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[bioontology-support] Can't generate ChEBI mappings in my OntoPortal 3 VM

Miller, Mark markampa at pennmedicine.upenn.edu
Wed Sep 9 06:45:36 PDT 2020


Currently, one of my main uses for BioPortal/OntoPortal is retrieving all mappings between ChEBI, DrOn, and RxNorm. I prefer to do that from the VM because it’s faster and I can load new versions as soon as they become available. And it’s better citizenship, right?

I recently upgraded to OntoPortal 3, and I can’t seem to get mappings to or from ChEBI.

Are there caches that can be cleared besides the four on the Admin page?

Is there some way to force a rebuild of the mappings? I have tried re-processing and re-annotating from the Ontology Administration page.

I have included a lot of attachments. I hope they are helpful and not too distracting. I can send anything else you might like to see.

Thanks,
Mark

—   —   —



Here’s the Ontology Admin page:

[cid:4D43293E-A573-4932-A638-D8D46B3BD6F9]


I can retrieve mappings between RxNorm and STY, but I can’t get ChEBI mappings, at least through some of the web interfaces.

[cid:9CCC5668-3198-4DF9-8665-2286B44CF9BF]

[cid:3E5C0216-D07B-4C04-8EB5-D56047BFE78B]

Although some mappings are available via the API… but they look stale, from ontologies I have deleted from the VM. I HAVE cleared all of the caches accessible from the Site Administration page.

http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/mappings?apikey=XXX<http://192.168.0.201:8080/ontologies/RXNORM/classes/http://purl.bioontology.org/ontology/RXNORM/7646/mappings?apikey=XXX>

