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Items tagged with "rdf" (32)

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Workflows (26)

Taverna 1 Original Uploader Marco Roos	BioAID_EnirchBioModelWithProteinsFromText (v7) Created: 16/05/09 @ 01:06:26 \| Last updated: 16/05/09 @ 01:13:18 Credits: Marco Roos Sophia katrenko Andrew Gibson M. Scott Marshall Willem van Hage Edgar Martijn Schuemie AID License: Creative Commons Attribution-No Derivative Works 3.0 Unported License 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 Viewed: 149 times \| Downloaded: 31 times Tags (10): AIDA \| biorange_nl \| e-science \| hcls2009 \| owl \| protein \| rdf \| semantic_web \| text_mining \| VL-e	View Download (v7)
Taverna 2 Original Uploader Francois Belleau	Bio2RDF: Rdfiser for Bind protein interaction. (v1) Created: 19/02/09 @ 05:10:23 \| Last updated: 19/02/09 @ 05:24:29 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 57 times \| Downloaded: 28 times Tags (6): bind \| bio2rdf \| database \| protein \| rdf \| rdfiser	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Lists all Taverna 2 workflows (v1) Created: 21/08/09 @ 17:09:07 \| Last updated: 22/08/09 @ 05:54:06 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Uses Bioclipse and the MyExperiment SPARQL end point. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 82 times \| Downloaded: 20 times Tags (4): bioclipse \| myexperiment \| rdf \| sparql	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Extract RDF from HTML+RDFa (v2) Created: 30/09/09 @ 12:18:29 \| Last updated: 23/06/10 @ 20:04:25 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Small script for Bioclipse that extracts RDF from HTML+RDFa webpages. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 79 times \| Downloaded: 68 times Tags (5): bioclipse \| extraction \| html \| rdf \| rdfa	View Download (v2)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Visualize Molecules from DBPedia as Molecule Table (v3) Created: 14/03/10 @ 20:57:58 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 133 times \| Downloaded: 37 times Tags (7): bioclipse \| cdk \| cheminformatics \| chemistry \| dbpedia \| rdf \| sparql	View Download (v3)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Open PDB entries in Jmol for hits found for HIV in Bio2RDF (v3) Created: 14/03/10 @ 21:26:05 \| Last updated: 23/06/10 @ 20:20:41 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 3 \| Reviews: 1 \| Comments: 0 \| Citations: 0 Viewed: 119 times \| Downloaded: 28 times Tags (10): bio2rdf \| bioclipse \| cheminformatics \| drug development \| hiv \| jmol \| pdb \| proteins \| rdf \| sparql	View Download (v3)
Taverna 2 Original Uploader Francois Belleau	Triplify KEGG database list [myexperiments:kegg_namespace2rdf] (v2) Created: 28/11/09 @ 18:06:16 \| Last updated: 30/11/09 @ 20:17:03 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License TAG: knowledgescope, kegg, bio2rdf, banff_manifesto, rdf Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 22 times \| Downloaded: 15 times Tags (5): banff_manifesto \| bio2rdf \| cognoscope \| kegg \| rdf	View Download (v2)
Taverna 2 Original Uploader Francois Belleau	Triplify search results from all KEGG databases [myexperiments:kegg_search_all2rdf] (v3) Created: 30/11/09 @ 20:44:13 \| Last updated: 30/11/09 @ 20:44:55 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 37 times \| Downloaded: 21 times Tags (6): bfind \| bio2rdf \| cognoscope \| kegg \| rdf \| search_all	View Download (v3)
Taverna 2 Original Uploader Francois Belleau	Triplify UniProt database list [myexperiments:uniprotkb_namespace2rdf] (v1) Created: 30/11/09 @ 19:35:17 \| Last updated: 30/11/09 @ 19:43:03 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License TAG: knowledgescope, uniprotkb, bio2rdf, banff_manifesto Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 14 times \| Downloaded: 9 times Tags (5): banff_manifesto \| bio2rdf \| cognoscope \| rdf \| uniprotkb	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Triplify UniProt text search results [myexperiments:uniprotkb_search2rdf] (v1) Created: 30/11/09 @ 19:55:35 \| Last updated: 30/11/09 @ 19:56:33 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License TAG: knowledgescope, uniprotkb, bio2rdf, search, rdf Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 21 times \| Downloaded: 13 times Tags (5): bio2rdf \| cognoscope \| rdf \| search \| uniprotkb	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Triplify UniProt text search results from all databases [myexperiments:uniprotkb_search_all2rdf] (v2) Created: 30/11/09 @ 20:44:32 \| Last updated: 30/11/09 @ 20:45:08 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 31 times \| Downloaded: 14 times Tags (5): bio2rdf \| cognoscope \| rdf \| search_all \| uniprotkb	View Download (v2)
Taverna 2 Original Uploader Francois Belleau	Triplify EB-Eye databases list from EBI [myexperiments:eb-eye_namespace2rdf2rdf] (v1) Created: 30/11/09 @ 20:58:14 \| Last updated: 30/11/09 @ 20:59:49 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 27 times \| Downloaded: 15 times Tags (7): banff_manifesto \| bio2rdf \| cognoscope \| eb-eye \| ebi \| rdf \| soap	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Triplify NCBI databases external reference list [myexperiment:ncbi_xref_namespace2rdf] (v1) Created: 01/12/09 @ 03:01:28 \| Last updated: 01/12/09 @ 03:03:24 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 29 times \| Downloaded: 14 times Tags (5): banff_manifesto \| bio2rdf \| ncbi \| rdf \| xref	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Triplify LSRN record name list [myexperiment:lsrn_xref_namespace2rdf] (v1) Created: 01/12/09 @ 06:24:54 \| Last updated: 01/12/09 @ 06:27:20 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 10 times \| Downloaded: 9 times Tags (5): banff_manifesto \| bio2rdf \| lsrn \| rdf \| xref	View Download (v1)
