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 |
How to provide feedback
Review the Excel spreadsheet for:
- Errors in character and state descriptions, taxon list, and matrix
- Correct entity or quality term chosen. The fields for Entity, Quality, and Related Entity contain terms from the anatomy or quality ontologies. You can browse these ontologies on the BioPortal's website: browse anatomy ontology or quality ontology at the BioPortal.
- Comments or questions from the curator
Please return your comments in a Word or text file referencing the particular character or taxon for each comment.
