Difference between revisions of "Terminology"

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'''Phenotype''': An Entity-Quality (EQ) statement. Semantically, a phenotype is_a PATO:quality AND inheres_in some entity.
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__TOC__
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== Phenotypes ==
  
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* '''Taxon phenotype''': A phenotype that has been used in a taxon phenotype annotation.  A taxon phenotype may correspond to part or whole of a described character state (i.e. a character state may be decomposed into multiple phenotypes).
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=== Phenotypes and Characters ===
  
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* '''Gene phenotype''': A phenotype that has been used in a gene phenotype annotation.
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; Phenotype: An Entity-Quality (EQ) statement. Semantically, a phenotype is_a PATO:quality AND inheres_in some entity. In OWL, a phenotype is a class expression that is equivalent to the intersection of a PATO:quality with all things that inheres_in some entity (a property restriction).
  
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'''Distinct phenotype''': Property of a set of phenotypes. A distinct phenotype differs from others in entity, quality, related entity (where present), relation, or post-composition.
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; Attribute: High-level PATO quality term, such as PATO:shape. Attribute terms are superclasses (direct or indirect) of lower-level PATO quality terms.
  
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* '''Distinct taxon phenotype''': Phenotype assigned to taxon that is unique.  For example, the same taxon might be assigned the same phenotype (EQ) in different papers or the same taxon may be assigned the same phenotype for alternative character states (e.g., when annotating at high level of PATO granularity).  The number of distinct taxon phenotype annotations is typically lower than the total number of taxon phenotype annotations.
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; Character: Presumably homologous feature of an organism that varies across taxa.
  
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* '''Distinct gene phenotype''': Phenotype assigned to gene that is unique.
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; Character state: Variant of a character; assigned a code in a phylogenetic analysis.
  
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'''Phenotype annotation''' (synonym: phenotype assertion): The connection of a phenotype to a taxon or gene.
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; Composite character state: A character state with more than one phenotype.
  
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* '''Taxon phenotype annotation''': EQ statement associated with a taxon.
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; Phenotyped character: A character with one or more states assigned to a phenotype.
  
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* '''Gene phenotype annotation''': EQ statement associated with a gene.
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=== Phenotype annotations ===
  
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'''Attribute''': High-level PATO quality term.
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; Phenotype annotation: (synonym: phenotype assertion) The connection of a phenotype to a taxon or gene.
  
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'''Phenotype profile''': The union of phenotypes that are asserted for a particular gene or a particular taxon.  Washington et al. (2009) defined a phenotypic profile or gene phenotype profile as 'the sum-total of the EQ descriptions for an individual genotype'.
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; Phenotype profile: The union of phenotypes that are asserted for a particular gene or a particular taxon.  Washington et al. (2009) defined a phenotypic profile or gene phenotype profile as 'the sum-total of the EQ descriptions for an individual genotype'.
  
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'''Character''': Presumably homologous feature of an organism that varies across taxa.
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; Gene phenotype: A phenotype that has been used in a gene phenotype annotation.
  
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'''Character state''': Variant of a character; assigned a code in a phylogenetic analysis.
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; Gene phenotype annotation: EQ statement associated with a gene.
  
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'''Composite character''': A character state with more than one phenotype.
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; Taxon phenotype: A phenotype that has been used in a taxon phenotype annotation.  A taxon phenotype may correspond to part or whole of a described character state (i.e. a character state may be decomposed into multiple phenotypes).
  
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'''Phenotyped character''': A character with one or more states assigned to a phenotype.
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; Taxon phenotype annotation: EQ statement associated with a taxon.
  
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== Taxa: ==
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== Taxa, Taxon Names, and Taxon Summaries ==
  
 
; Publication (Taxon) Name: The taxon name used in a publication from which we have curated data.
 
; Publication (Taxon) Name: The taxon name used in a publication from which we have curated data.
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; Total (Number of) Publication Taxon Names:  Count of the total number of taxon names used in the publications that have annotations.  The same publication taxon name used in different publications is counted multiple times.
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; Distinct (Number of) Publication Taxon Names: Count of the unique number of taxon names used in the publications that have annotations.  The same taxon name used in different publications is counted only once.
  
 
; Incompletely Identified Taxon: A taxon that is identified in a publication less specific than genus and species. Typically, these are of the form "''Genus'' sp. (Author Year)", where (Author Year) cites the publication in which it appears.
 
; Incompletely Identified Taxon: A taxon that is identified in a publication less specific than genus and species. Typically, these are of the form "''Genus'' sp. (Author Year)", where (Author Year) cites the publication in which it appears.
  
