any chemical means.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
other_residue_function
mao.obo
A user specified activity or function associated with a residue.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
pdb_name
mao.obo
msa_3d_superposition
mao.obo
msa_reference_structure_name
mao.obo
msa_superposed_regions
mao.obo
msa_symmetry_operator
mao.obo
msa_rmsd
mao.obo
tissue_type
mao.obo
The tissue from which the sequence was extracted.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
developmental_stage
mao.obo
The developmental stage of the organism's life cycle during which the sequence was extracted nMGED Interface
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
exposed
mao.obo
surface_residue
A residue on the surface of the protein that is accessible to solvent.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
residue_salt_bridge
mao.obo
An interaction between positive and negative charges on side chains of a protein.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
ramanchandran_plot
mao.obo
The Ramachandran plot is a graph of the protein backbone torsional angles psi (Calpha-C bond) versus phi (N-Calpha bond). The psi and phi angles cover the ranges from -180 to +180.
MAO:pk
http://purl.org/obo/owl/MAO#MAO_pk
phi_angle
mao.obo
The phi (N-Calpha bond) protein backbone torsional angles of the Ramachandran plot. The phi angle cover the range from -180 to +180.
MAO:pk
http://purl.org/obo/owl/MAO#MAO_pk
3d_coordinate_x
mao.obo
psi_angle
mao.obo
The psi (C-Calpha bond) protein backbone torsional angles of the Ramachandran plot. The phi angle cover the range from -180 to +180.
MAO:pk
http://purl.org/obo/owl/MAO#MAO_pk
3d_coordinate_y
mao.obo
3d_coordinate_z
mao.obo
bonded_residue
mao.obo
The other residue bonded to the reference residue.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
msa_freetext_line
mao.obo
aln_text
A line of free text in the msa, containing annotation associated with a sequence or group of sequences.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
msa_freetext_owner
mao.obo
The alignment_sequence or sub_family that the msa_freetext is attached to.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
aln_text_owner
msa_freetext_type
mao.obo
The type of text supplied in the msa_freetext.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
aln_text_type
consensus_sequence_construction_method
mao.obo
The method used to determine the consensus sequence.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
sequence_type
mao.obo
The type of sequence e.g. protein or dna.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
column_score_calculation_method
mao.obo
The method used to calculate the score associated with a given column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
column_weight_calculation_method
mao.obo
The method used to calculate the weight associated with a given column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
amino_acid_residue
mao.obo
An organic compound that generally contains an amino (-NH2) and a carboxyl (-COOH) group. There are 20 different kinds of amino acids. A protein consists of a specific sequence of amino acids.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
amino_acid
aa
aa_residue
nucleotide_residue
mao.obo
base
A DNA sequence consists of a specific sequence of nucleotides. A nucleotide is made of a molecule of sugar, a molecule of phosphoric acid, and a molecule called a base. The bases are the "letters" that spell out the genetic code. In DNA, the code letters are A, T, G, and C, which stand for the chemicals adenine, thymine, guanine, and cytosine, respectively. In base pairing, adenine always pairs with thymine, and guanine always pairs with cytosine. [NHGRI] A DNA sequence consists of a specific sequence of nucleotides.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
base_pair
nucleotide
atom_name
mao.obo
motif
mao.obo
A pattern of conserved residues in a sequence that are located within a certain distance from each other in the sequence.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
enzyme_active_site
mao.obo
The active site of an enzyme is the binding site where catalysis occurs. The structure and chemical properties of the active site allow the recognition and binding of the substrate. The active site consists of the catalytic amino acids and one or more binding sites that bind the substrate(s).
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
substrate_binding_site
mao.obo
A residue that is directly involved in the binding of a specific substrate.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
mutation
mao.obo
A mutation is a permanent, transmissible change to the genetic material (usually DNA or RNA) of a cell.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
point_mutation
mao.obo
A point mutation is usually caused by chemicals or malfunction of DNA replication and exchanges a single nucleotide for another. Most common is the transition that exchanges a purine for a purine or a pyrimidine for a pyrimidine (A ? G, C ? T). Less common is a transversion, which exchanges a purine for a pyrimidine or a pyrimidine for a purine (C/T ? A/G).
