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Administrator:

Marco Roos

e-science support team for NBIC

Unique name: eScienceSupportTeam4NBIC Created: Sunday 16 March 2008 @ 22:23:11 (GMT)

4 shared items

Uploader:

Marco Roos

Discover_entities (v2)

Created: 10/12/07 @ 21:48:33 | Updated: 10/12/07 @ 22:54:42

Credits: Marco Roos Sophia katrenko AID

License: Creative Commons Attribution-Share Alike 3.0 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: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 486 times | Downloaded: 436 times

Uploader:

Marco Roos

Flatten_and_make_unique (v1)

Created: 10/12/07 @ 22:12:00 | Updated: 10/12/07 @ 22:12:00

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 License

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

Viewed: 443 times | Downloaded: 356 times

Uploader:

Marco Roos

Lucene_bioquery_optimizer_MR1 (v1)

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

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 License

This workflow does four things: 1. it retrieves documents relevant for the query string 2. it discovers entities in those documents, these are considered relevant entities 3. it filters proteins from those entities (on the tag protein_molecule) 4. 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...

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

Viewed: 464 times | Downloaded: 360 times

Uploader:

Marco Roos

Retrieve_documents_MR1 (v1)

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

Credits: Marco Roos Edgar AID

License: Creative Commons Attribution-Share Alike 3.0 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.

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

Viewed: 427 times | Downloaded: 376 times

Uploader:

Marco Roos

BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html (v8)

Created: 29/02/08 @ 01:34:46 | Updated: 28/07/08 @ 21:43:42

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; the AIDA...

Rating: 0.0 / 5 (0 ratings) | Versions: 8 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 728 times | Downloaded: 580 times