Workflows

EUADR Relationship Extraction Workflow (1)

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The workflow offers the ability to automatically determine if an ADR and a Drug are co-mentioned in any of the indexed resources. However the actual relationship between a Drug and an ADR can only be determined by referring to the actual resource The co-occurance relationship workflow seeks to automate the search for resources (publications, drug labels) related to ADRs corresponding to a given drug/ adverse event association. To enable this concept profiles for drugs and adverse effects wer...

Created: 2011-07-27 | Last updated: 2012-09-07

Credits: Bharat Singh

Download Structures from PubChem given che... (1)

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This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned.  The pubchem compound_ID is then used to download structures from PubChem.  

Created: 2011-05-24 | Last updated: 2011-05-24

Credits: Kalai Michael Gerlich

Attributions: Download Entries from PubChem

XPath Pubmed Ids (2)

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This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml. The xml is then parsed to retrieve a list of PubMed ids

Created: 2011-03-23 | Last updated: 2011-03-30

Credits: Paul Fisher

Attributions: XPath Pubmed Ids

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

retrive dpas data for all ics instruments ... (1)

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This workflow demonstrates the standard query where events for a period of time are requested from the HEC service, available instruments for this time come from the ICS and data only for the times of the events are requested from the DPAS. In this version data from only 3 random events (out of the HEC list) will be requested from the DPAS.

Created: 2010-09-14 | Last updated: 2010-09-14

Credits: Anja Le Blanc

Attributions: retrive dpas data for all ics instruments for HEC event data

retrive dpas data for all ics instruments ... (1)

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This workflow demonstrates the standard query there events for a period of time are requested from the HEC service, available instruments for this time come from the ICS and data only for the times of the events are requested from the DPAS.

Created: 2010-09-14 | Last updated: 2010-09-14

Credits: Anja Le Blanc

Attributions: Extracting data from VOTable format by using XPath query Retrieve all data for all instruments for a given periode of time

instruments in sxr and euv spectrum (1)

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ICS use case 5

Created: 2010-08-20 | Last updated: 2010-08-20

Credits: Anja Le Blanc

Call VSO web service with HELIO input data (1)

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  date transformation from 2000-10-02T23:00:00 to 20001002230000 HELIO instrument names as in http://helio-dev.i4ds.ch/xsd/instruments.xsd spitt into source and instrument names; if these pair don't exist only first part (source) is tried.

Created: 2010-08-04 | Last updated: 2010-08-04

Credits: Anja Le Blanc

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