Ontology parsing error adds extra column

[caufieldjh]

Parsing ABD results in the edges including the following:

urn:uuid:c95fa7fd-b1f0-4f35-83d4-4fce72d8bbc0	http://brd.bsvgateway.org/api/organism/?id=620	biolink:subclass_of	http://brd.bsvgateway.org/api/organism/	rdfs:subClassOf	BioPortal	Anthology of Biosurveillance Diseases
urn:uuid:7a7d352b-0ebb-42a4-a950-fcf914d72fd4	http://brd.bsvgateway.org/api	ransmission/	biolink:subclass_of	owl:Thing	rdfs:subClassOf	BioPortal	Anthology of Biosurveillance Diseases
urn:uuid:b9b23088-74d8-45be-b1d8-9ef0085b1a8d	http://brd.bsvgateway.org/api/organism/?id=628	biolink:subclass_of	http://brd.bsvgateway.org/api/organism/	rdfs:subClassOf	BioPortal	Anthology of Biosurveillance Diseases

The middle line is the issue - this breaks any merge in which these edges are included, raising a pandas.errors.ParserError: Error tokenizing data. C error: Expected 7 fields in line 1017, saw 8

It looks like there's some truncation/extra whitespace in the id. This ontology has a class named Transmission so this is likely something with the prefix http://brd.bsvgateway.org/api/transmission/
ABD has some other weirdness too, with lots of Error classes. See on Bioportal at https://bioportal.bioontology.org/ontologies/ABD/?p=classes&conceptid=root

[caufieldjh]

This same error is likely to happen with other malformed edge values though, e.g., in ACESO:

urn:uuid:0b5fa719-01c3-41c7-acc1-815dd3edee05	http://purl.bioontology.org/ontology/SNOMEDCT/247997008	biolink:subclass_of	http://ontology.apa.org/apaonto	ermsonlyOUT%20(5).owl#Bullying	rdfs:subClassOf	BioPortal	Adverse Childhood Experiences Ontology

In this case, there's some weird parsing going on with an imported SNOMED term: https://bioportal.bioontology.org/ontologies/SNOMEDCT?p=classes&conceptid=247997008

Same result - wrong number of columns in that entry, pandas raises ParserError, merge fails.

[caufieldjh]

Here's another example from ADALAB:

urn:uuid:f5b2b9c3-7ba3-45e4-8f91-8186dc2a5f7d	http://rdf.adalab-project.org/ontology/adalab	ranscriptionFactor	biolink:type	OBO:INO_0000008	type

This must have something to do with tabs - all the impacted values are missing "/t", but parsed literally rather than as a tab.

[caufieldjh]

Regenerating each transform with version as of commit 76b2709 appears to resolve the issue, e.g. with ADALAB:

urn:uuid:b3e7008f-1a2a-440b-89c6-45fdba059072	http://rdf.adalab-project.org/ontology/adalab/transcriptionFactor	biolink:type	OBO:INO_0000008	type	BioPortal	AdaLab ontology