]> Don's unique tag experiment <p>This is a test experiment where I will run the Unique Tags example workflow a few times.</p> 2008-07-25T15:09:08Z 2008-07-25T15:09:08Z 183 69 Job_20080910-1319_Don Cruickshank 2008-09-10T13:20:23Z 2008-09-10T13:21:05Z Job_20080910-1323_Don Cruickshank 2008-09-10T13:24:38Z 2008-09-10T14:24:38Z 2008-09-10T14:25:40Z COMPLETE 2009-01-30T14:45:14Z 2008-09-10T13:24:13Z 2009-01-30T14:45:14Z BioAID_ProteinDiscovery_filterOnHumanUniprot_perDoc_html <p>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 &quot;Enhancer of Zeste&quot;). 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 service inside is based on LingPipe. This subworkflow also 'filters' false positives from the discovered protein by requiring a discovery has a valid UniProt ID. Martijn Schuemie's service to do that contains only human UniProt IDs, which is why this workflow only works for human proteins. Workflow by Marco Roos (AID = Adaptive Information Disclosure, University of Amsterdam; http://adaptivedisclosure.org) Text mining services by Sophia Katrenko and Edgar Meij (AID), and Martijn Schuemie (BioSemantics, Erasmus University Rotterdam). Changes to our original BioAID_DiseaseDiscovery workflow: * Stops at protein discovery * Use of Martijn Schuemie's synsets service to * add synonyms to the query. * provide uniprot ids to discovered proteins * filter false positive discoveries, only proteins with a uniprot id go through; this introduces some false negatives (e.g. discovered proteins with a name shorter than 3 characters) * Counting of results in various ways, but no outputs defined in this simplified workflow. * Output into simple html table.</p> 8 0 2008-02-29T01:34:46Z 2008-10-29T09:29:36Z bioaid_proteindiscovery_filteronhumanuniprot_perdoc_html_14081.xml Test runner for AID Test runner for testing the run option of myExperiment for AID and NBIC marco 2008-03-23T10:48:56Z 2008-03-23T10:48:56Z aida runner aida runner marco 2008-04-10T16:05:45Z 2008-12-03T11:20:58Z --- query_protein: P53 http://aida.science.uva.nl:9999/remotetaverna/v1/data/d782bc1b-9a2e-4a80-a71e-21e19a643470 --- query_protein: P53 http://aida.science.uva.nl:9999/remotetaverna/v1/data/578c39d6-4a94-494b-81ac-a520e00eeac6 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2008-07-13T22:56:51Z 2011-06-28T17:27:44Z 2011-06-28T17:27:44Z 2011-06-28T17:27:44Z 2011-06-28T17:27:44Z 2011-06-28T17:27:44Z 2011-06-28T17:27:44Z 2011-06-28T17:27:44Z