Relation
type: AnnotationProperty
description: Recommended best practice is to reference the resource by means of a string or number conforming to a formal identification system.
comment: A reference to a related resource.

Description
type: AnnotationProperty
comment: An account of the content of the resource.
description: 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
type: AnnotationProperty
comment: An entity responsible for making contributions to the content of the resource.
description: 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
type: AnnotationProperty
comment: A language of the intellectual content of the resource.
description: 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
type: AnnotationProperty
comment: The nature or genre of the content of the resource.
description: 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
type: AnnotationProperty
comment: A reference to a resource from which the present resource is derived.
description: 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
type: AnnotationProperty
comment: An entity primarily responsible for making the content of the resource.
description: 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
type: AnnotationProperty
comment: An entity responsible for making the resource available
description: 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
type: AnnotationProperty
comment: The topic of the content of the resource.
description: 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
type: AnnotationProperty
description: 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.
comment: The extent or scope of the content of the resource.

Resource Identifier
type: AnnotationProperty
comment: An unambiguous reference to the resource within a given context.
description: 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
type: AnnotationProperty
comment: A date associated with an event in the life cycle of the resource.
description: 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
type: AnnotationProperty
comment: The physical or digital manifestation of the resource.
description: 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
type: AnnotationProperty
description: Typically, a Title will be a name by which the resource is formally known.
comment: A name given to the resource.

Rights Management
type: AnnotationProperty
description: 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.
comment: Information about rights held in and over the resource.

part_of
type: ObjectProperty
type: TransitiveProperty
has OBO namespace: mao.obo

is_annotation
type: ObjectProperty
has OBO namespace: mao.obo

is_attribute
type: ObjectProperty
has OBO namespace: mao.obo

is_name
type: ObjectProperty
has OBO namespace: mao.obo

belongs to
type: ObjectProperty
description: Generic property that links a concept to another concept it is a constituent of. The property is a synonym of part_of.
equivalent property: part of
range: The Character Data Analysis Ontology
domain: The Character Data Analysis Ontology

belongs to Edge
type: ObjectProperty
description: The property links a Node to one of the edges that are incident on such node.
range: Edge
domain: Node
sub property of: belongs to

belongs to Edge as Child
type: ObjectProperty
description: The property links a Node to the Edge it belongs to in the child position.
range: DirectedEdge
domain: Node
sub property of: belongs to Edge
inverse of: has Child Node

belongs to Edge as Parent
type: ObjectProperty
description: The property links a Node to one of the Edges where the node appears in the parent position (i.e., closer to the root).
range: DirectedEdge
domain: Node
sub property of: belongs to Edge
inverse of: has Parent Node

belongs to TU
type: ObjectProperty
type: FunctionalProperty
description: This property relates a character-state datum to its TU.
domain: CharacterStateDatum
range: TU
sub property of: belongs to

has
type: ObjectProperty
description: Generic 'has' property.

has Amino Acid Datum
type: ObjectProperty
description: 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).
range: AminoAcidResidueStateDatum
sub property of: has Molecular Datum
domain: Class
  union of: AminoAcidResidueCharacter
  union of: TU

has Amino Acid State
type: ObjectProperty
description: This property associates a amino acid character-state instance with a state value from the domain of amino acid states.
domain: AminoAcidResidueStateDatum
sub property of: has State
range: Class
  union of: AminoAcidResidue
  union of: Generic State

has Ancestor
type: ObjectProperty
type: TransitiveProperty
description: The property links a node to any of the other nodes that are its ancestors in a rooted tree.
domain: Node
range: Node
sub property of: has
inverse of: has Descendant

has Change Component
type: ObjectProperty
description: This property relates a transformation to the components that compose it.
sub property of: has
domain: hereditaryChange

has Character
type: ObjectProperty
description: This property associates a character data matrix with a character (a column) represented in the matrix.
range: Character
domain: CharacterStateDataMatrix
sub property of: has

has Child
type: ObjectProperty
description: The property links a node to a node that is an immediate descendant in the tree.
domain: Node
range: Node
sub property of: has Descendant
inverse of: has Parent
property chain axiom: belongs to Edge as Parent
property chain axiom: has Child Node

has Child Node
type: ObjectProperty
type: FunctionalProperty
description: 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.
domain: DirectedEdge
range: Node
sub property of: has Node

has Compound Datum
type: ObjectProperty
description: This property relates a compound character (a character with some states that are subdividable) to a state datum for the character.
range: CompoundStateDatum
sub property of: has Categorical Datum
domain: Class
  union of: CompoundCharacter
  union of: TU

has Compound State
type: ObjectProperty
description: This property associates a compound character-state instance with its compound state value.
domain: CompoundStateDatum
sub property of: has State
range: Class
  union of: Compound
  union of: Generic State

has Continuous Datum
type: ObjectProperty
description: This property relates a continuous character to a state datum for the character.
range: ContinuousStateDatum
sub property of: has Datum
domain: Class
  union of: ContinuousCharacter
  union of: TU

has Continuous State
type: ObjectProperty
description: This property associates a character-state instance with a state value on a continuous numeric scale.
range: Continuous
domain: ContinuousStateDatum
sub property of: has State

has Coordinate System
type: ObjectProperty
description: This property links a coordinate to the coordinate system it references.
range: CoordinateSystem
domain: DatumCoordinate

has Datum
type: ObjectProperty
description: This property relates a character to a state datum for the character.
range: CharacterStateDatum
sub property of: has
domain: Class
  union of: Character
  union of: TU

has Descendant
type: ObjectProperty
type: TransitiveProperty
description: A property that links a node to any of its descendants in a rooted tree.
range: Node
domain: Node
sub property of: has

has External Reference
type: ObjectProperty
comment: Associates a TU to some external taxonomy reference.
domain: TU
range: The Character Data Analysis Ontology

has First Coordinate Item
type: ObjectProperty
description: The property that relates a coordinate list to the first item in the list.
domain: CoordinateList
sub property of: has
range: Class
  union of: CoordinatePoint
  union of: CoordinateRange

has Left Node
type: ObjectProperty
description: This property relates a transformation to a 'left' node (the node that has the 'left' state).
range: Node
sub property of: has Change Component
domain: hereditaryChange

has Left State
type: ObjectProperty
description: This property relates a transformation to a 'left' state (the state associated with the 'left' node).
range: CharacterStateDomain
sub property of: has Change Component
domain: hereditaryChange

has Node
type: ObjectProperty
description: Property that associates to each Edge the Nodes it connects.
domain: Edge
range: Node
sub property of: has

