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Network-member Bio2RDF

Unique name: bio2rdf
Created: Saturday 24 January 2009 @ 17:20:54 (GMT)

The goal of this community is to explore the possibilities of using Taverna  platform with Virtuoso SPARQL engine to build useful workflow capable of answering complex question by using the distributed network of RDF data available over the web.

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Latest announcement:: A new workflow

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Blob Murin.owl ontology designed with Ontowiz

Created: 17/02/09 @ 04:45:12 | Last updated: 17/02/09 @ 05:00:49

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The ontology of the Murin protocol was designed with Protege Ontowiz tool.

File type: GIF image

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Blob Murin.owl ontology from Bio2RDF project

Created: 17/02/09 @ 05:02:44

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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File type: Binary data

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Blob Bio2RDF first released version of cognoscope at BioH...

Created: 12/02/10 @ 05:39:32 | Last updated: 13/02/10 @ 09:27:01

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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File type: Trident (Package)

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Workflows (41)
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Workflow Text search within sparql point (1)

Created: 19/01/09 @ 16:37:53

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow make possible full text search within different sparql point made available by the Bio2RDF project.

Rating: 1.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 111 times | Downloaded: 49 times

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Workflow Author's collaborators according to pubmed (1)

Created: 20/01/09 @ 02:22:32 | Last updated: 20/01/09 @ 03:41:26

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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SELECT distinct ?s2 FROM <http://atlas.bio2rdf.org/sparql> WHERE {   ?s1 ?p1 ?o1 .   ?o1 bif:contains "author" .   ?s2 ?p2 ?s1 .   FILTER( regex(?s1, "pubmed") ) } followed by SELECT ?creator, count() FROM <http://localhost:8890/sparql> WHERE {   ?s1 ?p1 .   ?s1 ?p2 ?o2 .   FILTER( regex(?o2, "author"))   ?s1 ?creator . } ORDER BY DESC(count())

Rating: 3.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 170 times | Downloaded: 76 times

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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

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Workflow What is known about HIV using Bio2RDF's SP... (2)

Created: 05/02/09 @ 06:13:53 | Last updated: 05/02/09 @ 06:15:22

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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To answer this question Bio2RDF Atlas about mouse and human genome sparql endpoint available at http://atlas.bio2rdf.org/sparql is searched.  The selected URIs are then loaded into your local Virtuoso triplestore at http://localhost:8890/sparql. You must enable insert mode into the graph. Once the mashup is built, two SPARQL queries analyze the obtained graph.  Finally you can submit queries to the RDF mashup about HIV as you like.  Enjoy. This is the queries present in t...

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

Viewed: 272 times | Downloaded: 72 times

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Workflow Initialize triplestore with Murin's protoc... (1)

Created: 17/02/09 @ 04:40:17 | Last updated: 17/02/09 @ 04:42:28

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow initialize the Sesame triplestore with initial data.  The 5 rdfiser in JSP are needed, they are executed on localhost.

Rating: 1.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 45 times | Downloaded: 27 times

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Workflow Sesame triplestore loader from a dereferen... (2)

Created: 19/02/09 @ 05:02:34 | Last updated: 19/02/09 @ 05:03:08

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Load triples obtained from an URL in N3 or XML format and load them into your local Sesame Triplestore locally installed and available at http://localhost/sesame. The http://localhost/sesame/servlets/uploadURL service of Sesame is used in HTTP POST mode.

Rating: 1.0 / 5 (1 rating) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 135 times | Downloaded: 32 times

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Original Uploader
Original Uploader

Workflow Bio2rdf: Bind search, rdfise and load demo (1)

Created: 19/02/09 @ 05:07:30 | Last updated: 19/02/09 @ 05:39:51

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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INSERT IN GRAPH <http://localhost/sesame/mem_rdf_db> {     CONSTRUCT { ?s, ?p, ?o . }     FROM <http://soap.bind.ca/wsdl/bind.wsdl>     WHERE {         SELECT ?s         FROM <http://soap.bind.ca/wsdl/bind.wsdl>         WHERE {              ?s, ?p, ?o .        ...

