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Items tagged with "rdf" (23)

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Groups (4)

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Network-member Semantic_BioAID_collaboration

Created: Friday 22 August 2008 @ 10:49:27 (BST)

Group for collaboration of Andy, Scott, and Marco.

5 shared items   |   1 announcements

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Network-member CWA working group 2.6: Nanopublications

Created: Wednesday 12 August 2009 @ 14:12:31 (BST)

The Concept Web Alliance is an organization founded to promote the semantically rich publication and dissemination of life science data and knowledge. The basic underlying units of this knowledge will be 'triples' - concept-relationship-concept - represented using the Resource Description Framework (RDF) specification of the W3C. Technologies that are built around RDF such as RDF Triplestores,...

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Latest announcement:: Nanopublication / Format Working Group Mailing List

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Network-member CWA working group 2.1 - Content Capture

Unique name: CWA_ContentCapture Created: Tuesday 01 September 2009 @ 13:06:04 (BST)

Concept Web Alliance working group on content capture CWA wants to help disclose experiment-derived knowledge from within the scientific community via concepts and relations between concepts, stored as concept-relation-concept triples that together form a 'nano-publication'. A nano-publication contains a single 'unit of though', and minimal provenance about who made it, where it was stated, ho...

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Network-member CWA Working Group 2.6: Storage and maintenance

Created: Friday 27 November 2009 @ 19:39:12 (GMT)

A fundamental challenge facing the Semantic Web and the Concept Web Alliance is making essential information available from triple stores. The scale of the information that users eventually want to share and access is generally larger than will fit into a single triple store. Also, it is impossible to centralize all knowledge in a CWA knowledge warehouse. For this reason, federation of data sou...

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Files (1)

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Blob myExperiment RDF slides for F2F 15/07/2009

Created: 15/07/09 @ 10:16:03 | Last updated: 15/07/09 @ 10:17:09

Credits: User David R Newman

License: Creative Commons Attribution-Share Alike 3.0 Unported License

These slides are an update from those given at the May 2009 myExperiment hackfest.  In particular and extra slide about linked data has been added.

File type: PowerPoint presentation

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 11 times | Downloaded: 13 times

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Workflows (18)
Taverna 1

Original Uploader

Workflow BioAID_EnirchBioModelWithProteinsFromText (v7)

Created: 22/08/08 @ 11:00:51 | Last updated: 16/05/09 @ 01:13:19

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

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

Roosetal_paper14_swat4ls_figure_06
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...

Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 1 | Citations: 0

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Taverna 2

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Workflow Bio2RDF: Rdfiser for Bind protein interaction. (v1)

Created: 19/02/09 @ 05:10:23 | Last updated: 19/02/09 @ 05:24:30

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Bind_describe
CONSTRUCT{ <bmuri>, ?p, ?o . } FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE { <bmuri>, ?p, ?o . }

Rating: 5.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 33 times | Downloaded: 14 times

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Bioclipse Scripting Language

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Workflow Lists all Taverna 2 workflows (v1)

Created: 21/08/09 @ 17:09:07 | Last updated: 22/08/09 @ 05:54:07

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Myexp890
Uses Bioclipse and the MyExperiment SPARQL end point.

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

Viewed: 47 times | Downloaded: 9 times

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Bioclipse Scripting Language

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Workflow Extract RDF from HTML+RDFa (v1)

Created: 30/09/09 @ 12:18:30 | Last updated: 30/09/09 @ 12:18:31

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Importrdfa
Small script for Bioclipse 2.2 that extracts RDF from HTML+RDFa webpages.

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

Viewed: 36 times | Downloaded: 18 times

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Bioclipse Scripting Language

Original Uploader

Workflow Visualize Molecules from DBPedia as Molecule Table (v3)

Created: 11/10/09 @ 13:29:52 | Last updated: 14/03/10 @ 20:57:59

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Visualizedbpediahits
Downloads entries from DBPedia which have a SMILES and creates a molecule table with 2D structures of the hits found with SPARQL.

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

Viewed: 47 times | Downloaded: 7 times

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Bioclipse Scripting Language

Original Uploader

Workflow Open PDB entries in Jmol for hits found for HIV in Bio2RDF (v2)

Created: 11/10/09 @ 21:25:59 | Last updated: 14/03/10 @ 21:26:06

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Downloadhivprotein
Queries Bio2RDF for proteins of which the title contains 'HIV', downloads them using the EMBL webservices and opens them in Bioclipse for visualization with Jmol.

Rating: 1.0 / 5 (2 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 40 times | Downloaded: 9 times

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Taverna 2

Original Uploader

Workflow Triplify KEGG database list [myexperiments:kegg_namespace2rdf] (v2)

Created: 28/11/09 @ 17:59:38 | Last updated: 30/11/09 @ 20:17:04

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Triplify_kegg_database_list__myexperiments_kegg_namespace2rdf_
TAG: knowledgescope, kegg, bio2rdf, banff_manifesto, rdf

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

Viewed: 3 times | Downloaded: 3 times

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Taverna 2

Original Uploader

Workflow Triplify search results from all KEGG databases [myexperiments:kegg_search_all2rdf] (v3)

Created: 30/11/09 @ 16:50:06 | Last updated: 30/11/09 @ 20:44:57

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Triplify_search_results_from_all_kegg_databases__myexperiments_kegg_search_all2rdf_
Search all KEGG databases using bfind SOAP service and merge results into a bmuri list and a ntriples string. 

