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Items tagged with "GO" (15)

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Workflows (13)
Original Uploader

Workflow EBI_OLS_TermInfo (1)

Created: 09/07/08 @ 05:36:40

Credits: User Hamish McWilliam

License: Creative Commons Attribution 3.0 Unported License

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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: 90 times | Downloaded: 44 times

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Original Uploader

Workflow What is Paget's disease sparql query example (3)

Created: 20/01/09 @ 03:34:08

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 320 times | Downloaded: 80 times

Tags (8):

Original Uploader

Workflow Clean GO Filter (1)

Created: 19/08/09 @ 16:07:27

Credits: User Paul Fisher

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 28 times | Downloaded: 1 time

Tags (8):

Original Uploader

Workflow Triplify GO database external reference [... (1)

Created: 01/12/09 @ 06:28:26 | Last updated: 01/12/09 @ 06:29:35

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 39 times | Downloaded: 15 times

Tags (5):

Original Uploader

Workflow KEGG Pathways and Additional Information f... (2)

Created: 29/03/11 @ 11:16:17 | Last updated: 30/03/11 @ 16:09:01

Credits: User Morgan Taschuk

Attributions: Workflow extract_uniprot_embl_gi.xml

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 51 times | Downloaded: 24 times

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Original Uploader

Workflow Gene expression interpretation by the Glob... (1)

Created: 26/04/11 @ 08:31:51 | Last updated: 26/04/11 @ 08:31:52

Credits: User Marco Roos

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 42 times | Downloaded: 0 times

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Original Uploader

Workflow [untitled] (1)

Created: 26/04/11 @ 14:50:37 | Last updated: 26/04/11 @ 15:04:28

Credits: User Dennis Leenheer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 22 times | Downloaded: 15 times

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Original Uploader

Workflow Get names of proteins similar to RNA bindi... (1)

Created: 18/05/11 @ 15:24:56 | Last updated: 18/05/11 @ 15:39:02

Credits: User hindlem

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 27 times | Downloaded: 17 times

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Original Uploader

Workflow Get a list of proteins from a Gene Ontolog... (1)

Created: 20/02/12 @ 23:00:06 | Last updated: 22/02/12 @ 21:08:54

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Get a list of UniProt proteins that have been annotated with the same Gene Ontology (GO) term. This workflow uses the the QuickGO service

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

Viewed: 18 times | Downloaded: 5 times

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Original Uploader

Workflow DatabaseID_to_ConceptID (4)

Created: 25/06/12 @ 20:48:28 | Last updated: 14/09/12 @ 10:03:01

Credits: User Marco Roos User Martijn Schuemie User Reinout van Schouwen Network-member BioSemantics

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose: This workflow maps input Identifiers, common database identifiers, to the Concept Identifiers from the EMC ontology. Result: Concept Identifiers from the EMC ontology. Resources: Table of database identifiers and concept identifiers. Database identifiers from ... EMC ontology compiled from ... Comments: This workflow can be used together with other workflows in this pack: http://www.myexperiment.org/packs/282 for functional gene and SNP annotation and knowledge discovery.

Rating: 0.0 / 5 (0 ratings) | Versions: 4 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 28 times | Downloaded: 6 times

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Original Uploader

Workflow SNPs to Concept Set through Concept Profil... (5)

Created: 26/06/12 @ 10:27:33 | Last updated: 14/09/12 @ 10:10:23

Credits: User Kristina Hettne User Eleni User Harish Dharuri User Reinout van Schouwen User Marco Roos User Martijn Schuemie Network-member BioSemantics

Attributions: Workflow Find Supporting Documents Workflow SNP_ID2EntrezGene_ID Workflow DatabaseID_to_ConceptID Workflow Match gene lists based on information in literature Workflow Match concept profiles Workflow Explain concept scores

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Purpose: Currently, this workflow takes one SNP and a concept set as input, calculates the matching score between these, finds co-occuring documents between the query concept and the match concept, finds the concept that contributes the most to the match, and the documents that support this finding. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www...

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

Viewed: 48 times | Downloaded: 6 times

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Original Uploader

Workflow Get a list of proteins annotated with an O... (2)

Created: 22/08/12 @ 08:05:33 | Last updated: 24/08/12 @ 02:45:18

Credits: User Rafael C. Jimenez

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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A service to look for models in BioModels using an Ontology Id as input. First the workflow will look in QuickGO for UniProt accessions annotated with the provided Ontology Id. Then it will look for models using the list of proteins. If one of the input protein is found in one model the workflow will provide the BioModels Id, the SBML and a link to the BioModels database. Please use taverna 2.4 or above.

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

Viewed: 4 times | Downloaded: 0 times

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Packs (2)
Creator

Pack 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...

2 items in this pack

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Creator

Pack Functional annotation of SNPs using next-generation ...


Created: 26/06/12 @ 10:41:38 | Last updated: 14/09/12 @ 10:53:41

This pack implements the concept profile matching pipeline in the knowledge discovery tool Anni (http://biosemantics.org/anni), and adapts it to interpret the top SNPs from a GWAS. The underlying literature and concept profile databases are the same as the for the current version of Anni (2.1). The pack consists of three main workflows (http://www.myexperiment.org/workflows/2999, http://www.myexperiment.org/workflows/2973, http://www.myexperiment.org/workflows/2972). Workflow 2999 returns a ...

0 items in this pack

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