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

Viewed: 61 times | Downloaded: 32 times

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Original Uploader

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

Created: 19/02/09 @ 05:10:23 | Last updated: 19/02/09 @ 05:24:29

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 62 times | Downloaded: 29 times

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Original Uploader

Workflow Bio2RDF: Bind fulltext search service retu... (1)

Created: 19/02/09 @ 05:18:44 | Last updated: 19/02/09 @ 05:26:17

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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SELECT ?s FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE {   ?s, ?p, ?o .   FILTER ( regex(?o, "query")) . }

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

Viewed: 40 times | Downloaded: 23 times

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Original Uploader

Workflow Bio2RDF: CPath search, rdfise and load dem... (1)

Created: 19/02/09 @ 07:06:58 | Last updated: 19/02/09 @ 07:08:28

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Search for a list of genes into the Pathway Commons interaction database and load the fetched triples into a triplestore. INSERT IN GRAPH < http://localhost/sesame/mem_rdf_db> {     CONSTRUCT{ ?s, ?p, ?o . }     FROM < http://www.pathwaycommons.org/pc/webservice.do>     WHERE {         SELECT ?s         FROM <http://www.pathwaycommons.org/pc/webservice.do>  ...

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

Viewed: 52 times | Downloaded: 29 times

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

Created: 14/03/10 @ 21:26:05 | Last updated: 01/03/13 @ 14:37:58

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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.

Rating: 1.3 / 5 (3 ratings) | Versions: 3 | Reviews: 2 | Comments: 0 | Citations: 0

Viewed: 165 times | Downloaded: 34 times

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Original Uploader

Workflow What is [query] from NCBI, EBI, UniProt an... (2)

Created: 03/11/09 @ 04:29:15 | Last updated: 03/11/09 @ 04:29:19

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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test values: query = paget disease query = pdb4 query = hk1 query = h1n1 This rdfiser query those four federated search services EB-Eye, KEGG LinkDB, NCBI Entrez and UniProt knowledgebase. RDF triples are returned for search statistics with Bio2RDF normalised URIs. This workflow should be used responsibly because it can generate high load at the provider resources. test values: query = paget disease query = pdb4 query = hk1 query = h1n1 query = paget disease query = pdb4 query = hk1 que...

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

Viewed: 134 times | Downloaded: 30 times

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Workflow Search for BMURI in PubMed [myexperiment:p... (1)

Created: 17/11/09 @ 06:59:06

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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test values: subkecttest values: query = bio2rdf graph = http://bio2rdf query = nur77 AND Rouillard,C graph = http://nur77 test values: query = bio2rdf graph = http://bio2rdf query = nur77 AND Rouillard,C graph = http://nur77 query = labrie graph = http://labrie

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

Viewed: 41 times | Downloaded: 23 times

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Workflow Search for citations and related article i... (1)

Created: 17/11/09 @ 07:02:11

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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graph = http://nur77 bmuri = http://bio2rdf.org/pubmed:18843482 http://bio2rdf.org/pubmed:18466322 http://bio2rdf.org/pubmed:17201484 http://bio2rdf.org/pubmed:14603264 http://bio2rdf.org/pubmed:12629527

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

Viewed: 73 times | Downloaded: 14 times

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Workflow Sponge into Virtuoso triplestore the neede... (2)

Created: 17/11/09 @ 07:09:01 | Last updated: 27/11/09 @ 03:32:15

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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query = labrie,f query = labrie query = labrie,f query = labrie query = h1n1 query = morissette,j query = labrie,f query = labrie query = h1n1 Get a list of paper from pubmed.

