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Showing 9 results. Use the filters on the left and the search box below to refine the results.
Category: Workflow Type: Taverna 1 Tag: AIDA Group: AID

Workflow BioAID_DiseaseDiscovery_RatHumanMouseUnipr... (4)

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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...

Created: 2008-12-15 | Last updated: 2011-08-11

Credits: User Marco Roos Network-member AID

Workflow BioAID_ProteinDiscovery_filterOnHumanUnipr... (11)

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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...

Created: 2009-05-28

Credits: User Marco Roos User Martijn Schuemie Network-member AID Network-member AID_myGrid_collaboration

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

Workflow BioAID_ProteinToDiseases (1)

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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: A user query: a single protein name Add synonyms (service courtesy of Martijn Scheumie, Erasmus University Rotterdam) Retrieve documents: finds relevant documents (abstract+title) based on query Discover proteins: extract proteins discovered in the set of relevant abstracts 5. Link proteins ...

Created: 2007-11-14 | Last updated: 2007-11-15

Credits: User Marco Roos User Martijn Schuemie Network-member AID

Attributions: Workflow BioAID_DiseaseDiscovery_RatHumanMouseUniprotFilter

Workflow DiscoverProteinLink (2)

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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 ...

Created: 2007-10-03 | Last updated: 2007-11-15

Credits: User Marco Roos Network-member AID

Workflow BioAID_EnirchBioModelWithProteinsFromText (7)

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This workflow is for demonstration purposes only. Please contact the authors if you wish to try it. We will gladly collaborate with you. Summary This workflow extracts proteins and protein relations from Medline. Extracted protein names (symbols of at least 3 characters) are validated against mouse, rat, and human UniProt symbols, so the results are limited to these species. This workflow follows the following basic steps: it retrieves documents relevant for the query string i...

Created: 2009-05-16 | Last updated: 2009-05-16

Credits: User Marco Roos User Sophia katrenko User Andrew Gibson User M. Scott Marshall User Willem van Hage User Edgar User Martijn Schuemie Network-member AID

Workflow Discover_proteins_from_text (2)

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This workflow discovers proteins from plain text. It is built around 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.

Created: 2007-11-15 | Last updated: 2007-11-15

Credits: User Marco Roos Network-member AID

Workflow ProteinSynonymsToQuery (2)

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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

Created: 2007-10-03 | Last updated: 2007-11-13

Credits: User Marco Roos User Martijn Schuemie Network-member AID

Workflow BioAID_Discover_proteins_from_text_plus_sy... (1)

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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.

Created: 2007-11-15

Credits: User Marco Roos User Martijn Schuemie Network-member AID

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Workflow Index MyExperiment Workflow (2)

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This workflow uses AIDA components to index all of the workflows on MyExperiment. First, it lists and downloads each workflow's xml file. Then, the titles and descriptions are parsed and submitted to an Indexer webservice. After it's finished, your index will be searchable by visiting http://aida.science.uva.nl:9999/search.

Created: 2009-05-26 | Last updated: 2009-05-27

Credits: User Edgar

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