search

monarch-initiative / monarch-legacy

Monarch web application and API
BSD 3-Clause "New" or "Revised" License
42 stars 37 forks source link

df not showing up for noto #767

Open nlwashington opened 9 years ago

nlwashington commented 9 years ago

on the page for noto: http://beta.monarchinitiative.org/gene/ZFIN:ZDB-GENE-990415-75

the deficiency http://zfin.org/action/feature/view/ZDB-ALT-991201-146 is not showing up. not sure if this is a scigraph issue, an interface issue, or a data issue. need to investigate.

nlwashington commented 9 years ago

also, none of the genotypes are showing up, but they are clearly here: http://zfin.org/action/marker/view/ZDB-GENE-990415-75

nlwashington commented 9 years ago

furthermore, the name of the gene isn't showing up. this is odd... when i look it up by id, the label is not there, despite it being in the turtle.

http://duckworth.crbs.ucsd.edu:9000/scigraph/graph/ZFIN:ZDB-GENE-990415-75?project=%2A

vs

ZFIN:ZDB-GENE-990415-75 a owl:Class ; rdfs:label "noto" ; OBO:RO_0002162 OBO:NCBITaxon_7955 ; OBO:RO_0002525 OBO:CHR_ZDB-REFCROSS-000320-1chr13 ; OBO:RO_HOM0000017 http://www.ncbi.nlm.nih.gov/gene/344022 ; dc:description "notochord homeobox" ;

@ccondit why do you think there is this difference?

ccondit commented 9 years ago

It's because the most recent zfin.ttl actually didn't load:

Parser: TurtleOntologyParser
uk.ac.manchester.cs.owl.owlapi.turtle.parser.ParseException: Encountered " <ERROR> "% "" at line 1005785, column 42.
Was expecting:
    "." ...

so none of the axioms were added.

nlwashington commented 9 years ago

ah ha. the chemical environments had percent signs in the ids i was creating...

_:physical-light-100-% a OBO:XCO_0000000

getting rid of those now...

jmcmurry commented 8 years ago

Some progress appears to have been made on this ticket.

Nevertheless

Same on beta.