Workflows

Free text search to Concept Wiki URI (4)

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Free text search of concept wiki using the Openphacts "Map free text to a concept url based on semantic tag" ie /search/byTag. Search for either compounds or targets depending on the input uuid for "searchType" and filter by source authority with the "branch" input

Created: 2013-06-24 | Last updated: 2013-06-24

Credits: Ian Dunlop Katy Wolstencroft Marco Roos paul groth

Make XML Parameters (1)

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Reformats a SNP list with optional p-value into the required XML input for the 'Define Associated Regions and Genes' workflow. Additional parameters can be supplied to add to the XML document.

Created: 2012-02-08 | Last updated: 2012-02-08

Credits: Paul martin

Longitude with beanshell (1)

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This workflow takes in a string value or list of values and pulls out longitude coordinates formatted as ###-##(N or S) using the following regular expression: \d\d\d-\d\d(E|W). The coordinates are processed and formatted to be in the form required by the web service used in my "Elevation plot" workflow. This workflow primarily contains string manipulation. For many of the text and list services used, the beanshell script needed to be modified in order to produce the formatti...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Chrisser

Latitude with beanshell (1)

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This workflow takes in a string value or list of values and pulls out latitude coordinates formatted as ##-##(N or S) using the following regular expression: \d\d-\d\d(N|S). The coordinates are processed and formatted to be in the form required by the web service used in my "Elevation plot" workflow. This workflow contains primarily string manipulation. For many of the text and list services used, the beanshell script needed to be modified in order to produce the formatting I requi...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Chrisser

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

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