Re: Protein representation with and without BioChemEntity

Hi all,


> If we are going to use a second context with aliases defined by Bioschemas
> profiles, would it not make sense for that second context be one provided
> by Bioschemas? If we have a Bioschemas context, that context will take care
> of define the aliases and collate the possible corresponding ontology
> terms. In this way we keep it simple for users and avoid multiple cases
> (camel and others), for minimum and recommended properties at least. A
> third party property would always be possible for optional properties,
> giving proority to any of those already coined in schema.org


I love any idea that keeps things simple! If I understand correctly, this
proposal would push the Bioschemas community to converge on choices for
both terms and IRIs, but it would still allow for using different terms.

It could look like this for annotating a pre-existing JSON API
<https://www.oclc.org/developer/news/2016/retrofitting-an-existing-api-with-linked-data.en.html>.
The
Bioschemas context would specify one alias, e.g.:

> { ...,

  transcribedFrom: http://semanticscience.org/resource/is-transcribed-from,

  ... }


But if the pre-existing API uses the term "transcfrom" then it would need
to use a combined context like this:

> [

  { ...,

    transcfrom: http://semanticscience.org/resource/is-transcribed-from,

    ... } ,

  "http://bioschemas.org/context.jsonld"

]


One point of caution: the JSON-LD spec says
<https://json-ld.org/spec/latest/json-ld/#advanced-context-usage>,
"Multiple contexts may be combined using an array, which is processed in
order," but that doesn't necessarily mean the Bioschemas term would take
precedence for the combined context above. For example, if the output from
the API were to be expanded and re-compacted with that combined context,
the result could use the term "transcfrom" instead of "transcribedFrom", as
specified by the term selection algorithm
<https://www.w3.org/TR/json-ld-api/#term-selection> and discussed in this
comment
<https://github.com/digitalbazaar/jsonld.js/issues/75#issuecomment-61841449>
.

Regards,
Anders Riutta