Failing ontologies on data load

[serjoshua]

OBO

Fixed	ID	Status	Download	Parsing	EBI Override	PURL	Notes	Pipeline Error
	cido	active	❌			http://purl.obolibrary.org/obo/cido.owl	failed import http://purl.obolibrary.org/obo/DrugsNoChEBI_interactions_with_targets.owl	[line: 2, col: 207] {E202} Expecting XML start or end element(s). String data "aeo.obo" not allowed. Maybe there should be an rdf:parseType='Literal' for embedding mixed XML content in RDF. Maybe a striping error.
	cto	active	❌			http://purl.obolibrary.org/obo/cto.owl		[line: 25, col: 32] {E201} Multiple children of property element
	cvdo	active	❌			http://purl.obolibrary.org/obo/cvdo.owl	failed import http://purl.obolibrary.org/obo/cvdo/external/doid_import.owl	[line: 2, col: 207] {E202} Expecting XML start or end element(s). String data "aeo.obo" not allowed. Maybe there should be an rdf:parseType='Literal' for embedding mixed XML content in RDF. Maybe a striping error.
	upheno	active	❌			http://purl.obolibrary.org/obo/upheno.owl	failed import http://purl.obolibrary.org/obo/upheno/upheno_root_alignments.owl	[line: 1, col: 1 ] Content is not allowed in prolog.
	mamo	orphaned	❌		✅	http://purl.obolibrary.org/obo/mamo.owl		[line: 17, col: 74] {E201} Multiple children of property element
	vario	orphaned	❌			http://purl.obolibrary.org/obo/vario.owl		[line: 1, col: 1 ] Content is not allowed in prolog.
	olatdv	inactive	❌			http://purl.obolibrary.org/obo/olatdv.owl		Not found
	pdumdv	inactive	❌			http://purl.obolibrary.org/obo/pdumdv.owl		Not found
	rnao	inactive	❌			http://purl.obolibrary.org/obo/rnao.owl	failed import http://www.obofoundry.org/ro/ro.owl	Not found
	dinto	inactive	❌			http://purl.obolibrary.org/obo/dinto.owl		[line: 13, col: 4 ] {E201} The attributes on this property element, are not permitted with any content; expecting end element tag.
	eo	inactive	❌			http://purl.obolibrary.org/obo/eo.owl		Not found
	epo	inactive	❌			http://purl.obolibrary.org/obo/epo.owl		Not found
	ero	inactive	❌			http://purl.obolibrary.org/obo/ero.owl		[line: 4, col: 27] {E202} Expecting XML start or end element(s). String data "redirecting" not allowed. Maybe there should be an rdf:parseType='Literal' for embedding mixed XML content in RDF. Maybe a striping error.
	flu	inactive	❌			http://purl.obolibrary.org/obo/flu.owl	failed import http://purl.obolibrary.org/obo/ido/2010-12-02/ido-main-workaround.owl	Not found
	mfo	inactive	❌			http://purl.obolibrary.org/obo/mfo.owl		[line: 1, col: 3 ] The markup in the document preceding the root element must be well-formed.
	mirnao	inactive	❌			http://purl.obolibrary.org/obo/mirnao.owl		Not found
	mo	inactive	❌			http://purl.obolibrary.org/obo/mo.owl		[line: 2, col: 207] {E202} Expecting XML start or end element(s). String data "aeo.obo" not allowed. Maybe there should be an rdf:parseType='Literal' for embedding mixed XML content in RDF. Maybe a striping error.
	nmr	inactive	❌			http://purl.obolibrary.org/obo/nmr.owl		[line: 2, col: 207] {E202} Expecting XML start or end element(s). String data "aeo.obo" not allowed. Maybe there should be an rdf:parseType='Literal' for embedding mixed XML content in RDF. Maybe a striping error.
	ogi	inactive	❌			http://purl.obolibrary.org/obo/ogi.owl		Not found
	sep	inactive	✅	❌		http://purl.obolibrary.org/obo/sep.owl	redirects to http://ontologies.berkeleybop.org/sep.owl	Cannot read field "properties" because "this.ontologyNode" is null
	vhog	inactive	✅	❌		http://purl.obolibrary.org/obo/vhog.owl	redirects to file points to http://ontologies.berkeleybop.org/vhog.owl	Cannot read field "properties" because "this.ontologyNode" is null

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EBI OLS Ontologies

Fixed	ID	Download	Parsing	PURL	Notes	Pipeline Error
	phi	❌		file:/nfs/panda/ensembl/production/ensprod/ontologies/phi/PHI.obo		Not found
	atol	❌		http://www.atol-ontology.com/public/telechargement/atol.owl		javax.net.ssl.SSLHandshakeException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
	eol	❌		http://www.atol-ontology.com/public/telechargement/eol.owl		javax.net.ssl.SSLHandshakeException: PKIX path building failed: sun.security.provider.certpath.SunCertPathBuilderException: unable to find valid certification path to requested target
	lbo	❌		http://data.bioontology.org/ontologies/LBO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb		Failed to determine the content type: (URI=http://data.bioontology.org/ontologies/LBO/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb : stream=application/octet-stream)
	pride	❌		https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.obo	migrate away from OBO	Failed to determine the content type: (URI=https://raw.githubusercontent.com/PRIDE-Utilities/pride-ontology/master/pride_cv.obo : stream=text/plain)
	unimod	❌		http://www.unimod.org/obo/unimod.obo	migrate away from OBO	Failed to determine the content type: (URI=http://www.unimod.org/obo/unimod.obo : stream=null)
	hpath	❌		https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo	migrate away from OBO	Failed to determine the content type: (URI=https://raw.githubusercontent.com/Novartis/hpath/master/src/hpath.obo : stream=text/plain)
	vido	❌		https://raw.githubusercontent.com/infectious-disease-ontology-extensions/ido-virus/master/ontology/vido.owl		[line: 23, col: 18] {E201} Multiple children of property element

Original spreadsheet