[

  *
-
{
     *   "id": null,
     *   "source": "LOOM",
     *
-
"classes": [
        *
-
{
           *   "@id": "http://purl.bioontology.org/ontology/RXNORM/7646"<http://purl.bioontology.org/ontology/RXNORM/7646>,
           *   "@type": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
           *
-
"links": {
              *   "self": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646>,
              *   "ontology": "http://192.168.0.201:8080/ontologies/RXNORM"<http://192.168.0.201:8080/ontologies/RXNORM>,
              *   "children": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/children"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/children>,
              *   "parents": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/parents"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/parents>,
              *   "descendants": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/descendants"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/descendants>,
              *   "ancestors": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/ancestors"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/ancestors>,
              *   "instances": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/instances"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/instances>,
              *   "tree": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/tree"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/tree>,
              *   "notes": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/notes"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/notes>,
              *   "mappings": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/mappings"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/mappings>,
              *   "ui": "http://192.168.0.201/ontologies/RXNORM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646"<http://192.168.0.201/ontologies/RXNORM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646>,
              *
-
"@context": {
                 *   "self": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "ontology": "http://data.bioontology.org/metadata/Ontology"<http://data.bioontology.org/metadata/Ontology>,
                 *   "children": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "parents": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "descendants": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "ancestors": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "instances": "http://data.bioontology.org/metadata/Instance"<http://data.bioontology.org/metadata/Instance>,
                 *   "tree": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "notes": "http://data.bioontology.org/metadata/Note"<http://data.bioontology.org/metadata/Note>,
                 *   "mappings": "http://data.bioontology.org/metadata/Mapping"<http://data.bioontology.org/metadata/Mapping>,
                 *   "ui": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>
}
},
           *
-
"@context": {
              *   "@vocab": "http://data.bioontology.org/metadata/"<http://data.bioontology.org/metadata/>
}
},
        *
-
{
           *   "@id": "http://purl.obolibrary.org/obo/CHEBI_7772"<http://purl.obolibrary.org/obo/CHEBI_7772>,
           *   "@type": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
           *
-
"links": {
              *   "self": "http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772"<http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772>,
              *   "ontology": "http://192.168.0.201:8080/ontologies/CHEBI"<http://192.168.0.201:8080/ontologies/CHEBI>,
              *   "children": "http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/children"<http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/children>,
              *   "parents": "http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/parents"<http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/parents>,
              *   "descendants": "http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/descendants"<http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/descendants>,
              *   "ancestors": "http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/ancestors"<http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/ancestors>,
              *   "instances": "http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/instances"<http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/instances>,
              *   "tree": "http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/tree"<http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/tree>,
              *   "notes": "http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/notes"<http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/notes>,
              *   "mappings": "http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/mappings"<http://192.168.0.201:8080/ontologies/CHEBI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/mappings>,
              *   "ui": "http://192.168.0.201/ontologies/CHEBI?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772"<http://192.168.0.201/ontologies/CHEBI?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772>,
              *
-
"@context": {
                 *   "self": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "ontology": "http://data.bioontology.org/metadata/Ontology"<http://data.bioontology.org/metadata/Ontology>,
                 *   "children": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "parents": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "descendants": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "ancestors": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "instances": "http://data.bioontology.org/metadata/Instance"<http://data.bioontology.org/metadata/Instance>,
                 *   "tree": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "notes": "http://data.bioontology.org/metadata/Note"<http://data.bioontology.org/metadata/Note>,
                 *   "mappings": "http://data.bioontology.org/metadata/Mapping"<http://data.bioontology.org/metadata/Mapping>,
                 *   "ui": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>
}
},
           *
-
"@context": {
              *   "@vocab": "http://data.bioontology.org/metadata/"<http://data.bioontology.org/metadata/>
}
}
],
     *   "process": null,
     *   "@id": "",
     *   "@type": "http://data.bioontology.org/metadata/Mapping"<http://data.bioontology.org/metadata/Mapping>
},
  *
-
{
     *   "id": null,
     *   "source": "LOOM",
     *
-
"classes": [
        *
-
{
           *   "@id": "http://purl.bioontology.org/ontology/RXNORM/7646"<http://purl.bioontology.org/ontology/RXNORM/7646>,
           *   "@type": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
           *
-
"links": {
              *   "self": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646>,
              *   "ontology": "http://192.168.0.201:8080/ontologies/RXNORM"<http://192.168.0.201:8080/ontologies/RXNORM>,
              *   "children": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/children"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/children>,
              *   "parents": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/parents"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/parents>,
              *   "descendants": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/descendants"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/descendants>,
              *   "ancestors": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/ancestors"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/ancestors>,
              *   "instances": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/instances"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/instances>,
              *   "tree": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/tree"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/tree>,
              *   "notes": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/notes"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/notes>,
              *   "mappings": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/mappings"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/mappings>,
              *   "ui": "http://192.168.0.201/ontologies/RXNORM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646"<http://192.168.0.201/ontologies/RXNORM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646>,
              *
-
"@context": {
                 *   "self": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "ontology": "http://data.bioontology.org/metadata/Ontology"<http://data.bioontology.org/metadata/Ontology>,
                 *   "children": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "parents": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "descendants": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "ancestors": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "instances": "http://data.bioontology.org/metadata/Instance"<http://data.bioontology.org/metadata/Instance>,
                 *   "tree": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "notes": "http://data.bioontology.org/metadata/Note"<http://data.bioontology.org/metadata/Note>,
                 *   "mappings": "http://data.bioontology.org/metadata/Mapping"<http://data.bioontology.org/metadata/Mapping>,
                 *   "ui": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>
}
},
           *
-
"@context": {
              *   "@vocab": "http://data.bioontology.org/metadata/"<http://data.bioontology.org/metadata/>
}
},
        *
-
{
           *   "@id": "http://purl.obolibrary.org/obo/CHEBI_7772"<http://purl.obolibrary.org/obo/CHEBI_7772>,
           *   "@type": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