has Nucleotide Datum
type: ObjectProperty
description: 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).
range: DesoxiRibonucleotideResidueStateDatum
sub property of: has Molecular Datum
domain: Class
  union of: DesoxiRibonucleotideResidueCharacter
  union of: TU

has Nucleotide State
type: ObjectProperty
description: This property associates a nucleotide character-state instance with a state value from the domain of nucleotide states.
domain: DesoxiRibonucleotideResidueStateDatum
sub property of: has State
range: Class
  union of: DesoxiRibonucleotideResidue
  union of: Generic State

has Parent
type: ObjectProperty
description: The property that links a node to its unique parent in a rooted tree.
domain: Node
range: Node
sub property of: has Ancestor
property chain axiom: belongs to Edge as Child
property chain axiom: has Parent Node

has Parent Node
type: ObjectProperty
type: FunctionalProperty
description: 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)
domain: DirectedEdge
range: Node
sub property of: has Node

has Remaining Coordinate List
type: ObjectProperty
description: The property that relates a coordinate list to the item in the list beyond the first item.
domain: CoordinateList
range: CoordinateList
sub property of: has

has Right Node
type: ObjectProperty
description: This property relates a transformation to a 'right' node (the node that has the 'right' state).
range: Node
sub property of: has Change Component
domain: hereditaryChange

has Right State
type: ObjectProperty
description: This property relates a transformation to a 'right' state (the state associated with the 'right' node).
range: CharacterStateDomain
sub property of: has Change Component
domain: hereditaryChange

has Root
type: ObjectProperty
type: FunctionalProperty
description: The property links a rooted tree to the specific node that represents the unique root of the tree.
range: Node
domain: RootedTree
sub property of: has

has State
type: ObjectProperty
description: This property associates a character-state instance with its state value, e.g., a state value expressed in terms of an imported domain ontology.
domain: CharacterStateDatum
range: CharacterStateDomain
sub property of: has

has TU
type: ObjectProperty
description: This property associates a character data matrix with a TU (a row) represented in the matrix.
domain: CharacterStateDataMatrix
range: TU
sub property of: has

hereditary change of
type: ObjectProperty
description: 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.
range: Character

homologous to
type: ObjectProperty
description: 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).
domain: CharacterStateDatum
range: CharacterStateDatum

represented by Node
type: ObjectProperty
description: This property relates a TU to a node that represents it in a network.
range: Node
domain: TU
inverse of: represents TU

represents TU
type: ObjectProperty
type: FunctionalProperty
description: This property relates a TU or taxonomic unit (typically associated with character data) to a phylogenetic history (Tree).
domain: Node
range: TU

subtree of
type: ObjectProperty
description: This property links two networks where the latter is a substructure of the former
range: Network
domain: Network

exampleInput
type: DatatypeProperty
comment: 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.
domain: unitTest
range: string

hasConfiguredInstanceExample
type: DatatypeProperty
comment: This is a link to an executable version of the service. This will normally be represented by a workflow containing just the service
domain: operation
domain: serviceDescription
range: anyURI

hasDefaultValue
type: DatatypeProperty
comment: describes preconfigured values for input parameters
domain: parameter
range: string

isMandatory
type: DatatypeProperty
comment: describes whether an input parameter is required or optional to execute the service
domain: parameter
range: boolean

validOutputXML
type: DatatypeProperty
comment: 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.
domain: unitTest
range: string

validREGEX
type: DatatypeProperty
comment: value is a regular expression that should match the output from the service given the associated input from the unit test
domain: unitTest
range: string

validXPath
type: DatatypeProperty
comment: value is an XPath statement that can be used to validate the output of a service given the associated input in the unit test
domain: unitTest
range: string

multiple_sequence_alignment
type: Class
has OBO namespace: mao.obo
has related synonym: msa
has definition: Definition
  label: 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.
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

structural_location
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: amino_acid_residue
has OBO namespace: mao.obo
has definition: The location of the residue in the 3D structure.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

residue_function
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: amino_acid_residue
has OBO namespace: mao.obo
has definition: Function of the residue, such as catalysis, binding or post-translational modification. A residue may exhibit zero, one or more activities.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

column_conservation_level
type: Class
subclass of: Restriction
  on property: part_of
  some values from: column_conservation
has OBO namespace: mao.obo
has definition: The level of conservation associated with a given column. This may be specified by either a qualitative score or a quantitative score.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

conserved_residue_list
type: Class
subclass of: column_conservation_type
has OBO namespace: mao.obo
has definition: A user specified list of conserved residues.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

biological_process
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: GeneOntology interface
  type: Definition
  has db xref: GO:0008150
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_0008150

cellular_component
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: GeneOntology interface
  type: Definition
  has db xref: GO:0005575
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_0005575

molecular_function
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: GeneOntology interface
  type: Definition
  has db xref: GO:0003674
    type: DbXref
    has URI: http://purl.org/obo/owl/GO#GO_0003674

conserved_small_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: mao.obo
has definition: A conserved small residue e.g. PAGST
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

conserved_negatively_charged_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: mao.obo
has definition: A conserved negatively charged residue e.g. DE
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

conserved_hydrophobic_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: mao.obo
has definition: A conserved hydrophobic residue e.g. ACFGLIMVWY
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

conserved_hydrophilic_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: mao.obo
has definition: A conserved hydrophilic residue e.g. DEHKNQRST
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

quantitative_conservation_level
type: Class
subclass of: column_conservation_level
has OBO namespace: mao.obo
has definition: A quantitative score for the conservation associated with a given column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

qualitative_conservation_level
type: Class
subclass of: column_conservation_level
has OBO namespace: mao.obo
has definition: A qualitative description of the level of conservation associated with a given column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

low_conservation
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: mao.obo
has definition: A low level of conservation associated with a given column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

medium_conservation
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: mao.obo
has definition: A medium level of conservation associated with a given column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

high_conservation
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: mao.obo
has definition: A high level of conservation associated with a given column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

catalytic_site
type: Class
subclass of: enzyme_active_site
has OBO namespace: mao.obo
has definition: A residue that is directly involved in some aspect of the reaction catalysed by the enzyme.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

domain
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo
has definition: Definition
  label: 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]
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

post translational modification
type: Class
subclass of: residue_function
has OBO namespace: mao.obo
has definition: Definition
  label: 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
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: ptm

psi_mutation
type: Class
subclass of: mutation
has OBO namespace: mao.obo
has definition: PSI interface
  type: Definition
  has db xref: MI:0118
    type: DbXref
    has URI: http://purl.org/obo/owl/MI#MI_0118

msa_construction_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: multiple_sequence_alignment
has OBO namespace: mao.obo
has definition: The method used to construct the multiple sequence alignment.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

surface_accessibility
type: Class
subclass of: structural_location
has OBO namespace: mao.obo
has definition: Surface area accessible to solvent
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

