Search InChI in NCBI eSearch (pccompound)

Created: 2009-03-30 09:26:25 Last updated: 2009-03-30 09:47:00

Download Workflow

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.

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/740/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (1)

Name	Description
terms

Processors (8)

Name	Type	Description
NCBI_eSearch	arbitrarywsdl
fetch_compound_info	local
fetch_compound_image	local
Beanshell_scripting_host	beanshell
parametersXML	local
run_eSummary	arbitrarywsdl
requestXML	local
NCBI_database	stringconstant

Beanshells (1)

Name	Description	Inputs	Outputs
Beanshell_scripting_host		xml db_search	image info db id

Outputs (3)

Name	Description
webpage
image
out

Links (13)

Source	Sink
Beanshell_scripting_host:id	requestXML:id
Beanshell_scripting_host:image	fetch_compound_image:url
Beanshell_scripting_host:info	fetch_compound_info:url
NCBI_database:value	Beanshell_scripting_host:db_search
NCBI_database:value	parametersXML:db
fetch_compound_image:image	image
fetch_compound_info:contents	webpage
parametersXML:output	NCBI_eSearch:parameters
terms	parametersXML:term
Beanshell_scripting_host:db	requestXML:db
NCBI_eSearch:parameters	Beanshell_scripting_host:xml
requestXML:output	run_eSummary:request
run_eSummary:result	out

Coordinations (0)

Information Workflow Type

Taverna 1

Information Uploader

Michael Gerlich

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

Michael Gerlich

Information Attributions (0)

(Workflows/Files)

None

Information Tags (12)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

2661 viewings

2210 downloads

[ see breakdown ]

Citations (0)

None

Version History

In chronological order:

Search InChI in NCBI eSearch (pccompound)

Created by Michael Gerlich on Monday 30 March 2009 09:26:25 (UTC)

Last edited by Michael Gerlich on Monday 30 March 2009 09:47:01 (UTC)

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (31)

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

Taverna 1

Uploader

Michael Gerlich

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

Taverna 2

Uploader

Paul Fisher

microRNA to KEGG Pathways and Abstracts (1)

Workflow takes in a text file of microRNAs from microCOSM (at the EBI) and outputs a list of KEGG pathway information, including genes in pathways and pathway abstracts from PubMed. The results can then be used in various text mining applications/workflows to rank the results against a given disease.Workflow takes in a file of microRNAs

Created: 2010-03-17

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region