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Creator:

Marco Roos

AIDA toolbox

Created: 01/08/08 @ 11:33:03 | Updated: 01/08/08 @ 11:54:45

8 items in this pack

Comments: 0 | Viewed: 92 times |

Uploader:

Marco Roos

From biologist to web service to Taverna to myExperiment to biologist

Created: 21/03/08 @ 19:00:12 | Updated: 23/03/08 @ 10:39:27

Credits: Marco Roos Martijn Schuemie AID myGrid

Attributions: BioAID_DiseaseDiscovery_byHumanUniprot

License: Creative Commons Attribution-Share Alike 3.0 License

File type: video/x-msvideo

Rating: 1.0 / 5 (1 rating) | Comments: 0 | Viewed: 361 times | Downloaded: 289 times

Uploader:

Marco Roos

ProteinSynonymsToQuery (v2)

Created: 03/10/07 @ 18:36:10 | 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

Viewed: 705 times | Downloaded: 571 times

Uploader:

Marco Roos

BioAID_protein_discovery (v1)

Created: 14/11/07 @ 12:46:33 | Updated: 15/11/07 @ 09:01:12

Credits: Marco Roos AID

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 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 2. Retrieve documents: finds relevant documents (abstract+title) based on query (edit maxHits to change the default maximum number of documents returned) 3. Discover proteins: extract proteins discovered in the set of relevant abstracts. Servic...

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Uploader:

Marco Roos

DiscoverProteinLink (v2)

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

Credits: Marco Roos AID

License: Creative Commons Attribution-Share Alike 3.0 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 ...

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

Viewed: 746 times | Downloaded: 624 times

Uploader:

Marco Roos

BioAID_Discover_proteins_from_text_plus_synonyms (v1)

Created: 15/11/07 @ 09:40:24 | Updated: 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.

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

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Uploader:

Marco Roos

BioAID_DiseaseDiscovery_byHumanUniprot (v3)

Created: 05/12/07 @ 23:11:42 | Updated: 15/05/08 @ 21:10:32

Credits: Marco Roos Martijn Schuemie AID

License: Creative Commons Attribution-Share Alike 3.0 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 Apache's Luce...

Rating: 0.0 / 5 (0 ratings) | Versions: 3 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 771 times | Downloaded: 718 times

Uploader:

Marco Roos

Extract_proteins (v2)

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

Credits: Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 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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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...

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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