Minerva seems to garble some models when creating JSON (for over the wire)

[kltm]

Examining "RAS signaling template" (https://github.com/geneontology/noctua-models/blob/master/models/5667fdd400000802) as an OWL file, it looks fairly normal. However, when requesting it from a client, weirdness ensues; it looks like only annotations:

{
 "id": "gomodel:5667fdd400000802",
 "modified-p": false,
 "annotations": [
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0043849>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000837>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0005096>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000815>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0005525>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0003924>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000826>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0009898>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0009898>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/y> \"468\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Types",
   "value": ""
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Prefix",
   "value": "xsd: <http://www.w3.org/2001/XMLSchema#>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0004311>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000066>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000848>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#AnnotationProperty",
   "value": "<http://www.geneontology.org/formats/oboInOwl#id>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000838>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Ontology",
   "value": "<http://model.geneontology.org/5667fdd400000802>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0019003>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//www.geneontology.org/formats/oboInOwl#id> \"gomodel:5667fdd400000802\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#ObjectProperty",
   "value": "<http://purl.obolibrary.org/obo/RO_0002406>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.org/dc/elements/1.1/source> \"PMID:2336011\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000851>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/x> \"104\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#AnnotationProperty",
   "value": "<http://purl.org/dc/elements/1.1/title>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0005783>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000833>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/ECO_0000304>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000808>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://purl.org/dc/elements/1.1/contributor> \"http://orcid.org/0000-0001-7476-6306\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000811>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/x> \"713\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000813>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0080120>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0004671>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000835>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000816>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/y> \"235\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000860>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000819>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000841>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#ObjectProperty",
   "value": "<http://purl.obolibrary.org/obo/RO_0002413>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0008233>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000853>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/x> \"1113\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#AnnotationProperty",
   "value": "<http://geneontology.org/lego/modelstate>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000066>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000820>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000847>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/y> \"631\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0004311>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000066>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000850>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000843>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/ECO_0000304>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#AnnotationProperty",
   "value": "<http://purl.org/dc/elements/1.1/date>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000842>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000852>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#AnnotationProperty",
   "value": "<http://geneontology.org/lego/evidence>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.org/dc/elements/1.1/date> \"2015-12-16\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/x> \"896\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/x> \"516\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000817>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/x> \"81\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000824>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.org/dc/elements/1.1/date> \"2015-12-22\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000825>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/RO_0002406>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000833>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000860>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000066>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000846>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/x> \"982\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000808>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.org/dc/elements/1.1/contributor> \"http://orcid.org/0000-0001-7476-6306\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/RO_0002406>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000805>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000846>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/RO_0002411>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000833>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000066>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000856>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0007265>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/derived> \"true\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000050>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000803>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000830>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000827>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000803>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/y> \"14\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000844>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000810>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000849>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0005623>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000831>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000066>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000852>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.org/dc/elements/1.1/date> \"2015-12-16\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000826>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.org/dc/elements/1.1/title> \"RAS signaling template\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000050>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000829>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000845>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0019003>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Datatype",
   "value": "xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000849>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000812>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Facts",
   "value": ""
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000804>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/RO_0002408>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000839>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000066>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000804>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/RO_0002413>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000827>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0005096>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#ObjectProperty",
   "value": "<http://purl.obolibrary.org/obo/BFO_0000066>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000856>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000817>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.org/dc/elements/1.1/source> \"PMID:19201597\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000854>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000835>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000850>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000831>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000814>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000821>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400002147>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000859>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/x> \"329\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000816>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000843>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/RO_0002408>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000833>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/y> \"434\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000829>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": ""
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0005525>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000066>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000858>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0080120>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/ECO_0000033>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Prefix",
   "value": "rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/y> \"309\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000809>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000847>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000066>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000812>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000050>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000803>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#AnnotationProperty",
   "value": "<http://geneontology.org/lego/hint/layout/y>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#ObjectProperty",
   "value": "<http://purl.obolibrary.org/obo/BFO_0000050>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#ObjectProperty",
   "value": "<http://purl.obolibrary.org/obo/RO_0002411>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000824>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000858>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#AnnotationProperty",
   "value": "<http://purl.org/dc/elements/1.1/contributor>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000838>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000857>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/RO_0002413>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000814>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/x> \"1082\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0005829>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Prefix",
   "value": "owl: <http://www.w3.org/2002/07/owl#>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000822>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/x> \"146\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.org/dc/elements/1.1/contributor> \"http://orcid.org/0000-0001-7476-6306\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000840>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000832>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/modelstate> \"development\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000859>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000841>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000839>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0005829>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000821>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000810>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000853>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#AnnotationProperty",
   "value": "<http://purl.org/dc/elements/1.1/source>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/ECO_0000033>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000066>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000809>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000855>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/y> \"306\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0007265>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0003924>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000845>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000855>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0005623>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#AnnotationProperty",
   "value": "<http://geneontology.org/lego/hint/layout/x>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000837>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000050>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000823>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000848>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000823>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400002147>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000828>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0008233>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/x> \"630\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0004671>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0090002>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.org/dc/elements/1.1/source> \"PMID:23360111\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/y> \"4\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000805>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0005085>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0090002>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000840>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000830>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.org/dc/elements/1.1/date> \"2015-12-22\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000825>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/RO_0002413>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000819>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/y> \"69\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Prefix",
   "value": "rdfs: <http://www.w3.org/2000/01/rdf-schema#>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000844>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/GO_0043849>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/y> \"510\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000066>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000815>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/x> \"472\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Prefix",
   "value": "xml: <http://www.w3.org/XML/1998/namespace>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.org/dc/elements/1.1/source> \"PMID:2336011\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000828>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000822>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0005085>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000820>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#ObjectProperty",
   "value": "<http://purl.obolibrary.org/obo/RO_0002408>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/BFO_0000066>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000854>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//geneontology.org/lego/hint/layout/y> \"165\"^^xsd:string"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000813>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/RO_0002408>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000833>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Annotations",
   "value": "<http://geneontology.org/lego/evidence> <http://model.geneontology.org/5667fdd400000802/5667fdd400000851>,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Import",
   "value": "<http://purl.obolibrary.org/obo/go/extensions/go-lego.owl>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.org/dc/elements/1.1/source> \"PMID:23360111\"^^xsd:string,"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Class",
   "value": "<http://purl.obolibrary.org/obo/GO_0005783>"
  },
  {
   "key": "http://www.geneontology.org/formats/oboInOwl#Individual",
   "value": "<http://model.geneontology.org/5667fdd400000802/5667fdd400000857>"
  }
 ],
 "facts": [],
 "individuals": [],
 "properties": []
}

