Snapshot of the Pack: Visualize PAV provenance as SVG (from myExperiment)

Pack Details

Title	Visualize PAV provenance as SVG
Items	11
Created by	Stian Soiland-Reyes
Created at	09:18:51 on Friday, 05 April 2013
Last updated at	11:39:09 on Thursday, 04 January 2018

Description

A workflow that converts PAV provenance to SVG by inferring PROV-O statements.

VoID descriptions following the Open PHACTS Dataset descriptions specification are fetched as Turtle , cleaned up to be valid OWL2 ontology and include useful labels, processed through the OWL reasoner Pellet ; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox , generating an SVG visualization of the provenance.

Note that this workflow downloads CWM , Pellet and ProvToolbox on demand, and uses UNIX command line tools like wget and md5 which are unlikely to work in Windows. This workflow has been tested on Ubuntu 12.10 with Taverna 2.4.0.

This pack is licensed as AGPL 3.0 (not GPL 2.0 as myExperiment states) as includes (links to) the Pellet source code/binary. The workflow does not bundle Pellet, but it downloads it on demand.

Downloaded Items (3)

File: Workflow run: Pav2Svg using ChemSpider VoID [ open local copy ]
Uploader: Stian Soiland-Reyes

Added to pack by: Stian Soiland-Reyes (05/04/2013 @ 09:28:44)
Comment: none
File: Visualization of ChemSpider VoiD provenance [ open local copy ]
Uploader: Stian Soiland-Reyes

Added to pack by: Stian Soiland-Reyes (05/04/2013 @ 09:23:41)
Comment: none
Workflow: Visualize PAV provenance as SVG [ open local copy ]
Type: Taverna 2
Originally uploaded by: Stian Soiland-Reyes
Version: 2 (created on: 05/03/2013, last edited on: 05/04/2013)
Version uploaded by: Stian Soiland-Reyes

Added to pack by: Stian Soiland-Reyes (05/04/2013 @ 09:20:59)
Comment: none

Not Downloaded Items (8)

Packs within this pack (0)

None

External items (8)

PAV ontology: Provenance, Authoring and Versioning - https://doi.org/10.1186/2041-1480-4-37
Alternate link: http://arxiv.org/abs/1304.7224

Added to pack by: Stian Soiland-Reyes (01/05/2013 @ 14:49:58)
Comment:

Paper in Journal of Biomedical Semantics 2013, 4:37
Pellet 2.3.0 source code/binary - http://clarkparsia.com/pellet/download/pellet-2.3.0
Alternate link: https://dl.dropbox.com/sh/baz8nld080x49yz/uMG8YBw_GP/pellet-2.3.0.zip

Added to pack by: Stian Soiland-Reyes (05/04/2013 @ 09:51:49)
Comment:

(c) Copyright 2011 Clark & Parsia LLC

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License
along with this program. If not, see <http: />.
Link - http://www.w3.org/2000/10/swap/cwm.tar.gz
Alternate link: none

Added to pack by: Stian Soiland-Reyes (05/04/2013 @ 09:51:11)
Comment: none
Link - http://www.openphacts.org/specs/2012/WD-datadesc-20121019/examples/chembl-rdf-void.ttl
Alternate link: none

Added to pack by: Stian Soiland-Reyes (05/04/2013 @ 09:20:31)
Comment: none
Link - http://www.openphacts.org/specs/2012/WD-datadesc-20121019/
Alternate link: none

Added to pack by: Stian Soiland-Reyes (05/04/2013 @ 09:20:18)
Comment: none
Link - http://purl.org/pav/
Alternate link: none

Added to pack by: Stian Soiland-Reyes (05/04/2013 @ 09:20:08)
Comment: none
Link - http://www.w3.org/2000/10/swap/doc/cwm.html
Alternate link: none

Added to pack by: Stian Soiland-Reyes (05/04/2013 @ 09:19:58)
Comment: none
Link - https://github.com/lucmoreau/ProvToolbox
Alternate link: none

Added to pack by: Stian Soiland-Reyes (05/04/2013 @ 09:19:38)
Comment: none

Items that can be viewed, but not downloaded (0)

None

Items that cannot be viewed (0)

None

Packs within this pack:	0
External items:	8
Items that can be viewed, but not downloaded:	0; ( 0 workflows, 0 files )
Items that cannot be viewed:	0

Workflows:	1
Files:	2

Snapshot of the Pack: Visualize PAV provenance as SVG

Pack Details

Description

Summary of Pack Items (11)

Downloaded Items (3)

Not Downloaded Items (8)

Packs within this pack (0)

External items (8)

Items that can be viewed, but not downloaded (0)

Items that cannot be viewed (0)