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 from a subset of Medline that is about Homo Sapiens according to mesh annotation. Protein names (symbols of at least 3 characters) are validated against human UniProt symbols.

This workflow follows the following basic steps:

  1. it retrieves documents relevant for the query string (documents tagged with mesh term 'Humans' only)
  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)

Protein discoveries are filtered on their presence in UniProt (human only)

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