N_terminal
type: Class
subclass of: structural_location
has OBO namespace: mao.obo
has definition: A residue in a protein chain that has a free amino group.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: amino_terminus

C_terminal
type: Class
subclass of: structural_location
has OBO namespace: mao.obo
has definition: A residue in a protein chain that has a free carboxyl group.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: carboxyl_terminus

in_domain
type: Class
subclass of: structural_location
has OBO namespace: mao.obo
has definition: 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]
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

in_hinge_region
type: Class
subclass of: structural_location
has OBO namespace: mao.obo
has definition: A residue in a hinge region i.e. a flexible region of the protein between two globular domains.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

in_transmembrane_region
type: Class
subclass of: structural_location
has OBO namespace: mao.obo
has definition: Definition
  label: 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].
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

in_helix
type: Class
subclass of: structural_location
has OBO namespace: mao.obo
has definition: Definition
  label: 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].
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

in_strand
type: Class
subclass of: structural_location
has OBO namespace: mao.obo
has related synonym: in_beta_strand
has definition: Definition
  label: 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].
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

in_loop
type: Class
subclass of: structural_location
has OBO namespace: mao.obo
has definition: 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].
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

sub_alignment
type: Class
subclass of: Restriction
  on property: part_of
  some values from: multiple_sequence_alignment
has OBO namespace: mao.obo
has related synonym: cluster
has related synonym: group
has related synonym: sub_group
has definition: 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.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

residue
type: Class
subclass of: Restriction
  on property: part_of
  some values from: alignment_sequence
subclass of: Restriction
  on property: part_of
  some values from: alignment_column
has OBO namespace: mao.obo
has definition: Definition
  label: 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.
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

gap_character
type: Class
subclass of: Restriction
  on property: part_of
  some values from: alignment_column
subclass of: Restriction
  on property: part_of
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: The character used to represent an insertion/deletion.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

unknown_residue_function
type: Class
subclass of: residue_function
has OBO namespace: mao.obo

unknown_structural_location
type: Class
subclass of: structural_location
has OBO namespace: mao.obo

kegg_id
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: KEGG interface
  type: Definition
  has db xref: KEGG:xref
    type: DbXref
    has URI: http://purl.org/obo/owl/KEGG#KEGG_xref

alignment_sequence
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sub_alignment
has OBO namespace: mao.obo
has definition: The order of residues and insertions/deletions represented by gap characters in a single sequence. For proteins, this is known as the primary structure.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

sequence_name
type: Class
subclass of: Restriction
  on property: is_name
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: The name given to the sequence.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

column_score
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_column
has OBO namespace: mao.obo
has definition: A score associated with a given column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

column_conservation_type
type: Class
subclass of: Restriction
  on property: part_of
  some values from: column_conservation
has OBO namespace: mao.obo
has definition: The type of residue conserved in a given column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

organism
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: The organism that was the source of the sequence.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

sequence_feature
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: A region of the sequence, defined by a start and stop residue, that has a specific property.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: fitem

feature_start_residue
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sequence_feature
has OBO namespace: mao.obo
has definition: The residue at the beginning of the feature.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

feature_stop_residue
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sequence_feature
has OBO namespace: mao.obo
has definition: The residue at the end of the feature.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

consensus_sequence
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sub_alignment
has OBO namespace: mao.obo
has definition: A pseudo-sequence that summarises the residue information contained in an aligned set of sequences.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

column_weight
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_column
has OBO namespace: mao.obo
has definition: A weight associated with a given column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

sequence_weight
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: A weight assigned to a sequence.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

feature_description
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sequence_feature
has OBO namespace: mao.obo
has definition: A general text description of the feature.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

protein:protein interactions
type: Class
subclass of: residue_function
has OBO namespace: mao.obo
has definition: PSI interface
  type: Definition
  has db xref: MI:0000
    type: DbXref
    has URI: http://purl.org/obo/owl/MI#MI_0000

msa_name
type: Class
subclass of: Restriction
  on property: is_name
  some values from: multiple_sequence_alignment
has OBO namespace: mao.obo
has definition: The name given to the multiple sequence alignment.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

ec_number
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: Enzyme Commission interface
  type: Definition
  has db xref: EC:xref
    type: DbXref
    has URI: http://purl.org/obo/owl/EC#EC_xref

hydrophobicity
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: A measure of how insoluble a given molecule is when in water or other polar liquids.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

feature_name
type: Class
subclass of: Restriction
  on property: is_name
  some values from: sequence_feature
has OBO namespace: mao.obo
has definition: The name given to the feature.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

sequence_feature_type
type: Class
subclass of: sequence_feature
has OBO namespace: mao.obo
has definition: The type of the sequence feature.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

interpro_domain
type: Class
subclass of: domain
has OBO namespace: mao.obo
has definition: Interpro interface
  type: Definition
  has db xref: IPR:xref
    type: DbXref
    has URI: http://purl.org/obo/owl/IPR#IPR_xref

transmembrane_helix
type: Class
subclass of: residue_hydrogen_bond
has OBO namespace: mao.obo
has related synonym: tm

coiled_coil
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo

msa_core_block
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo
has definition: A conserved region in the sub_alignment.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

helix
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo
has definition: Definition
  label: 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.
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has narrow synonym: alpha_helix

strand
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo
has definition: Definition
  label: 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.
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: beta_strand

accession_number
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has related synonym: accession
has definition: A unique identifier in the sequence databases.Accession numbers should remain static between database updates.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

sequence_description
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: A general description of the sequence.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

taxid
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: NCBI taxonomy database interface
  type: Definition
  has db xref: taxid:xref
    type: DbXref
    has URI: http://purl.org/obo/owl/taxid#taxid_xref

sequence_repeat
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo
has definition: A region which has multiple copies in the sequence. Repeats range from short stretches of adjacent, similar residues to multiple copies of complete domains.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

signal
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo
has definition: Extent of a signal sequence (prepeptide).
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

sequence_variant
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo
has related synonym: varsplic
has definition: A region where an alternative sequence has been observed.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

low_complexity_region
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo
has definition: Definition
  label: 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).
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

site
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo
has definition: A generic term for the extent of a user-specified site.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

sequence_keyword_list
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: 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.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

buried
type: Class
subclass of: structural_location
has OBO namespace: mao.obo
has definition: A residue in the core of the protein that has no surface area accessible to solvent.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: core_residue

