Difference between revisions of "Terminology"

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'''Phenotype''': An EQ statement. A phenotype, i.e. EQ statement, corresponds to 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. <font color=red>''- used in all papers''</font>
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__TOC__
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== Phenotypes ==
  
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'''Distinct phenotype''': Phenotype that differs from others in entity, quality, related entity (where present), relation, or postcomposition (order of parens) <font color=red>''not used''</font> though used currently in Phenoscape paper
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=== Phenotypes and Characters ===
  
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'''Phenotype assertion''': <font color=red>not defined, used in TAO paper only''</font>
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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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**'Another alternative would take advantage of phenotype annotations to infer a taxonomically variable relationship. In thiscase, a rule could be constructed that would allow a reasoner to infer from the (separately asserted) presence of Weberian apparatus in a taxon (e.g., Otophysi) that vertebra 1 is a Weberian vertebra in that taxon. Because the presence of the Weberian apparatus is a morphological character state and as such a phenotype, this strategy would use <B>phenotype assertions </B> to inject additional and taxon-specific relationships into the anatomy ontology, without the need for an ontology curator to maintain those separately.'
 
  
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'''Annotation''': part of title of Phenex paper, not defined; defined in TAO paper: 'One common use of ontologies is the  <B>annotation </B> or “tagging” of objects or observations, such as genetic sequences, gene expression patterns, or whole organism phenotypes, with ontology terms. The convention used by model organism databases to  <B>annotate </B> mutant phenotypes is entity-quality (EQ) syntax in which an entity from an anatomical ontology is combined with a quality or nontaxon specific modifier (Gkoutos et al. 2004; Sprague et al. 2008). The Phenoscape project has adopted and extended EQ to  <B>annotate </B> evolutionary phenotypes, specifically systematic characters for ostariophysan fishes. '
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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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'''Asserted annotation''': used in Phenoscape paper
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; Character: Presumably homologous feature of an organism that varies across taxa.
  
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'''Inferred annotation''': used in Phenoscape paper
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; Character state: Variant of a character; assigned a code in a phylogenetic analysis.
  
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'''Phenotype annotation''': <font color=red>''- used in all papers, not defined!''</font>
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; Composite character state: A character state with more than one phenotype.
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**From SB paper: 'Because the active use of ontologies is relatively new to evolutionary biology in general and systematics in particular, the biological research project currently driving development of TAO is the  <B>phenotype annotation </B> of the systematic literature for teleost fishes by the Phenoscape project.'
 
  
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**From SB paper: 'For example, a character state might be “Antorbital, triangular.” This phenotype can be expressed using the TAO term antorbital and the PATO term triangular. Such  <B>phenotype annotations </B> corresponding to systematic characters require the association of the anatomical term with a taxonomic name. Thus, TAO terms are associated with species or higher taxa through annotations to teleost scientific names from the Teleost Taxonomy On- tology (www.phenoscape.org; OBO CVS repository: http://obofoundry.org).'
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; Phenotyped character: A character with one or more states assigned to a phenotype.
  
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**From Phenex paper:'Here, we address this problem at its root by development of a configurable software tool that employs standard ontologies and syntax to create computable  <B>phenotype annotations </B>.'
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=== Phenotype annotations ===
  
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**'Specialized software has been developed to assist human curators in  <B>annotating </B> the phenotypes of mutant genotypes using EQ syntax...'
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; Phenotype annotation: (synonym: phenotype assertion) The connection of a phenotype to a taxon or gene.
  
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'''Zebrafish phenotype annotations''': - used currently in Phenoscape paper to mean 'Zebrafish phenotypes' or Zebrafish EQ statements'
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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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** E.g.: 'Zebrafish phenotype annotations recorded in the ZFIN database (21,476 as of 13 Jan 2011) are associated with genes (3,865) that are mutated or knocked down using morpholinos'
 
  
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'''Gene phenotype''': used in Phenoscape paper to describe the phenotypes associated with genes in the zebrafish database.  See kb where we use '<b>Gene phenotype annotations</b>' and 'Complex query for: annotated genes'.  We use 'mutant phenotypes' in the TAO paper (not defined).  The Washington et al. paper uses  'zebrafish phenotypes' or 'mutant phenotypes' (but they only use the mutant data, vs. we are using also morpholino data). KB reports also uses 'Count of genotype-phenotype assertions (including morpholinos as genotypes)' and report delivered says 'genotype annotations'.  KB reports uses 'Count of <b>distinct gene-phenotype assertions</b> (implied by genotype assertions)' and report delivered says '<b>gene annotations</b>'.
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; Gene phenotype: A phenotype that has been used in a gene phenotype annotation.
  
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'''Phenotype-taxon assertion (=Taxon-Phenotype annotations?)''': Phenotype that is assigned to a taxon <font color=red>''- not used in Phenex, TAO, or Curation papers, however, '<B>Taxon-Phenotype annotation</B> used in Phenex paper''</font>:
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; Gene phenotype annotation: EQ statement associated with a gene.
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**'From this knowledgebase, similar  <B>taxon–phenotype annotations </B> can be easily discovered by searching higher level anatomical or quality terms.'
 
  
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'''Taxon phenotype''' (used synonymously with '''Taxon phenotype annotations''' in current Phenoscape paper).  Used in the same sense as 'Taxon-phenotype annotations' above in Phenex paper. We have discussed the use of the term '''Evolutionary phenotype'''. See kb for our use of 'Taxonomic phenotype annotations' -- but then we also use 'taxon phenotype annotations'.
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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 phenotype-taxon 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. <font color=red>''- not used''</font>
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; Taxon phenotype annotation: EQ statement associated with a taxon.
  
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'''
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== Taxa, Taxon Names, and Taxon Summaries ==
  
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'''Attribute''': Higher level PATO quality term used to group "value qualities".  NOTE: In current Phenoscape paper we define as 'Attributes are relatively high-level nodes in the PATO quality ontology, such as shape, position, etc.'
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; Publication (Taxon) Name: The taxon name used in a publication from which we have curated data.
  
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'''Value qualities''': Nodes at a lower level than 'Attribute' in the PATO hierarchy
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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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'''Phenotype Group''': combination of an attribute with some entity, such as basihyal bone shape, tooth count, etc.<font color=red>''- not used -- PM recommends getting rid of this''</font>
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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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'''Phenotype profile''': union of phenotypes that are asserted for a particular gene or a particular taxon. Washington et al. define phenotypic profile as 'the sum-total of the EQ descriptions for an individual genotype' (but they also refer to gene phenotype profile.
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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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= Taxa: =
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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 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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; 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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[*side note not for report: should be around 3,400 for 47 publications]
 
  
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'''Distinct Publication Names''': Count of the unique number of publication taxa used in the publications that have annotations.  The same publication name used in different publications is counted only once.
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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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'''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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; 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>
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'''Total Mismatches''': Count of the total number of mismatches between Total Publication Names 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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'''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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'''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. <font color=red>''- used in Curation paper''</font>
 
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''' Character''':
 
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'''Character state''': variant of a Character, assigned a code in a phylogenetic analysis <font color=red>''- used''</font>
 
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'''Composite character''': character state with more than one phenotype. <font color=red>''- used in Curation paper, Phenex paper''</font>
 
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'''Phenotyped character''': Character with one or more states assigned to a phenotype <font color=red>''- not used''</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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