Account created on 9 July 2023, over 1 year ago
  • Bioinformatics Training Technician - Data Management at BioData.ptΒ 
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@gpo Can you please post your bioschemas CSV for types and properties somewhere on GitHub? If I have an absolute URL to the data, I can test importing it.

Here they are:
https://github.com/BioData-PT/bioschemas-data/tree/schemadotorg

Found the root of the issue, turned out to be specific for my setup, my apologies for not realizing it before submitting the issue.

Yeah, I'm going to have to update the code to strip out https://bioschemas.org/. I think the module is going to have to assume that all types and properties are unique, independent of their domain.

I just gave it a try, replacing bioschemas.org with schema.org and the property I added still doesn't show up in the form, although it appears on the reports.

That would be awesome! Thank you so much!

If it doesn’t work I can maybe try to work around it using something like
schema.org/bioschemas-xxxxx

But the added versatility may help people using other controlled vocabularies…

Okay... found another hiccup.... the new properties I've added are not showing up on the "Manage Schema.org fields" form of the respective content type, although their respective entries appear in the property reports.

Example, I rewrote Organization like so

"https://schema.org/Organization","Organization","Bioschemas specification for describing a Organization in the life-science. Provides a way to describe bioscience organizations on the World Wide Web. It defines metadata terms that can be used in the code of web pages and applications, and builds on top of existing technologies and standards. The goal of the specification is to make it easier to discover, exchange and integrate life science organization profiles across the Internet.","https://schema.org/Thing","","","https://schema.org/description, https://schema.org/legalName, https://schema.org/name, https://schema.org/rdf:type, https://schema.org/sameAs, https://schema.org/topic, https://schema.org/alternateName, https://schema.org/contactPoint, https://bioschemas.org/fundingModel, https://schema.org/keywords, https://schema.org/location, https://schema.org/logo, https://schema.org/member, https://schema.org/memberOf, https://bioschemas.org/membershipCategory, https://schema.org/sameAs, https://bioschemas.org/status, https://schema.org/url, https://bioschemas.org/attachment, https://schema.org/budget, https://bioschemas.org/dateModified, https://schema.org/department, https://schema.org/dissolutionDate, https://bioschemas.org/founderMember, https://schema.org/foundingDate, https://schema.org/owns, https://schema.org/parentOrganization, https://bioschemas.org/socialMedia, https://schema.org/subOrganization","","","","https://bioschemas.org"

Notice how the second to last property is https://bioschemas.org/socialMedia, which I then defined in the properties CSV:

"https://bioschemas.org/socialMedia","socialMedia","Link to social media websites like twitter or facebook.","","","","https://schema.org/Organization","https://schema.org/URL","","","","https://bioschemas.org"

Yet it doesn't appear when adding a new Organization content type. Any chance I'm missing something?

Maybe the simplest solution is to make the source the CSV configurable. It would default to the local files, but you could use the below URLs

Definitely! As my version overrides some original schema.org definitions.

it probably seems to be just a matter of compiling the terms which haven't been added to the shemas.org spec and appending them to the CSV, which I haven't gotten around of trying yet

Just gave it a go using some CSVs I generated and everything seems to work!

For now, manually merging the data should work. If it does work as expected, we can explore adding a hook or a programmatic approach to importing other schemas.

Having some sort of programmatic way of adding additional schemas seems perfect!

Yeah Bioschemas can be a bit all over the place. Yes, some terms were incorporated into the main spec, but others (the ones that I'm actually more interested about, like ComputationalTool, TrainingMaterial) were not, and as such they don't show up on the CSV on the repo that they forked from the main schema.org repository.
From what I'm getting it probably seems to be just a matter of compiling the terms which haven't been added to the shemas.org spec and appending them to the CSV, which I haven't gotten around of trying yet.

The Bioschemas spec is here https://github.com/BioSchemas/specifications

I'm not the best PHPer but from looking at </code> would I be correct to assume that if I can find a way to add Bioschemas' properties and types to <code>schemaorg-current-https-properties.csv schemaorg-current-https-properties.csv, I'd be all set, right?

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