Term Requests

The ontologies developed by Phenoscape are updated regularly, and requests from the community for improvement to the ontologies are welcome. These requests are typically for addition of new terms and synonyms, new and refined definitions and relationships, and corrections for spelling errors. Requests are submitted to one of the SourceForge trackers, and automatically forwarded to the teleost-discuss mailing list so that other users can provide feedback on the request. Below is a flowchart showing the term request process for the anatomy ontology (TAO):

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Submit requests related to any aspect of fish anatomy to the Teleost Anatomy Ontology (TAO) tracker. Requests related to taxonomic names and museum codes should be submitted to the Teleost Taxonomy Ontology (TTO) tracker.

Create Your SourceForge Account

Go to the SourceForge homepage to create your account (click on the "create account" link on the upper right corner of the page). Although requests can be submitted without logging in, creating your own account has the advantage of allowing you to track the progress of your request by email and through your sourceforge account page.

Request Procedures

Anatomy or Taxonomy Requests

1. Log on to your SourceForge account
2. Go to the tracker page approporiate for your request: teleost anatomy tracker or taxonomy tracker. Once you have submitted your first request, you can also navigate to the tracker page by clicking on the "Tracker" link within your Personal Page.
3. Click "submit new"
4. In the Category field, pick the approporiate category for your request (new term request, obsoletion request, or other term-related request)
5. In the Assigned to field, choose the appropriate curator for your request: wdahdul if anatomy, pmidford if taxonomy related.
6. In the Summary field, type in the name of the requested term, or short description of the subject. The text entered here will appear in the Subject line of the subsquent email created for this request.
7. Describe your request in the Detailed Description field. It is helpful to include the following information when possible: name of new term, proposed definition, relationships, synonyms, and relevant citations. Definitions for anatomy terms should be given in genus-differentia form
8. When finished, click the Submit button. You will then receive two emails related to this request: a confirmation email of your submission and the teleost-discuss email summarizing the request. All subsequent discussion of the request will take place on the teleost-discuss mailing list. You'll receive a third email once the request is fulfilled and the tracker item closed by a Phenoscape curator.

Collection Code requests

The Collection Code ontology is maintained as a shared spreadsheet on Google Docs (ask a PhenoScaper for access to the spreadsheet). Requests for codes are submitted to the TTO tracker and added to the shared spreadsheet at the same time.

1. Submit the museum code request to the TTO tracker.
   1. Log on to your SourceForge account
   2. Go to the taxonomy tracker.
   3. Click "submit new"
   4. In the Assigned to field, choose pmidford.
   5. In the Summary field, type "museum code: [insert relevant code]" The text entered here will appear in the Subject line of the subsquent email created for this request.
   6. Describe your request in the Detailed Description field. Include museum abbreviation, description, and synonym if needed.
   7. When finished, click the Submit button. You will then receive two emails related to this request: a confirmation email of your submission and the teleost-discuss email summarizing the request. All subsequent discussion of the request will take place on the teleost-discuss mailing list. You'll receive a third email once the request is fulfilled and the tracker item closed by a Phenoscape curator.
2. Add code and description to the *last line* of the fish collection codes spreadsheet. If you are adding a synonym to an existing collection code, use columns C or D as necessary.
3. Update your entry to Google Docs if comments on your request are made on the teleost-discuss mailing list.

If you are creating a Taxon List that requires a new code or synonym addition, make a note in the Curator Notes column that the change has been requested.

An OBO file will be generated from the spreadsheet at least once per month.

Links

Bookmark the following links within your internet browser, as clicking on the bookmarks is the easiest way to go to the tracker page after logging onto SourceForge.

Teleost Anatomy Tracker

Teleost Taxonomy Tracker