residue_hydrogen_bond
type: Class
subclass of: residue_structural_bond
has OBO namespace: mao.obo
has definition: A type of attractive intermolecular force that exists between two partial electric charges of opposite polarity.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

conserved_aliphatic_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: mao.obo
has definition: A conserved aliphatic residue e.g. AGLIV
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

conserved_aromatic_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: mao.obo
has definition: A conserved aromatic residue e.g. YWFH
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

conserved_basic_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: mao.obo
has definition: A conserved basic residue e.g. HKR
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

conserved_hydroxyl_residue
type: Class
subclass of: column_conservation_type
has OBO namespace: mao.obo
has definition: A conserved hydroxyl residue e.g. STY
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

dna_binding_site
type: Class
subclass of: residue_function
has OBO namespace: mao.obo
has definition: A residue that is directly involved in binding to dna.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

column_conservation
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_column
has OBO namespace: mao.obo
has definition: The conservation associated with a given column in the msa.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

residue_function_detection_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: residue_function
has OBO namespace: mao.obo
has definition: The method used to detect the activity or function of the residue.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

column_conservation_construction_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: column_conservation
has OBO namespace: mao.obo
has definition: The method used to construct the conservation score associated with a given column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

user_conservation_value
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: mao.obo
has definition: A user defined conservation term e.g. mixed conservation from different methods
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

strict_conservation
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: mao.obo
has definition: A strictly conserved column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

no_conservation
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: mao.obo
has definition: An unconserved column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

in_cavity
type: Class
subclass of: structural_location
has OBO namespace: mao.obo
has related synonym: in_pocket
has definition: The residue is touching a cavity.
  type: Definition
  has db xref: MAO:pk
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_pk

alignment_column
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sub_alignment
has OBO namespace: mao.obo
has definition: Definition
  label: 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.
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

sub_alignment_construction_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: sub_alignment
has OBO namespace: mao.obo
has related synonym: sub_group_construction_method
has definition: The method used to determine the sub_alignment or sub_families.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: cluster_construction_method
has related synonym: group_construction_method

loop
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo
has definition: Definition
  label: 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.
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

interresidue_contact_list
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: residue
has OBO namespace: mao.obo
has related synonym: residue_contact_list
has definition: List of spatial contacts between two residues
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

contact_residue1
type: Class
subclass of: Restriction
  on property: part_of
  some values from: interresidue_contact_list
has OBO namespace: mao.obo
has definition: First residue involved in contact
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

interresidue_contact
type: Class
subclass of: Restriction
  on property: part_of
  some values from: interresidue_contact_list
has OBO namespace: mao.obo
has related synonym: residue_contact
has definition: Spatial contact between two residues
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

differential_conservation
type: Class
subclass of: qualitative_conservation_level
has OBO namespace: mao.obo
has definition: 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.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

conserved_gap_character
type: Class
subclass of: column_conservation_type
has OBO namespace: mao.obo
has definition: A conserved insertion/deletion.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

structural_location_detection_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: structural_location
has OBO namespace: mao.obo
has definition: The method used to determine the location of the residue in the 3d structure.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

3d_atomic_coordinates
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: atom
has OBO namespace: mao.obo
has definition: The coordinates of the atom in 3-dimensional space.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

atom
type: Class
subclass of: Restriction
  on property: part_of
  some values from: nucleotide_residue
subclass of: Restriction
  on property: part_of
  some values from: amino_acid_residue
has OBO namespace: mao.obo
has definition: The fundamental building blocks of chemistry, which cannot be broken by any chemical means.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

other_residue_function
type: Class
subclass of: residue_function
has OBO namespace: mao.obo
has definition: A user specified activity or function associated with a residue.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

pdb_name
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo

msa_3d_superposition
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo

msa_reference_structure_name
type: Class
subclass of: Restriction
  on property: part_of
  some values from: msa_3d_superposition
has OBO namespace: mao.obo

msa_superposed_regions
type: Class
subclass of: Restriction
  on property: part_of
  some values from: msa_3d_superposition
has OBO namespace: mao.obo

msa_symmetry_operator
type: Class
subclass of: Restriction
  on property: part_of
  some values from: msa_3d_superposition
has OBO namespace: mao.obo

msa_rmsd
type: Class
subclass of: Restriction
  on property: part_of
  some values from: msa_3d_superposition
has OBO namespace: mao.obo

tissue_type
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: The tissue from which the sequence was extracted.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

developmental_stage
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: The developmental stage of the organism's life cycle during which the sequence was extracted nMGED Interface
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

exposed
type: Class
subclass of: structural_location
has OBO namespace: mao.obo
has related synonym: surface_residue
has definition: A residue on the surface of the protein that is accessible to solvent.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

residue_salt_bridge
type: Class
subclass of: residue_structural_bond
has OBO namespace: mao.obo
has definition: An interaction between positive and negative charges on side chains of a protein.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

ramanchandran_plot
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: amino_acid_residue
has OBO namespace: mao.obo
has definition: 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.
  type: Definition
  has db xref: MAO:pk
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_pk

phi_angle
type: Class
subclass of: ramanchandran_plot
has OBO namespace: mao.obo
has definition: The phi (N-Calpha bond) protein backbone torsional angles of the Ramachandran plot. The phi angle cover the range from -180 to +180.
  type: Definition
  has db xref: MAO:pk
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_pk

3d_coordinate_x
type: Class
subclass of: Restriction
  on property: part_of
  some values from: 3d_atomic_coordinates
has OBO namespace: mao.obo

psi_angle
type: Class
subclass of: ramanchandran_plot
has OBO namespace: mao.obo
has definition: The psi (C-Calpha bond) protein backbone torsional angles of the Ramachandran plot. The phi angle cover the range from -180 to +180.
  type: Definition
  has db xref: MAO:pk
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_pk

3d_coordinate_y
type: Class
subclass of: Restriction
  on property: part_of
  some values from: 3d_atomic_coordinates
has OBO namespace: mao.obo

