Author Guide

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

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