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: 35 times \| Downloaded: 14 times Tags (5): banff_manifesto \| bio2rdf \| GO \| rdf \| xref	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Triplify namespace XREF list from GO, LSRN, NCBI and UniProt [myexperiment:xref_namespace2rdf] (v1) Created: 01/12/09 @ 06:56:54 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 46 times \| Downloaded: 15 times Tags (5): banff_manifesto \| bio2rdf \| mashup \| rdf \| xref	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Download all data sets from a OpenTox API capable web resource (v3) Created: 01/04/10 @ 12:20:18 \| Last updated: 13/11/10 @ 13:53:22 Credits: License: Creative Commons Attribution-Share Alike 3.0 Unported License Uses the OpenTox API (REST+RDF) to query all data sets, downloads them as MDL SD file, and opens the results in the Bioclipse molecules table. Rating: 0.0 / 5 (0 ratings) \| Versions: 3 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 22 times \| Downloaded: 16 times Tags (7): bioclipse \| cheminformatics \| data \| opentox \| rdf \| rest \| toxicity	View Download (v3)
SPARQL Original Uploader Annsofie Anderssson	Query chEMBL for ion channel PCM data (v1) Created: 16/03/10 @ 09:25:25 Credits: Annsofie Anderssson 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: 10 times \| Downloaded: 6 times Tags (4): chembl \| proteochemometrics \| rdf \| sparql	View Download (v1)
SPARQL Original Uploader Annsofie Anderssson	SPARQL query for QSAR data (v1) Created: 16/03/10 @ 11:26:40 Credits: 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: 18 times \| Downloaded: 20 times Tags (4): chembl \| qsar \| rdf \| sparql	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	List all algorithms and descriptors an OpenTox service provides (v2) Created: 01/04/10 @ 12:25:01 \| Last updated: 13/11/10 @ 13:49:17 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Uses the OpenTox API 1.1 to discover all the available algorithms and descriptors for a given service. Rating: 0.0 / 5 (0 ratings) \| Versions: 2 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 45 times \| Downloaded: 21 times Tags (5): bioclipse \| opentox \| rdf \| sparql \| toxicity	View Download (v2)
SPARQL Original Uploader David De Roure	Similar Workflows (v1) Created: 09/07/10 @ 20:46:14 Credits: David De Roure David R Newman Danius Michaelides License: Creative Commons Attribution-Share Alike 3.0 Unported License SPARQL query to to test for workflows that should be attributed or may just be copies of earlier workflows. Use with rdf.myexperiment.org Rating: 4.0 / 5 (1 rating) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 20 times \| Downloaded: 15 times Tags (3): myexperiment \| rdf \| sparql	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Calculate molecular descriptors with OpenTox services (v1) Created: 30/10/10 @ 17:03:27 \| Last updated: 30/10/10 @ 17:03:31 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Queries an OpenTox ontology server for available molecular descriptor, picks one, and calculates the descriptor value for a few molecules. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 16 times \| Downloaded: 8 times Tags (10): bioclipse \| cheminformatics \| descriptor \| molecular \| ontology \| opentox \| qsar \| rdf \| services \| toxicology	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Search OpenTox data sets by title. (v1) Created: 14/11/10 @ 11:40:43 \| Last updated: 14/11/10 @ 11:40:46 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License Use of an OpenTox ontology server to find data sets with a particular string in the title, such as 'EPA' as in this case. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 14 times \| Downloaded: 6 times Tags (7): bioclipse \| data \| epa \| ontology \| opentox \| rdf \| toxicology	View Download (v1)
RapidMiner Original Uploader mansoor khan	Mining Semantic Web data using FastMap - ExampleSet (v1) Created: 25/06/11 @ 12:11:37 \| Last updated: 25/06/11 @ 13:17:51 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow describes how to learn from the Semantic Web's data. The input to the workflow is a feature vector developed from a RDF resource. The loaded example set is then divided into training and test parts. These sub-example sets are used by the FastMap operators (encapsulate the FastMap data transformation technique), which processes each feature at a time and transform the data into a different space. This transformed data is more meaningful and helps the learner to improve classfica... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 1 Viewed: 49 times \| Downloaded: 20 times Tags (7): data transformation \| fastmap \| machine learning \| plug-in \| rapidminer \| rdf \| semantic web	View Download (v1)
RapidMiner Original Uploader mansoor khan	Mining Semantic Web data using Correspondence Analysis - ExampleSet (v1) Created: 25/06/11 @ 14:10:49 \| Last updated: 25/06/11 @ 14:22:30 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow describes how to learn from the Semantic Web's data using a data transformation algorithm 'Correspondence Analysis'. The input to the workflow is a feature vector developed from a RDF resource. The loaded example set is divided into training and test parts. These sub-example sets are used by the Correspondence Analysis operators (encapsulate the Correspondence Analysis data transformation technique) which processes each feature at a time and transform the data into a different... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 1 Viewed: 71 times \| Downloaded: 26 times Tags (7): correspondence analysis \| data transformation \| machine learning \| plug-in \| rapidminer \| rdf \| semantic web	View Download (v1)
RapidMiner Original Uploader mansoor khan	Mining Semantic Web data using Correspondence Analysis - Read RDF (v1) Created: 25/06/11 @ 14:48:59 \| Last updated: 25/06/11 @ 15:01:59 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License This workflow will explain that how an example set can be extracted from an RDF resource using the provided SPARQL query. This example set is then divided into training and test parts. These sub-example sets are used by the Correspondencce Analysis operators (encapsulate the Correspondencce Analysis data transformation technique) which processes each feature at a time and transform the data into a different space. This transformed data is more meaningful and helps the learner to improve clas... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 1 Viewed: 76 times \| Downloaded: 26 times Tags (7): correspondence analysis \| data transformation \| machine learning \| plug-in \| rapidminer \| rdf \| semantic web	View Download (v1)

