About | Mailing List | Publications

Give us Feedback |

Invite

Home
»
Workflows
»
Download Entries from PubChem

Workflow Entry: Download Entries from PubChem

Created at: 30/03/09 @ 09:20:42 Last updated: 30/03/09 @ 09:34:37

Version 1 (of 1)

Version created on: 30/03/09 @ 09:20:42 by: Michael Gerlich | Revision comments Expand

Last edited on: 30/03/09 @ 09:34:38 by: Michael Gerlich

Title: Download Entries from PubChem

Type: Taverna 1

Preview

(Click on the image to get the full size)

Download Scalable Diagram (SVG)

Description

Given a list of identifiers (e.g. CID) and their appropriate type (eID_CID - note that these differ slightly from the original identifier name -> CID <-> eID_CID), this workflow queries PubChem via PUG to retrieve a download URL for the resulting XML file containing the results.

Adding support for downloading this XML file and writing it to filesystem is planned.

Download

Download Workflow File/Package (SCUFL)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Launch in Taverna

Note: you need to have both the WHIP Launcher and the Taverna myExperiment/WHIP plugin installed on your machine for this to work. See here for information.

Option 2:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/737/download?version=1
[ More Info Expand ]

Workflow Components

Inputs (2)

Name	Description
ID	1, 2, 3, 4, 5, 6, 7, 8, 9, 10
idType	eID_CID

Processors (12)

Name	Type	Description
Compression	stringconstant
Format	stringconstant
Download_out	local
GetDownloadUrl_in	local
InputListText_in	local
GetDownloadUrl_out	local
InputListText_out	local
Download_in	local
GetDownloadUrl	arbitrarywsdl	Given a download key, return an FTP URL that may be used to download the requested file. Synchronous. See the Service entry for this web service.
InputListText	arbitrarywsdl	Input a set of identifiers for a PubChem database, as a simple string of integer values separated by commas and/or whitespace. Returns a list key. Synchronous. See the Service entry for this web service.
Download	arbitrarywsdl	Given a list key, prepare for download a file containing those records in the selected format. See the web download service documentation (http://pubchem.ncbi.nlm.nih.gov/pc_fetch/pc_fetch-help.html) for more detail on the supported formats and file types. Returns a download key. Asynchronous. See the Service entry for this web service.
Status_Check	workflow

Beanshells (1)

Name	Description	Inputs	Outputs
CheckForSuccess		status	success

Outputs (1)

Name	Description
URL

Links (14)

Source	Sink
Compression:value	Download_in:eCompress
Download:parameters	Download_out:input
Download_in:output	Download:parameters
Download_out:DownloadKey	Status_Check:KeyIn
Format:value	Download_in:eFormat
GetDownloadUrl:parameters	GetDownloadUrl_out:input
GetDownloadUrl_in:output	GetDownloadUrl:parameters
ID	InputListText_in:ids
InputListText:parameters	InputListText_out:input
InputListText_in:output	InputListText:parameters
InputListText_out:ListKey	Download_in:ListKey
Status_Check:KeyOut	GetDownloadUrl_in:DownloadKey
idType	InputListText_in:idType
GetDownloadUrl_out:url	URL

Coordinations (0)

Information Workflow Type

Taverna 1

Information Original Uploader

Michael Gerlich

Information License

All versions of this Workflow are licensed under:

Information Credits (1)

(People/Groups)

Michael Gerlich

Information Attributions (0)

(Workflows/Files)

None

Information Tags (4)

Original 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 Ratings (0)

Current:

0.0 / 5

(0 ratings)

Log in to rate and see breakdown of ratings

Information Attributed By (1)

(Workflows/Files)

Download Structures from PubChem given chemical names

Information Favourited By (0)

No one

Information Statistics

505 viewings

697 downloads

[ see breakdown ]

Citations (0)

None

Version History

Earliest Version:
[1] - Download Entries from PubChem

Created on: Monday 30 March 2009 @ 09:20:42 (GMT)

Created by: Michael Gerlich

Last edited on: Monday 30 March 2009 @ 09:34:38 (GMT)

Last edited by: Michael Gerlich

Revision comments:

None

This Workflow only has one version.

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 (7)

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

Taverna 2

Original Uploader

Kalai

Download Structures from PubChem given chemical names (v1)

Created: 24/05/11 @ 13:13:52 | Last updated: 24/05/11 @ 14:19:24

Credits: Kalai Michael Gerlich

Attributions: Download Entries from PubChem

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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.

Rating: 0.0 / 5 (0 ratings) | Versions: 1 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 39 times | Downloaded: 19 times

Tags (26):

View

Download (v1)

Taverna 2

Original Uploader

Peter Li

download (v2)

Created: 16/07/10 @ 10:41:38 | Last updated: 16/07/10 @ 10:53:32

Credits: Peter Li

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Given a list key, prepare for download a file containing those records in the selected format. The original workflow was written by the PubChem team @ NCBI (http://pubchem.ncbi.nlm.nih.gov/).

Rating: 0.0 / 5 (0 ratings) | Versions: 2 | Reviews: 0 | Comments: 0 | Citations: 0

Viewed: 29 times | Downloaded: 24 times

Tags (2):

View

Download (v2)

What is this?

Linked Data

Non-Information Resource URI: http://www.myexperiment.org/workflows/737/versions/1

Alternative Formats