Difference between revisions of "Author Guide"

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This page provides background information for authors whose publication(s) has been curated for the Phenoscape Knowledgebase.  The goal of the Phenoscape Project is to link evolutionary data to genomics using ontologies and Phenoscape is developing a curated knowledgebase of morphological characters and prototyping the approach with ostariophysan fishes, beginning with the papers that have published data matrices. Learn more about the project and the ontologies used by Phenoscape here.
 
This page provides background information for authors whose publication(s) has been curated for the Phenoscape Knowledgebase.  The goal of the Phenoscape Project is to link evolutionary data to genomics using ontologies and Phenoscape is developing a curated knowledgebase of morphological characters and prototyping the approach with ostariophysan fishes, beginning with the papers that have published data matrices. Learn more about the project and the ontologies used by Phenoscape here.
  
== Annotation of evolutionary phenotypes using Entity-Quality syntax ==  
+
== How to provide feedback ==
  
The morphological variation reported in systematic character data is documented in phenotype statements recorded in Entity-Quality syntax.  Entities are terms taken from the anatomy ontology to represent anatomical structures and qualities are terms taken from the quality ontology to describe the variable aspect of the structure. For example, an author may describe a “rectangularly shaped supraorbital bone.” This is represented as:
+
Review the Excel spreadsheet for:
  
E: supraorbital, Q: rectangular
+
* Errors in character and state descriptions, taxon list, and matrix
 +
* Comments or questions from the curator (please see Comments columns)
  
Additional information about EQ sytax is available here [EQ_for_character_matrices] and here.
+
Please return your comments by email or in a Word or text file referencing the particular character or taxon for each comment.
 +
 
 +
 
 +
== Annotation of evolutionary phenotypes using Entity-Quality syntax ==
 +
 
 +
The morphological variation reported in systematic character data is documented in phenotype statements recorded in Entity-Quality syntax.  '''Entities''' are terms taken from the anatomy ontology to represent anatomical structures and '''qualities''' are terms taken from the quality ontology to describe the variable aspect of the structure. For example, an author may describe a “rectangularly shaped supraorbital bone.” This is represented as:
 +
 
 +
E: supraorbital, Q: shape
 +
 
 +
Phenotype annotations for characters involving more than one entity require a 'related entity' (RE) in annotation:
 +
 
 +
  E: supraorbital, Q: relational structural quality, RE: antorbital
 +
 
 +
Complex characters may also require more than one phenotype statement. For example, a character state might describe: "antorbital large and sigmoid shaped." Two EQ statements are recorded:
 +
 
 +
E: antorbital, Q: size
 +
E: antorbital, Q: shape
 +
 
 +
Additional information about EQ syntax is available [[EQ_for_character_matrices | here]].
 +
 
 +
Phenoscape is currently annotating characters to a coarse level of entity and quality. We are using a small set of quality terms to categorize phenotype variation into broad categories which will guide future annotation and ontology development efforts. See the [[Guide_to_Character_Annotation | '''Guide to Character Annotation''']] for the list of quality terms, and for further examples of how characters are annotated in Phenoscape.
  
 
== Data spreadsheet ==
 
== Data spreadsheet ==
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! Description
 
! Description
 
|-
 
|-
| Publication Taxon || Taxon name used in the publication
+
| Publication Taxon || Free text field for the taxon name used in the publication
 
|-
 
|-
| TTO Taxon || Valid taxon name from the Teleost Taxonomy Ontology (based on Catalog of Fishes)
+
| TTO Taxon || Term from the Teleost Taxonomy Ontology for the valid taxon name (based on Catalog of Fishes)
 
|-
 
|-
|Matrix Taxon ||  Taxon used in the publication's matrix
+
|Matrix Taxon ||  Free text field for the taxon name used in the publication's matrix
 
|-
 
|-
|Taxon Comment || notes or questions made by a curator
+
|Taxon Comment || Notes or questions made by a curator regarding a particular taxon
 
|-
 
|-
|Specimens || voucher specimens from the materials list
+
|Specimens || Voucher specimen(s) from the materials list
 
|}
 
|}
  
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! Description
 
! Description
 
|-
 
|-
|Character Number ||  
+
|Character Number ||
 
|-
 
|-
|Character Description || free-text description of the character from the publication
+
|Character Description || Free-text description of the character from the publication
 
|-
 
|-
|Character Comment:
+
|Character Comment || Notes or questions made by a curator regarding a particular character
 