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
insertion_mutation
mao.obo
The addition of one or more extra nucleotides into the DNA. They are usually caused by transposable elements, or errors during replication of repeating elements (e.g. AT repeats). Insertions in a gene can cause a shift in the reading frame (frameshift) or alter splicing of the mRNA, both of which can significantly alter the gene product.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
deletion_mutation
mao.obo
Deletions remove one or more nucleotides from the DNA. Like insertions, these mutations can alter the reading frame of the gene. Deletions in a gene can cause a shift in the reading frame (frameshift) or alter splicing of the mRNA, both of which can significantly alter the gene product.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
silent_mutation
mao.obo
A silent mutation is a DNA mutation that does not alter the final amino acid, and hence does not affect the final protein. Anaylsis of mutations in genes causing genetic disorders has shown that silent mutations can affect gene transcription, leading to the formation of truncated protein with reduced or no function.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
synonymous_mutation
missense_mutation
mao.obo
A missense mutations is a type of point mutation where a nucleotide is changed which results in a different amino acid. This in turn can render the resulting protein nonfunctional.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
nonsynonymous_mutation
nonsense_mutation
mao.obo
A nonsense mutation is a point mutation that results in a premature stop codon in the transcribed mRNA, and possibly a truncated (and often nonfunctional) protein product.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
mutation_type
mao.obo
The type fo mutation. e.g. germline mutation, which can be passed on to progeny or somatic mutation, which often leads to the malfunction or death of a cell and can cause cancer.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
metal_binding_site
mao.obo
A residue that is directly involved in the binding of a metal ion.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
CSA_catalytic_site
mao.obo
CSA Interface
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
ligand_binding_site
mao.obo
A residue that is directly involved in the binding of a specific ligand.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
mutation_phenotypic_manifestation
mao.obo
OBO_phenotype_ontology interface
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
resid_ptm
mao.obo
RESID database interface
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
acetylation
mao.obo
N-terminal of some residues and side chain of lysine or cysteine
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
amidation
mao.obo
Generally at the C-terminal of a mature active peptide after oxidative cleavage of last glycine
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
blocked
mao.obo
Unidentified N- or C-terminal blocking group
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
formylation
mao.obo
Of the N-terminal methionine
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
gamma_carboygluamic_acid
mao.obo
Of glutamate
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
hydroxylation
mao.obo
Generally of asparagine, aspartate, proline or lysine
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
methylation
mao.obo
Generally of N-terminal phenylalanine, side chain of lysine, arginine, histidine, asparagine or glutamate, and C-terminal cysteine
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
phosphorylation
mao.obo
Of serine, threonine, tyrosine, aspartate, histidine or cysteine
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
pyrrolidone_carboxylic_acid
mao.obo
N-terminal glutamine which has formed an internal cyclic lactam. This is also called 'pyro-Glu'. Very rarely, pyro-Glu can be produced by modification of a N-terminal glutamate
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
sulfation
mao.obo
Of tyrosine, serine or threonine
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
carbohydrate_binding_site
mao.obo
lipid_binding_site
mao.obo
A residue that is directly involved in the binding of a lipid.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
residue_disulfide_bond
mao.obo
A strong covalent bond between two sulfhydryl groups. This bond is very important to the folding, structure, and function of proteins.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
disulfide_bridge
residue_structural_bond
mao.obo
contact_residue2
mao.obo
Second residue involved in spatial contact
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
n_terminal_extension
mao.obo
c_terminal_extension
mao.obo
sequence_weight_calculation_method
mao.obo
sequence_insertion
mao.obo
column_consensus
mao.obo
A consensus character that summarises the residue information contained in an alignment_column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
feature_calculation_method
mao.obo
The method used to determine the feature.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
column_consensus_calculation_method
mao.obo
The method used to determine the consensus character associated with a column.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
so_mutation
mao.obo
SO interface
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
sequence_keyword
mao.obo
A keyword provides information that can be used to generate indexes of the sequence entries based on functional, structural, or other categories.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
hydrophobicity_calculation_method
mao.obo
The method used to calculate the hydrophobicity measure.
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
contact_distance
mao.obo
Distance between two residues in spatial contact
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
contact_description
mao.obo
Textual comment describing spatial contact between two residues
MAO:jt
http://purl.org/obo/owl/MAO#MAO_jt
Alanine
Cysteine
Aspartate
TODO: Aspartate?
Glutamate
Phenylalanine
Glycine
Histidine
Isoleucine
Lysine
Leucine
Methionine
Asparagine
TODO: Should this be Aliphatic?
Proline
Glutamine
Arginine
Serine
Threonine
Valine
Tryptophan
Tyrosine
0
0
This class will be declared equivalent ot the amino acid class description imported
1
2
'Branch' is the domain-specific synonym for an edge of a (Phylogenetic) Tree or Network. Branches may have properties such as length and degree of support.
2
The base class of annotations in CDAO.
Its possible that this base class should be discarded and that annotations should inherit from an imported base class if one exists.
