BioAID_EnirchBioModelWithProteinsFromText

Created: 2009-05-16 01:06:26      Last updated: 2009-05-16 01:13:18

This workflow extracts proteins and protein relations from Medline. Extracted protein names (symbols of at least 3 characters) are validated against mouse, rat, and human UniProt symbols, so the results are limited to these species.

This workflow follows the following basic steps:

  1. it retrieves documents relevant for the query string
  2. it discovers proteins in those documents, considered relevant to the query string (colocation in text mining terms)
  3. it extract protein-protein relations (slightly stronger than colocation)

In addition, the results are added to a biological model to support hypthesis formation and a procedural model to log trails to evidence. The models are based on description logic (RDF/OWL format).

Acknowledgements:

Synonyms and Uniprot services: Martijn Scheumie, BioSemantics Group, University of Rotterdam, The Netherlands (BioRange project)

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  • Friday 27 November 2009 11:43:02 (UTC)

    This workflow may need some work because of a recent server migration... Our apologies.




Workflow Other workflows that use similar services (1)

Workflow BioAID_ProteinDiscovery_filterOnHumanUnipr... (11)

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This workflow finds proteins relevant to the query string via the following steps: A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste"). Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene) Discover proteins: extract proteins discovered in the set of relevant abstracts with a 'named entity recognizer' trained on genomic terms using a Bayesian approach; the AIDA serv...

Created: 2009-05-28

Credits: User Marco Roos User Martijn Schuemie Network-member AID Network-member AID_myGrid_collaboration

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter