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InviteWorkflow Entry: BioAID_Discover_proteins_from_text_plus_synonyms
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 Version 1
(of 1)
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Version created on:
15/11/07 @ 09:40:24
by:
Marco Roos
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Title: BioAID_Discover_proteins_from_text_plus_synonyms
Type: Taverna 1
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Description
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.
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[1] - BioAID_Discover_proteins_from_text_plus_synonyms
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Original Uploader |
Created: 15/12/08 @ 20:46:09 | Last updated: 11/08/11 @ 09:22:23
Credits:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
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); consider adding 'ProteinSynonymsToQuery' in front of the input if your query is a protein. 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apa...
Rating: 4.0 / 5 (2 ratings) | Versions: 4 | Reviews: 0 | Comments: 3 | Citations: 0 Viewed: 4034 times | Downloaded: 616 times Tags (9): |
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Original Uploader |
Created: 10/12/07 @ 21:48:33 | Last updated: 10/12/07 @ 22:54:42
Credits:
License: Creative Commons Attribution-Share Alike 3.0 Unported License
This workflow contains the 'Named Entity Recognize' web service from the AIDA toolbox, created by Sophia Katrenko. It can be used to discover entities of a certain type (determined by 'learned_model') in documents provided in a lucene output format.
Known issues:
The output of NErecognize contains concepts with / characters, breaking the xml. For post-processing its results it is better to use string manipulation than xml manipulations.
The output is per document, which means entities will ...
Rating: 5.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0 Viewed: 103 times | Downloaded: 50 times Tags (4): |
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Non-Information Resource URI: http://www.myexperiment.org/workflows/81
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