August 24, 2008
As we proposed in an earlier post, we have been developing an alternative to the traditional approach of representing taxonomy in ontologies. This alternative represents species (and currently higher taxa) as individuals in the ontology.
There is another phenoscape ontology that would benefit from the use of individuals: our ontology (ok, it’s really a vocabulary) of research collections of fish. Part of our process for curating anatomy papers involves constructing a list of all the specimens reported in the paper (generally the author includes this in the paper, but we enter it to facilitate annotation). The specimen lists consist of collection names and numbers. Although research collections are supposed to have standardize names and abbreviations, practice does not always reflect these standards: the same collection may be abbreviated in different ways by different authors, and collections occasionally merge and the smaller collections might disappear into larger ones or be renamed.
So we constructed a vocabulary of fish collections with their 4-5 letter abbreviations, longer name and possible synonyms. Now a research collection contains individual specimens, but these are parts of a collection, not subtypes of a particular collection, and therefore, the collection is best represented as an individual, not a class. So, the collections vocabulary, represented as an OBO ontology, should ideally use OBO instances (which exist to represent individuals), rather than terms for the collections.
Unfortunately, the current version of OBO-Edit, although it will read and save ontologies containing Individuals, provides no facility for either viewing or editing these individuals. Furthermore, although there are several OWL editors that would allow us to work with Individuals, there are no OBO<->OWL translators that understand what to do with OWL individuals, so they are just omitted in the OBO translation, even though the OBO file format, since version 1.2, has supported Instance ’stanzas.’ Read the rest of this entry »
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Collections Vocabulary, Ontology, Taxonomy Ontology | 
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Posted by pmidford
July 11, 2008
Our first educational and outreach event “Evolutionary Biology & Ontologies Workshop” was held at the Evolution meetings in Minneapolis, Minnesota (June 20, 2008), and we felt it was a big success. We had lots of enthusiasm and over 50 attendees for this all day workshop, which was organized by the Phenoscape PIs (Paula Mabee, Todd Vision, Monte Westerfield), NESCent and Barry Smith from the National Center for Biomedical Ontologies (NCBO).
We need to especially thank all our speakers for their excellent presentations, They not only gave the audience a varied introduction to ontologies, but also a set of examples of the integrative questions that can be answered using them. The slideshows for all of these talks are on our wiki but I thought I would provide a brief overview of each one right below as a summary of the workshop. The use of ontologies is just emerging in evolutionary biology, and it is an exciting time to be involved in this field. As we move forward to use ontologies in evolutionary biology, we discover new requirements and challenges — for example, the challenge of how we create ontologies that are interoperable — so that we can ask big questions that span not only taxonomic groups (such as bees and fishes and mouse and fly) but different knowledge domains (such as phenotype, evolution, and genetics, genomics, medicine). Read the rest of this entry »
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Curation Tools, Data Curation, Ontology, Workshops | Tagged: Evolution Conference, Outreach, RCN | 
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Posted by pmabee
June 10, 2008
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.
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Anatomy Ontology, Ontology | Tagged: Relations | 
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Posted by wdahdul
May 22, 2008
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.
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No Comments » | Anatomy Ontology, Morphology, Ontology, Relations | Tagged: Anatomy Ontology, Ontology | Permalink
Posted by wdahdul
May 14, 2008
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.
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2 Comments | Ontology, Taxonomy Ontology, Teleosts | Tagged: NCBO, taxonomy | Permalink
Posted by pmidford
