OMEX metadata specification ratification (v1.2)

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John Gennari

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Jul 21, 2021, 12:48:46 AM7/21/21

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COMBINE annotation community:

As you may know, in April of 2020, we ratified version 1.0 of the OMEX metadata specification. At the time, we only had early versions of tool support for this standard. We have now developed a much more robust library, libOmexMeta (and pyomexmeta) that provides library support for the standard. (See our 2021 publication in Bioinformatics) During development, we made some minor changes to the specifications, resulting in version 1.1. Most recently, the editors have engaged in another round of improvements and changes to the specification, and these are reflected in version 1.2.

We are now asking for ratification of version 1.2. The specifications are available at

https://drive.google.com/file/d/1d_tkxWOkHO6FnNR4EXM5KiTQsQLJNDKJ/view?usp=sharing

As before, we have set up a Google forms survey at

https://forms.gle/6ZwDfVs4J823uKmd6

Please respond within the next two weeks (by August 4, 2021). Thanks in advance for casting your ballot!

Sincerely,

The Editors of the OMEX Metadata Specification: John Gennari, Matthias König, Goksel Misirli, Max Neal, David Nickerson, Dagmar Waltemath

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For those who care, some brief words about what is new in version 1.2:

First, the spirit and goals of the document remain the same, thus all changes are considered "minor" and as improvements to the recommended RDF in annotation files.

** The largest change from version 1.0 is the addition of some "model-level" annotations. (These were largely omitted in v1.0.) These include authors, publication, and date of creation. We leverage Dublin Core for many of these terms. We also advocate the use of orcid IDs to identify authors and contributors. We recognize that more work needs to be done in this area.

**In version 1.2, we use absolute URIs, rather than the relative "./" conventions used in version 1.0. To do this, we have introduced a placeholder URI, omex-library.org to use as the root of all annotations.

** There are many other syntactic and clarity changes. For example, we now provide a more clear (we hope) distinction between how composite annotations occur for SBML models versus CellML models. We also use Turtle rather than XML/RDF syntax in the document.

Of course, you are always welcome to provide feedback to me or any of the editors!