Draft OMEX metadata spec, version 1.1
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John Gennari
Aug 19, 2020, 2:00:53 AM8/19/20
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(Apologies if you receive two of these messages; I'm not clear on the best way to post this)
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
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
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