Pack: Visualize PAV provenance as SVG

Created: 2013-04-05 09:18:51 Last updated: 2018-01-04 11:39:09

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Title: Visualize PAV provenance as SVG

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.

Items (11)

File: Visualization of ChemSpider VoiD provenance (Stian Soiland-Reyes)

Added by Stian Soiland-Reyes ... more than 1 year ago (2013-04-05 09:23:41)

Workflow: Visualize PAV provenance as SVG (Stian Soiland-Reyes)

Added by Stian Soiland-Reyes ... more than 1 year ago (2013-04-05 09:20:59)

File: Workflow run: Pav2Svg using ChemSpider VoID (Stian Soiland-Reyes)

Added by Stian Soiland-Reyes ... more than 1 year ago (2013-04-05 09:28:44)

External: PAV ontology: Provenance, Authoring and Versioning - (https://doi.org/10.1186/2041-1480-4-37)

Alternate link

Paper in Journal of Biomedical Semantics 2013, 4:37

Added by Stian Soiland-Reyes ... more than 1 year ago (2013-05-01 14:49:58)

External: Pellet 2.3.0 source code/binary - (http://clarkparsia.com/pellet/download/pellet-2.3.0)

Alternate link

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://www.gnu.org/licenses/>.

Added by Stian Soiland-Reyes ... more than 1 year ago (2013-04-05 09:51:49)

External: Link - (http://www.w3.org/2000/10/swap/cwm.tar.gz)

Added by Stian Soiland-Reyes ... more than 1 year ago (2013-04-05 09:51:11)

External: Link - (http://www.openphacts.org/specs/2012/WD-datadesc-20121019/examples/chembl-rdf-void.ttl)

Added by Stian Soiland-Reyes ... more than 1 year ago (2013-04-05 09:20:31)

External: Link - (http://www.openphacts.org/specs/2012/WD-datadesc-20121019/)

Added by Stian Soiland-Reyes ... more than 1 year ago (2013-04-05 09:20:18)

External: Link - (http://purl.org/pav/)

Added by Stian Soiland-Reyes ... more than 1 year ago (2013-04-05 09:20:08)

External: Link - (http://www.w3.org/2000/10/swap/doc/cwm.html)

Added by Stian Soiland-Reyes ... more than 1 year ago (2013-04-05 09:19:58)