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

Viewed: 68 times | Downloaded: 23 times

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

Created: 28/11/09 @ 18:06:16 | Last updated: 30/11/09 @ 20:17:03

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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TAG: knowledgescope, kegg, bio2rdf, banff_manifesto, rdf

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

Viewed: 29 times | Downloaded: 17 times

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

Created: 30/11/09 @ 20:44:13 | Last updated: 30/11/09 @ 20:44:55

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 44 times | Downloaded: 25 times

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

Created: 30/11/09 @ 19:35:17 | Last updated: 30/11/09 @ 19:43:03

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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TAG: knowledgescope, uniprotkb, bio2rdf, banff_manifesto

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

Viewed: 17 times | Downloaded: 10 times

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

Created: 30/11/09 @ 19:55:35 | Last updated: 30/11/09 @ 19:56:33

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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TAG: knowledgescope, uniprotkb, bio2rdf, search, rdf

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

Viewed: 25 times | Downloaded: 14 times

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

Created: 30/11/09 @ 20:44:32 | Last updated: 30/11/09 @ 20:45:08

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 42 times | Downloaded: 16 times

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

Created: 30/11/09 @ 20:58:14 | Last updated: 30/11/09 @ 20:59:49

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 31 times | Downloaded: 16 times

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Original Uploader
Original Uploader

Workflow Triplify NCBI databases list [myexperiment... (1)

Created: 30/11/09 @ 21:47:05 | Last updated: 01/12/09 @ 02:49:34

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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List NCBI's database name. Using this URL service: http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? This is NCBI's namespace list supported by Bio2RDF : pubmed protein nucleotide gene=geneid homologene mesh omim pccompound=cid pcsubstance=sid taxonomy unigene unists

Rating: 1.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 42 times | Downloaded: 13 times

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

Created: 01/12/09 @ 03:01:28 | Last updated: 01/12/09 @ 03:03:24

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 37 times | Downloaded: 16 times

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Workflow Triplify UniProt database external referen... (2)

Created: 01/12/09 @ 04:08:08 | Last updated: 01/12/09 @ 04:09:39

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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

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

Viewed: 33 times | Downloaded: 14 times

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Workflow Triplify search results from KEGG bfind SO... (3)

Created: 30/11/09 @ 16:21:05 | Last updated: 30/11/09 @ 20:48:50

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow use KEGG's SOAP service provided to do a BFIND serch within one of the KEGG's official database. The results are returned in RDF ntriples format. 

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

Viewed: 30 times | Downloaded: 26 times

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

Created: 01/12/09 @ 06:24:54 | Last updated: 01/12/09 @ 06:27:20

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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: 17 times | Downloaded: 10 times

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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

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

Created: 01/12/09 @ 06:56:54

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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

Viewed: 55 times | Downloaded: 16 times

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Original Uploader

Workflow Rdfise Riken SciNes Database Repository [m... (1)

Created: 01/02/10 @ 20:10:43 | Last updated: 01/02/10 @ 20:13:51

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow rdfise Riken SciNes Database Repository available at https://database.riken.jp/sw/links/en/crib151s2i/. There is a bug with main page listing databases: version 2p and 3p are similar to 1p.

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

Viewed: 30 times | Downloaded: 11 times

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Workflow ChEBI mashup from searched string (1)

Created: 29/04/10 @ 14:09:37

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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A demo showing hoe to use SOAP services from Bio2RDF ChEBI SPARQL endpoint.A demo showing hoe to use SOAP services from Bio2RDF ChEBI SPARQL endpoint. First a full text search query is done, then we do a reverse link query to get all the related topic. Finally with a describe queries we obtain the complete graph of each topic. The ntriples result is a mashup of what is known about this searched topic form ChEBI. This graph can then be loaded in a triplestore for further exploration.

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

Viewed: 25 times | Downloaded: 13 times

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Workflow Who is Dr Labrie according to Pubmed publi... (2)

Created: 08/07/10 @ 07:18:09 | Last updated: 08/07/10 @ 07:32:26

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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To use this wokflow you need to import services from To use this wokflow you need to import services from http://proxy.bio2rdf.org/bio2rdf/services.txt you can explore the loaded data at http://proxy.bio2rdf.org/fct

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

Viewed: 23 times | Downloaded: 10 times

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