BioPAX Pathway URIs

[IgorRodchenkov]

I just discovered that Biofactoid is already included in bioregistry.io registry and can resolve links. See http://bioregistry.io/biofactoid

So why don't you use those resolvable/linkable URIs for the Biofactoid Pathways in the BioPAX model and output file?

Can we use e.g. "http://bioregistry.io/biofactoid:3e4476c1-e3ec-4635-969b-6a02de4e581a" URI instead of current "3e4476c1-e3ec-4635-969b-6a02de4e581a" (or use whatever ID resolves to the right thing)?

In the BioPAX file it looks like this:

<bp:Pathway rdf:about="3e4476c1-e3ec-4635-969b-6a02de4e581a">

but likely should look like this

PS: (more importantly) By the way, the examle ID above is from a biopax data file (0a49a0c9-1cb4-4f67-b78f-eaa5cc5f0ebf.owl) from the archive that I downloaded from https://biofactoid.org/api/document/zip/biopax?idMapping=true on 13 May 2024. Why the Pathway ID/URI there is "3e4476c1-e3ec-4635-969b-6a02de4e581a" instead of that from the file name: "0a49a0c9-1cb4-4f67-b78f-eaa5cc5f0ebf", which is in fact perfectly resolvable: http://bioregistry.io/biofactoid:0a49a0c9-1cb4-4f67-b78f-eaa5cc5f0ebf? Also, the example from the bioregistry.io/biofactoid page also works (gets resolved): http://bioregistry.io/biofactoid:fdb8a927-45c3-48b7-9743-cbb5e16837fa

[IgorRodchenkov]

On the second thought.., as I understand, Biofactoid stable IDs are document IDs, not bioentity IDs... A document can have more than one Pathway or interactions or no pathways. So likely not using the document ID for any of the bioentities was a good decision indeed. So ignore my suggestion then.

Though, it would be great to make sure you generate the same ID/URIs for the same Things (bioentities and refs inside the BioPAX files) every time one calls: https://biofactoid.org/api/document/zip/biopax?idMapping=true