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Using Literature for Biological Discovery Lars Juhl Jensen EMBL Heidelberg
Introduction ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Genes2Diseases: utilizing Medline for finding disease related genes in the human genome ,[object Object],[object Object],[object Object],[object Object],[object Object],http://www.bork.embl.de/g2d
“Biologists would rather share their toothbrush than share a gene name” ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],The synonyms and orthologs lists can be downloaded from: http://www.bork.embl.de/synonyms
Retraining TreeTagger for Medline abstracts ,[object Object],[object Object],[object Object],[object Object]
Tagging is really easy ... compared to extracting the information you are after ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
“Biologists tend to ask simple questions: Here’s a frog ... is he happy?” ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
A mini-ontology of transcription regulation ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Parsing abstracts to identify relationships between genes/proteins ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Using text mining of Medline abstract to support predicted regulatory interactions ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
The next step: mining full text scientific papers ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]
Summary ,[object Object],[object Object],[object Object],[object Object]
Acknowledgments ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

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