format identifier: Combine Archive Metadata & new metadata specification

[Frank Bergmann]

Dear all, 

it has been brought to my attention, that there is currently an interoperability issue using combine archives and the new metadata specification format. The issue is, that when we created the combine archive and looked for minimal metadata to exchange about the archive (description, authors, dates), we took a page from the SBML specification and formulated a specific subset of RDF that libraries would implement to support so users of the libraries would not need to generate the RDF themselves. Similarly, when reading in a combine archive, the utility classes would be used to provide the information obtained. What decides whether these utility classes come into play or not is the format identifier. 

http://identifiers.org/combine.specifications/omex-metadata

if that identifier is given, then the archive metadata is expected to follow the format as described in section 3.8 of: 

http://co.mbine.org/specifications/omex.version-1.pdf

Unfortunately, what has happened now, is that the page has been rewritten citing the new metadata specification. I also have seen a first archive, that uses this identifier to identify a file not with metadata about the archive, but other information, that is unrecoverable by software that implemented the reduced and recommended subset from 2014. 

I hope we can resolve this issue, without having to change software for those people that have supported the format before. The only way I can see this happen, is by choosing a different identifier for the new metadata specification. 

Thanks

Frank

[John Gennari]

Very interesting. Indeed, we had also recently noticed this problem (thanks to Ciaran Welsh, cc'd).

It's short notice, but would you (Frank) happen to be available today (Tues) at 3pm Pacific time?  We have a weekly meeting at that time, and this would be a good time to discuss this.

Although if that doesn't work, we should schedule a different time. As Ciaran is in England, he can't join us at our weekly Tues afternoon meetings. Max, Ciaran and myself are probably some of the key players to chat about this conflict. I'm free this Thursday and Friday morning, if that helps scheduling.

-John G.

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[Nicolas Rodriguez]

one solution would be to add a "level 2" for the new omex-metadata to differentiate it from the original one.

Nico

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[John Gennari]

Dear all:

As part of the work of the Center for Reproducible Biomedical Modeling,
we have been working to update and extend the OMEX metadata
specification. As you may recall, version 1.0 was approved back in
April. Attached, please find a draft of version 1.1.

There are some significant extensions in the attached. First, we have
re-organized the way that namespaces are used, and we have reserved
"omex-library.org" as a holding spot for these URIs. Version 1.1 does
not use relative paths, unlike version 1.0. Second, we have added 6
types of model-level annotations, such as the creator of the model, the
publication for the model, etc.  As a smaller matter, for readability,
the document uses Turtle format for RDF, rather than XML/RDF. But either
serialization is sanctioned.

This is a draft specification, as we are currently developing software
libraries that support this version (the developers are Ciaran Welsh for
C and Python, and Max Neal for Java). Our intention is that software
will be backwards compatible with version 1.0. (It will be able to read
OMEX files stored in version 1.0 and convert them to version 1.1.)

Let me know if you have any comments or questions. Of course, we will
also be presenting this material at the COMBINE 2020 meeting. Thanks!

-John Gennari