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Creator:

Marco Roos

AIDA demo pack

Created: 14/12/08 @ 21:35:44 | Last updated: 01/05/09 @ 17:35:26

5 items in this pack

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Creator:

Marco Roos

Supporting material for Roos et al., BMC Bioinformatics, SWAT4LS supplement (2009)

Created: 15/05/09 @ 15:45:33 | Last updated: 15/05/09 @ 16:05:01

4 items in this pack

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Administrator:

Marco Roos

Semantic_BioAID_collaboration

Created: Friday 22 August 2008 @ 10:49:27 (BST)

5 shared items   |   1 announcements

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 Unported 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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Original Uploader

Marco Roos

BioAID_protein_discovery (v1)

Created: 14/11/07 @ 12:46:33 | Last updated: 15/11/07 @ 09:01:13

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow finds proteins 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 Retrieve documents: finds relevant documents (abstract+title) based on query (edit maxHits to change the default maximum number of documents returned) Discover proteins: extract proteins discovered in the set of relevant abstracts. Services by...

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Original Uploader

Marco Roos

DiscoverProteinLink (v2)

Created: 03/10/07 @ 18:36:12 | Last updated: 15/11/07 @ 09:02:44

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

COMPETITION: For friends only: If you find any two topics that return true positives with this workflow I will buy you a bottle of wine (or equivalent). Terms: if we confirm that the protein was indeed never mentioned together with both input topics in one article, we will publish this together. ---- This workflow implements Swanson's prinicple with services from the AIDA toolbox. It tries to find proteins that link two topics, while they never mentioned together with both topics in ...

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Viewed: 197 times | Downloaded: 41 times

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 Unported 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

Extract_proteins (v2)

Created: 10/12/07 @ 22:10:51 | Last updated: 10/12/07 @ 22:30:53

Credits: Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This workflow filters protein_molecule-labeled terms from an input string(list). The result is a tagged list of proteins (disregarding false positives in the input). Internal information: This workflow is a copy of 'filter_protein_molecule_MR3' used for the NBIC poster (now in Archive).

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Original Uploader

Marco Roos

Lucene_bioquery_optimizer_MR1 (v1)

Created: 10/12/07 @ 22:14:26

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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, ...

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Original Uploader

Marco Roos

Retrieve_documents_MR1 (v1)

Created: 10/12/07 @ 22:17:00

Credits: Marco Roos Edgar AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

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Original Uploader

Marco Roos

BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html (v11)

Created: 29/02/08 @ 01:34:47 | Last updated: 28/05/09 @ 12:21:06

Credits: Marco Roos Martijn Schuemie AID AID_myGrid_collaboration

Attributions: BioAID_DiseaseDiscovery

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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...

Rating: 0.0 / 5 (0 ratings) | Versions: 11 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 256 times | Downloaded: 71 times