Text-mining using OSCAR to obtain a list of Chemical names and Identifiers

Created: 2013-04-18 13:01:50

This service extracts chemical names from text and obtains identifiers for these names. It outputs a HTML string that can be opened in a browser providing a table of information and links to ChemSpider.
Known issues
 - Character limit ~3000
 - Unable to produce InChIs or CSID for some names
 - Error sometimes encountered when a trivial and systematic name for the same compound are used
 - Some issues with identifiers being recognised but not able to be processed

requires access to an OSCAR3 service and ChemSpider
more information is contained within the text constant "Instructions"  

Information Preview

Information Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
[ More InfoExpand ]

Information Workflow Components

Information Authors (0)
Information Titles (0)
Information Descriptions (0)
Information Dependencies (0)
Inputs (2)
Processors (17)
Beanshells (2)
Outputs (1)
Datalinks (21)
Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (2)


Information Attributions (1)


Information Tags (12)

Log in to add Tags

Information Shared with Groups (0)


Information Featured In Packs (0)


Log in to add to one of your Packs

Information Attributed By (0)



Information Favourited By (0)

No one

Information Statistics


Citations (0)


Version History

In chronological order:

Reviews Reviews (0)

No reviews yet

Be the first to review!

Comments Comments (0)

No comments yet

Log in to make a comment

Workflow Other workflows that use similar services (15)

Only the first 2 workflows that use similar services are shown. View all workflows that use these services.


Workflow Generate inChi (1)

Generates an inChi string for a given chemical represented by its SMILES string, SDF or MOL file using the inchi web service provided by ChemSpider

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li


Workflow Generate inChi information (1)

Uses the GenerateInchiInfo web service operation from ChemSpider to generate information relating to the InChi string for a given chemical compound

Created: 2010-07-09 | Last updated: 2010-07-09

Credits: User Peter Li