Releases · allysonlister/swo

05 Mar 15:11

v2023-03-05

839b92d

Refactoring final 'efo' style IRIs Latest

Latest

This release is is for ticket #59, where IRIs that had 'efo' in them were refactored to no longer include them. The old IRIs were obsoleted as per our best practices, and new IRIs of the correct form were minted. See this directory for all work, and this diff for all changes since the previous releases.

Before the automated work outlined below, the following manual changes were performed:

obsolete_MathWorks

During the initial creation of the efo IRIs, we noticed that http://www.ebi.ac.uk/efo/swo/SWO_0000291 (obsolete_MathWorks) had been incorrectly obsoleted some years ago (the owl:deprecated flag hadn't been set), causing it to appear as though it was not yet obsolete. This was dealt with manually, and committed separately, within swo-edit before the more automated steps below were "officially" run.

OBI_0000245_1

Please note I also obsoleted the following individuals which seem to have been added erroneously:

http://www.ebi.ac.uk/efo/swo/OBI_0000245_1

obsoleted_in_version and reason_for_obsolescence

We noticed that there were also these two EFO properties, and decided to keep one and refactor the other:

Kept http://www.ebi.ac.uk/efo/obsoleted_in_version,obsoleted as it is still present within EFO. However, we don't plan to use this in future, as the related issue will provide more context.
Refactored http://www.ebi.ac.uk/efo/reason_for_obsolescence,reason for obsolescence --> http://www.w3.org/2000/01/rdf-schema#comment as EFO no longer has this property within its release files. We will do this by adding it to the mapping file (refactor-efo-swo-mappings.csv) manually, and stripping out all of the annotations assigned to it to prevent it being added to rdfs:comment.

Automated refactoring

The modified IRIs are all instances except for 4 object properties (http://www.ebi.ac.uk/efo/swo/SWO_0000394,is developed by, http://www.ebi.ac.uk/efo/swo/SWO_0000740, implements, http://www.ebi.ac.uk/efo/swo/SWO_0000741,is encoded in and also http://www.ebi.ac.uk/efo/reason_for_obsolescence). The efo refactoring for classes happened in 2019.

Suggestions/Comments?

This is a relatively large change affecting a number of IRIs. Please let us know if you have any questions, or you think something was done incorrectly. Thanks!

Assets 2

11 Oct 21:12

allysonlister

v2022-10-11

152ed33

2022-10-11 Alignment with ODK Build Procedure

This release is the first one utilising 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

Please note that, due to the way the files are built, there will be non-trivial changes to the ontology. Most will not be visible, but some may be. Please let us know if you see anything odd or if you have any questions about this release.

Assets 2

28 Nov 11:24

allysonlister

v1.7

f2ce994

SWO Release version 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.

Please see https://github.com/allysonlister/swo/tree/master/release/1.7 for more information.

Assets 2

01 Feb 11:56

allysonlister

v1.6

db387ab

SWO Release 1.6

Release 1.6 is characterized mainly by the move to GitHub and the addition of a number of new license classes to align more closely with BioSharing.org.

Assets 2

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obsolete_MathWorks

OBI_0000245_1

obsoleted_in_version and reason_for_obsolescence

Automated refactoring

Suggestions/Comments?

Releases: allysonlister/swo

Refactoring final 'efo' style IRIs

obsolete_MathWorks

OBI_0000245_1

obsoleted_in_version and reason_for_obsolescence

Automated refactoring

Suggestions/Comments?

2022-10-11 Alignment with ODK Build Procedure

SWO Release version 1.7

SWO Release 1.6