Difference between revisions of "Terminology"

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= Character: =
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__TOC__
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== Phenotypes ==
  
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Character state: variant of a Character, assigned a code in a phylogenetic analysis
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=== Phenotypes and Characters ===
  
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Phenotype: An EQ version of a part or whole character state (i.e. a character state may have multiple phenotypes). Semantically, a phenotype is_a PATO:quality AND inheres_in some entity.
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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: Phenotype that differs from others in entity, quality, related entity (where present), relation, or postcomposition (order of parens)
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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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Phenotyped character: Character with one or more states assigned to a phenotype
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; Character: Presumably homologous feature of an organism that varies across taxa.
  
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Phenotype assertion [phenotype statement]: Phenotype that is assigned to a taxon
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; Character state: Variant of a character; assigned a code in a phylogenetic analysis.
  
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Distinct phenotype assertions: phenotypes assigned to taxa that are 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 (EQ) for alternative character states (when annotating at high level of PATO granularity, e.g.).  Thus the number of distinct phenotype assertions is lower than the number of phenotype assertions.
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; Composite character state: A character state with more than one phenotype.
  
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Attribute: Higher level PATO quality term used to group "value qualities"
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; Phenotyped character: A character with one or more states assigned to a phenotype.
  
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Value qualities: Nodes at a lower level than 'Attribute' in the PATO hierarchy
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=== Phenotype annotations ===
  
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Phenotype Group: combination of an attribute with some entity, such as basihyal bone shape, tooth count, etc.
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; Phenotype annotation: (synonym: phenotype assertion) The connection of a phenotype to a taxon or gene.
  
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= Taxa: =
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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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Total Publication Names: Count of the total number of taxa used in the publications that have annotations. Includes repeated uses of the same publication name in different publications.
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; Gene phenotype: A phenotype that has been used in a gene phenotype annotation.
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[*side note not for report: should be around 3,332 for 47 publications]
 
  
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Distinct 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 'publication-specific' names, meaning those referring to Author and Year in parentheses.
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; Gene phenotype annotation: EQ statement associated with a gene.
  
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Total Mismatches: Count of the total number of mismatches between publication and valid taxon names.  Each mismatch, including the same mismatch in different publications, is counted for the total. Also, do not count any 'publication-specific' names, meaning those refering to Author and Year in parentheses.
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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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Distinct Mismatches: Count of the unique mismatches between publication names and valid taxon names.  The same publication name used in different publications is counted only once.  Also, do not count any 'publication-specific' names, meaning those referring to Author and Year in parentheses.
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; Taxon phenotype annotation: EQ statement associated with a taxon.
  
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Total Publication-Specific Names: Count of the unique Valid Taxon names that refer to the Author and Year in parentheses.  For example, 'Danio sp. (Smith 1992)' is counted as a publication-specific name.
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== Taxa, Taxon Names, and Taxon Summaries ==
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; 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.
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; 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.
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; 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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; 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)).
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; 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).
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; 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).
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; 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).  <font color=red>''- used in Curation paper''</font>
  
 
[[Category:Curation]]
 
[[Category:Curation]]

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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