           *
-
"links": {
              *   "self": "http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772"<http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772>,
              *   "ontology": "http://192.168.0.201:8080/ontologies/CHEBI1"<http://192.168.0.201:8080/ontologies/CHEBI1>,
              *   "children": "http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/children"<http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/children>,
              *   "parents": "http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/parents"<http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/parents>,
              *   "descendants": "http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/descendants"<http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/descendants>,
              *   "ancestors": "http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/ancestors"<http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/ancestors>,
              *   "instances": "http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/instances"<http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/instances>,
              *   "tree": "http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/tree"<http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/tree>,
              *   "notes": "http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/notes"<http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/notes>,
              *   "mappings": "http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/mappings"<http://192.168.0.201:8080/ontologies/CHEBI1/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/mappings>,
              *   "ui": "http://192.168.0.201/ontologies/CHEBI1?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772"<http://192.168.0.201/ontologies/CHEBI1?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772>,
              *
-
"@context": {
                 *   "self": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "ontology": "http://data.bioontology.org/metadata/Ontology"<http://data.bioontology.org/metadata/Ontology>,
                 *   "children": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "parents": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "descendants": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "ancestors": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "instances": "http://data.bioontology.org/metadata/Instance"<http://data.bioontology.org/metadata/Instance>,
                 *   "tree": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "notes": "http://data.bioontology.org/metadata/Note"<http://data.bioontology.org/metadata/Note>,
                 *   "mappings": "http://data.bioontology.org/metadata/Mapping"<http://data.bioontology.org/metadata/Mapping>,
                 *   "ui": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>
}
},
           *
-
"@context": {
              *   "@vocab": "http://data.bioontology.org/metadata/"<http://data.bioontology.org/metadata/>
}
}
],
     *   "process": null,
     *   "@id": "",
     *   "@type": "http://data.bioontology.org/metadata/Mapping"<http://data.bioontology.org/metadata/Mapping>
},
  *
-
{
     *   "id": null,
     *   "source": "LOOM",
     *
-
"classes": [
        *
-
{
           *   "@id": "http://purl.bioontology.org/ontology/RXNORM/7646"<http://purl.bioontology.org/ontology/RXNORM/7646>,
           *   "@type": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
           *
-
"links": {
              *   "self": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646>,
              *   "ontology": "http://192.168.0.201:8080/ontologies/RXNORM"<http://192.168.0.201:8080/ontologies/RXNORM>,
              *   "children": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/children"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/children>,
              *   "parents": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/parents"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/parents>,
              *   "descendants": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/descendants"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/descendants>,
              *   "ancestors": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/ancestors"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/ancestors>,
              *   "instances": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/instances"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/instances>,
              *   "tree": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/tree"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/tree>,
              *   "notes": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/notes"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/notes>,
              *   "mappings": "http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/mappings"<http://192.168.0.201:8080/ontologies/RXNORM/classes/http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646/mappings>,
              *   "ui": "http://192.168.0.201/ontologies/RXNORM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646"<http://192.168.0.201/ontologies/RXNORM?p=classes&conceptid=http%3A%2F%2Fpurl.bioontology.org%2Fontology%2FRXNORM%2F7646>,
              *
-
"@context": {
                 *   "self": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "ontology": "http://data.bioontology.org/metadata/Ontology"<http://data.bioontology.org/metadata/Ontology>,
                 *   "children": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "parents": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "descendants": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "ancestors": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "instances": "http://data.bioontology.org/metadata/Instance"<http://data.bioontology.org/metadata/Instance>,
                 *   "tree": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "notes": "http://data.bioontology.org/metadata/Note"<http://data.bioontology.org/metadata/Note>,
                 *   "mappings": "http://data.bioontology.org/metadata/Mapping"<http://data.bioontology.org/metadata/Mapping>,
                 *   "ui": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>
}
},
           *
-
"@context": {
              *   "@vocab": "http://data.bioontology.org/metadata/"<http://data.bioontology.org/metadata/>
}
},
        *
-
{
           *   "@id": "http://purl.obolibrary.org/obo/CHEBI_7772"<http://purl.obolibrary.org/obo/CHEBI_7772>,
           *   "@type": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
           *
-
"links": {
              *   "self": "http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772"<http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772>,
              *   "ontology": "http://192.168.0.201:8080/ontologies/DRON"<http://192.168.0.201:8080/ontologies/DRON>,
              *   "children": "http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/children"<http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/children>,
              *   "parents": "http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/parents"<http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/parents>,
              *   "descendants": "http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/descendants"<http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/descendants>,
              *   "ancestors": "http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/ancestors"<http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/ancestors>,
              *   "instances": "http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/instances"<http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/instances>,
              *   "tree": "http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/tree"<http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/tree>,
              *   "notes": "http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/notes"<http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/notes>,
              *   "mappings": "http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/mappings"<http://192.168.0.201:8080/ontologies/DRON/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772/mappings>,
              *   "ui": "http://192.168.0.201/ontologies/DRON?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772"<http://192.168.0.201/ontologies/DRON?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_7772>,
              *
-
"@context": {
                 *   "self": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "ontology": "http://data.bioontology.org/metadata/Ontology"<http://data.bioontology.org/metadata/Ontology>,
                 *   "children": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "parents": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "descendants": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "ancestors": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "instances": "http://data.bioontology.org/metadata/Instance"<http://data.bioontology.org/metadata/Instance>,
                 *   "tree": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>,
                 *   "notes": "http://data.bioontology.org/metadata/Note"<http://data.bioontology.org/metadata/Note>,
                 *   "mappings": "http://data.bioontology.org/metadata/Mapping"<http://data.bioontology.org/metadata/Mapping>,
                 *   "ui": "http://www.w3.org/2002/07/owl#Class"<http://www.w3.org/2002/07/owl#Class>
}
},
           *
-
"@context": {
              *   "@vocab": "http://data.bioontology.org/metadata/"<http://data.bioontology.org/metadata/>
}
}
],
     *   "process": null,
     *   "@id": "",
     *   "@type": "http://data.bioontology.org/metadata/Mapping"<http://data.bioontology.org/metadata/Mapping>
}