Some of those are pretty iffy looking, like:

  {
   "key": "http://www.geneontology.org/formats/oboInOwl#<http",
   "value": "//purl.obolibrary.org/obo/RO_0002408>  <http://model.geneontology.org/5667fdd400000802/5667fdd400000833>,"
  }

As well, the following report from the client, unhappy about empty values:

bad annotation k/v set:  { key: 'http://www.geneontology.org/formats/oboInOwl#Types',
  value: '' }
bad annotation k/v set:  { key: 'http://www.geneontology.org/formats/oboInOwl#Facts',
  value: '' }
bad annotation k/v set:  { key: 'http://www.geneontology.org/formats/oboInOwl#Annotations',
  value: '' }

It looks like something is going wrong somewhere in there?

[kltm]

GAF output fairly void as well, so something earlier, maybe during parsing, as there did not seem to be any problems before the restart?

[kltm]

From Chris's email comments, the only thing that a noctua client could have done here (that wasn't done more seriously in the case of the Scratch model becoming unreadable/unparsable) would be to add an annotation and then remove it. However, I'm not sure I every tried to apply the annotation to this model (the extra "template" annotation does not exist here).

[kltm]

tagging @cmungall

[hdietze]

There are two underlying issues here:

• While saving, we decorate the model with additional information and tag this axioms as inferred. This tag uses an undeclared annotation property. After save any attempt to read the model fails on this undeclared property (as the Manchester writer did not fix/add the declaration)
• Due to the syntax error, the OWL-API tries all other parser, including OBO. The OBO parser sees no syntax error and thus accepts the file, but produces garbage and renders this non-sense in JSON.

I have addressed both in the commits, but to fix all already saved model, we need to add the declaration to all models.

[hdietze]

The required additional lines in each model are:

AnnotationProperty:  <http://geneontology.org/lego/derived>

[kltm]

With a scripted model fix and PR from @cmungall (https://github.com/geneontology/noctua-models/pull/13), it looks like it is cleared.