Current behavior is mangling OBO ids.
See this selection of ID remappings it attempted to make for OGSF:
Old ID New ID
OBO:OGI.owl#CpG_Island CPG:ISLAND
OBO:OGI.owl#Biological_Macromolecule BIOLOGICAL:MACROMOLECULE
OBO:OGI.owl#isLocatedAfter ISLOCATEDAFTER
OBO:so_variant_of SO:VARIANT:OF
OBO:OGI.owl#Genomic_DNA GENOMIC:DNA
OBO:OGI.owl#Polymer POLYMER
OBO:OGI.owl#Polypeptide POLYPEPTIDE
OBO:OGI.owl#Primary_Transcript PRIMARY:TRANSCRIPT
OBO:OGI.owl#isAdjacentBefore ISADJACENTBEFORE
OBO:Contig3 CONTIG3
OBO:Contig4 CONTIG4
OBO:OGI.owl#isAdjacentAfter ISADJACENTAFTER
OBO:Gap4 GAP4
OBO:Gap2 GAP2
OBO:Gap3 GAP3
OBO:OGI.owl#Transcript TRANSCRIPT
OBO:REO_0000826 REO:0000826
OBO:so_has_part SO:HAS:PART
OBO:REO_0000826 is parsed as expected.
OBO:Contig3 shouldn't be here so there are a few options, including leaving it unchanged.
OBO:OGI.owl#CpG_Island is referring to OGI, so this could be OGI:CpG_Island, but that won't resolve back to anything - its ID in OGI.owl is still http://purl.obolibrary.org/obo/OGI.owl#CpG_Island. So we can either leave it unchanged or assign it the new project-specific ID.
Underscores are converted to colons, which is normally fine as long as we're looking at a CURIE already.
Current behavior is mangling OBO ids. See this selection of ID remappings it attempted to make for OGSF:
OBO:REO_0000826
is parsed as expected.OBO:Contig3
shouldn't be here so there are a few options, including leaving it unchanged.OBO:OGI.owl#CpG_Island
is referring to OGI, so this could beOGI:CpG_Island
, but that won't resolve back to anything - its ID inOGI.owl
is stillhttp://purl.obolibrary.org/obo/OGI.owl#CpG_Island
. So we can either leave it unchanged or assign it the new project-specific ID.Underscores are converted to colons, which is normally fine as long as we're looking at a CURIE already.