Traits shown to be relevant for phylogenetic classification
A matrix of character-state data, typically containing observed data, though in some cases the states in the matrix might be simulated or hypothetical. Synonyms: character Data matrix, character-state matrix
Meta-information associated with a character matrix, such as, for the case of a sequence alignment, the method of alignment.
1
1
The instance of a given character for a given TU. Its state is an object property drawn from a particular character state domain, e.g., the state of an Amino_Acid_State_Datum is an object property drawn from the domain Amino_Acid.
The universe of possible states for a particular type of character, e.g., the states of an Amino_Acid character come from the Amino_Acid domain.
A character that could be divided into separate characters but is not due to the non-independence of changes that would result, e.g., as in the case of a subsequence that is either present or absent as a block.
1
This class describes a continuous value. The link to the actual float value is through the property has_Value. It could have also other properties attached (e.g., has_Precision).
A reference to an external coordinate system. Coordinates for data must refer to some such external coordinate system.
1
A positional coordinate giving the source of a character state, used for molecular sequences.
drawing from seqloc categories from NCBI at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/SEQLOC.HTML#_Seq-loc:_Locations_on
1
1
A directed edge. Rooted trees have directed edges. The direction is specified by way of the parent and child relationships of nodes that the edge connects.
2
An edge connecting two nodes in a (Phylogenetic) Tree or Network, also known as a 'branch'. Edges may have attributes such as length, degree of support, and direction. An edge can be a surrogate for a 'split' or bipartition, since each edge in a tree divides the terminal nodes into two sets.
Its possible that this should not be classed as an 'annotation' since it contains data rather than meta-data.
The length of an edge (branch) of a Tree or Network, typically in units of evolutionary changes in character-state per character.
This concept is tied to the verbally ambiguous 'gap' concept and to the use of a gap character (often the en dash '-') in text representations of sequence alignments. In general, this represents the absence of any positively diagnosed Character-State. As such, the gap may be interpreted as an additional Character-State, as the absence of the Character, or as an unknown value. In some cases it is helpful to separate these.
This class should be renamed. These are not generic states but non-concrete states including gap, unknown and missing.
1
Description of a model of transformations.
This is a non-computible description of a model, not the fully specified mathematical model, which typically relates the probability of a transformation to various parameters.
1
1
1
3
2
1
1
A set of ordered states, typically the residues in a macromolecular sequence.
The class is used to describe either colletions of characters or higher order grouping (e.g., groups of groups of characters). This extends the CharSet block of NEXUS.
A unit of analysis that may be tied to a node in a tree and to a row in a character matrix. It subsumes the traditional concepts of 'OTU' and 'HTU'.
Link to an externally defined taxonomic hierarchy.
1
1
1
1
1
1
parameterType
serviceDescription
input and output are different representations of the same thing - syntax translation
input and output are different representations of the same thing - syntax translation
input is equivalent to output
output is part of input
input uniquely identifies output
The biological sense of the word. The process of converting a sequence of nucleic acid (mRNA) into an amino acid sequence
$Date: 2011/04/15 12:36:54 $
$Id: cdao.owl,v 1.36 2011/04/15 12:36:54 astoltzfus Exp $
Comparison of two or more biological entities of the same class when the similarities and differences of the entities are treated explicitly as the product of an evolutionary process of descent with modification.
GNU General Public License (GPL)
The Character Data Analysis Ontology
The Comparative Data Analysis Ontology (CDAO) provides a framework for understanding data in the context of evolutionary-comparative analysis. This comparative approach is used commonly in bioinformatics and other areas of biology to draw inferences from a comparison of differently evolved versions of something, such as differently evolved versions of a protein. In this kind of analysis, the things-to-be-compared typically are classes called 'OTUs' (Operational Taxonomic Units). The OTUs can represent biological species, but also may be drawn from higher or lower in a biological hierarchy, anywhere from molecules to communities. The features to be compared among OTUs are rendered in an entity-attribute-value model sometimes referred to as the 'character-state data model'. For a given character, such as 'beak length', each OTU has a state, such as 'short' or 'long'. The differences between states are understood to emerge by a historical process of evolutionary transitions in state, represented by a model (or rules) of transitions along with a phylogenetic tree. CDAO provides the framework for representing OTUs, trees, transformations, and characters. The representation of characters and transformations may depend on imported ontologies for a specific type of character.
http://cdao.cvs.sourceforge.net/*checkout*/cdao/cdao/OWL/cdao.owl
http://www.evolutionaryontology.org/CDAO
OWL (RDF-XML)
CDAO Team
comparative analysis; comparative data analysis; evolutionary comparative analysis; evolution; phylogeny; phylogenetics