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 1. Download Most Recent Version of Phenex
- 2 2. Access Project Files
- 3 3. Access PDFs for Curation
- 4 4. Use Ontologies to Annotate Characters
- 5 5. Update Taxon Lists
- 6 6. Request New Terms for Ontologies
- 7 7. Edit the Anatomy Ontology
- 8 8. Subscribe to Curator and Ontology Request Mailing Lists
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
- In finder > Go > Connect to Server
- Type in
- Accept security warning about certificate
- enter username and password
- Go to "My Network Places"
- Add a Network Place (pulls up wizard)
- Click Next twice
- In internet or Network address box, type in
- Accept certificate warning, if given.
- Give the share a meaningful name. Default is usually fine.
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