A new paper entitled "Semi-automated ontology generation within OBO-Edit" has just appeared in the journal Bioinformatics [1]. The paper describes a system called 'DOG4DAG', which supports the creation and extension of OBO ontologies by semi- automatically generating terms, definitions and parent-child relations from text in PubMed, the web and PDF repositories.
Submitted by Trish Whetzel on November 25, 2009 - 12:21
Stephanie Dutchen from the National Institute of General Medical Sciences (NIGMS) writes on “What is an ontology” explaining how ontologies can be used to organize biological knowledge by providing a common vocabulary for scientists in different organizations and specialties and by representing the relationships between terms providing added knowledge.
Submitted by Barry Smith on November 12, 2009 - 13:47
At the IBCO there were a number of talks of interest to Phenoscapers, including one from the BGEE group on Homolonto and Chris Mungall’s on GO cross products and Uberon. Read more.See also here.
Submitted by Barry Smith on November 9, 2009 - 17:53
It is not only in the biomedical domain that ontologies are increasingly being used to advance data information and analysis. Similar developments can be witnessed in many other domains, for example in the military domain of what is called 'C2' or 'Command and Control', which requires agile information sharing with an increasingly wide variety of military and non-military partners. This paper describes an initiative to develop a C2 domain ontology in order to improve C2 data and service integration. It provides an overview of ontology, examples of existing ontologies (including biomedical ontologies), and key C2 areas of potential application.Click here to read the paper.
Submitted by Barry Smith on November 9, 2009 - 13:51
I would like to take this opportunity to describe the type of work that the Semantic Technologies Group in Statistical and Quantitative Sciences has been involved with over the past five or so years. Since most SQS and DDS members are unfamiliar with this area, this letter will be a bit longer than is customary.We start with a brief history lesson.
Submitted by Trish Whetzel on November 6, 2009 - 14:10
The ICBO meeting impressed me by how much of it focused on the science of biomedicine itself, using the language of ontology for clarification and communication. This was a refreshing change from many of the earlier meetings in this subject area, where the discussion centered primarily on whether one person's opinion on the organization and naming of a subject area was any better or worse than another's and whether we had a right to even say.
Some 200 participants enjoyed 3 days of biomedical ontology at the first ICBO conference, preceded by 4 days of classes and tutorials on topics ranging from spatial ontology and qualitative reasoning to the metaphysical foundations of biomedical ethics. The meeting itself included 38 presentations, 43 posters, 6 software demonstrations, 2 panels, and 1 plenary lecture (by Howard Garner, on the use of high-powered text-mining software applied to PubMed for drug discovery).
