https://github.com/cthoyt/swo

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

https://github.com/cthoyt/swo

Repository

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

https://github.com/cthoyt/swo/blob/master/

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# The Software Ontology
The Software Ontology (SWO) is a resource for describing software tools, their types, tasks, versions, licensing, provenance and associated data. The latest release is 1.7.

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](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](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](LicenceHierarchy.md) page.

# Files

Each directory contains a README describing its contents. Broadly, the `dev` directory contains the working files which are updated in an ongoing manner. The `release` directory is only updated when a release has been built.

## Development files

Within the `dev/ontology` subdirectory, you will find a number of OWL files. Details of these files can be found in the [ontology directory's README](dev/ontology/README.md).

## Release files

Within the release/ subdirectory are the various files that are published with each SWO release. Details of releases are available in the [release directory README](release/README.md).

# 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/tree/master/release.

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 the *obsolete SWO class* (child of *DeprecatedClass*) 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 as a README.md and will outline major changes to the ontology.

Release files are created using [ROBOT](http://robot.obolibrary.org/) via a controlling [Makefile](dev/Makefile).

# Tools Used

[Ontofox](http://ontofox.hegroup.org/) has been used to build [swo-external](https://github.com/allysonlister/swo/blob/master/dev/ontology/swo-external.owl) containing all of the imported classes and associated axioms. [Protege](https://protege.stanford.edu/) (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](http://robot.obolibrary.org/) has been used to merge and build the release files as well as perform a number of housekeeping tasks.

- [Ontofox](http://ontofox.hegroup.org/) - Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. OntoFox: web-based support for ontology reuse.
BMC Research Notes. 2010, 3:175. PMID: 20569493
- [Protege](http://protege.stanford.edu/) - Musen, M.A. [The Protg project: A look back and a look forward.](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4883684/) AI Matters. Association of Computing Machinery Specific Interest Group in Artificial Intelligence, 1(4), June 2015. DOI: 10.1145/2557001.25757003.
- [ROBOT](http://robot.obolibrary.org/) - R.C. Jackson, J.P. Balhoff, E. Douglass, N.L. Harris, C.J. Mungall, and J.A. Overton. [ROBOT: A tool for automating ontology workflows](https://rdcu.be/bMnHT). BMC Bioinformatics, vol. 20, July 2019.

# Licensing

The SWO License is available at [LICENSE.md](LICENSE.md).

For license information for the external ontologies used to create SWO, please see our [Licensing Compliance](https://github.com/allysonlister/swo/blob/master/LicensingCompliance.md) page.


# 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](https://github.com/allysonlister/swo/issues/10) in the issue tracker.

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