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Showing 22 results. Use the filters on the left and the search box below to refine the results.
Category: Workflow Tag: search

Workflow BioAID_ProteinDiscovery (8)

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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.

Created: 2010-05-10 | Last updated: 2013-08-16

Credits: User Marco Roos Network-member AID

Workflow DOI2PMID (2)

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

Created: 2007-10-03

Workflow MassBank to KEGG (1)

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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)

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: User Michael Gerlich

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

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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...

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

Credits: User Francois Belleau

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

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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.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: User Michael Gerlich

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

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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...

Created: 2010-03-13 | Last updated: 2010-03-19

Credits: User Samuel Lampa

Workflow Triplify search results from KEGG bfind SO... (3)

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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. 

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

Credits: User Francois Belleau

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

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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

Created: 2009-11-17

Credits: User Francois Belleau

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

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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 .        ...

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

Credits: User Francois Belleau

Workflow Triplify UniProt text search results [myex... (1)

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TAG: knowledgescope, uniprotkb, bio2rdf, search, rdf

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

Credits: User Francois Belleau

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