User: Martijn Schuemie

Uploader:

Marco Roos

From biologist to web service to Taverna to myExperiment to biologist

Created: 21/03/08 @ 19:00:24 | Last updated: 23/03/08 @ 10:39:27

Credits: Marco Roos Martijn Schuemie AID myGrid

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 License

File type: video/x-msvideo

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Original Uploader

Marco Roos

BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html (v9)

Created: 29/02/08 @ 01:34:47 | Last updated: 14/12/08 @ 21:44:19

Credits: Marco Roos Martijn Schuemie AID AID_myGrid_collaboration

Attributions: BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow finds proteins relevant to the query string via the following steps: 1. A user query: a single gene/protein name. E.g.: (EZH2 OR "Enhancer of Zeste"). 2. Retrieve documents: finds 'maximumNumberOfHits' relevant documents (abstract+title) based on query (the AIDA service inside is based on Apache's 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...

Rating: 0.0 / 5 (0 ratings) | Versions: 9 | Reviews: 0 | Comments: 1 | Citations: 0

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Original Uploader

Marco Roos

BioAID_Discover_proteins_from_text_plus_synonyms (v1)

Created: 15/11/07 @ 09:40:24

Credits: Marco Roos Martijn Schuemie AID

License: Creative Commons Attribution-Share Alike 3.0 License

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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Original Uploader

Marco Roos

BioAID_ProteinToDiseases (v1)

Created: 14/11/07 @ 12:47:57 | Last updated: 15/11/07 @ 09:00:44

Credits: Marco Roos Martijn Schuemie AID

Attributions: BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow was based on BioAID_DiseaseDiscovery, changes: expects only one protein name, adds protein synonyms). This workflow finds diseases relevant to the query string via the following steps: 1. A user query: a single protein name 2. Add synonyms (service courtesy of Martijn Scheumie, Erasmus University Rotterdam) 3. Retrieve documents: finds relevant documents (abstract+title) based on query 4. Discover proteins: extract proteins discovered in the set of relevant abstracts 5. Link pr...

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Original Uploader

Marco Roos

ProteinSynonymsToQuery (v2)

Created: 03/10/07 @ 18:36:10 | Last updated: 13/11/07 @ 23:47:41

Credits: Marco Roos Martijn Schuemie AID

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow uses Martijn Schuemie's protein synonym service to produce synonyms and a new query string from the input query term. The service is limited to proteins, enzymes and genes. An input query that is a boolean string will be split and processed, but the boolean logic of the input query will be lost. Workflow URL: http://rdf.adaptivedisclosure.org/~marco/BioAID/Public/Workflows/BioAID/ProteinSynonymsToQuery.xml

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

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