Bioschemas or other schemas support

The first and simplest question is where are bioschemas stored.

Theoretically, someone can override the schemadotorg.installer service (\Drupal\schemadotorg\SchemaDotOrgInstaller) and import any custom types and properties.

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?

In theory, you should be able to append the below files...

https://github.com/BioSchemas/schemaorg/blob/master/data/releases/3.9/ex...
https://github.com/BioSchemas/schemaorg/blob/master/data/releases/3.9/ex...

...to...

https://git.drupalcode.org/project/schemadotorg/-/blob/1.0.x/data/22.0/s...
https://git.drupalcode.org/project/schemadotorg/-/blob/1.0.x/data/22.0/s...

...and the Bioschemas types and properties will become available via the UI after running `drush schemadotorg:update-schema`

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.

It looks like I am wrong about the CSV file hosted via https://github.com/BioSchemas/schemaorg/blob/master/data/releases/.

We need to find or generate a CSV that contains the bioschemas.

I'm having a hard time figuring out what needs to be done. Keep in mind that I am not an expert on Schem.org.

I see that the http://bioschemas.org specification is being partially incorporated into https://schema.org as a pending spec.

@see Introduce BioSchemas terms into pending #2863
@see https://bioschemas.org/types/BioChemEntity/0.7-RELEASE-2019_06_19
@see https://schema.org/BioChemEntity

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.

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!

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

https://raw.githubusercontent.com/GilOliveira/schemadotorg/bioschemas/da...
https://raw.githubusercontent.com/GilOliveira/schemadotorg/bioschemas/da...

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.

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?

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.

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…

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.

@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.

The MR allows you to enter an external URL.
@see /admin/config/search/schemadotorg/settings/general

I did not implement any code to strip https://bioschemas.org/

@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

I am getting a 404 via https://github.com/BioData-PT/bioschemas-data/tree/schemadotorg. Maybe you need to adjust the access to the file.

My bad! Should be working now.

Steps to review

• Switch to branch
• Reinstall module
• Login as admin
• Go to /admin/config/search/schemadotorg/settings/general
• Set Schema.org data file/URL to https://raw.githubusercontent.com/BioData-PT/bioschemas-data/schemadotorg/schemaorg-current-https-[TABLE].csv
• Click 'Save configuration'

Attached is a diff of the latest cleaned up MR to make this easier to review.

@gpo I updated the MR. Are you using the MR? If yes, I am OK with merging the code.

I think I like having this option available to allow people to import their own schemas. I am going to merge it and see if people use it.

Automatically closed - issue fixed for 2 weeks with no activity.

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

I can second that, there are a lot more than schema.org, e.g. https://lov.linkeddata.es/dataset/lov/

Also, I don't fully understand why we import the vocabularies and application profiles as CSV data (vs linked data/triples)?

It was simpler and more performant. Keep in mind the Schema.org data is all managed via the 'schemadotorg.installer' and 'schemadotorg.schema_type_manager' are services and could be reworked to not use CSV data.

The [Schema.org configuration tool (RDF UI)]( https://www.drupal.org/project/rdfui → ) does use linked data/triples.
@see https://git.drupalcode.org/project/rdfui/-/blob/8.x-1.x/src/EasyRdfConve...