|-
 
|-
|State Number:
+
|State Number ||
 
|-
 
|-
|State Description || free-text description of the character state from the publication
+
|State Description || Free-text description of the character state from the publication
 
|-
 
|-
|State Comment ||
+
|State Comment || Notes or questions made by a curator regarding a particular state
 
|-
 
|-
|Entity || term from the Teleost Anatomy Ontology (sometimes combined with term from the Spatial Ontology)
+
|Entity || Term from the Teleost Anatomy Ontology (sometimes combined with a Spatial Ontology term)
 
|-
 
|-
|Quality || term from the Phenotype and Trait Ontology (sometimes combined with term from the Spatial Ontology)
+
|Quality || Term from the Phenotype and Trait Ontology (sometimes combined with a Spatial Ontology term)
 
|-
 
|-
|Related Entity || term from the Teleost Anatomy Ontology (sometimes combined with term from the Spatial Ontology)
+
|Related Entity || Term from the Teleost Anatomy Ontology (sometimes combined with a Spatial Ontology term)
 
|-
 
|-
|Count
+
|Count || Numerical value or range
 
|-
 
|-
|Comment
+
|Comment || Notes or questions made by a curator regarding a phenotype statement
 
|}
 
|}
  
 
[[Category:Curation]]
 
[[Category:Curation]]
 
[[Category: Training]]
 
[[Category: Training]]
 +
[[Category: Help]]

Latest revision as of 21:32, 15 June 2009

This page provides background information for authors whose publication(s) has been curated for the Phenoscape Knowledgebase. The goal of the Phenoscape Project is to link evolutionary data to genomics using ontologies and Phenoscape is developing a curated knowledgebase of morphological characters and prototyping the approach with ostariophysan fishes, beginning with the papers that have published data matrices. Learn more about the project and the ontologies used by Phenoscape here.

How to provide feedback

Review the Excel spreadsheet for:

  • Errors in character and state descriptions, taxon list, and matrix
  • Comments or questions from the curator (please see Comments columns)

Please return your comments by email or in a Word or text file referencing the particular character or taxon for each comment.


Annotation of evolutionary phenotypes using Entity-Quality syntax

The morphological variation reported in systematic character data is documented in phenotype statements recorded in Entity-Quality syntax. Entities are terms taken from the anatomy ontology to represent anatomical structures and qualities are terms taken from the quality ontology to describe the variable aspect of the structure. For example, an author may describe a “rectangularly shaped supraorbital bone.” This is represented as:

E: supraorbital, Q: shape

Phenotype annotations for characters involving more than one entity require a 'related entity' (RE) in annotation:

 E: supraorbital, Q: relational structural quality, RE: antorbital

Complex characters may also require more than one phenotype statement. For example, a character state might describe: "antorbital large and sigmoid shaped." Two EQ statements are recorded:

E: antorbital, Q: size
E: antorbital, Q: shape

Additional information about EQ syntax is available here.

Phenoscape is currently annotating characters to a coarse level of entity and quality. We are using a small set of quality terms to categorize phenotype variation into broad categories which will guide future annotation and ontology development efforts. See the Guide to Character Annotation for the list of quality terms, and for further examples of how characters are annotated in Phenoscape.

Data spreadsheet

The spreadsheet sent to you contains data curated by students and at least one data curator (a taxonomic expert). The various columns contained in the spreadsheet are summarized below:

Taxa and Matrix fields:

Field Description
Publication Taxon Free text field for the taxon name used in the publication
TTO Taxon Term from the Teleost Taxonomy Ontology for the valid taxon name (based on Catalog of Fishes)
Matrix Taxon Free text field for the taxon name used in the publication's matrix
Taxon Comment Notes or questions made by a curator regarding a particular taxon
Specimens Voucher specimen(s) from the materials list


Characters and EQ fields:

Field Description
Character Number
Character Description Free-text description of the character from the publication
Character Comment Notes or questions made by a curator regarding a particular character
State Number
State Description Free-text description of the character state from the publication
State Comment Notes or questions made by a curator regarding a particular state
Entity Term from the Teleost Anatomy Ontology (sometimes combined with a Spatial Ontology term)
Quality Term from the Phenotype and Trait Ontology (sometimes combined with a Spatial Ontology term)
Related Entity Term from the Teleost Anatomy Ontology (sometimes combined with a Spatial Ontology term)
Count Numerical value or range
Comment Notes or questions made by a curator regarding a phenotype statement