Tag Results

Items tagged with "bio2rdf" (48)

Note: some items may not be visible to you, due to viewing permissions.


Files (3)
Uploader

Blob Murin.owl ontology designed with Ontowiz

Created: 2009-02-17 04:45:12 | Last updated: 2009-02-17 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

Comments: 0 | Viewed: 54 times | Downloaded: 34 times

Tags:

Uploader

Blob Murin.owl ontology from Bio2RDF project

Created: 2009-02-17 05:02:44

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: Binary data

Comments: 0 | Viewed: 65 times | Downloaded: 63 times

Tags:

Uploader

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

Created: 2010-02-12 05:39:32 | Last updated: 2010-02-13 09:27:01

Credits: User Francois Belleau

License: Creative Commons Attribution-Share Alike 3.0 Unported License

No description

File type: Trident (Package)

Comments: 0 | Viewed: 56 times | Downloaded: 40 times

Tags:

Groups (1)

Network-member Bio2RDF

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

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.

0 shared items   |   1 announcements

Tags:

Latest announcement:: A new workflow

Workflows (44)

Workflow Text search within sparql point (1)

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

Created: 2009-01-19

Credits: User Francois Belleau

Workflow Author's collaborators according to pubmed (1)

Thumb
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())

Created: 2009-01-20 | Last updated: 2009-01-20

Credits: User Francois Belleau

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

Thumb
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  

Created: 2009-01-20

Credits: User Francois Belleau

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

Thumb
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...

Created: 2009-02-05 | Last updated: 2009-02-05

Credits: User Francois Belleau

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

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

Created: 2009-02-17 | Last updated: 2009-02-17

Credits: User Francois Belleau

Workflow Load affymetrix experiments results into S... (1)

Thumb
The affymetrix data source is not public.

Created: 2009-02-17

Credits: User Francois Belleau

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

Thumb
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.

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

Credits: User Francois Belleau

Workflow Bio2RDF: Sesame triplestore loader from tr... (2)

Thumb
INSERT IN GRAPH

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

Credits: User Francois Belleau

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

Thumb
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 .        ...

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

Credits: User Francois Belleau

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

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

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

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

Credits: User Francois Belleau

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

Thumb
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>  ...

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

Credits: User Francois Belleau

Workflow Bio2RDF: CPath describe interaction (1)

Thumb
No description

Created: 2009-02-19

Credits: User Francois Belleau

Workflow Bio2RDF: CPath reverse links (1)

Thumb
No description

Created: 2009-02-19

Credits: User Francois Belleau

Workflow Bio2RDF: CPath search in taxon (1)

Thumb
No description

Created: 2009-02-19

Credits: User Francois Belleau

Workflow Load GO terms in the triplestore (1)

Thumb
No description

Created: 2009-05-01

Credits: User Francois Belleau

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

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

Thumb
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...

Created: 2009-11-03 | Last updated: 2009-11-03

Credits: User Francois Belleau

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

Thumb
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

Created: 2009-11-17

Credits: User Francois Belleau

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

Thumb
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

Created: 2009-11-17

Credits: User Francois Belleau

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

Thumb
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.

Created: 2009-11-17 | Last updated: 2009-11-27

Credits: User Francois Belleau

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

Thumb
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)

Thumb
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)

Thumb
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)

Thumb
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)

Thumb
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)

Thumb
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 namespace list from global search... (1)

Thumb
No description

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

Credits: User Francois Belleau

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

Thumb
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

Created: 2009-11-30 | Last updated: 2009-12-01

Credits: User Francois Belleau

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

Thumb
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 UniProt database external referen... (2)

Thumb
Get UniProt 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 search results from KEGG bfind SO... (3)

Thumb
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. 

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

Credits: User Francois Belleau

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

Thumb
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)

Thumb
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)

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

Thumb
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.

Created: 2010-02-01 | Last updated: 2010-02-01

Credits: User Francois Belleau

Workflow ChEBI mashup from searched string (1)

Thumb
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.

Created: 2010-04-29

Credits: User Francois Belleau

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

Thumb
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

Created: 2010-07-08 | Last updated: 2010-07-08

Credits: User Francois Belleau

Workflow Bio2RDF Talend workflow to populate PARP s... (1)

Thumb
Talend worflow to populate a semantic mashup about PARP family proteins. The mashup uploaded in Virtuoso triplestore is available at http://parp.bio2rdf.org.

Created: 2013-01-30 | Last updated: 2013-01-31

Credits: User Francois Belleau

Workflow HGNC 2 Bio2RDF rdfizer workflow (1)

Thumb
Talend workflow to convert in RDF with Bio2RDF URIs, the HGNC description of genes available at http://www.genenames.org/cgi-bin/hgnc_stats.

Created: 2013-02-27

Credits: User Francois Belleau

Workflow A Talend mashup to discover PARP proteins ... (3)

Thumb
A Talend workflow to answer this specific question :What is known about PARP family proteins involved in pathway according to Reactome ?by fetching RDF data from Bio2RDF`s HGNC, UniProt REST service and EBI Reactome SPARQL endpoint, all Semantic Web public resources.

Created: 2014-02-10 | Last updated: 2014-04-07

Credits: User Francois Belleau

What is this?

Linked Data

Non-Information Resource URI: http://www.myexperiment.org/tags/1139


Alternative Formats

HTML
RDF
XML