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Items tagged with "rdf" (37)

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Files (2)
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Blob myExperiment RDF slides for F2F 15/07/2009

Created: 2009-07-15 10:16:03 | Last updated: 2009-07-15 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

Comments: 0 | Viewed: 42 times | Downloaded: 40 times

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Uploader

Blob Janus provenance graph (RDF)

Created: 2010-06-08 23:02:53 | Last updated: 2010-06-09 22:48:46

Credits: User 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

Comments: 0 | Viewed: 55 times | Downloaded: 35 times

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Groups (5)
Owner

Network-member Semantic_BioAID_collaboration


Created: Friday 22 August 2008 10:49:27 (UTC)

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 (UTC)

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

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Latest announcement:: Nanopublication / Format Working Group Mailing List

Owner

Network-member CWA working group 2.1 - Content Capture

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

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

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Network-member CWA Working Group 2.6: Storage and mainten...


Created: Friday 27 November 2009 19:39:12 (UTC)

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

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Network-member BioSemantics

Unique name: biosemantics
Created: Thursday 30 June 2011 13:06:48 (UTC)

Group for members of the BioSemantics group and their close collaborators.BiosemanticsWith the explosion of information in the biomolecular field, there is a dire need for information technology that assists in retrieving, extracting, and relating information and knowledge in the biomedical literature and databases. Biosemantics researchers and developers develop, evaluate, and apply such techn...

70 shared items   |   0 announcements

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Packs (1)

Pack Visualize PAV provenance as SVG


Created: 2013-04-05 09:18:51 | Last updated: 2013-05-01 14:50:57

A workflow that converts PAV provenance to SVG by inferring PROV-O statements.VoID descriptions following the Open PHACTS Dataset descriptions specification are fetched as Turtle, cleaned up to be valid OWL2 ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance.Note that this workflow downloads CWM, Pellet and ProvToolbox on dema...

11 items in this pack

Comments: 0 | Viewed: 74 times | Downloaded: 10 times

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Workflows (29)

Workflow BioAID_EnirchBioModelWithProteinsFromText (7)

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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...

Created: 2009-05-16 | Last updated: 2009-05-16

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

Workflow Bio2RDF: Rdfiser for Bind protein interact... (1)

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

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: User Francois Belleau

Workflow Lists all Taverna 2 workflows (1)

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Uses Bioclipse and the MyExperiment SPARQL end point.

Created: 2009-08-21 | Last updated: 2009-08-22

Credits: User Egon Willighagen

Workflow Extract RDF from HTML+RDFa (2)

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

Created: 2009-09-30 | Last updated: 2010-06-23

Credits: User Egon Willighagen

Workflow Visualize Molecules from DBPedia as Molecu... (3)

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

Created: 2010-03-14

Credits: User Egon Willighagen

Workflow Open PDB entries in Jmol for hits found fo... (3)

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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.

Created: 2010-03-14 | Last updated: 2010-06-23

Credits: User Egon Willighagen

Workflow Triplify KEGG database list [myexperiments... (2)

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TAG: knowledgescope, kegg, bio2rdf, banff_manifesto, rdf

Created: 2009-11-28 | Last updated: 2009-11-30

Credits: User Francois Belleau

Workflow Triplify search results from all KEGG data... (3)

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

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Workflow Triplify UniProt database list [myexperime... (1)

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TAG: knowledgescope, uniprotkb, bio2rdf, banff_manifesto

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Workflow Triplify UniProt text search results [myex... (1)

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TAG: knowledgescope, uniprotkb, bio2rdf, search, rdf

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Workflow Triplify UniProt text search results from ... (2)

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

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Workflow Triplify EB-Eye databases list from EBI [m... (1)

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

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Workflow Triplify NCBI databases external reference... (1)

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

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: User Francois Belleau

Workflow Triplify LSRN record name list [myexperim... (1)

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

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: User Francois Belleau

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

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Get GO external database list from http://www.geneontology.org/doc/GO.xrf_abbs 

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: User Francois Belleau

Workflow Triplify namespace XREF list from GO, LSRN... (1)

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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

Created: 2009-12-01

Credits: User Francois Belleau

Workflow Download all data sets from a OpenTox API ... (3)

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 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.

Created: 2010-04-01 | Last updated: 2010-11-13

Credits: User

Workflow Query chEMBL for ion channel PCM data (1)

No description

Created: 2010-03-16

Credits: User Annsofie Anderssson

Workflow SPARQL query for QSAR data (1)

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

Created: 2010-03-16

Credits: User Annsofie Anderssson

Workflow List all algorithms and descriptors an Ope... (2)

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 Uses the OpenTox API 1.1 to discover all the available algorithms and descriptors for a given service.

Created: 2010-04-01 | Last updated: 2010-11-13

Credits: User Egon Willighagen

Workflow Similar Workflows (1)

SPARQL query to to test for workflows that should be attributed or may just be copies of earlier workflows. Use with rdf.myexperiment.org

Created: 2010-07-09

Credits: User David De Roure User David R Newman User Danius Michaelides

Workflow Calculate molecular descriptors with OpenT... (1)

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 Queries an OpenTox ontology server for available molecular descriptor, picks one, and calculates the descriptor value for a few molecules.

Created: 2010-10-30 | Last updated: 2010-10-30

Credits: User Egon Willighagen

Workflow Search OpenTox data sets by title. (1)

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 Use of an OpenTox ontology server to find data sets with a particular string in the title, such as 'EPA' as in this case.

Created: 2010-11-14 | Last updated: 2010-11-14

Credits: User Egon Willighagen

Workflow Mining Semantic Web data using FastMap - E... (1)

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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...

Created: 2011-06-25 | Last updated: 2011-06-25

Workflow Mining Semantic Web data using Corresponde... (1)

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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...

Created: 2011-06-25 | Last updated: 2011-06-25

Workflow Mining Semantic Web data using Corresponde... (1)

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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...

Created: 2011-06-25 | Last updated: 2011-06-25

Workflow Visualize PAV provenance as SVG (2)

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VoID descriptions are fetched as Turtle, cleaned up to be valid OWL ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance. Note that this workflow downloads CWM, Pellet and ProvToolbox on demand, and uses UNIX command line tools like wget and md5 which are unlikely to work in Windows. This workflow has been tested on Ubuntu 12.10 wit...

Created: 2013-03-05 | Last updated: 2013-04-05

Credits: User Stian Soiland-Reyes

Workflow Get HPO concept label and synonym (1)

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This workflow queries bioportal for label and synonyms of Human Phenotype Ontology concepts.Note: this workflow requires a BioPortal API key to work. It can be requested from bioportal.bioontology.org

Created: 2014-10-20 | Last updated: 2014-10-20

Credits: User Rajireturn Network-member BioSemantics

Workflow Groovy script to convert (part of) CGN dat... (1)

Converts CGN data from [0] to RDF. It uses intermedia TSV files (never mind the file extensions) for the data tab. The 3char ISO country codes are available at [1], but ideally these are pulled out of Wikidata directly. The RDF uses the Darwin Core ontology, QUDT, and Wikidata (on top of regular stuff). This Groovy script uses Bioclipse (www.bioclipse.net) with the RDF plugin.Menting, Frank (2015): CGN tomato passport data. figshare. http://dx.doi.org/10.608...

Created: 2015-01-22

Credits: User Egon Willighagen

What is this?

Linked Data

Non-Information Resource URI: http://www.myexperiment.org/tags/607


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