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Items tagged with "sparql" (23)

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Workflows (21)

Taverna 2 Original Uploader Francois Belleau	Text search within sparql point (v1) Created: 19/01/09 @ 16:37:53 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 100 times \| Downloaded: 45 times Tags (3): bio2rdf \| sparql \| text_mining	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Author's collaborators according to pubmed (v1) Created: 20/01/09 @ 02:22:32 \| Last updated: 20/01/09 @ 03:41:26 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 159 times \| Downloaded: 69 times Tags (4): bio2rdf \| pubmed \| sparql \| text_mining	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	What is Paget's disease sparql query example (v3) Created: 20/01/09 @ 03:34:08 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 291 times \| Downloaded: 70 times Tags (8): bio2rdf \| example \| GO \| OMIM \| pubmed \| sparql \| text_mining \| uniprot	View Download (v3)
Taverna 2 Original Uploader Francois Belleau	What is known about HIV using Bio2RDF's SPARQL endpoints ? (v2) Created: 05/02/09 @ 06:13:53 \| Last updated: 05/02/09 @ 06:15:22 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 217 times \| Downloaded: 68 times Tags (8): bio2rdf \| geneid \| hiv \| OMIM \| pubmed \| sparql \| uniprot \| virtuoso	View Download (v2)
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	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	Search for citations and related article in PubMed [myexperiment:pubmed_step2_link] (v1) Created: 17/11/09 @ 07:02:11 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 66 times \| Downloaded: 13 times Tags (6): bio2rdf \| citation \| cognoscope \| pubmed \| search \| sparql	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Sponge into Virtuoso triplestore the needed ressource from PubMed [myexperiment:pubmed_step3_describe] (v2) Created: 17/11/09 @ 07:09:01 \| Last updated: 27/11/09 @ 03:32:15 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 61 times \| Downloaded: 22 times Tags (6): bio2rdf \| cognoscope \| describe \| pubmed \| rdfiser \| sparql	View Download (v2)
SPARQL Original Uploader Egon Willighagen	Query DBPedia for all entries with an InChI (v1) Created: 20/11/09 @ 23:23:35 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License SPARQL against http://dbpedia.org/sparql that retrieves the first 100 ChemicalCompounds which has an InChI. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 83 times \| Downloaded: 43 times Tags (3): dbpedia \| inchi \| sparql	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Search for BMURI in PubMed [myexperiment:pubmed_step1_search] (v1) Created: 17/11/09 @ 06:59:06 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 37 times \| Downloaded: 20 times Tags (5): bio2rdf \| cognoscope \| pubmed \| search \| sparql	View Download (v1)
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)
SPARQL Original Uploader Annsofie Anderssson	Keyword search against chEMBL (v1) Created: 24/03/10 @ 15:57:59 Credits: Annsofie Anderssson License: Creative Commons Attribution-Share Alike 3.0 Unported License By entergin a keyword to the query this SPARQL query will find targets related to that word. The keyword looks at the provided description about the protein for a match. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 12 times \| Downloaded: 10 times Tags (2): chembl \| 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)
RapidMiner Original Uploader Lawrynka	Semantic clustering (with AHC) of SPARQL query results over RDF version of videolectures.net dataset (v1) Created: 29/01/12 @ 09:38:32 \| Last updated: 29/01/12 @ 09:39:22 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License The workflow uses RapidMiner extension named RMonto (http://semantic.cs.put.poznan.pl/RMonto/) to perform clustering of SPARQL query results based on chosen semantic similarity measure. The measure used in this particualr workflow is a kernel that exploits membership of clustered individuals to OWL classes from a background ontology ("Common classes" kernel from [1]). Since the semantics of the backgound ontology is used in this way, we use the name "semantic clustering". ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 15 times \| Downloaded: 6 times Tags (8): clustering \| dmro ontology \| ontologies \| rapidminer \| rmonto \| semantic web \| sparql \| videolectures.net	View Download (v1)
RapidMiner Original Uploader Lawrynka	Semantic clustering (with k-medoids) of SPARQL query results over RDF version of videolectures.net dataset (v1) Created: 29/01/12 @ 09:28:33 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License The workflow uses RapidMiner extension named RMonto (http://semantic.cs.put.poznan.pl/RMonto/) to perform clustering of SPARQL query results based on chosen semantic similarity measure. Since the semantics of the backgound ontology is used in this way, we use the name "semantic clustering". The SPARQL query is entered in a parameter of "SPARQL selector" operator. The clustering operator (k-medoids) allows to specify which of the query variables are to be used as clustering criteria. If more ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 7 times \| Downloaded: 2 times Tags (8): clustering \| dmro ontology \| ontologies \| rapidminer \| rmonto \| semantic web \| sparql \| videolectures.net	View Download (v1)
RapidMiner Original Uploader Lawrynka	Semantic clustering (with alpha-clustering) of SPARQL query results over RDF version of videolectures.net dataset (v1) Created: 29/01/12 @ 15:52:57 \| Last updated: 30/01/12 @ 16:10:25 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License The workflow uses RapidMiner extension named RMonto (http://semantic.cs.put.poznan.pl/RMonto/) to perform clustering of SPARQL query results based on chosen semantic similarity measure. The measure used in this particualr workflow is a kernel that exploits membership of clustered individuals to OWL classes from a background ontology ("Epistemic" kernel from [1]). Since the semantics of the backgound ontology is used in this way, we use the name "semantic clustering". This ... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 13 times \| Downloaded: 4 times Tags (8): clustering \| dmro ontology \| ontologies \| rapidminer \| rmonto \| semantic web \| sparql \| videolectures.net	View Download (v1)
RapidMiner Original Uploader Lawrynka	Loading OWL files (RDF version of videolectures.net dataset) to Sesame/OWLIM repository (v1) Created: 29/01/12 @ 16:11:36 \| Last updated: 29/01/12 @ 16:47:06 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License The workflow uses RapidMiner extension named RMonto (http://semantic.cs.put.poznan.pl/RMonto/). Operator "Build knowledge base" is responsible for collecting data either from OWL files or SPARQL endpoints or RDF repositories and provide it to the subsequent operators in a workflow. In this workflow it is parametrized in this way, that is builds a Sesame/OWLIM repository from the files specified in "Load file" operators. Paths to OWL files are specified as parameter va... Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 12 times \| Downloaded: 4 times Tags (8): clustering \| dmro ontology \| ontologies \| rapidminer \| rmonto \| semantic web \| sparql \| videolectures.net	View Download (v1)
Taverna 2 Original Uploader Stian Soiland-Reyes	Find workflow ancestors (v1) Created: 08/05/12 @ 11:15:30 \| Last updated: 08/05/12 @ 11:19:37 Credits: Stian Soiland-Reyes License: Creative Commons Attribution 3.0 Unported License Given a t2flow file (Taverna 2 workflow), extract ancestor workflow UUIDs and search myExperiment for matching workflow entries. Note that this will also match the workflow itself and nested workflows, but does not match against other workflows having the same ancestors (but newer UUIDs). This workflow requires Taverna 2.4 or later and uses myExperiment's SPARQL endpoint, which is refreshed weekly and contains only public workflow entries. Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 9 times \| Downloaded: 5 times Tags (9): ancestor \| identifier \| myexperiment \| rest \| sparql \| t2flow \| uuid \| workflow \| xpath	View Download (v1)

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Administrator:

Francois Belleau

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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