Metadata in RDF

Moving the conversation from to the forums:

Just caught up with # I2K … I wonder when “metadata” (standards) enters stage? Or tools outputting knowledge in form of triplets which could be saved in wikidata and queried via SPARQL. … Result # interoperability

I wanted to point at recent work from @norio.kobayashi to add support for RDF/OWL to OME:

He unfortunately wasn’t able to attend I2K because he was presenting his work at SWAT4HLS.

A few next steps from our side include:

There were a few others who were interested in similar efforts at I2K. General brain-storming and suggestions welcome from all.


see also: Create minimal YAML metadata file using BioFormats

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Hi Josh, thanks for starting this topic!

I probably should follow those links and investigate @norio.kobayashi’s work with this, but to summarize what we are thinking about at JAX:

-We want a triple store that covers all of our data resources at JAX, so having the ability to export from OMERO metadata of all types as RDF triples would be amazing

-Anything that would make it easier for our users to adopt controlled vocabularies for their experimental metadata would be welcome (e.g., autocomplete). Our current thinking is to implement something through our LIMS(s) and pull metadata from the LIMS to populate OMERO, making use of OMERO’s namespace support. But users will still want to annotate through OMERO.web sometimes

-we want to implement a minimal metadata policy for data ingested into OMERO, similar to what the IDR requires. You showed something in your talk at I2K–I will look into that

I definitely want to be a part of this conversation and am happy to discuss our specific plans in further detail if anyone is interested, but we still have a lot of decisions to make about how we are handling our internal- and external-facing data resources and welcome input!

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