Resources for Data Contributors

The following instructions outline the resources used by Phenoscape curators for the annotation of evolutionary phenotypes. If you are a student intern, please refer to the Student Instructions page for more information and links.

Data uploaded to the Phenoscape Knowledgebase are made available under a Creative Commons Attribution 3.0 Unported license (see Phenoscape data policy)

1. Download Most Recent Version of Phenex

Phenex was developed by Phenoscape for annotation of evolutionary phenotypes. You can find instructions for downloading and installing Phenex at the Phenex homepage.

2. Access Project Files

Phenoscape project files are XML files (more specifically, they are in NeXML format) created using Phenex and housed in a shared DropBox folder (named 'Phenoscape-data'). Please contact Wasila or Paula if you are interested in perusing or adding to them.

3. Access PDFs for Curation

Phenoscape uses Mendeley to maintain the collection of PDFs for curation. Please ask project personnel (Wasila or Paula) for an invitation to join the group.

Phenoscape also maintains a collection of PDFs for teleost publications on the Phenoscape file share. Directions for connecting to the file share are below. Please ask a Phenoscaper for the username and password.

Mac OS X

1. In finder > Go > Connect to Server
2. Type in

https://webdav.nescent.org/phenoscape-data

1. Accept security warning about certificate
2. enter username and password

Windows XP

1. Go to "My Network Places"
2. Add a Network Place (pulls up wizard)
3. Click Next twice
4. In internet or Network address box, type in

https://webdav.nescent.org/phenoscape-data

1. Accept certificate warning, if given.
2. Give the share a meaningful name. Default is usually fine.
3. Finish

4. Use Ontologies to Annotate Characters

The primary activity of a curator is to annotate the free-text characters from systematic studies using ontologies. Instructions for this activity can be found in the Phenoscape Guide to Character Annotation.

5. Update Taxon Lists

Most project files require a taxonomic expert to review the taxonomy used in a publication and update to reflect current taxonomy. Please see instructions for creating taxon lists in Phenex or instructions for updating taxon lists with valid taxon names.

6. Request New Terms for Ontologies

Curation drives ontology development and many new terms and relationships need to be added. Term requests for updates to ontologies used in Phenoscape can be submitted to the following term trackers:

• Uber Anatomy Ontology (Uberon) term tracker
• Phenotype and Trait Ontology (PATO) term tracker
• Vertebrate Taxonomy Ontology (VTO) term tracker
• Collection Codes Vocabulary

7. Edit the Anatomy Ontology

• Ontology Editing Guidelines

8. Subscribe to Curator and Ontology Request Mailing Lists

• Phenoscape Curators mailing list (for discussion and communication of data curation issues, solutions, and progress): phenoscape-curators
• Discussion of EQ formalism, phenotype description, PATO terms: obo-phenotype
• Discussion of anatomy ontology issues obo-anatomy