Recruiting NLP-crowdsourcing-semantic-web postdoc or staff scientist

Our laboratory at the The Scripps Research Institute in beautiful San Diego, California is recruiting a talented individual to help us use crowdsourcing to push the boundaries of biomedical information extraction and its applications.   We are looking for someone with experience in natural language processing (statistical or linguistic), machine learning, and knowledge representation....
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The Network of BioThings

I offer an idea, and a proposal… What: We want to structure biological knowledge by annotating BioThings (genes, proteins, mutations, diseases, and drugs) in biomedical research articles. We want to comprehensively annotate the mentions of these BioThings in research articles, and also want to describe the nature of the relationships between these entities. Finally, we want to do it in...
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Integrating Knowledge Presentation at SMWCon

Our presentation at the Semantic MediaWiki Conference was a smashing hit! I discussed the software we developed to create GeneWiki+, which we’ve christened mwsync. Mwsync is a cool little Java framework that makes it easy to maintain a live mirror of any MediaWiki site that exposes the standard MediaWiki API. The framework copies over any changes made to the source site on a repeating...
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Gene Wiki SPARQL endpoint

Thanks to Leyla and Alex Garcia-Castro from UniProt and Florida State University respectively, we now have access to a SPARQL endpoint for the data in the Gene Wiki.  Access it live here:http://virtuoso.idiginfo.org/sparql(update on 4-28-12 , that is down and a live one is currently available athttp://199.102.237.69:8890/sparql)Here is one query that you might like to try that finds...
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Semantic Wiki Links article published

A while back, I posted an entry here called "Stepping towards a Semantic Wikipedia" that quickly became the most-visited post on this blog.  Today, after several months of waiting, I discovered by accident that the official peer-reviewed article on the same subject is now available (the editors never bothered to tell us that it came out).  The article elaborates on a pattern that...
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Publication review 2011

As the end of 2011 was a busy time grant-writing, I didn’t get an opportunity to highlight several recent publications that came out from our lab. Better late than never: Hu Y, Galkin AV, Wu C, Reddy V, Su AI (2011) CAFET Algorithm Reveals Wnt/PCP Signature in Lung Squamous Cell Carcinoma.PLoS ONE 6(10): e25807. (Full text) This paper described CAFET, a novel algorithm for enrichment-based...
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