Add first version of enhanced mapping metadata

[matentzn]

LinkML-Map transformation specifications previously had minimal metadata — just id, title, and schema references. This made it difficult to track provenance, authorship, licensing, and versioning of mapping specifications.

The FAIR Mappings Schema defines a minimal metadata standard for mapping specifications. By aligning LinkML-Map's TransformationSpecification with this schema (at least a little closer), we enable:

• Provenance tracking: who created, authored, and reviewed a mapping specification
• FAIR compliance: publication date, license, version, and documentation URLs
• Interoperability: metadata can be transformed to/from FAIR Mappings Schema format using LinkML-Map itself

Summary of changes

Schema (transformer_model.yaml):

• Added metadata fields to TransformationSpecification: publication_date, license, version, creator, author, reviewer, mapping_method, documentation, content_url
• Added Agent class hierarchy (Agent, Person, Organization, Software) aligned with FAIR Mappings Schema, supporting polymorphic contributor modeling via designates_type

Examples:

• Enriched the personinfo-to-agent example with real metadata (ORCIDs, license, publication date)
• Added FAIR Mappings metadata example with sample data, transform specs, and expected output demonstrating linkml-map-to-FAIR and SSSOM-to-FAIR transformations

Tests:

• Updated existing tests to reflect enriched example metadata

What's not included (future work)

• Structured Source objects for source_schema/target_schema (see Convert source_schema and target_schema slot values into complex tasks #161)
• Schema version tracking (source_schema_version, target_schema_version)

[amc-corey-cox]

The description field you added to TransformationSpecification is actually already inherited from SpecificationComponent (the parent class), so that addition can be removed. The other new fields (publication_date, license, version, creator_id, author_id, mapping_method) are the actual new additions.

I'll fix up the conflicts with main and update the tests so this is ready to go.

[amc-corey-cox]

@matentzn I fixed the conflicts you were running into and I think this could be ready to merge in. If you're happy with what we have here just click the "Ready for review" button to take this off of draft mode. I'll review it and merge it in.

[matentzn]

@amc-corey-cox Thank you for looking into this! I still need to review some of these changes with my collaborators; I will let you know when I am happy with it!

PS: I will join you soon in your LinkML-map efforts - my funds where approved (yay)

[matentzn]

@amc-corey-cox there is no huge rush here, but I think this is in a good enough stage now to merge. Let me know if you have any feedback!

[amc-corey-cox]

@matentzn I'm working on this one. I had Claude Code help me review it and came up with a bunch of things, some I don't agree with. I'm working through it and trying to get a reasonable review for you.

[amc-corey-cox]

@matentzn - I just have a couple comments here. I don't think any of this needs to be blocking. I would prefer if we get the tests in before the merge but feel free to merge if you just want to get it in. This was sitting a while and took a fair bit of effort to get ready to merge again so we may just want to merge and avoid that happening again.

[amc-corey-cox]

Sounds good! I'm going to merge.