Workflows

DOI Record Generator (1)

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This workflow generates DOI record files for deposit, using data set metadata for the FLOSSmole project. It reads in an input file generated from a SQL query from an eprints database, and transforms the parts of the source file as necessary to create a comprehensive DOI deposit record. It also generates DOIs for the data sets. These metadata are inserted into an XML record template (based on the std-doi.xsd schema) and the individual resources are aggregated into a single file.

Created: 2009-04-29

Credits: Andrea Wiggins

Attributions: Data Set Metadata Generator

Data Set Metadata Generator (1)

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This workflow generates ePrints XML import files with data set metadata for the FLOSSmole project. It reads in an input file generated from a Notre Dame SourceForge dump SQL query and uses regular expressions to parse the filename for the data set's source repository, download URL, and basic description. It also translates the epoch date into a sql format suitable for import, and the file size from bytes into larger units, e.g. GB, MB, etc. These data are inserted into an XML eprint record te...

Created: 2008-08-19 | Last updated: 2008-08-19

Credits: Andrea Wiggins

MassBank to KEGG (1)

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: Michael Gerlich

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: Michael Gerlich

blastp using the MRS system (1)

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This blastp workflow uses the blast service of MRS (http://mrs.cmbi.ru.nl). Inputs are a sequence (only amino acids, not a fasta sequence) and a database name. Valid database names that can be used are "sprot", "uniprot", "trembl", "pdb", "refseq", "ipi" and "gpcrdb". Output is returned in XML.

Created: 2008-11-28 | Last updated: 2008-11-28

Credits: Bas Vroling

Transform XML with parameters (1)

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Similar to Transform_XML local widget but accepts transformation parameters and skips the part with writing to the output file. The essence, i.e. Transform_XML beanshell works with Strings representing file contents, not with file URLs. The XML transfomation parameters are given as a list of strings in the "param_name = param_value" format.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: trybik

retrieve protein sequence and do a BLAST a... (1)

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retrieve protein sequence and do a BLAST and extract position from DDBJ Web services   informations on Web services available at http://xml.nig.ac.jp/index.html example accession : Q9NRA8 database : UNIPROT program : blastp  

Created: 2010-07-21 | Last updated: 2010-07-21

Credits: Lebreton

Attributions: BLAST using DDBJ service