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The Software Ontology

The Software Ontology

The Software Ontology (SWO) is an OBO Foundry ontology describing software tools, their types, tasks, versions, licensing, provenance and associated data. The latest release is 1.7.

Its OBO Foundry entry can be found at http://obofoundry.org/ontology/swo

You can cite SWO with the following publication:

Malone, J., Brown, A., Lister, A.L. et al. The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation. J Biomed Semant 5, 25 (2014). https://doi.org/10.1186/2041-1480-5-25

You can also view SWO in the EBI's Ontology Lookup Service (OLS) at https://www.ebi.ac.uk/ols/ontologies/swo.

Licenses in SWO

As part of SWO, we have developed a hierarchy of license types which can organize licenses based on their clauses. For more information on this work, please see the LicenceHierarchy page.

Releases and Versions

Stable release versions

The latest version of the ontology can always be found at:

http://purl.obolibrary.org/obo/swo.owl

(note this will not show up until the request has been approved by obofoundry.org)

Editors' version

Editors of this ontology should use the edit version, src/ontology/swo-edit.owl

Release Policy

  1. Releases occur on an ad hoc basis, as required by our users. All releases of the Software Ontology can always be found at https://github.com/allysonlister/swo/releases.
  2. Assigned identifiers will remain on a class and will not be deleted from the OWL files. Classes that are no longer required will be subclassed under http://www.geneontology.org/formats/oboInOwl#ObsoleteClass and stripped of axioms but the URI and original annotation will remain.
  3. Classes that change their intended meaning significantly (i.e. they denote a new entity) will be assigned a new URI and the old URI will be made obsolete as per the above.
  4. A release notes file will be attached to each release and will outline major changes to the ontology.

Tools Used

This ontology repository was created using the Ontology Development Kit (ODK). Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P Balhoff, Seth Carbon, Anita R Caron, William D Duncan, Joe E Flack, Melissa Haendel, Nomi L Harris, William R Hogan, Charles Tapley Hoyt, Rebecca C Jackson, HyeongSik Kim, Huseyin Kir, Martin Larralde, Julie A McMurry, James A Overton, Bjoern Peters, Clare Pilgrim, Ray Stefancsik, Sofia MC Robb, Sabrina Toro, Nicole A Vasilevsky, Ramona Walls, Christopher J Mungall, David Osumi-Sutherland, Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies, Database, Volume 2022, 2022, baac087, https://doi.org/10.1093/database/baac087

Licensing

The SWO is licensed under the CC BY 4.0 license. Exact text is available at LICENSE.

For license information for the external ontologies used to create SWO, please see our Licensing Compliance page.

Contact

Please use this GitHub repository's Issue tracker to request new terms/classes or report errors or specific concerns related to the ontology.

Of Historical Interest

Directory/File restructuring for the ODK

In October 2022, SWO converted from a project-specific Makefile to the Ontology Development Kit. This resulted in a complete restructuring of the directories and files within the repository. For now, these are contained within the historical_files directory.

Please note that this also resulted in a change to how the release numbering happens; SWO now builds releases that contain the date within the ontology version IRI, rather than a release number. This is consistent with OBO Foundry best practices.

Restructuring for Release 1.7

Due to improvements in automatically building an ontology via Ontofox and ROBOT, we no longer needed to import all of EDAM. Release 1.7 was the first to employ these semi-automated updates. This allows SWO to be easily aligned with any new releases of its imported ontologies and creates a much simpler build procedure.

Previously, SWO was built with a series of modular OWL files labelled swo_*.owl. While this made things easier in previous years, the number of development files was getting unwieldy. Currently, the only file imported by the development version of SWO is the automatically-generated one produced by Ontofox, which pulls in all of the latest annotation and hierarchies for the imported classes.

Finally, the IRIs across all SWO classes were reconciled according to the official SWO IRI naming scheme. As such, many IRIs were deprecated and new IRIs issued. Full details are available at the IRI Refactoring Issue in the issue tracker.

Tools Used for 1.7 and earlier

Ontofox has been used to build swo-external containing all of the imported classes and associated axioms. Protege (including versions 4.3.0 and 5.2.0) has been used to create the core OWL file and to view and check all development ontology files. ROBOT has been used to merge and build the release files as well as perform a number of housekeeping tasks.

Acknowledgements

This ontology repository was created using the Ontology Development Kit (ODK).

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The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, licences, provenance and associated data.

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