3d_coordinate_z
type: Class
subclass of: Restriction
  on property: part_of
  some values from: 3d_atomic_coordinates
has OBO namespace: mao.obo

bonded_residue
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: residue_structural_bond
has OBO namespace: mao.obo
has definition: The other residue bonded to the reference residue.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

msa_freetext_line
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sub_alignment
has OBO namespace: mao.obo
has related synonym: aln_text
has definition: A line of free text in the msa, containing annotation associated with a sequence or group of sequences.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

msa_freetext_owner
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: msa_freetext_line
has OBO namespace: mao.obo
has definition: The alignment_sequence or sub_family that the msa_freetext is attached to.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: aln_text_owner

msa_freetext_type
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: msa_freetext_line
has OBO namespace: mao.obo
has definition: The type of text supplied in the msa_freetext.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: aln_text_type

consensus_sequence_construction_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: consensus_sequence
has OBO namespace: mao.obo
has definition: The method used to determine the consensus sequence.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

sequence_type
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_sequence
has OBO namespace: mao.obo
has definition: The type of sequence e.g. protein or dna.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

column_score_calculation_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: column_score
has OBO namespace: mao.obo
has definition: The method used to calculate the score associated with a given column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

column_weight_calculation_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: alignment_column
has OBO namespace: mao.obo
has definition: The method used to calculate the weight associated with a given column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

amino_acid_residue
type: Class
subclass of: residue
has OBO namespace: mao.obo
has definition: 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.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: amino_acid
has related synonym: aa
has related synonym: aa_residue

nucleotide_residue
type: Class
subclass of: residue
has OBO namespace: mao.obo
has related synonym: base
has definition: Definition
  label: 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.
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: base_pair
has related synonym: nucleotide

atom_name
type: Class
subclass of: Restriction
  on property: is_name
  some values from: atom
has OBO namespace: mao.obo

motif
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo
has definition: A pattern of conserved residues in a sequence that are located within a certain distance from each other in the sequence.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

enzyme_active_site
type: Class
subclass of: residue_function
has OBO namespace: mao.obo
has definition: Definition
  label: 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).
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

substrate_binding_site
type: Class
subclass of: enzyme_active_site
has OBO namespace: mao.obo
has definition: A residue that is directly involved in the binding of a specific substrate.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

mutation
type: Class
subclass of: residue_function
has OBO namespace: mao.obo
has definition: A mutation is a permanent, transmissible change to the genetic material (usually DNA or RNA) of a cell.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

point_mutation
type: Class
subclass of: mutation
has OBO namespace: mao.obo
has definition: Definition
  label: 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).
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

insertion_mutation
type: Class
subclass of: mutation
has OBO namespace: mao.obo
has definition: Definition
  label: 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.
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

deletion_mutation
type: Class
subclass of: mutation
has OBO namespace: mao.obo
has definition: Definition
  label: 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.
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

silent_mutation
type: Class
subclass of: point_mutation
has OBO namespace: mao.obo
has definition: Definition
  label: 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.
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: synonymous_mutation

missense_mutation
type: Class
subclass of: point_mutation
has OBO namespace: mao.obo
has definition: 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.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: nonsynonymous_mutation

nonsense_mutation
type: Class
subclass of: point_mutation
has OBO namespace: mao.obo
has definition: 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.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

mutation_type
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: mutation
has OBO namespace: mao.obo
has definition: 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.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

metal_binding_site
type: Class
subclass of: ligand_binding_site
has OBO namespace: mao.obo
has definition: A residue that is directly involved in the binding of a metal ion.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

CSA_catalytic_site
type: Class
subclass of: catalytic_site
has OBO namespace: mao.obo
has definition: CSA Interface
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

ligand_binding_site
type: Class
subclass of: residue_function
has OBO namespace: mao.obo
has definition: A residue that is directly involved in the binding of a specific ligand.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

mutation_phenotypic_manifestation
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: mutation
has OBO namespace: mao.obo
has definition: OBO_phenotype_ontology interface
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

resid_ptm
type: Class
subclass of: post translational modification
has OBO namespace: mao.obo
has definition: RESID database interface
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

acetylation
type: Class
subclass of: post translational modification
has OBO namespace: mao.obo
has definition: N-terminal of some residues and side chain of lysine or cysteine
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

amidation
type: Class
subclass of: post translational modification
has OBO namespace: mao.obo
has definition: Generally at the C-terminal of a mature active peptide after oxidative cleavage of last glycine
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

blocked
type: Class
subclass of: post translational modification
has OBO namespace: mao.obo
has definition: Unidentified N- or C-terminal blocking group
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

formylation
type: Class
subclass of: post translational modification
has OBO namespace: mao.obo
has definition: Of the N-terminal methionine
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

gamma_carboygluamic_acid
type: Class
subclass of: post translational modification
has OBO namespace: mao.obo
has definition: Of glutamate
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

hydroxylation
type: Class
subclass of: post translational modification
has OBO namespace: mao.obo
has definition: Generally of asparagine, aspartate, proline or lysine
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

methylation
type: Class
subclass of: post translational modification
has OBO namespace: mao.obo
has definition: Generally of N-terminal phenylalanine, side chain of lysine, arginine, histidine, asparagine or glutamate, and C-terminal cysteine
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

phosphorylation
type: Class
subclass of: post translational modification
has OBO namespace: mao.obo
has definition: Of serine, threonine, tyrosine, aspartate, histidine or cysteine
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

pyrrolidone_carboxylic_acid
type: Class
subclass of: post translational modification
has OBO namespace: mao.obo
has definition: 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
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

sulfation
type: Class
subclass of: post translational modification
has OBO namespace: mao.obo
has definition: Of tyrosine, serine or threonine
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

carbohydrate_binding_site
type: Class
subclass of: ligand_binding_site
has OBO namespace: mao.obo

lipid_binding_site
type: Class
subclass of: ligand_binding_site
has OBO namespace: mao.obo
has definition: A residue that is directly involved in the binding of a lipid.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

residue_disulfide_bond
type: Class
subclass of: residue_structural_bond
has OBO namespace: mao.obo
has definition: A strong covalent bond between two sulfhydryl groups. This bond is very important to the folding, structure, and function of proteins.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt
has related synonym: disulfide_bridge

residue_structural_bond
type: Class
subclass of: residue_function
has OBO namespace: mao.obo

contact_residue2
type: Class
subclass of: Restriction
  on property: part_of
  some values from: interresidue_contact
has OBO namespace: mao.obo
has definition: Second residue involved in spatial contact
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

n_terminal_extension
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo

c_terminal_extension
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo

sequence_weight_calculation_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: sequence_weight
has OBO namespace: mao.obo

sequence_insertion
type: Class
subclass of: sequence_feature_type
has OBO namespace: mao.obo

column_consensus
type: Class
subclass of: Restriction
  on property: is_attribute
  some values from: alignment_column
has OBO namespace: mao.obo
has definition: A consensus character that summarises the residue information contained in an alignment_column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

feature_calculation_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: sequence_feature
has OBO namespace: mao.obo
has definition: The method used to determine the feature.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

column_consensus_calculation_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: column_consensus
has OBO namespace: mao.obo
has definition: The method used to determine the consensus character associated with a column.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

so_mutation
type: Class
subclass of: mutation
has OBO namespace: mao.obo
has definition: SO interface
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

sequence_keyword
type: Class
subclass of: Restriction
  on property: part_of
  some values from: sequence_keyword_list
has OBO namespace: mao.obo
has definition: A keyword provides information that can be used to generate indexes of the sequence entries based on functional, structural, or other categories.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

hydrophobicity_calculation_method
type: Class
subclass of: Restriction
  on property: is_annotation
  some values from: hydrophobicity
has OBO namespace: mao.obo
has definition: The method used to calculate the hydrophobicity measure.
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

contact_distance
type: Class
subclass of: Restriction
  on property: part_of
  some values from: interresidue_contact
has OBO namespace: mao.obo
has definition: Distance between two residues in spatial contact
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

contact_description
type: Class
has OBO namespace: mao.obo
has definition: Textual comment describing spatial contact between two residues
  type: Definition
  has db xref: MAO:jt
    type: DbXref
    has URI: http://purl.org/obo/owl/MAO#MAO_jt

