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Tag: BioAID User: Marco Roos

Workflow BioAID_Discover_proteins_from_text_plus_sy... (1)

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This workflow discovers proteins from plain text and adds synonyms using Martijn Schuemie's proteins synonym service. Proteins are discovered with the AIDA 'Named Entity Recognize' web service by Sophia Katrenko (service based on LingPipe), from which output it filters out proteins. The Named Recognizer services uses the pre-learned genomics model, named 'MedLine', to find genomics concepts in plain text.

Created: 2007-11-15

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

Workflow Demo_DiseaseDiscovery_byHumanUniprot_scaffold (1)

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This workflow finds disease relevant to the query string via the following steps: 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); consider adding 'ProteinSynonymsToQuery' in front of the input if your query is a protein. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's Lucene)...

Created: 2007-12-10

Credits: User Marco Roos Network-member AID

Workflow Retrieve_documents_MR1 (1)

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This workflow applies the search web service from the AIDA toolbox. Comments: This search service is based on lucene defaults; it may be necessary to optimize the querystring to adopt the behaviour to what is most relevant in a particular domain (e.g. for medline prioritizing based on publication date is useful). Lucene favours shorter sentences, which may be bad for subsequent information extraction.

Created: 2007-12-10

Credits: User Marco Roos User Edgar Network-member AID

Workflow Lucene_bioquery_optimizer_MR1 (1)

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This workflow does four things: it retrieves documents relevant for the query string it discovers entities in those documents, these are considered relevant entities it filters proteins from those entities (on the tag protein_molecule) it removes all terms from the list produced by 3 (query terms temporarily considered proteins) ToDo Replace step 4 by the following procedure: 1. remove the query terms from the output of NER (probably by a regexp matching on what is inside the tag, ...

Created: 2007-12-10

Credits: User Marco Roos Network-member AID

Creator

Pack AIDA demo pack


Created: 2008-12-14 21:35:43 | Last updated: 2009-05-01 17:35:26

 Pack with AIDA demo material

5 items in this pack

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Pack Supporting material for Roos et al., BMC Bioinformat...


Created: 2009-05-15 15:45:32 | Last updated: 2011-08-11 10:01:23

Supporting material for BMC Bioinformatics, supplement for Semantic Web Applications and Tools for Life Science (2009) Structuring and extracting knowledge for the support of hypothesis generation in molecular biology Marco Roos, M. Scott Marshall, Andrew P. Gibson, Martijn Schuemie, Edgar Meij, Sophia Katrenko, Willem Robert van Hage, Konstantinos Krommydas, Pieter W. Adriaans Acknowledgements We thank the myGrid team and OMII-UK for their support in applying their e-Science tools, and M...

5 items in this pack

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Workflow Link_protein_to_OMIM_disease (1)

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Created: 2007-12-10

Credits: User Marco Roos Network-member AID

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