]

I have tried submitting ChEBI as both the OBO and OWL files, and as the full or lite edition.

I don’t see the words “error” or “warn” anywhere in the ChEBI parsing log. Here’s an excerpt:

Log file: CHEBI/1/parsing.log
# Logfile created on 2020-09-07 15:59:17 +0000 by logger.rb/v1.4.2
I, [2020-09-07T15:59:17.864488 #2539]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/CHEBI/submissions/1"]
I, [2020-09-07T15:59:17.868818 #2539]  INFO -- : ["Starting to process CHEBI/submissions/1"]
I, [2020-09-07T15:59:18.196865 #2539]  INFO -- : ["Java call [java -DentityExpansionLimit=2500000 -Xmx10240M -jar /srv/ontoportal/ncbo_cron/vendor/bundle/ruby/2.6.0/bundler/gems/ontologies_linked_data-613a5c836099/bin/owlapi-wrapper-1.3.6.jar -m /srv/ontoportal/data/repository/CHEBI/1/chebi_lite.obo -o /srv/ontoportal/data/repository/CHEBI/1 -r true]"]
I, [2020-09-07T16:00:12.628030 #2539]  INFO -- : ["2020-09-07T15:59:18 [main] INFO  o.s.n.o.OntologyParserCommand - Parsing invocation with values: ParserInvocation [inputRepositoryFolder=null, outputRepositoryFolder=/srv/ontoportal/data/repository/CHEBI/1, masterFileName=/srv/ontoportal/data/repository/CHEBI/1/chebi_lite.obo, invocationId=0, parserLog=, userReasoner= true]\n\n2020-09-07T15:59:18 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - executor ...\n\n2020-09-07T15:59:19 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Input repository folder is null. Unique file being parsed.\n\n2020-09-07T15:59:19 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.binary.BinaryRDFParserFactory\n\n2020-09-07T15:59:19 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.n3.N3ParserFactory\n\n2020-09-07T15:59:19 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.nquads.NQuadsParserFactory\n\n2020-09-07T15:59:19 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.ntriples.NTriplesParserFactory\n\n2020-09-07T15:59:19 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.rdfjson.RDFJSONParserFactory\n\n2020-09-07T15:59:19 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.jsonld.JSONLDParserFactory\n\n2020-09-07T15:59:19 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.rdfxml.RDFXMLParserFactory\n\n2020-09-07T15:59:19 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.trix.TriXParserFactory\n\n2020-09-07T15:59:19 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.turtle.TurtleParserFactory\n\n2020-09-07T15:59:19 [main] DEBUG o.e.rdf4j.rio.RDFParserRegistry - Registered service class org.eclipse.rdf4j.rio.trig.TriGParserFactory\n\n2020-09-07T15:59:19 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.XMLSchemaDatatypeHandler\n\n2020-09-07T15:59:19 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.RDFDatatypeHandler\n\n2020-09-07T15:59:19 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.DBPediaDatatypeHandler\n\n2020-09-07T15:59:19 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.VirtuosoGeometryDatatypeHandler\n\n2020-09-07T15:59:19 [main] DEBUG o.e.r.rio.DatatypeHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.datatypes.GeoSPARQLDatatypeHandler\n\n2020-09-07T15:59:19 [main] DEBUG o.e.r.rio.LanguageHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.languages.RFC3066LanguageHandler\n\n2020-09-07T15:59:19 [main] DEBUG o.e.r.rio.LanguageHandlerRegistry - Registered service class org.eclipse.rdf4j.rio.languages.BCP47LanguageHandler\n\n2020-09-07T15:59:33 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Calculating metrics for /srv/ontoportal/data/repository/CHEBI/1/chebi_lite.obo\n\n2020-09-07T15:59:33 