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

Viewed: 2 times | Downloaded: 2 times

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Taverna 2

Original Uploader

Workflow Triplify UniProt database list [myexperiments:uniprotkb_namespace2rdf] (v1)

Created: 30/11/09 @ 19:35:17 | Last updated: 30/11/09 @ 19:43:04

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

_myexperiments_uniprot_namespace2rdf_
TAG: knowledgescope, uniprotkb, bio2rdf, banff_manifesto

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

Viewed: 2 times | Downloaded: 1 time

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Taverna 2

Original Uploader

Workflow Triplify UniProt text search results [myexperiments:uniprotkb_search2rdf] (v1)

Created: 30/11/09 @ 19:55:35 | Last updated: 30/11/09 @ 19:56:34

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Triplify_uniprot_text_search_results__myexperiments_uniprotkb_search2rdf_
TAG: knowledgescope, uniprotkb, bio2rdf, search, rdf

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

Viewed: 5 times | Downloaded: 1 time

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Taverna 2

Original Uploader

Workflow Triplify UniProt text search results from all databases [myexperiments:uniprotkb_search_all2rdf] (v2)

Created: 30/11/09 @ 20:24:52 | Last updated: 30/11/09 @ 20:45:09

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Triplify_uniprot_text_search_results_from_all_databases__myexperiments_uniprotkb_search_all2rdf__
Search all UniProt databases using search URL service and merge results into a bmuri list and a ntriples string. 

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

Viewed: 10 times | Downloaded: 2 times

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Taverna 2

Original Uploader

Workflow Triplify EB-Eye databases list from EBI [myexperiments:eb-eye_namespace2rdf2rdf] (v1)

Created: 30/11/09 @ 20:58:14 | Last updated: 30/11/09 @ 20:59:50

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Triplify_eb-eye_databases_list_from_ebi__myexperiments_eb-eye_namespace2rdf2rdf__
TAG: knowledgescope, eb-eye, bio2rdf, banff_manifesto, rdf, ebi, soap

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

Viewed: 9 times | Downloaded: 2 times

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Taverna 2

Original Uploader

Workflow Triplify NCBI databases external reference list [myexperiment:ncbi_xref_namespace2rdf] (v1)

Created: 01/12/09 @ 03:01:28 | Last updated: 01/12/09 @ 03:03:25

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Triplify_ncbi_databases_external_reference_list__myexperiment_ncbi_xref_namespace2rdf_
Get NCBI external database list from http://www.ncbi.nlm.nih.gov/projects/collab/db_xref.html

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

Viewed: 8 times | Downloaded: 4 times

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Taverna 2

Original Uploader

Workflow Triplify LSRN record name list [myexperiment:lsrn_xref_namespace2rdf] (v1)

Created: 01/12/09 @ 06:24:54 | Last updated: 01/12/09 @ 06:27:21

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Triplify_lsrn_record_name_list___myexperiment_lsrn_xref_namespace2rdf_
Get LSRN list from http://www.lsrn.org/lsrn/registry-2009-04-26-32404.rdf 

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

Viewed: 3 times | Downloaded: 0 times

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Taverna 2

Original Uploader

Workflow Triplify GO database external reference [myexperiment:go_xref_namespace2rdf] (v1)

Created: 01/12/09 @ 06:28:26 | Last updated: 01/12/09 @ 06:29:37

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Triplify_go_database_external_reference___myexperiment_go_xref_namespace2rdf_
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: 20 times | Downloaded: 2 times

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Taverna 2

Original Uploader

Workflow Triplify namespace XREF list from GO, LSRN, NCBI and UniProt [myexperiment:xref_namespace2rdf] (v1)

Created: 01/12/09 @ 06:56:56

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Triplify_namespace_xref_list_from_go__lsrn__ncbi_and_uniprot___myexperiment_xref_namespace2rdf__
TAG: banff_manifesto, xref, bio2rdf, rdfTAG: banff_manifesto, xref, bio2rdf, rdf, mashup Triplify namespace XREF list from GO, LSRN, NCBI and UniProt [myexperiment:xref_namespace2rdf] TAG: banff_manifesto, xref, bio2rdf, rdf TAG: banff_manifesto, xref, bio2rdf, rdf

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

Viewed: 33 times | Downloaded: 3 times

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SPARQL

Original Uploader

Workflow Query chEMBL for ion channel PCM data (v1)

Created: 16/03/10 @ 09:25:26 | Last updated: 16/03/10 @ 09:25:28

Credits: User Annsofie Anderssson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

Viewed: 3 times | Downloaded: 0 times

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SPARQL

Original Uploader

Workflow SPARQL query for QSAR data (v1)

Created: 16/03/10 @ 11:26:40 | Last updated: 16/03/10 @ 11:26:42

Credits: User Annsofie Anderssson

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This query collects valuable data such as activity-, assay-, target-id's, confidence values, SMILES, activity values and units for QSAR projects.

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

Viewed: 1 time | Downloaded: 2 times

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