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 appropriate mailing list. For example, TAO term requests are forwarded to obo-teleost-discuss@lists.sourceforge.net - List subscription and archives 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

Making Your Requests

1. Log on to your SourceForge account
2. Go to the tracker page appropriate for your request: teleost anatomy tracker, taxonomy tracker, and phenotype and trait ontology (PATO) 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 the "Add new" link to begin submission of a new tracker item
4. In the 'Category' field, pick the appropriate category for your request (new term request, obsoletion request, or other term-related request)
5. If the 'Assigned To' field appears, 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 "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 "Add Artifact' 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.

Note about taxonomic requests

There are several types of taxonomic requests typically submitted after reviewing a taxon list. This includes addition of synonyms or valid species names missing from the taxonomy ontology, and addition of unknown or unnamed species. For more details, see Update Taxon Lists. For example, Smith (2008) may have Danio sp. and Danio aff. dangila in their materials list. These names should be added to the taxonomy ontology with reference to the publication. The request for new species names would be:

• Danio sp. (Smith 2008)
• Danio aff. dangila (Smith 2008)

Warning about unavailable names

When constructing taxon requests for material that is either unpublished or in the publication process, it is important not to expose unpublished names as that may prevent them from being published or recognized by taxonomic authorities. To avoid this, it is important to construct temporary names such as 'Genus1 species1 (Smith 2008).' In this case it is especially important to include author and year (as best known) to distinguish the name from other temporary names as well as simplifying the process of making the temporary obsolete if the material is published.

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 taxonomy (TTO) tracker and added to the shared spreadsheet at the same time; it is important to remember to edit the spreadsheet if comments relevant to your request are made on teleost-discuss.

1. Submit the museum code request to the taxonomy tracker.
   1. Log on to your SourceForge account
   2. Go to the taxonomy tracker.
   3. Click the "add new artifact" link to begin submission of a new tracker item
   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 requested code to the Fish Collection Codes spreadsheet on Google Docs:
   1. Add code and description to the *last line* of the spreadsheet. If you are adding a synonym to an existing collection code, use columns C or D as necessary.
   2. In the Status field, type "pending", and record the date of request and your initials in the Request Notes field.
   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 in Phenote that requires a new code or synonym addition, make a note in the Curator Notes column of your Phenote file indicating that the change has been requested.

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

Links to Trackers

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

PATO tracker