OBOFoundry / OBOFoundry.github.io

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry
http://obofoundry.org
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Create CI job that checks for consistency between OBO central metadata and ontology header (e.g. license) #515

Closed cmungall closed 3 years ago

cmungall commented 6 years ago

currently this is done by a TWG member by running this:

~/repos/OBOFoundry.github.io(master) $ make sparql-consistency-report.txt

The output produced is like this

bfo license INCONSISTENT: REMOTE:http://creativecommons.org/licenses/by/3.0/ != LOCAL:http://creativecommons.org/licenses/by/4.0/
bfo title UNDECLARED_REMOTE
bfo description UNDECLARED_REMOTE
bfo homepage INCONSISTENT: REMOTE:http://ifomis.org/bfo,http://code.google.com/p/bfo/ != LOCAL:http://ifomis.org/bfo/
chebi license UNDECLARED_REMOTE
chebi title UNDECLARED_REMOTE
chebi description UNDECLARED_REMOTE
chebi homepage UNDECLARED_REMOTE
doid license UNDECLARED_REMOTE
doid title UNDECLARED_REMOTE
doid description UNDECLARED_REMOTE
doid homepage UNDECLARED_REMOTE
go license UNDECLARED_REMOTE
go title UNDECLARED_REMOTE
go description UNDECLARED_REMOTE
go homepage UNDECLARED_REMOTE
obi license CONSISTENT
obi title INCONSISTENT: REMOTE:Ontology for Biomedical Investigation != LOCAL:Ontology for Biomedical Investigations
obi description INCONSISTENT: REMOTE:The Ontology for Biomedical Investigations (OBI) is build in a collaborative, international effort and will serve as a resource for annotating biomedical investig
ations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigat
ion Ontology (FuGO) and will contain both terms that are common to all biomedical investigations, including functional genomics investigations and those that are more domain specific. != LOCAL:An int
egrated ontology for the description of life-science and clinical investigations
obi homepage UNDECLARED_REMOTE
pato license UNDECLARED_REMOTE
pato title UNDECLARED_REMOTE
pato description UNDECLARED_REMOTE
pato homepage UNDECLARED_REMOTE
po license UNDECLARED_REMOTE
po title UNDECLARED_REMOTE
po description UNDECLARED_REMOTE
po homepage UNDECLARED_REMOTE
pr license UNDECLARED_REMOTE
pr title UNDECLARED_REMOTE
pr description UNDECLARED_REMOTE
pr homepage UNDECLARED_REMOTE
xao license UNDECLARED_REMOTE
xao title UNDECLARED_REMOTE
xao description UNDECLARED_REMOTE
xao homepage UNDECLARED_REMOTE
zfa license UNDECLARED_REMOTE
zfa title UNDECLARED_REMOTE
zfa description UNDECLARED_REMOTE
zfa homepage UNDECLARED_REMOTE
aeo license UNDECLARED_REMOTE
aeo title UNDECLARED_REMOTE
aeo description UNDECLARED_REMOTE
aeo homepage UNDECLARED_REMOTE
agro license UNDECLARED_REMOTE

(note in some cases the obo curated info may be more accurate, e.g. we actively curate to avoid things like homepages on defunct google code)

The task here is to set up a CI job that runs this e.g. daily

Next we need someone who will follow up on this

cmungall commented 6 years ago

See also #540

nlharris commented 3 years ago

is this still needed?

jamesaoverton commented 3 years ago

This is covered by the Dashboard.