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Items tagged with "GO" (10)

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Workflows (9)

Taverna 1 Original Uploader Hamish McWilliam	EBI_OLS_TermInfo (v1) Created: 09/07/08 @ 05:36:40 Credits: Hamish McWilliam License: Creative Commons Attribution 3.0 Unported License Get details of an ontology term given its identifer. This workflow uses the EBI's Ontology Lookup Service (OLS) to get the details of the ontology term. The OLS suports a wide range of biological and bioinformatic ontologies. See http://www.ebi.ac.uk/ontology-lookup/ for more information. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 84 times \| Downloaded: 41 times Tags (9): bioinformatics \| ebi \| gene ontology \| GO \| go terms \| ols \| ontologies \| ontology \| ontology lookup service	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	What is Paget's disease sparql query example (v3) Created: 20/01/09 @ 03:34:08 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License SELECT distinct ?s1 FROM <http://atlas.bio2rdf.org/sparql> WHERE { ?s1 ?p1 ?o1 . ?o1 bif:contains "paget" . FILTER( regex(?s1, "omim") OR regex(?s1, "geneid") OR regex(?s1, "uniprot")) } followed by SELECT ?type1, count() FROM <http://localhost:8890/sparql> WHERE { ?s1 ?p1 ?o1 . ?o1 bif:contains "paget" . ?s1 Rating:* 3.0 / 5 (1 rating) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 280 times \| Downloaded: 68 times Tags (8): bio2rdf \| example \| GO \| OMIM \| pubmed \| sparql \| text_mining \| uniprot	View Download (v3)
Taverna 2 Original Uploader Francois Belleau	Load GO terms in the triplestore (v1) Created: 01/05/09 @ 14:36:50 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 88 times \| Downloaded: 35 times Tags (4): bio2rdf \| GO \| hcls2009 \| virtuoso	View Download (v1)
Taverna 1 Original Uploader Paul Fisher	Clean GO Filter (v1) Created: 19/08/09 @ 16:07:27 Credits: Paul Fisher License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow filters an Ondex graph, by cleaning up any GO terms within the Graph (?). The result is a new Ondex graph. The parameters that can be used with this service are as follows: graphId - the ID of the input Graph. outputGraphId - the ID of the output Graph (Optional). If no output graph is specified filtered items will be removed from the input graph. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 23 times \| Downloaded: 1 time Tags (8): filter \| GO \| go terms \| graph \| ondex \| ovtk \| oxl \| terms	View
Taverna 2 Original Uploader Francois Belleau	Triplify GO database external reference [myexperiment:go_xref_namespace2rdf] (v1) Created: 01/12/09 @ 06:28:26 \| Last updated: 01/12/09 @ 06:29:35 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License Get GO external database list from http://www.geneontology.org/doc/GO.xrf_abbs Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 34 times \| Downloaded: 13 times Tags (5): banff_manifesto \| bio2rdf \| GO \| rdf \| xref	View Download (v1)
Taverna 2 Original Uploader Morgan Taschuk	KEGG Pathways and Additional Information from BLAST (v2) Created: 29/03/11 @ 11:16:17 \| Last updated: 30/03/11 @ 16:09:01 Credits: Morgan Taschuk Attributions: extract_uniprot_embl_gi.xml License: Creative Commons Attribution-Share Alike 3.0 Unported License Takes in a tab-delimited BLAST file and finds additional information about the target proteins from KEGG, Gene Ontology, Interpro and PubMed. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 32 times \| Downloaded: 16 times Tags (6): BLAST \| GO \| interpro \| medline \| pathway \| uniprot	View Download (v2)
Taverna 2 Original Uploader Marco Roos	Gene expression interpretation by the Global Test (v1) Created: 26/04/11 @ 08:31:51 \| Last updated: 26/04/11 @ 08:31:52 Credits: Marco Roos License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow adds meaning to gene expresion values by performing a standard and a literature weighted Global Test. Gene expression is expected to be from Affymetrix microarrays, for which an RMA normalization and entrez Gene ID mapping/summation is performed. Original workflow is by Dennis Leenheer, edits by Marco Roos. Scripts by Kristina Hettne, acknowledging Rob Jellier, Jelle Goeman, and Peter-Bram 't Hoen. The workflow was created for the LUMC BioSemantics group, part of the Human Gen... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 0 times Tags (8): biosemantics \| e-science \| entrez \| gene expression \| GO \| normalization \| phenotype \| text_mining	View
Taverna 2 Original Uploader Dennis Leenheer	[untitled] (v1) Created: 26/04/11 @ 14:50:37 \| Last updated: 26/04/11 @ 15:04:28 Credits: Dennis Leenheer License: Creative Commons Attribution-Share Alike 3.0 Unported License This workflow allows the user to search for processes that are involved with a certain gene. Using microarray-files (CEL-files), consisting of wild type and KO mice to which a stimulant is induced, the user can get an idea of the processes involved. (This is done using the global test and the literature weighted global test.) The results are then given as a text-file. Warning: workflow is not working (needs some revisions), all input is currently hardcoded! (You will have to change the file... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 11 times \| Downloaded: 7 times Tags (16): bioinformatics \| biosemantics \| datamining \| global test \| GO \| kegg \| literature weighted global test \| mapping \| normalization \| rma \| sommation \| taverna \| taverna 2 \| textmining \| weighted global test \| workflow	View Download (v1)
Taverna 2 Original Uploader hindlem	Get names of proteins similar to RNA binding proteins (Simple example SADI workflow) (v1) Created: 18/05/11 @ 15:24:56 \| Last updated: 18/05/11 @ 15:39:02 Credits: hindlem License: Creative Commons Attribution-Share Alike 3.0 Unported License A very simple demo workflow using some existing SADI services. It finds UniProt proteins of GO function "RNA Binding", it then runs a BLAST service to find similar UniProt proteins and then outputs their names. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 13 times \| Downloaded: 6 times Tags (5): bioinformatics \| BLAST \| GO \| sadi \| uniprot	View Download (v1)

Packs (1)

Creator:

Marco Roos

wf4ever Deliverable 6.3 Pack

Created: 02/12/11 @ 09:31:26 | Last updated: 02/12/11 @ 10:21:03

This pack contains (references to) the workflows for GWAS analysis by workflows that perform pathway and GO analysis and biosemantics data interpretation (a special form of text mining). This pack aggregates the deliverable materials for month 8 for Work Package 6. The workflows have not been published in the scientific domain yet, so its content cannot yet be made public. They are available upon request, in particular for reviewers. Please contact Kristina Hettne or Marco Roos (see credit...

6 items in this pack

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