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Finished metrics calculation for /srv/ontoportal/data/repository/CHEBI/1/chebi_lite.obo in 57 milliseconds\n\n2020-09-07T15:59:33 [main] INFO  o.s.ncbo.oapiwrapper.OntologyMetrics - Generated metrics CSV file for /srv/ontoportal/data/repository/CHEBI/1/chebi_lite.obo\n\n2020-09-07T15:59:33 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Ontology document format: org.semanticweb.owlapi.formats.OBODocumentFormat\n\n2020-09-07T15:59:34 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - isPrefixOWLOntologyFormat: false\n\n2020-09-07T15:59:38 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Adding version: 191\n\n2020-09-07T15:59:45 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - isOBO: true\n\n2020-09-07T15:59:47 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Serializing ontology in RDF ...\n\n2020-09-07T16:00:12 [main] INFO  o.s.ncbo.oapiwrapper.OntologyParser - Serialization done!\n\n2020-09-07T16:00:12 [main] INFO  o.s.n.o.OntologyParserCommand - Parse result: true\n\n2020-09-07T16:00:12 [main] INFO  o.s.n.o.OntologyParserCommand - Output triples in: {}/srv/ontoportal/data/repository/CHEBI/1/owlapi.xrdf\n\n2020-09-07T16:00:12 [main] INFO  o.s.n.o.OntologyParserCommand - Finished parsing!\n"]
I, [2020-09-07T16:00:12.628684 #2539]  INFO -- : ["OWLAPI Java command: parsing finished successfully."]
I, [2020-09-07T16:00:12.630502 #2539]  INFO -- : ["Output size 193129660 in `/srv/ontoportal/data/repository/CHEBI/1/owlapi.xrdf`"]
I, [2020-09-07T16:01:16.993478 #2539]  INFO -- : ["Triples /srv/ontoportal/data/repository/CHEBI/1/owlapi.xrdf appended in <http://data.bioontology.org/ontologies/CHEBI/submissions/1>"]
I, [2020-09-07T16:01:18.487491 #2539]  INFO -- : ["1: page 1 of 58 - 2500 ontology terms retrieved in 1.22956868 sec."]
I, [2020-09-07T16:01:19.250110 #2539]  INFO -- : ["Asserting 2500 labels in <http://data.bioontology.org/ontologies/CHEBI/submissions/1>"]
I, [2020-09-07T16:01:19.451892 #2539]  INFO -- : ["Labels asserted in 0.199278285 sec."]
---snip---
I, [2020-09-07T16:03:13.058429 #2539]  INFO -- : ["1: page 58 of 58 - 2149 ontology terms retrieved in 0.919392601 sec."]
I, [2020-09-07T16:03:13.605387 #2539]  INFO -- : ["Asserting 2149 labels in <http://data.bioontology.org/ontologies/CHEBI/submissions/1>"]
I, [2020-09-07T16:03:13.810954 #2539]  INFO -- : ["Labels asserted in 0.204242249 sec."]
I, [2020-09-07T16:03:13.811189 #2539]  INFO -- : ["Asserting 4298 mappings in <http://data.bioontology.org/ontologies/CHEBI/submissions/1>"]
I, [2020-09-07T16:03:14.060541 #2539]  INFO -- : ["Mapping labels asserted in 0.246911618 sec."]
I, [2020-09-07T16:03:14.060640 #2539]  INFO -- : ["end generate_missing_labels traversed 144649 classes"]
I, [2020-09-07T16:03:14.060693 #2539]  INFO -- : ["Saved generated labels in /srv/ontoportal/data/repository/CHEBI/1/labels.ttl"]
I, [2020-09-07T16:03:14.060823 #2539]  INFO -- : ["Completed Missing Labels Generation: 1 in 116.91650822501106 sec. 144649 classes."]
I, [2020-09-07T16:03:14.677001 #2539]  INFO -- : ["Indexing ontology terms: CHEBI..."]
I, [2020-09-07T16:03:14.747152 #2539]  INFO -- : ["Removed ontology terms index (0.069995754s)"]
I, [2020-09-07T16:03:17.420513 #2539]  INFO -- : ["Thread 1: Page 1 of 145 - 1000 ontology terms retrieved in 1.0482e-05 sec."]
I, [2020-09-07T16:03:18.050454 #2539]  INFO -- : ["Thread 1: Page 1 of 145 attributes mapped in 0.629807943 sec."]
I, [2020-09-07T16:03:44.499101 #2539]  INFO -- : ["Thread 1: Page 1 of 145 - 1000 ontology terms indexed in 26.448257779 sec."]

