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Discuss how to prefix or fix entities #17
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By the way, I would suggest to always roll a bespoke VFB id for site, because URLs can change so easily. |
LIcenses
This should be OK though:
|
DOIs: - allowing '/' in short_form is a problem for short_form generation code assumptions (VFB_neo4j). Not sure of best soln. |
Maybe the best thing to do is not using DOIs as IRIs in VFB.. the only alternative I can think of that does not involve DOI1, DOI2 etc is what Robbie has being doing, str replacing the |
I've gone with @matentzn IIRC you will fix nesting issues for curies arising from this by enforcing ordering on the curie spec. Is this correct? |
For DOIs, I'm happy to use virtualflybrain/reports/ as base but we need a standard transformation of ID to short_form that curators can work with when loading content linked to preprints and that we can use for ontology term xrefs to preprints. I think the two options are |
I am assuming having publication ids minted is out of the question? Both of these require some kind of hacky development work (if short_form contains '' replace by '_', which also needs to be made configurable).. If you want to do it I estimate getting this into both the neo4j2owl importer and SOLR will be about 90 min, with testing etc. |
@matentzn - I don't think I need you to do more on this. I see this being managed on the database side. I think the key question is whether the escaped short_form will work for your short_form generator. |
Probably not - I am relying on URI get fragment - having a backslash will probably cause a malformed URI exception. But I am not sure I understand - how will pdb know about this new short form? PDB regenerates short forms from IRI, so are you going to actually change the IRI from |
The internal VFB issue is that, with the current schema, we need a short_form for pub that is either an external pub ID or some minimal transformation of one. This is distinct from whether the IRI is resolvable. For most pubs we use a FlyBase identifier and FlyBase iri: flybase.org/reports/FBrf0001234, which makes a well behaved short_form of the FlyBase ID. We indicate that this is resolvable using the tag |
Ok sounds good :) |
@Robbie1977 - Are you happy with |
Some entities in the current triplestore are not very well amenable to CURIEfication; but I think some of them are simply mistakes that should be fixed. Here is a preliminary categorisation.
Probably fine, but not prefixable
Maybe we should just ignore these and add the full IRI in the short form and curie fields for SOLR? As an aside I dont think its a good idea to have URL parameters in an entity IRI, but hell, why not :P
I would suggest @dosumis you check [x] the ones that you know about, but I think they are all fine (just in case you want to delete one of them). Trick: if you dont know something, navigate to the triple store entity explorer and paste the IRI in (mind the
<>
).Site
again)Site
)Site
)Site
)Site
)Entities we should look into (probably typos in IRIs):
Missing URL parts like site or data
Broken RO relation (in DPO, ticket!)
Entities with regular IRI, but hard to prefix
unless you accept
/
in the short name:https://doi.org/10.1101/2020.01.10.902478
doi:10.1101/2020.01.10.902478
This is probably the right way, given how Zenodo seems to do it.
DOI:
creativecommons:
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