Many license annotations don't match what's in the ontology

[cthoyt]

As a follow-up to #1635, it's worth noting the Bioregistry is tracking conflicts between the OBO Foundry's license metadata (which is manually curated) and the OLS's license metadata (which I think is parsed from the ontology). There are several remaining conflicts to address, listed at https://biopragmatics.github.io/bioregistry/warnings/#license-conflicts.

You could also use the following Python code to generate the table

from tabulate import tabulate

from bioregistry import manager

if __name__ == '__main__':
    print(tabulate(
        manager.get_license_conflicts(),
        headers=['prefix', 'override', 'obo', 'ols'],
        tablefmt='github',
    ))

I'll include it here in addition to the one on the website

prefix	obo	ols
aism	CC-BY	https://creativecommons.org/licenses/by/4.0/
amphx	CC-BY	https://creativecommons.org/licenses/by/3.0/
apollosv	CC-BY 3.0	https://creativecommons.org/licenses/by/4.0/
bspo	CC-BY	https://creativecommons.org/licenses/by/3.0/
chmo	CC-BY	http://creativecommons.org/licenses/by/4.0/
cido	CC-BY	http://creativecommons.org/licenses/by/4.0/
cl	CC-BY	http://creativecommons.org/licenses/by/4.0/
clao	CC-0	https://creativecommons.org/licenses/by/4.0/
cto	CC-BY	http://creativecommons.org/licenses/by/4.0
dpo	CC-BY	https://creativecommons.org/licenses/by/3.0/
dron	CC-BY	https://creativecommons.org/licenses/by/3.0/
duo	CC-BY	http://creativecommons.org/licenses/by/4.0/
envo	CC-BY	https://creativecommons.org/publicdomain/zero/1.0/
eupath	CC-BY	http://creativecommons.org/licenses/by/4.0/
fbbt	CC-BY	https://creativecommons.org/licenses/by/3.0/
fbcv	CC-BY	https://creativecommons.org/licenses/by/3.0/
fbdv	CC-BY	https://creativecommons.org/licenses/by/3.0/
fobi	CC-BY	http://creativecommons.org/licenses/by/4.0/
foodon	CC-BY	https://creativecommons.org/licenses/by/3.0/
fypo	CC-BY	https://creativecommons.org/licenses/by/4.0/
genepio	CC-BY	http://creativecommons.org/licenses/by/3.0/
hso	CC-BY	http://creativecommons.org/licenses/by/3.0/
iao	CC-BY	http://creativecommons.org/licenses/by/4.0/
iceo	CC-BY	http://creativecommons.org/licenses/by/4.0/
ico	CC-BY	http://creativecommons.org/licenses/by/3.0/
maxo	CC-BY	https://creativecommons.org/licenses/by/4.0/
mf	CC-BY	https://creativecommons.org/licenses/by/3.0/
mfoem	CC-BY	https://creativecommons.org/licenses/by/3.0/
mro	CC-BY	http://creativecommons.org/licenses/by/3.0/
oae	CC-BY	http://creativecommons.org/licenses/by/3.0/
obib	CC-BY	http://creativecommons.org/licenses/by/4.0/
ogg	CC-BY	http://creativecommons.org/licenses/by/3.0/
ogms	CC-BY	http://creativecommons.org/licenses/by/4.0/
ogsf	CC-BY 3.0	New BSD license
ohpi	CC-BY	http://creativecommons.org/licenses/by/4.0/
ons	CC-BY	https://creativecommons.org/licenses/by/4.0/
ontoneo	CC-BY	http://creativecommons.org/licenses/by/4.0/
oostt	CC-BY	http://creativecommons.org/licenses/by/4.0/
opmi	CC-BY	http://creativecommons.org/licenses/by/4.0/
pato	CC-BY	https://creativecommons.org/licenses/by/3.0/
phipo	CC-BY	https://creativecommons.org/licenses/by/3.0/
plana	CC-BY	https://creativecommons.org/licenses/by/3.0/
planp	CC-BY	https://creativecommons.org/licenses/by/3.0/
pr	CC-BY	http://creativecommons.org/licenses/by/4.0/
psdo	CC-BY	https://creativecommons.org/licenses/by/4.0/
rbo	CC-BY	http://creativecommons.org/licenses/by/3.0/
stato	CC-BY	http://creativecommons.org/licenses/by/3.0/
txpo	CC-BY 3.0	http://creativecommons.org/licenses/by/4.0/
uberon	CC-BY	http://creativecommons.org/licenses/by/3.0/
vo	CC-BY	http://creativecommons.org/licenses/by/4.0/
xao	CC-BY	https://creativecommons.org/licenses/by/3.0/
xpo	CC-BY	https://creativecommons.org/licenses/by/3.0/
zeco	CC-BY	https://creativecommons.org/licenses/by/3.0/
zfa	CC-BY	https://creativecommons.org/licenses/by/3.0/

[matentzn]

Great effort to look for conflicts here! I think two things are conflated here:

1. in OBO metadata the license has two fields, url and label. The first thing to check would be whether these two are in conflict - the current validator allows all sorts of variations on the label, and I wouldn't be surprised if there was a CC-BY 3.0 label paired with a 4.0 URL. So this I would check first
2. OLS always uses OBO metadata directly. So there cant be any conflicts - the table you present here looks like it is comparing the OBO license.label property with the dc:license annotation in the ontology. Can you clarify where what information comes from? OLS uses the OBO metadata file directly!

license:
  url: https://creativecommons.org/licenses/by/4.0/
  label: CC-BY

[cthoyt]

Thanks for the feedback, Nico. I'm going to close this issue and open a clean one with a better table