Add support for extension slots #375
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We add a new slot to the MappingSet object , representing the definitions of extension slots that may be used within the set (as a list of "extension definition" objects). Each "extension definition" is made of up to three elements: * the name of the extension slot, * the identifier of an associated property, * a type hint. We also add a sample file that demonstrates the use of such extension slots.
We add a section in the description of the data model to explain what extension slots are and how they should be used. We add a section in the specification of the SSSOM/TSV format to explain how extension slots should be managed in that format.
We add the two following prefix names: * xsd: http://www.w3.org/2001/XMLSchema# * linkml: https://w3id.org/linkml/ to the list of built-in prefix names. They are intended to be used when defining "extension slots" (as the value of the `type_hint` slot, to define the expected type of the slot), so for convenience we make them built-in.
The IRI of the "uriorcurie" data type is `https://w3id.org/linkml/Uriorcurie`, _not_ `.../uriOrCurie`. Not sure where I got the incorrect casing from.
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matentzn
reviewed
Aug 3, 2024
Clear out possible ambiguity when referring to the "LinkML model". Clarify the possible types of extension values.
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matentzn
reviewed
Aug 4, 2024
Clarify reference to `slot_name` in the description of the `property` slot. Fix incorrect reference to a SSSOM/TSV _writer_ (not _reader_) when we state that unknown slots MUST NOT be written in SSSOM/TSV files. Replace "catenate" by "concatenate". My understanding is that the two terms are actually equivalent, but "concatenate" is for some reason more widely used at least in computer science.
matentzn
previously approved these changes
Aug 4, 2024
hrshdhgd
previously approved these changes
Aug 5, 2024
matentzn
previously approved these changes
Aug 5, 2024
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Ready to merge! |
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To re-reviewers: the only change was to the changelog, to fix the merge conflict caused by the merge of #386. This is the expected consequence of the requirement (stated in the PR template) that the changelog must be updated in every PR (instead of updating it in one go before a release). All additions to the changelog are done at exactly the same place, so when there are several concurrent PR there cannot not be a merge conflict. |
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This PR is next in line for the merging, can you update the branch and resolve conflicts? |
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Will do by this evening. :) |
hrshdhgd
approved these changes
Aug 6, 2024
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Resolves #328
docs/have been added/updated if necessarymake testhas been run locallyIf you are proposing a change to the SSSOM metadata model, you must
examples/see_alsofield of the linkml modelsee_alsofield of the linkml modelThis PR updates the SSSOM model to allow for defined extensions as proposed in #328.
It also updates the description of the data model to describe the use of both defined and undefined extension, and the specification of the SSSOM/TSV format to explain how SSSOM/TSV parsers and writers should deal with such extensions.
Overall, this is exactly what was proposed in this comment in #328, except that here we need to split the specification in two parts (one about extensions in general, independently of the serialisation format, and one about the SSSOM/TSV serialisation of extensions), while the initial proposition was in a single block.