---snip---
I, [2020-09-07T16:44:32.335034 #2539]  INFO -- : ["Thread 1: Page 145 of 145 - 649 ontology terms retrieved in 7.343e-06 sec."]
I, [2020-09-07T16:44:32.686103 #2539]  INFO -- : ["Thread 1: Page 145 of 145 attributes mapped in 0.350929584 sec."]
I, [2020-09-07T16:44:41.926707 #2539]  INFO -- : ["Thread 1: Page 145 of 145 - 649 ontology terms indexed in 9.240427009 sec."]
I, [2020-09-07T16:44:42.116333 #2539]  INFO -- : ["Ontology terms index commit in 0.188457243 sec."]
I, [2020-09-07T16:44:42.116492 #2539]  INFO -- : ["Completed indexing ontology terms: CHEBI in 2487.790310148004 sec. 144649 classes."]
I, [2020-09-07T16:44:42.238956 #2539]  INFO -- : ["Indexing ontology properties: CHEBI..."]
I, [2020-09-07T16:44:42.261297 #2539]  INFO -- : ["Removed ontology properties index in 0.02218551 seconds."]
I, [2020-09-07T16:44:42.462311 #2539]  INFO -- : ["Indexing a total of 1 pages of 2500 properties each."]
I, [2020-09-07T16:44:42.524558 #2539]  INFO -- : ["Page 1 of ontology properties indexed in 0.062042124 seconds."]
I, [2020-09-07T16:44:42.547796 #2539]  INFO -- : ["Ontology properties index commit in 0.02297986 seconds."]
I, [2020-09-07T16:44:42.547940 #2539]  INFO -- : ["Completed indexing ontology properties of CHEBI in 0.30903106299228966 sec. Total of 38 properties indexed."]
I, [2020-09-07T16:44:42.666989 #2539]  INFO -- : ["metrics_for_submission start"]
I, [2020-09-07T16:45:45.772482 #2539]  INFO -- : ["Metrics groupby_children retrieved 12321 in 4.306272875 sec."]
I, [2020-09-07T16:45:45.777303 #2539]  INFO -- : ["Metrics count_classes retrieved 144649 in 0.000317321 sec."]
I, [2020-09-07T16:45:46.325177 #2539]  INFO -- : ["Metrics count cls with def 118708 in 0.547730875 sec."]
I, [2020-09-07T16:45:46.325947 #2539]  INFO -- : ["Class metrics finished in 63.658839633 sec."]
I, [2020-09-07T16:45:46.325989 #2539]  INFO -- : ["class_metrics finished"]
I, [2020-09-07T16:45:46.326441 #2539]  INFO -- : ["individuals finished"]
I, [2020-09-07T16:45:46.326651 #2539]  INFO -- : ["properties finished"]
I, [2020-09-07T16:45:46.326961 #2539]  INFO -- : ["generation of metrics file finished"]
I, [2020-09-07T16:45:46.564402 #2539]  INFO -- : ["Bubastis diff: no older submissions available for http://data.bioontology.org/ontologies/CHEBI/submissions/1."]
I, [2020-09-07T16:45:46.569379 #2539]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/CHEBI/submissions/1 completed successfully"]
D, [2020-09-07T16:45:46.605989 #2539] DEBUG -- : ["Archiving submissions previous to http://data.bioontology.org/ontologies/CHEBI/submissions/1..."]
D, [2020-09-07T16:45:46.623654 #2539] DEBUG -- : ["Completed archiving submissions previous to http://data.bioontology.org/ontologies/CHEBI/submissions/1"]
I, [2020-09-07T16:45:46.646961 #2539]  INFO -- : [["Caching classes of CHEBI"]]
I, [2020-09-07T16:45:46.647023 #2539]  INFO -- : ["Caching classes of CHEBI"]
I, [2020-09-07T16:45:48.748482 #2539]  INFO -- : [["Page 1 of 58 - 2500 classes retrieved in 2.101163434 sec."]]
I, [2020-09-07T16:45:48.748509 #2539]  INFO -- : ["Page 1 of 58 - 2500 classes retrieved in 2.101163434 sec."]
