Phenoscape

Peter Midford and I recently attend the two-day Relations Ontology workshop in Denver, Colorado. The goal of the meeting was to further develop the Relations Ontology (RO) by moving relations from RO proposed (ontology for relations yet to be officially added to RO) to RO, and adding any new relations proposed by attendees. Impressively, almost all of the items on the original agenda were covered, and an ‘action list’ was produced to focus efforts subsequent to the meeting.

Phenoscape had several relations on the agenda, and Peter and I have summarized the discussion, definitions, and examples used.

Read the rest of this entry »

The Teleost Anatomy Ontology (TAO) is a multi-species anatomy ontology for teleost fishes.  In this first post about the TAO, I’ll introduce the structure of the ontology and its development, and discuss some of the challenges we’ve come across in building a multi-species ontology. You can browse the TAO by using the NCBO BioPortal.

Read the rest of this entry »

Searching as well as visualizing the Teleost Anatomy Ontology (TAO) on the NCBO Bioportal was broken for more than a week but has been fixed since Friday.

The other good update from the Bioportal development is that terms can now be found by their synonyms as well. For example, try searching TAO for the ‘dermosphenotic’, which at present isn’t the name of a term in the ontology. Instead, you get the ‘infraorbital 5‘, for which dermosphenotic is a synonym.

Fish morphologists will note that this is actually problematic, since in reality the dermosphenotic is the synonym for the last infraorbital bone. In zebrafish, with which we seeded the TAO, this is indeed the 5th in the series of infraorbitals, but in other clades of teleosts it is the 6th or yet another one. But that’s another story, which we’ll highlight in a forthcoming post on building the TAO.

We have created a new mailing list, obo-taxonomy, under the OBO (Open Biomedical Ontologies) umbrella. Our motivation for this new forum is to really open up the discussion surrounding the issues of what should be a proper ontological representation of taxonomy and phylogeny, for example proper semantics of the relationship between taxonomic groups, and between specimens and species. If you care about or have thoughts or opinions on these and related questions, we encourage you to subscribe to this new list.

Read the rest of this entry »

One of the two main ontologies developed and used by the Phenoscape project is the Teleost Taxonomy Ontology (TTO). Although the Phenoscape project is focused on the Ostariophysi, the TTO covers not just teleosts, but all the species listed in Bill Eschmeyer’s Catalog of Fish. This post will discuss how the current TTO was constructed and the work flow we use to update it. A later posting will discuss the effort to update the ontology to better represent current thinking about metaphysical status of species and other taxonomic terms.

Read the rest of this entry »

Aside from the Evolutionary Biology and Ontologies Workshop that we organize together with the NCBO at the Evolution Meeting 2008 in Minneapolis, we will also be presenting a poster. For your advance pleasure, here is the abstract that we wrote, only to realize that registration for a poster presentation actually did not require or even offer any abstract submission.

Read the rest of this entry »

We finally set up a Phenoscape project on SourceForge.net. At this moment there isn’t much there in the code repository, but within the next days we’ll deposit some scripts that we had to develop for OBO-format ontology generation (for example, for initiating the TTO from the Catalog of Fishes) and for massaging the tracker messages auto-generated by the OBO term request trackers to be more user-friendly. The source code repository will also be the home for some controlled vocabularies that (only?) we need for our project (such as the one for museum codes).

Read the rest of this entry »

The first Phenoscape Data Jamboree (we are scheduled to have one each year) is starting today at NESCent. The event brings three fish morphologists external to the project (Miles Coburn, Kevin Conway, Mário de Pinna) together with our morphologist, ontology, and informatics personnel. In addition, Nicole Washington (NCBO) and Martin Ringwald (Jackson Laboratory), two experts from communities that have made considerable strides in bringing ontology-driven and semantically explicit approaches to bear on annotating gene function and mouse phenotypes and gene expression, respectively, are here to serve in an advisory role.

Read the rest of this entry »

Released new Phenote version (download). It has the following new features:

• Changed version scheme again, hopefully for the last time
• Bug fixes to in-table editing
• Added TAO to the Quality field for use in post-composition
• Included built-in Phenoscape interface layout
• Re-ordered input fields to better match curation workflow

Released new Phenote version (download). It has the following new features:

• Annotations can now be edited directly in the table