Groups (4)

Administrator: Marco Roos	Semantic_BioAID_collaboration Created: Friday 22 August 2008 @ 10:49:27 (GMT) Group for collaboration of Andy, Scott, and Marco. 5 shared items \| 1 announcements Members (4): Marco Roos M. Scott Marshall Barend Andrew Gibson Tags: BioAID \| e-science \| owl \| rdf \| semantic_web \| text_mining	View
Administrator: Andrew Gibson	CWA working group 2.6: Nanopublications Created: Wednesday 12 August 2009 @ 14:12:31 (GMT) 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,... 1 shared item \| 1 announcements Members (24): Andrew Gibson Chr... Mha... Veeranna Ronad Ala... Egon Willighagen paul groth Stefano Bocconi Jgr... Gudmundur 'Mummi' Thorisson Peter-Jan Roes Hailiang (Leon) Mei Rob Hooft Dmitry Katsubo Bharat Singh Antoine van Kampen Ravi Kalaputapu Andrea Jacintha Valk Christine Chichester Alejandra Gonzalez Beltran Karsten uil Nigam Shah Barend Tags: cwa \| rdf \| triplestore Latest announcement:: Nanopublication / Format Working Group Mailing List	View
Administrator: Marco Roos	CWA working group 2.1 - Content Capture Unique name: CWA_ContentCapture Created: Tuesday 01 September 2009 @ 13:06:04 (GMT) 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... 1 shared item \| 1 announcements Members (12): Marco Roos Mat... Franck Tanoh Katy Wolstencroft Rajiv Salimath Lis... Jiten Bhagat Christine Chichester Nigam Shah Richard Cave Segolene Ayme Andrew Su Tags: e-science \| hcls2009 \| rdf \| semantic_web \| support	View
Administrator: M. Scott Marshall	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... 0 shared items \| 0 announcements Members (6): M. Scott Marshall Andrew Gibson Christine Chichester Mat... Barend Dmitry Katsubo Tags: cwa \| hcls \| rdf \| repository \| semantic web	View

Files (2)

Uploader:

David R Newman

myExperiment RDF slides for F2F 15/07/2009

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

Credits: 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: 18 times | Downloaded: 20 times

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Uploader:

Paolo

Janus provenance graph (RDF)

Created: 08/06/10 @ 23:02:53 | Last updated: 09/06/10 @ 22:48:46

Credits: Paolo

License: Creative Commons Attribution-Share Alike 3.0 Unported License

RDF instance file containing the entire provenance graph for once run of the PC1 mockup workflow. The RDF graph complies with the Janus ontology, which can be viewed here Caveat: implementation still under testing, file may still contain bugs

File type: RDF data

Rating: 0.0 / 5 (0 ratings) | Comments: 0 | Viewed: 18 times | Downloaded: 16 times

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