Alanine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasPolarity
  some values from: Non-Polar
subclass of: Restriction
  on property: hasSize
  all values from: Tiny
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasPolarity
  all values from: Non-Polar
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophobic
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophobic
subclass of: Restriction
  on property: hasSize
  some values from: Tiny
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
disjoint with: Cysteine
disjoint with: Aspartate
disjoint with: Glutamate
disjoint with: Phenylalanine
disjoint with: Glycine
disjoint with: Histidine
disjoint with: Isoleucine
disjoint with: Lysine
disjoint with: Leucine
disjoint with: Methionine
disjoint with: Asparagine
disjoint with: Proline
disjoint with: Glutamine
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Cysteine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasPolarity
  some values from: Polar
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophobic
subclass of: Restriction
  on property: hasSize
  some values from: Small
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasPolarity
  all values from: Polar
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophobic
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasSize
  all values from: Small
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
disjoint with: Aspartate
disjoint with: Glutamate
disjoint with: Phenylalanine
disjoint with: Glycine
disjoint with: Histidine
disjoint with: Isoleucine
disjoint with: Lysine
disjoint with: Leucine
disjoint with: Methionine
disjoint with: Asparagine
disjoint with: Proline
disjoint with: Glutamine
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Aspartate
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasCharge
  some values from: Negative
subclass of: Restriction
  on property: hasSize
  some values from: Small
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasPolarity
  all values from: Polar
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasSize
  all values from: Small
subclass of: Restriction
  on property: hasCharge
  all values from: Negative
subclass of: Restriction
  on property: hasPolarity
  some values from: Polar
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophilic
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophilic
disjoint with: Glutamate
disjoint with: Phenylalanine
disjoint with: Glycine
disjoint with: Histidine
disjoint with: Isoleucine
disjoint with: Lysine
disjoint with: Leucine
disjoint with: Methionine
disjoint with: Asparagine
disjoint with: Proline
disjoint with: Glutamine
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine
version info: TODO: Aspartate?

Glutamate
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophilic
subclass of: Restriction
  on property: hasPolarity
  some values from: Polar
subclass of: Restriction
  on property: hasSize
  some values from: Small
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasPolarity
  all values from: Polar
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasCharge
  some values from: Negative
subclass of: Restriction
  on property: hasSize
  all values from: Small
subclass of: Restriction
  on property: hasCharge
  all values from: Negative
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophilic
disjoint with: Phenylalanine
disjoint with: Glycine
disjoint with: Histidine
disjoint with: Isoleucine
disjoint with: Lysine
disjoint with: Leucine
disjoint with: Methionine
disjoint with: Asparagine
disjoint with: Proline
disjoint with: Glutamine
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Phenylalanine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophobic
subclass of: Restriction
  on property: hasSize
  all values from: Large
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aromatic
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophobic
subclass of: Restriction
  on property: hasPolarity
  all values from: Non-Polar
subclass of: Restriction
  on property: hasSize
  some values from: Large
subclass of: Restriction
  on property: hasPolarity
  some values from: Non-Polar
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aromatic
disjoint with: Glycine
disjoint with: Histidine
disjoint with: Isoleucine
disjoint with: Lysine
disjoint with: Leucine
disjoint with: Methionine
disjoint with: Asparagine
disjoint with: Proline
disjoint with: Glutamine
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Glycine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophobic
subclass of: Restriction
  on property: hasPolarity
  some values from: Non-Polar
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophobic
subclass of: Restriction
  on property: hasPolarity
  all values from: Non-Polar
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasSize
  some values from: Tiny
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasSize
  all values from: Tiny
disjoint with: Histidine
disjoint with: Isoleucine
disjoint with: Lysine
disjoint with: Leucine
disjoint with: Methionine
disjoint with: Asparagine
disjoint with: Proline
disjoint with: Glutamine
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Histidine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasPolarity
  some values from: Polar
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophilic
subclass of: Restriction
  on property: hasCharge
  all values from: Positive
subclass of: Restriction
  on property: hasSize
  all values from: Large
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aromatic
subclass of: Restriction
  on property: hasSize
  some values from: Large
subclass of: Restriction
  on property: hasPolarity
  all values from: Polar
subclass of: Restriction
  on property: hasCharge
  some values from: Positive
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophilic
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aromatic
disjoint with: Isoleucine
disjoint with: Lysine
disjoint with: Leucine
disjoint with: Methionine
disjoint with: Asparagine
disjoint with: Proline
disjoint with: Glutamine
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Isoleucine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasPolarity
  all values from: Non-Polar
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophobic
subclass of: Restriction
  on property: hasSize
  some values from: Large
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasPolarity
  some values from: Non-Polar
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophobic
subclass of: Restriction
  on property: hasSize
  all values from: Large
disjoint with: Lysine
disjoint with: Leucine
disjoint with: Methionine
disjoint with: Asparagine
disjoint with: Proline
disjoint with: Glutamine
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Lysine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasSize
  some values from: Large
subclass of: Restriction
  on property: hasCharge
  all values from: Positive
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophilic
subclass of: Restriction
  on property: hasPolarity
  all values from: Polar
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophilic
subclass of: Restriction
  on property: hasPolarity
  some values from: Polar
subclass of: Restriction
  on property: hasCharge
  some values from: Positive
subclass of: Restriction
  on property: hasSize
  all values from: Large
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
disjoint with: Leucine
disjoint with: Methionine
disjoint with: Asparagine
disjoint with: Proline
disjoint with: Glutamine
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Leucine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophobic
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophobic
subclass of: Restriction
  on property: hasSize
  all values from: Large
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasPolarity
  some values from: Non-Polar
subclass of: Restriction
  on property: hasSize
  some values from: Large
subclass of: Restriction
  on property: hasPolarity
  all values from: Non-Polar
disjoint with: Methionine
disjoint with: Asparagine
disjoint with: Proline
disjoint with: Glutamine
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Methionine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasPolarity
  some values from: Non-Polar
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophobic
subclass of: Restriction
  on property: hasSize
  all values from: Large
subclass of: Restriction
  on property: hasSize
  some values from: Large
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophobic
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasPolarity
  all values from: Non-Polar
disjoint with: Asparagine
disjoint with: Proline
disjoint with: Glutamine
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Asparagine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasPolarity
  all values from: Polar
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophilic
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasSize
  all values from: Small
subclass of: Restriction
  on property: hasPolarity
  some values from: Polar
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophilic
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasSize
  some values from: Small
disjoint with: Proline
disjoint with: Glutamine
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine
version info: TODO: Should this be Aliphatic?

