Weird Error classes in Dipper turtle output of monochrom about monochrom HOT 7 CLOSED

The corresponding turtle is this:

OBO:CHR_9606chr1 a owl:Class ;
    rdfs:label "chr1 (Human)" ;
    rdfs:subClassOf OBO:SO_0000340,
        <http://monarchinitiative.org/.well-known/genid/RO0002350_NCBITaxon9606genome>,
        <http://monarchinitiative.org/.well-known/genid/RO0002524CHR9606chr1p>,
        <http://monarchinitiative.org/.well-known/genid/RO0002524CHR9606chr1q> .

@cmungall can you fix this? It seems that this is not really valid OWL..

from monochrom.

(I mean, can you tell me what the intended syntax is here for that example class, I can piece the rest together)

from monochrom.

wild guess but suspect the subclass relation between chr1 and chr1[pq] is backwards.

Dippers original authors embraced a generous attitude towards blank nodes sometimes attempting to imbue them with characteristics bnodes do not technically support by giving them meaningful localid's or a handy base url. Both can be seen in this example.

I would interpret "OBO:CHR_9606chr1" as an attempt to have a URI for human chromosome 1 anchored at OBO.

My preference would be for an existing (resolvable) URI at Ensembl or UCSC.

First comment about the chr arms being subclasses of the chr still holds.
which is likely swapping argument order in dipper near here.

from monochrom.

@TomConlin will you ping me when you had a chance to rerun the dipper ingest without skolemisation? Thanks a lot :)

from monochrom.

Jenkins was updated to not Skolemized blank nodes for Monochrom any more.
The weekly dipper pipeline ran and the output is here:
https://data.monarchinitiative.org/dev/monochrom.ttl

from monochrom.

Hey @TomConlin , thanks, just checked this. There is still this issue:

_:RO0002350_NCBITaxon10090genome a owl:Restriction ;
    owl:onProperty OBO:RO_0002350 ;
    owl:someValuesFrom "_:NCBITaxon:10090genome" .

While this seems like legal RDF, in OWL, this is not possible; this would need to be an anymous expression like:

OBO:CHR_10090chr1 a owl:Class ;
    rdfs:label "chr1 (Mouse)" ;
    rdfs:subClassOf _:RO0002350_NCBITaxon10090genome, # <--- Not possible
        [ a owl:Restriction ; # <--- Correct
            owl:onProperty OBO:RO_0002524 ;
            owl:someValuesFrom OBO:CHR_10090chr1q ],
        OBO:SO_0000340 .

Thanks :)

from monochrom.

fixed by new pipeline

from monochrom.