Workflow Entry: BioAID_DiseaseDiscovery

This workflow finds disease relevant to the query string via the following steps: 1. A user query: a list of terms or boolean query – look at the Apache Lucene project for all details. E.g.: (EZH2 OR "Enhancer of Zeste" +(mutation chromatin) -clinical) 2. Retrieve documents: finds relevant documents (abstract+title) based on query (edit maxHits to change the default maximum number of documents returned; the AIDA service inside is based on Apache Lucene) 3. 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 service inside is based on LingPipe) 4. Link proteins to disease contained in the OMIM disease database (with a service from Japan that interrogates OMIM) Workflow by Marco Roos (AID = Adaptive Information Disclosure, University of Amsterdam; http://adaptivedisclosure.org) Text mining services by Sophia Katrenko and Edgar Meij (AID) OMIM service from the Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, director Hideaki Sugawara (see http://xml.nig.ac.jp) Workflow URL: http://adaptivedisclosure.org/workflows/BioAID/BioAID_DiseaseDiscovery.xml