Tag Results

Items tagged with "sparql" (27)

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


Files (1)
Uploader

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

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 (25)

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 Lists all Taverna 2 workflows (1)

Thumb
Uses Bioclipse and the MyExperiment SPARQL end point.

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

Credits: User Egon Willighagen

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

Thumb
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)

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 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 Query DBPedia for all entries with an InChI (1)

SPARQL against http://dbpedia.org/sparql that retrieves the first 100 ChemicalCompounds which has an InChI.

Created: 2009-11-20

Credits: User Egon Willighagen

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 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 Keyword search against chEMBL (1)

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.

Created: 2010-03-24

Credits: User Annsofie Anderssson

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

Thumb
 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

Uploader

Workflow Semantic clustering (with AHC) of SPARQL q... (1)

Thumb
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". ...

Created: 2012-01-29 | Last updated: 2012-01-29

Uploader

Workflow Semantic clustering (with k-medoids) of SP... (1)

Thumb
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 ...

Created: 2012-01-29

Uploader

Workflow Semantic clustering (with alpha-clustering... (1)

Thumb
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 ...

Created: 2012-01-29 | Last updated: 2012-01-30

Uploader

Workflow Loading OWL files (RDF version of videolec... (1)

Thumb
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...

Created: 2012-01-29 | Last updated: 2012-01-29

Workflow Find workflow ancestors (2)

Thumb
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).

Created: 2012-05-08 | Last updated: 2012-07-09

Credits: User Stian Soiland-Reyes

Workflow List all Kegg identifiers used for metabol... (1)

 List all Kegg identifiers used for metabolites in Wikipathways, using the SPARQL end point.

Created: 2013-03-08

Credits: User Egon Willighagen

Workflow List all human metabolites in Wikipathways (1)

 List all human metabolites in Wikipathways, using the SPARQL end point.

Created: 2013-03-08

Credits: User Egon Willighagen

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

Workflow Get HPO concept label and synonym (1)

Thumb
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

What is this?

Linked Data

Non-Information Resource URI: http://www.myexperiment.org/tags/1140


Alternative Formats

HTML
RDF
XML