Ontologies, controlled vocabularies with well-defined relations among terms, are a key tool in scientific data integration. By using ontologies, scientists from different disciplines can know when they are referring to the same entity by different names, and new discoveries are enabled by computer software being able to reason across disciplines and over large datasets. Already widely used in genomics, ontologies are of growing importance in systematics, ecology, behavior, genetics, morphology and physiology. This workshop aims to explore the utility of ontologies for ichthyology and herpetology, using the Teleost Anatomy Ontology and the Amphibian Anatomy Ontology as case studies of community resources that are being actively developed and used by members of ASIH. Read the rest of this entry »
Meeting with Deep Fin and other fishy folkApril 17, 2009
Phenoscapers met with Deep Fin and several associated fish groups in late February for ontology development, curation, web interface development and outreach. We had lots of good interactions with the 30+ ichthyologists attending. Read below for the details. Read the rest of this entry »
Second “Evolutionary Biology & Ontologies” workshopJanuary 9, 2009
Our second “Evolutionary Biology & Ontologies Workshop” was held at the Society of Integrative and Comparative Biology (SICB) meetings in Boston (January 5, 2009). It was organized by the Phenoscape PIs (Paula Mabee, Todd Vision, Monte Westerfield), NESCent and Barry Smith from the National Center for Biomedical Ontologies (NCBO). In our morning of talks, our speakers provided the audience with a solid introduction to ontologies, annotations, curation tools, databases, and examples of the integrative questions that can be answered using them. The speakers, titles, and slides for these talks are available through the links below, and they provide an instructive resource for the community. Read the rest of this entry »
Evolutionary Biology & Ontologies Workshop reportJuly 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 »