Proline
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasPolarity
  some values from: Non-Polar
subclass of: Restriction
  on property: hasSize
  some values from: Small
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophobic
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophobic
subclass of: Restriction
  on property: hasSize
  all values from: Small
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasPolarity
  all values from: Non-Polar
disjoint with: Glutamine
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Glutamine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasPolarity
  some values from: Polar
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasSize
  all values from: Large
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophilic
subclass of: Restriction
  on property: hasPolarity
  all values from: Polar
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasSize
  some values from: Large
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophilic
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
disjoint with: Arginine
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Arginine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophilic
subclass of: Restriction
  on property: hasPolarity
  some values from: Polar
subclass of: Restriction
  on property: hasCharge
  some values from: Positive
subclass of: Restriction
  on property: hasSize
  all values from: Large
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophilic
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasPolarity
  all values from: Polar
subclass of: Restriction
  on property: hasCharge
  all values from: Positive
subclass of: Restriction
  on property: hasSize
  some values from: Large
disjoint with: Serine
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Serine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophilic
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasPolarity
  all values from: Polar
subclass of: Restriction
  on property: hasPolarity
  some values from: Polar
subclass of: Restriction
  on property: hasSize
  all values from: Tiny
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophilic
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasSize
  some values from: Tiny
disjoint with: Threonine
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Threonine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasPolarity
  all values from: Polar
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophilic
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophilic
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasSize
  all values from: Tiny
subclass of: Restriction
  on property: hasSize
  some values from: Tiny
subclass of: Restriction
  on property: hasPolarity
  some values from: Polar
disjoint with: Valine
disjoint with: Tryptophan
disjoint with: Tyrosine

Valine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasSize
  some values from: Small
subclass of: Restriction
  on property: hasSize
  all values from: Small
subclass of: Restriction
  on property: hasPolarity
  some values from: Non-Polar
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aliphatic
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aliphatic
subclass of: Restriction
  on property: hasPolarity
  all values from: Non-Polar
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophobic
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophobic
disjoint with: Tryptophan
disjoint with: Tyrosine

Tryptophan
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophobic
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophobic
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aromatic
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aromatic
subclass of: Restriction
  on property: hasSize
  some values from: Large
subclass of: Restriction
  on property: hasPolarity
  all values from: Non-Polar
subclass of: Restriction
  on property: hasPolarity
  some values from: Non-Polar
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasSize
  all values from: Large
disjoint with: Tyrosine

Tyrosine
type: Class
subclass of: SpecificAminoAcid
subclass of: Restriction
  on property: hasCharge
  some values from: Neutral
subclass of: Restriction
  on property: hasSize
  some values from: Large
subclass of: Restriction
  on property: hasHydrophobicity
  some values from: Hydrophobic
subclass of: Restriction
  on property: hasPolarity
  some values from: Polar
subclass of: Restriction
  on property: hasHydrophobicity
  all values from: Hydrophobic
subclass of: Restriction
  on property: hasSize
  all values from: Large
subclass of: Restriction
  on property: hasSideChainStructure
  some values from: Aromatic
subclass of: Restriction
  on property: hasPolarity
  all values from: Polar
subclass of: Restriction
  on property: hasCharge
  all values from: Neutral
subclass of: Restriction
  on property: hasSideChainStructure
  all values from: Aromatic

EmptyList
type: Class
equivalent class: Class
  intersection of: OWLList
  intersection of: Restriction
    on property: hasContents
    max cardinality: 0
equivalent class: Class
  one of: nil
equivalent class: Class
  intersection of: OWLList
  intersection of: Restriction
    on property: hasNext
    max cardinality: 0

AminoAcidResidue
type: Class
subclass of: Molecular
description: This class will be declared equivalent ot the amino acid class description imported

AncestralNode
type: Class
subclass of: Node
subclass of: Restriction
  on property: part of
  on class: RootedTree
  min qualified cardinality: 1
subclass of: Restriction
  on property: has Descendant
  some values from: Node

Bifurcation
type: Class
equivalent class: Dichotomy
subclass of: AncestralNode
subclass of: Restriction
  on property: belongs to Edge as Parent
  cardinality: 2
disjoint with: Polytomy

Branch
type: Class
equivalent class: Edge
description: '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.

BranchingNode
type: Class
equivalent class: Restriction
  on property: belongs to Edge as Parent
  min cardinality: 2
subclass of: AncestralNode

CDAOAnnotation
type: Class
subclass of: The Character Data Analysis Ontology
description: The base class of annotations in CDAO.
comment: Its possible that this base class should be discarded and that annotations should inherit from an imported base class if one exists.

Character
type: Class
subclass of: Restriction
  on property: has Datum
  some values from: CharacterStateDatum
comment: Traits shown to be relevant for phylogenetic classification

CharacterStateDataMatrix
type: Class
subclass of: The Character Data Analysis Ontology
subclass of: Restriction
  on property: has TU
  some values from: TU
subclass of: Restriction
  on property: has
  some values from: CharacterStateDataMatrixAnnotation
subclass of: Restriction
  on property: has Character
  some values from: Character
description: 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

CharacterStateDataMatrixAnnotation
type: Class
subclass of: CDAOAnnotation
description: Meta-information associated with a character matrix, such as, for the case of a sequence alignment, the method of alignment.

CharacterStateDatum
type: Class
subclass of: The Character Data Analysis Ontology
subclass of: Restriction
  on property: belongs to Character
  on class: Character
  qualified cardinality: 1
subclass of: Restriction
  on property: belongs to TU
  on class: TU
  qualified cardinality: 1
description: 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.

CharacterStateDomain
type: Class
description: 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.

