Data dict for phonons

We met on 2021-06-09 wrt the phonons dataset (dataset: https://doi.org/10.6084/m9.figshare.c.3938023.v1, article: https://doi.org/10.1038/sdata.2018.65).

@stuchalk has agreed to be the technical lead for the subgroup, and will follow up with @gmrigna and @dwinston about how to enter metadata for the 34 terms of tables 1-6 in the article. We tentatively plan to document the approach to vocabulary re-use in a shared google doc, and to facilitate dictionary-term metadata entry in a shared google sheet.

The next meeting of the phonons subgroup has not yet been scheduled. Hoping for early-to-mid July (one month after the last one).

Re: vocabulary reuse, noting here that search results for https://lov.linkeddata.es/dataset/lov/terms?q=chemical+composition included https://w3id.org/mdo/structure/Composition, which led me to https://w3id.org/mdo/structure/ReducedFormula, which is granularly resolvable via browser as https://huanyu-li.github.io/mdo/structure/1.0/index.html#ReducedFormula.

This vocabulary was co-authored by @rar. With some work, we may be able to use this. For example,


curl --head -L \
    -H "Accept: application/ld+json;q=1,text/turtle;q=0.9,application/rdf+xml;q=0.8" \
    https://w3id.org/mdo/structure/ReducedFormula

returns a redirect to https://github.com/huanyu-li/Materials-Design-Ontology with Content-Type text/html. We would need to work to e.g. have such a request return structured data about the vocabulary term – in the example above, preferably serialized as JSON-LD, next best would be the terse triple (“turtle”) format, and finally XML would be acceptable, as e.g. the rdflib Python library (+ rdflib-jsonld plugin library) could convert amongst them.

1 Like

@stuchalk I started sketching out a SKOS vocabulary here. I’m not sure what you’d like me or @gmrigna to do in order to give you material to make scidata JSON-LD. Is something like this what you want? A spreadsheet in a certain format?

Sorry for the slow response. I am in the middle of getting ready for three presentations next week. Will get back to you on Tuesday when the slides are all done :slight_smile:

I finally got a chance to look at this and it looks like a great start. From my perspective the focal point is the need to create a JSON-LD context file for all the data elements that are specific to this data. Let me work on that this week and see where it gets to and how the vocab you sketched out aligns…

@stuchalk great, thanks! I’ll hold off on asserting triples for the skos:members of the other skos:Collections until I get feedback from you because, as you hinted at, I’m not confident that my method of intermediate (informal->formal) representation will align well with your preferred method for producing a JSON-LD context file.

mp-10653.jsonld (23.9 KB)
OK, I have reworked the example file slightly (see attached) and created a ‘phonons.jsonld’ context file that can be found at ‘https://stuchalk.github.io/scidata/contexts/phonons.jsonld’. I had to create an ‘mp.owl’ ontology for a couple of ontological definitions that I could not find elsewhere (see ‘https://stuchalk.github.io/scidata/ontology/mp.owl’). With all of this the JSON-LD converts to valid RDF. I will schedule another meeting of the group once you have had a chance to look at this.

2 Likes

thanks @stuchalk . I’ve looked it over, and it seems in good shape to discuss next steps. I’m particularly interested in you going over tooling for exploring the data, and how we might make links resolvable. Please go ahead and schedule our next meeting.

OK, I will schedule something a couple of weeks out as we have the abstract one next Wednesday…