Workflows

Retrieve full descriptions of bacteria str... (1)

• Download

This workflow retrieves the full description of bacteria strains that are available in the CABRI network services (see www.cabri.org). Input are the name of the involved CABRI catalogues (text/plain string with one catalogue name per line) and the scientific name of the desired bacteria strain (a text/plain string including genus and species separated by a blank space). Data are retrieved from the CABRI Web Services in two steps. First, all bacteria strains IDs are retrieved by using the ge...

Created: 2010-01-15

Credits: Achille Zappa

Search TP53 Somatic Mutation catalogue by ... (1)

• Download

This workflow takes the intron, the effect and the TP53 somatic mutation database as input and retrieves the full TP53 somatic mutation description(s) by first retrieving two different outputs and arranging them according to the boolean operators (and, or and butnot): - first output: a TP53 somatic mutation database unique IDs list associated with the input 'intron' (done via a call to the getP53MutationIdsByIntron web service) - second output: a TP53 somatic mutation database unique IDs list...

Created: 2010-01-15

Credits: Achille Zappa

Search TP53 Somatic Mutation catalogue by ... (1)

• Download

This workflow takes the exon, the effect and the TP53 somatic mutation database as input and retrieves the full TP53 somatic mutation description(s) by first retrieving two different outputs: - first output: a TP53 somatic mutation database unique IDs list associated with the input exon (done via a call to the getP53MutationIdsByExon web service) - second output: a TP53 somatic mutation database unique IDs list associated with the input effect (done via a call to the getP53MutationIdsByEffe...

Created: 2010-01-15

Credits: Achille Zappa

Pattern: Return errors instead of null (1)

• Download

 As Taverna can't (currently) handle null (see http://www.mygrid.org.uk/dev/issues/browse/TAV-653) - in Taverna 2 one can instead return exceptions on individual ports and inside lists. Exceptions are registered as error documents by Taverna, and are passed along. The ErrorBounce layer of processors downstream will prevent execution if they see this 'null'-exception - as showed in this example that the string concatination is just run for the two list elements that are not exceptio...

Created: 2010-01-04 | Last updated: 2010-01-04

Credits: Stian Soiland-Reyes

Triplify GO database external reference [... (1)

• Download

Get GO external database list from http://www.geneontology.org/doc/GO.xrf_abbs 

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: Francois Belleau

Triplify LSRN record name list [myexperim... (1)

• Download

Get LSRN list from http://www.lsrn.org/lsrn/registry-2009-04-26-32404.rdf 

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: Francois Belleau

Triplify NCBI databases list [myexperiment... (1)

• Download

List NCBI's database name. Using this URL service: http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? This is NCBI's namespace list supported by Bio2RDF : pubmed protein nucleotide gene=geneid homologene mesh omim pccompound=cid pcsubstance=sid taxonomy unigene unists

Created: 2009-11-30 | Last updated: 2009-12-01

Credits: Francois Belleau

Triplify EB-Eye databases list from EBI [m... (1)

• Download

TAG: knowledgescope, eb-eye, bio2rdf, banff_manifesto, rdf, ebi, soap

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

Credits: Francois Belleau

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

• Download

TAG: knowledgescope, uniprotkb, bio2rdf, search, rdf

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

Credits: Francois Belleau

Triplify UniProt database list [myexperime... (1)

• Download

TAG: knowledgescope, uniprotkb, bio2rdf, banff_manifesto

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

Credits: Francois Belleau