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Items tagged with "search" (20)

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Workflows (20)
Original Uploader

Workflow DOI2PMID (2)

Created: 03/10/07 @ 18:35:47

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

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Converts Digital Object Identifiers into their corresponding PubMed identifiers, if they exist.

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

Viewed: 92 times | Downloaded: 58 times

Tags (4):

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

Tags (4):

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

Tags (3):

Original Uploader

Workflow Search InChI in NCBI eSearch (pccompound) (1)

Created: 30/03/09 @ 09:26:25 | Last updated: 30/03/09 @ 09:47:00

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This workflow takes in a search term (e.g. InChI) for search in PubChem pccompound database. The result is an xml file containing summary information about the search term and also a compound image and the compound webpage fetched from Pubchem.

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

Viewed: 103 times | Downloaded: 50 times

Tags (12):

Original Uploader

Workflow MassBank to KEGG (1)

Created: 30/03/09 @ 09:30:32 | Last updated: 30/03/09 @ 09:49:13

Credits: User Michael Gerlich

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Workflow that queries MassBank DB to retrieve database identifiers (KEGG, PubChem, InChI) and continue search with them to retrieve pathways from KEGG for given compound identifier,searches PubChem via eutils and PUG, queries ChemSpider for compound information and image. Note: Usage of ChemSpider web services requires a valid security token - receive one by registering at ChemSpider (look at your profile to see your token)

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

Viewed: 215 times | Downloaded: 0 times

Tags (21):

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

Tags (8):

Original Uploader

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

Tags (5):

Original Uploader

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

Tags (6):

Original Uploader

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

Tags (5):

Original Uploader

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

Tags (6):

Workflow NMR Spectrum similarity search witn SWI-Pr... (1)

Created: 13/03/10 @ 02:07:23 | Last updated: 19/03/10 @ 13:15:41

Credits: User Samuel Lampa

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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With the SWI-Prolog (currently in experimental stage, and available from GitHub) plugin Prolog programs can be accessed inside Bioclipse’s scripting environment for querying and other processing of RDF triples. The prolog code in this Bioclipse script performs a simple spectrum similarity search based on a list of peak shift values, for which it tries to find spectra that contain peaks values close to those values, within a certian limit (<0.3 ppm in this case). The data which is u...

Rating: 5.0 / 5 (1 rating) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 50 times | Downloaded: 30 times

Tags (5):

Workflow Resolve an InChIKey on ChemSpider (1)

Created: 23/06/10 @ 21:16:09 | Last updated: 23/06/10 @ 21:16:10

Credits: User Egon Willighagen

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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 Resolves an InChIKey on ChemSpider and opens the search results in a molecules table.

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

Viewed: 18 times | Downloaded: 9 times

Tags (4):

Original Uploader

Workflow BioAID_ProteinDiscovery (7)

Created: 10/05/10 @ 16:21:09 | Last updated: 20/03/12 @ 17:16:11

Credits: User Marco Roos Network-member AID

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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This protein discovery workflow extracts protein names from documents retrieved from MedLine based on a user Query (cf Apache Lucene syntax). The protein names are filtered by checking if there exists a valid UniProt ID for the given protein name.

Rating: 0.0 / 5 (0 ratings) | Versions: 7 | Reviews: 0 | Comments: 1 | Citations: 0

Viewed: 389 times | Downloaded: 144 times

Tags (12):

Original Uploader

Workflow getFirstElementDFS (2)

Created: 13/01/12 @ 19:25:22 | Last updated: 13/02/12 @ 20:59:49

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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Returns the first element of a nested list using depth first search. The maximum depth of the input is set to 2. You can savely increase this by increasing the depth of the workflow input port and the beanshell input port. Taverna will wrap the input into a list with correct depth. However this will create a little overhead.

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

Viewed: 6 times | Downloaded: 4 times

Tags (6):

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