Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

Textmining activities at BioHackathon 2010

1,597 views

Published on

Summary of the activities developed by the text mining task force during the BioHackathon 2010

http://hackathon3.dbcls.jp/wiki/TextMining

Published in: Education, Technology
  • Be the first to comment

Textmining activities at BioHackathon 2010

  1. 1. Semantic Textmining Goals and achievements BioHackathon 2010
  2. 2. Team members • Hammad • Matthias • Venkata • Heiko • YAMAMOTO-san • Alberto
  3. 3. Original Proposal • Integration of text mining results – Reflect / Whatizit / Medie – Results as triplets • URI and predicates – Implementation with SADI – Result presentation using aTag • Explore relations • Interfaces
  4. 4. The work done • Integration of text mining results – Reflect / Whatizit / Medie – Results as triplets • URI and predicates – Future BioPython module and REST service • Explore relations – Sesame endpoint – Biogateway – ARQ for federated queries • Interfaces – Result presentation using aTag – Exhibit faceted interface
  5. 5. http://whatizit.neurocommons.org/
  6. 6. http://whatizit.neurocommons.org/
  7. 7. RDF schema for TM <rdf:Description> <rdf:type rdf:resource="http://rdfs.org/sioc/ns#Item"/> <sioc:about rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/9002550"/> <sioc:content>SBMA</sioc:content> <sioc:topic rdf:resource="http://purl.uniprot.org/uniprot/P10275"/> <rdfs:seeAlso rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/9002550"/> </rdf:Description>
  8. 8. http://reflect.ws
  9. 9. MEDIE and Enju APIs • MEDIE is an intelligent search engine to retrieve biomedical correlations from MEDLINE, based on indexing by Natural Language Processing and Text Mining techniques. • Enju is a syntactic parser for English.
  10. 10. Medie XML output http://www-tsujii.is.s.u-tokyo.ac.jp/medie/dbcls.cgi?pmid=19116711
  11. 11. Enju XML output http://docman.dbcls.jp/medieconv?pmid=17551671
  12. 12. http://togows.dbcls.jp/entry/pubmed/pmid.ttl http://www.uniprot.org/uniprot/P12345.rdf
  13. 13. Workflow Whatizit Reflect Medie Pubmed XML XML XML RDF RDF TogoWS RDF Uniprot
  14. 14. Substance A Interacts with Receptor B Region C axonal projections brain region D Region D aversive stimuli Interlink these entities with taxonomies & ontologies
  15. 15. TMOntology
  16. 16. http://hackathon3.dbcls.jp/wiki/TextMining

×