How to redirect to RDF (XML) version for OBO?

[yarikoptic]

In https://github.com/dandi/dandi-cli we relied on parsing XML provided for URLs like http://purl.obolibrary.org/obo/NCBITaxon_9606 . But now ( I guess after #1066) it redirects to HTML page... I wonder if there a way to negotiate the type of record to obtain back (like e.g. often API or DOI services do)?

attn @candleindark

refs:

• Failures in tests with marker obolibrary dandi/dandi-cli#1769

[jamesaoverton]

Yes, we had been sending the NCBITaxon PURLs to Ontobee, but got user feedback that made us switch to the NCBI pages instead.

The Ontobee pages still exist and I expect they will be maintained. So it would probably be easiest for you to just keep using Ontobee with URLs like https://ontobee.org/ontology/rdf/NCBITaxon?iri=http://purl.obolibrary.org/obo/NCBITaxon_1234175 -- like the upstream issue suggested. Is that an option for you?

We don't have content negotiation features on this PURL server itself, and I don't know if NCBI provides content negotiation or alternative formats that would work for you. NCBI also has newer pages like this https://www.ncbi.nlm.nih.gov/datasets/taxonomy/9606/ that may have more options.

[yarikoptic]

The Ontobee pages still exist and I expect they will be maintained. So it would probably be easiest for you to just keep using Ontobee with URLs like https://ontobee.org/ontology/rdf/NCBITaxon?iri=http://purl.obolibrary.org/obo/NCBITaxon_1234175 -- like the upstream issue suggested. Is that an option for you?

everything is an option when you are empowered with a Turing complete apparatus ;) I guess we will indeed just change to use that direct RDF url but I would recommend and appreciate keeping open an issue to do provide alternative views/redirects ("context negotiation") for the sake of machines!

[candleindark]

We at be sure that RDF/OWL is not supported by NCBI's service at this point per https://www.ncbi.nlm.nih.gov/datasets/docs/v2/reference-docs/file-formats/metadata-files/why-jsonl/#why-not-use-other-formats-such-as-json-ld-and-rdfowl.

[jamesaoverton]

Hypothetically, how would you configure an Apache2 HTTP server to do content negotiation for a given PURL that would redirect to from Ontobee if RDF/OWL is requested, and otherwise redirect to HTML from NCBI?

[yarikoptic]

here is full claude answer: https://claude.ai/share/6eecea9a-8c76-4bd8-b941-f2806edffa1c . In a nutshell:

RewriteEngine On

# JSON-LD or JSON
RewriteCond %{HTTP_ACCEPT} application/ld\\+json [OR]
RewriteCond %{HTTP_ACCEPT} application/json
RewriteRule ^/obo/MY_ONTO\\.owl$ https://example.org/my_onto.jsonld [R=303,L]

# RDF/XML
RewriteCond %{HTTP_ACCEPT} application/rdf\\+xml
RewriteRule ^/obo/MY_ONTO\\.owl$ https://example.org/my_onto.owl [R=303,L]

# Turtle
RewriteCond %{HTTP_ACCEPT} text/turtle
RewriteRule ^/obo/MY_ONTO\\.owl$ https://example.org/my_onto.ttl [R=303,L]

# Default to HTML (or whatever)
RewriteRule ^/obo/MY_ONTO\\.owl$ https://example.org/my_onto.html [R=303,L]