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):
tracker-flowchart.jpg
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.
Click the “Add new” link to begin submission of a new tracker
item
In the ‘Category’ field, pick the appropriate category for your
request (new term request, obsoletion request, or other term-related
request)
If the ‘Assigned To’ field appears, choose the appropriate curator
for your request: wdahdul if anatomy, pmidford if taxonomy related.
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.
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
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.
Submit the museum code request to the taxonomy tracker.
Click the “add new artifact” link to begin submission of a new
tracker item
In the Assigned to field, choose pmidford.
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.
Describe your request in the Detailed Description field. Include
museum abbreviation, description, and synonym if needed.
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.
Add requested code to the Fish Collection Codes spreadsheet on
Google Docs:
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.
In the Status field, type “pending”, and record the date of
request and your initials in the Request Notes field.
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.
