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Items tagged with "search" (20)

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Workflows (20)

Taverna 1 Original Uploader Duncan Hull	DOI2PMID (v2) Created: 03/10/07 @ 18:35:47 License: Creative Commons Attribution-No Derivative Works 3.0 Unported License 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: 83 times \| Downloaded: 52 times Tags (4): scampi \| search \| seed alignment \| SEG	View Download (v2)
Taverna 2 Original Uploader Francois Belleau	Bio2rdf: Bind search, rdfise and load demo (v1) Created: 19/02/09 @ 05:07:30 \| Last updated: 19/02/09 @ 05:39:51 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 53 times \| Downloaded: 28 times Tags (4): bind \| bio2rdf \| demo \| search	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Bio2RDF: Bind fulltext search service returning bmuris. (v1) Created: 19/02/09 @ 05:18:44 \| Last updated: 19/02/09 @ 05:26:17 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 33 times \| Downloaded: 19 times Tags (3): bind \| bio2rdf \| search	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Bio2RDF: CPath search in taxon (v1) Created: 19/02/09 @ 07:20:36 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License No description Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 2 \| Citations: 0 Viewed: 60 times \| Downloaded: 31 times Tags (4): bio2rdf \| cpath \| search \| taxonomy	View Download (v1)
Taverna 1 Original Uploader Michael Gerlich	Search InChI in NCBI eSearch (pccompound) (v1) Created: 30/03/09 @ 09:26:25 \| Last updated: 30/03/09 @ 09:47:00 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 89 times \| Downloaded: 44 times Tags (12): bioinformatics \| compound \| compound info + image \| database \| image \| inchi \| information \| ncbi \| pccompound \| pubchem \| search \| xml	View Download (v1)
Taverna 1 Original Uploader Michael Gerlich	MassBank to KEGG (v1) Created: 30/03/09 @ 09:30:32 \| Last updated: 30/03/09 @ 09:49:13 Credits: Michael Gerlich License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 193 times \| Downloaded: 0 times Tags (21): bget \| bioinformatics \| chemspider \| compound \| compound info + image \| database \| eutils \| image \| inchi \| information \| mass spectrometry \| massbank \| metabolomics \| ncbi \| pathway \| pccompound \| pubchem \| pug \| search \| summary \| xml	View
Taverna 2 Original Uploader Francois Belleau	What is [query] from NCBI, EBI, UniProt and KEGG ? (v2) Created: 03/11/09 @ 04:29:15 \| Last updated: 03/11/09 @ 04:29:19 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 120 times \| Downloaded: 25 times Tags (8): bio2rdf \| cognoscope \| eb-eye \| kegg \| ncbi \| rdfiser \| search \| uniprot	View Download (v2)
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: 36 times \| Downloaded: 18 times Tags (5): bio2rdf \| cognoscope \| pubmed \| search \| sparql	View Download (v1)
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: 61 times \| Downloaded: 11 times Tags (6): bio2rdf \| citation \| cognoscope \| pubmed \| search \| sparql	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Triplify UniProt text search results [myexperiments:uniprotkb_search2rdf] (v1) Created: 30/11/09 @ 19:55:35 \| Last updated: 30/11/09 @ 19:56:33 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License TAG: knowledgescope, uniprotkb, bio2rdf, search, rdf Rating: 0.0 / 5 (0 ratings) \| Versions: 1 \| Reviews: 0 \| Comments: 0 \| Citations: 0 Viewed: 19 times \| Downloaded: 12 times Tags (5): bio2rdf \| cognoscope \| rdf \| search \| uniprotkb	View Download (v1)
Taverna 2 Original Uploader Francois Belleau	Triplify search results from KEGG bfind SOAP service [myexperiments:kegg_search2rdf] (v3) Created: 30/11/09 @ 16:21:05 \| Last updated: 30/11/09 @ 20:48:50 Credits: Francois Belleau License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 18 times \| Downloaded: 20 times Tags (6): bfind \| bio2rdf \| cognoscope \| kegg \| search \| soap	View Download (v3)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Spectrum similarity search witn SWI-Prolog in Bioclipse (v1) Created: 13/03/10 @ 02:07:23 \| Last updated: 19/03/10 @ 13:15:41 Credits: Samuel Lampa License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 28 times \| Downloaded: 18 times Tags (5): bioclipse \| nmrshiftdb \| prolog \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in Jena with In-memory RDF Store (v1) Created: 14/05/10 @ 17:36:38 \| Last updated: 14/05/10 @ 17:43:00 Credits: Samuel Lampa 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: 12 times \| Downloaded: 7 times Tags (4): bioclipse \| nmrshiftdb \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in Jena with TDB RDF Store (v1) Created: 14/05/10 @ 17:37:47 \| Last updated: 14/05/10 @ 17:43:03 Credits: Samuel Lampa 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: 12 times \| Downloaded: 14 times Tags (4): bioclipse \| nmrshiftdb \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in Pellet with In-memory RDF Store (v1) Created: 14/05/10 @ 17:38:46 \| Last updated: 14/05/10 @ 17:43:09 Credits: Samuel Lampa 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: 11 times \| Downloaded: 6 times Tags (4): bioclipse \| nmrshiftdb \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in SWI-Prolog (v1) Created: 14/05/10 @ 17:40:14 \| Last updated: 14/05/10 @ 17:43:13 Credits: Samuel Lampa 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: 15 times \| Downloaded: 12 times Tags (6): benchmarks \| bioclipse \| nmrshiftdb \| prolog \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Samuel Lampa	NMR Shift Dereplication benchmark in SWI-Prolog, minimal version (v1) Created: 14/05/10 @ 17:41:04 \| Last updated: 14/05/10 @ 17:42:46 Credits: Samuel Lampa 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: 15 times \| Downloaded: 12 times Tags (6): benchmarks \| bioclipse \| nmrshiftdb \| prolog \| search \| similarity	View Download (v1)
Bioclipse Scripting Language Original Uploader Egon Willighagen	Resolve an InChIKey on ChemSpider (v1) Created: 23/06/10 @ 21:16:09 \| Last updated: 23/06/10 @ 21:16:10 Credits: Egon Willighagen License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 15 times \| Downloaded: 8 times Tags (4): bioclipse \| chemspider \| inchikey \| search	View Download (v1)
Taverna 2 Original Uploader Marco Roos	BioAID_ProteinDiscovery (v7) Created: 10/05/10 @ 16:21:09 \| Last updated: 12/01/12 @ 14:39:37 Credits: Marco Roos AID License: Creative Commons Attribution-Share Alike 3.0 Unported License The 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: 258 times \| Downloaded: 116 times Tags (12): AIDA \| BioAID \| biorange_nl \| lucene \| protein \| proteins \| pubmed \| search \| text_mining \| text_mining_network \| uniprot \| VL-e	View Download (v7)
Taverna 2 Original Uploader Markus Plangg	[untitled] (v2) Created: 13/01/12 @ 19:25:22 \| Last updated: 16/01/12 @ 00:09:51 License: Creative Commons Attribution-Share Alike 3.0 Unported License 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: 0 times \| Downloaded: 1 time Tags (6): beanshell \| dfs \| list \| nested list \| search \| tools	View Download (v2)