 
; Valid Taxon Name: The name of a taxon that is currently valid, according to an authoritative naming source (e.g., Catalog of Fishes) that is used in construction of the Taxonomy Ontology under consideration. This may or may not be the same as the Publication Taxon Name.
 
; Valid Taxon Name: The name of a taxon that is currently valid, according to an authoritative naming source (e.g., Catalog of Fishes) that is used in construction of the Taxonomy Ontology under consideration. This may or may not be the same as the Publication Taxon Name.
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; Total (Number of) Publication <font color=red>Taxon</font> Names:  Count of the total number of taxa used in the publications that have annotations.  Includes repeated uses of the same taxon name in different publications.<br/>[*''side note not for report: should be around 3,400 for 47 publications'']
 
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; Distinct (Number of) Publication <font color=red>Taxon</font> Names: Count of the unique number of publication taxa used in the publications that have annotations.  The same taxon name used in different publications is counted only once.
 
  
 
; Distinct (Number of) Valid Taxon Names: Count of unique Valid Taxon names appearing in publications. The same valid taxon name used in different publications is counted only once.  This includes incompletely identified taxa (which we cite to the publication in which it appears, such as ''Danio'' sp. (Smith 1992)).
 
; Distinct (Number of) Valid Taxon Names: Count of unique Valid Taxon names appearing in publications. The same valid taxon name used in different publications is counted only once.  This includes incompletely identified taxa (which we cite to the publication in which it appears, such as ''Danio'' sp. (Smith 1992)).

Latest revision as of 16:19, 4 June 2013

Phenotypes

Phenotypes and Characters

Phenotype
An Entity-Quality (EQ) statement. Semantically, a phenotype is_a PATO:quality AND inheres_in some entity. In OWL, a phenotype is a class expression that is equivalent to the intersection of a PATO:quality with all things that inheres_in some entity (a property restriction).
Attribute
High-level PATO quality term, such as PATO:shape. Attribute terms are superclasses (direct or indirect) of lower-level PATO quality terms.
Character
Presumably homologous feature of an organism that varies across taxa.
Character state
Variant of a character; assigned a code in a phylogenetic analysis.
Composite character state
A character state with more than one phenotype.
Phenotyped character
A character with one or more states assigned to a phenotype.

Phenotype annotations

Phenotype annotation
(synonym: phenotype assertion) The connection of a phenotype to a taxon or gene.
Phenotype profile
The union of phenotypes that are asserted for a particular gene or a particular taxon. Washington et al. (2009) defined a phenotypic profile or gene phenotype profile as 'the sum-total of the EQ descriptions for an individual genotype'.
Gene phenotype
A phenotype that has been used in a gene phenotype annotation.
Gene phenotype annotation
EQ statement associated with a gene.
Taxon phenotype
A phenotype that has been used in a taxon phenotype annotation. A taxon phenotype may correspond to part or whole of a described character state (i.e. a character state may be decomposed into multiple phenotypes).
Taxon phenotype annotation
EQ statement associated with a taxon.

Taxa, Taxon Names, and Taxon Summaries

Publication (Taxon) Name
The taxon name used in a publication from which we have curated data.
Total (Number of) Publication Taxon Names
Count of the total number of taxon names used in the publications that have annotations. The same publication taxon name used in different publications is counted multiple times.
Distinct (Number of) Publication Taxon Names
Count of the unique number of taxon names used in the publications that have annotations. The same taxon name used in different publications is counted only once.
Incompletely Identified Taxon
A taxon that is identified in a publication less specific than genus and species. Typically, these are of the form "Genus sp. (Author Year)", where (Author Year) cites the publication in which it appears.
Valid Taxon Name
The name of a taxon that is currently valid, according to an authoritative naming source (e.g., Catalog of Fishes) that is used in construction of the Taxonomy Ontology under consideration. This may or may not be the same as the Publication Taxon Name.
Distinct (Number of) Valid Taxon Names
Count of unique Valid Taxon names appearing in publications. The same valid taxon name used in different publications is counted only once. This includes incompletely identified taxa (which we cite to the publication in which it appears, such as Danio sp. (Smith 1992)).
Total (Number of) Mismatches
Count of the total number of mismatches between publication taxon names and their corresponding valid taxon names. Each mismatch, including the same mismatch in different publications, is counted for the total. This count excludes incompletely identified taxa (such as Danio sp. in Smith 1992).
Distinct (Number of) Mismatches
Count of the unique mismatches between publication names and valid taxon names. The same mismatche occurring in different publications is counted only once. This count excludes incompletely identified taxa (such as Danio sp. in Smith 1992).
Total (Number of) Publication-Specific Names
Count of the unique valid taxon names that are incompletely identified in (and thus specific to) a publication (such as Danio sp. in Smith 1992). - used in Curation paper
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