CompoundCharacter
type: Class
subclass of: CategoricalCharacter
subclass of: Restriction
  on property: has Compound Datum
  some values from: CompoundStateDatum
subclass of: Restriction
  on property: has Character
  some values from: Character
subclass of: Restriction
  on property: has Datum
  all values from: CompoundStateDatum
description: 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.

Continuous
type: Class
subclass of: CharacterStateDomain
subclass of: Restriction
  on property: has Value
  cardinality: 1
description: 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).

CoordinateSystem
type: Class
subclass of: The Character Data Analysis Ontology
description: A reference to an external coordinate system. Coordinates for data must refer to some such external coordinate system.

DatumCoordinate
type: Class
subclass of: The Character Data Analysis Ontology
subclass of: Restriction
  on property: has Coordinate System
  on class: CoordinateSystem
  qualified cardinality: 1
description: A positional coordinate giving the source of a character state, used for molecular sequences.
comment: drawing from seqloc categories from NCBI at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/SEQLOC.HTML#_Seq-loc:_Locations_on

DirectedEdge
type: Class
equivalent class: Class
  intersection of: Edge
  intersection of: Restriction
    on property: has Child Node
    on class: Node
    qualified cardinality: 1
  intersection of: Restriction
    on property: has Parent Node
    on class: Node
    qualified cardinality: 1
description: 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.

Edge
type: Class
subclass of: The Character Data Analysis Ontology
subclass of: Restriction
  on property: has Annotation
  some values from: EdgeAnnotation
subclass of: Restriction
  on property: has Node
  on class: Node
  qualified cardinality: 2
description: 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.

EdgeLength
type: Class
subclass of: EdgeAnnotation
subclass of: Restriction
  on property: has Type
  some values from: EdgeLengthType
subclass of: Restriction
  on property: has Value
  some values from: anySimpleType
comment: Its possible that this should not be classed as an 'annotation' since it contains data rather than meta-data.
description: The length of an edge (branch) of a Tree or Network, typically in units of evolutionary changes in character-state per character.

Generic State
type: Class
equivalent class: Class
  one of: absent
  one of: unknown
  one of: gap
subclass of: Categorical
description: 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.
comment: This class should be renamed. These are not generic states but non-concrete states including gap, unknown and missing.

MRCANode
type: Class
subclass of: CommonAncestralNode
subclass of: Restriction
  on property: nca node of
  on class: SetOfThings
  min qualified cardinality: 1

ModelDescription
type: Class
subclass of: CDAOAnnotation
description: Description of a model of transformations.
comment: 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.

Node
type: Class
subclass of: The Character Data Analysis Ontology
subclass of: Restriction
  on property: belongs to Edge as Child
  on class: DirectedEdge
  max qualified cardinality: 1
subclass of: Restriction
  on property: part of
  on class: Network
  min qualified cardinality: 1

PolymorphicStateDomain
type: Class
subclass of: CharacterStateDomain
subclass of: Restriction
  on property: has Uncertainty Factor
  has value: 1

Polytomy
type: Class
equivalent class: Restriction
  on property: belongs to Edge as Parent
  min cardinality: 3
subclass of: AncestralNode

ReconcileTree
type: Class
subclass of: Tree
subclass of: Restriction
  on property: reconciliation of
  on class: Tree
  min qualified cardinality: 2

RootedTree
type: Class
subclass of: Tree
subclass of: Restriction
  on property: has
  all values from: Class
    union of: DirectedEdge
    union of: Node
subclass of: Restriction
  on property: subtree of
  all values from: RootedTree
subclass of: Restriction
  on property: has Root
  on class: Node
  qualified cardinality: 1
disjoint with: UnrootedTree

Sequence
type: Class
subclass of: The Character Data Analysis Ontology
subclass of: Restriction
  on property: has
  all values from: Restriction
    on property: has Coordinate
    on class: DatumCoordinate
    min qualified cardinality: 1
subclass of: Restriction
  on property: has
  some values from: CharacterStateDatum
description: A set of ordered states, typically the residues in a macromolecular sequence.

SetOfThings
type: Class
subclass of: The Character Data Analysis Ontology
subclass of: Restriction
  on property: has Element
  all values from: Class
    union of: Character
    union of: SetOfCharacters
description: 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.

TU
type: Class
subclass of: The Character Data Analysis Ontology
description: 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'.

TaxonomicLink
type: Class
subclass of: TUAnnotation
description: Link to an externally defined taxonomic hierarchy.

evolutionaryTransition
type: Class
subclass of: hereditaryChange
subclass of: Restriction
  on property: hereditary change of
  on class: Character
  qualified cardinality: 1
subclass of: Restriction
  on property: has Right State
  on class: CharacterStateDomain
  qualified cardinality: 1
subclass of: Restriction
  on property: has Left State
  on class: CharacterStateDomain
  qualified cardinality: 1

hereditaryChange
type: Class
subclass of: Restriction
  on property: has Right State
  on class: CharacterStateDomain
  qualified cardinality: 1
subclass of: Restriction
  on property: hereditary change of
  on class: Character
  qualified cardinality: 1
subclass of: Restriction
  on property: has Left State
  on class: CharacterStateDomain
  qualified cardinality: 1

parameterType
type: Class

serviceDescription
type: Class

displaying
type: Class
subclass of: formatConverting
comment: input and output are different representations of the same thing - syntax translation

formatConverting
type: Class
subclass of: shim task
disjoint with: mapping
disjoint with: parsing
disjoint with: retrieving
comment: input and output are different representations of the same thing - syntax translation

mapping
type: Class
subclass of: shim task
disjoint with: parsing
disjoint with: retrieving
comment: input is equivalent to output

parsing
type: Class
subclass of: shim task
disjoint with: retrieving
comment: output is part of input

retrieving
type: Class
subclass of: shim task
comment: input uniquely identifies output

translating
type: Class
subclass of: bioinformatics task
subclass of: Restriction
  on property: task performed by
  some values from: translation algorithm
comment: The biological sense of the word. The process of converting a sequence of nucleic acid (mRNA) into an amino acid sequence

The Character Data Analysis Ontology
type: Class
date: $Date: 2011/04/15 12:36:54 $
version info: $Id: cdao.owl,v 1.36 2011/04/15 12:36:54 astoltzfus Exp $
Coverage: 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.
Rights Management: GNU General Public License (GPL)
description: 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.
Source: http://www.evolutionaryontology.org/CDAO
language: OWL (RDF-XML)
creator: CDAO Team
subject: comparative analysis; comparative data analysis; evolutionary comparative analysis; evolution; phylogeny; phylogenetics