I just got this announcement about an upcoming webinar from the NCBO–the National Center for Biomedical Ontology. It’s a project that’s new to me, so I can’t give you any insights on its utility for our readers. It sounds like text mining + evolution, and ways to extract information that’s not been extensively used previously. But I love to find out about new projects and tools in this arena and I think I’ll listen in.
Here’s the notice I got via the Biocurator mailing list:
The next NCBO Webinar will be presented by Dr. Hilmar Lapp, Assistant Director for Informatics at the National Evolutionary Synthesis Center (NESCent) on “Bringing reason to phenotype diversity, character change, and common descent” at 10:00am PST, Wednesday, November 17. Below is information on how to join the online meeting via WebEx and accompanying teleconference. For the full schedule of the NCBO Webinar presentations see: http://www.bioontology.org/webinar-series.
For more than a century, systematic biologists have meticulously documented the stunning biodiversity of phenotypes across the tree of life in the comparative systematics literature. This vast store of often complex character and character state descriptions informs our understanding of the evolutionary transitions that gave rise to the present diversity of life on earth. Yet, as free text in natural language, these descriptive data are not amenable to even simple computational processing, such as comparison of organisms by phenotype similarity, much less large-scale data integration and knowledge mining. I will present the approach that we have adopted within the Phenoscape project (http://phenoscape.org) to expose these data to machine reasoning. Phenoscape uses the Entity-Quality (EQ) model to transform characters and character states into formal phenotype assertions. Data transformed in this way from the systematics literature are integrated with mutant phenotype data from model organisms in a large knowledge base (http://kb.phenoscape.org), in order to generate hypotheses about the genetic causes of evolutionary character transitions. I will discuss both successes and challenges in blending formal knowledge representation methods with descriptive biology and hypotheses of descent. An important remaining challenge is a logic framework for reasoning over homology, i.e. descent from a common ancestor, which is required for many forms of evolutionary inference.
Hilmar Lapp is the Assistant Director for Informatics at the National Evolutionary Synthesis Center (NESCent). His research interests are in reusable and interoperable software and data, large-scale data integration, and building sustainable cyberinfrastructure. A biologist by training, he has also been programming for more than two decades, ranging from commercial applications to real-time data acquisition to bioinformatics data integration and standards. In his role at NESCent, he is involved in many of the Center’s cyberinfrastructure initiatives, and serves as senior personnel in the NSF-funded Phenoscape project (http://phenoscape.org), as well as the Dryad digital repository for data supporting scientific publications (http://datadryad.org). Before joining NESCent in 2006, he worked for almost 10 years in functional genome informatics in the biopharmaceutical sector. At the Genomics Institute of the Novartis Research Foundation (GNF) in San Diego, CA, he built SymAtlas, one of the first decidedly gene-centric database integrating genome annotation databases with gene function data.
And it also came with webinar details, but I’ll send you over to NCBO for that rather than posting them here. Go over to their webinar page: http://www.bioontology.org/webinar-series and click on this talk. The details about how to join and call in are over there.