I, [2020-09-07T16:45:50.456922 #2539]  INFO -- : [["Page 1 of 58 cached in Annotator in 1.708290642 sec."]]
I, [2020-09-07T16:45:50.456954 #2539]  INFO -- : ["Page 1 of 58 cached in Annotator in 1.708290642 sec."]
---snip---
I, [2020-09-07T16:49:11.988457 #2539]  INFO -- : ["Page 57 of 58 cached in Annotator in 1.358687309 sec."]
I, [2020-09-07T16:49:14.137903 #2539]  INFO -- : [["Page 58 of 58 - 2149 classes retrieved in 2.149309102 sec."]]
I, [2020-09-07T16:49:14.137929 #2539]  INFO -- : ["Page 58 of 58 - 2149 classes retrieved in 2.149309102 sec."]
I, [2020-09-07T16:49:15.348864 #2539]  INFO -- : [["Page 58 of 58 cached in Annotator in 1.210797795 sec."]]
I, [2020-09-07T16:49:15.348895 #2539]  INFO -- : ["Page 58 of 58 cached in Annotator in 1.210797795 sec."]
I, [2020-09-07T16:49:15.443946 #2539]  INFO -- : [["Completed caching ontology: CHEBI (http://data.bioontology.org/ontologies/CHEBI/submissions/1) in 208.70213225399493 sec. 144649 classes."]]
I, [2020-09-07T16:49:15.444113 #2539]  INFO -- : ["Completed caching ontology: CHEBI (http://data.bioontology.org/ontologies/CHEBI/submissions/1) in 208.70213225399493 sec. 144649 classes."]
D, [2020-09-07T16:50:16.528838 #2539] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/CHEBI/submissions/1 in 3058.8s"]
I, [2020-09-07T16:50:16.544463 #2539]  INFO -- : ["Running ontologies report for ontologies CHEBI...\n"]
I, [2020-09-07T16:50:16.544525 #2539]  INFO -- : ["Processing report for CHEBI - 1 of 1 ontologies."]
I, [2020-09-07T16:50:17.648376 #2539]  INFO -- : ["Finished report for CHEBI in 1.103617781001958 sec."]
I, [2020-09-07T16:50:17.651608 #2539]  INFO -- : ["Finished updating report for ontologies CHEBI. Wrote report data to /srv/ontoportal/data/reports/ontologies_report.json.\n"]
I, [2020-09-07T18:54:17.684928 #8073]  INFO -- : ["Starting to process http://data.bioontology.org/ontologies/CHEBI/submissions/1"]
I, [2020-09-07T18:54:17.687380 #8073]  INFO -- : ["Starting to process CHEBI/submissions/1"]
I, [2020-09-07T18:54:17.727812 #8073]  INFO -- : ["Submission processing of http://data.bioontology.org/ontologies/CHEBI/submissions/1 completed successfully"]
I, [2020-09-07T18:54:17.821911 #8073]  INFO -- : [["Caching classes of CHEBI"]]
I, [2020-09-07T18:54:17.821944 #8073]  INFO -- : ["Caching classes of CHEBI"]
I, [2020-09-07T18:54:18.688614 #8073]  INFO -- : [["Page 1 of 58 - 2500 classes retrieved in 0.865643534 sec."]]
I, [2020-09-07T18:54:18.688640 #8073]  INFO -- : ["Page 1 of 58 - 2500 classes retrieved in 0.865643534 sec."]
I, [2020-09-07T18:54:20.256994 #8073]  INFO -- : [["Page 1 of 58 cached in Annotator in 1.568235775 sec."]]
I, [2020-09-07T18:54:20.257039 #8073]  INFO -- : ["Page 1 of 58 cached in Annotator in 1.568235775 sec."]
---snip---
I, [2020-09-07T18:56:23.914798 #8073]  INFO -- : [["Page 58 of 58 - 2149 classes retrieved in 0.669476044 sec."]]
I, [2020-09-07T18:56:23.914825 #8073]  INFO -- : ["Page 58 of 58 - 2149 classes retrieved in 0.669476044 sec."]
I, [2020-09-07T18:56:25.117156 #8073]  INFO -- : [["Page 58 of 58 cached in Annotator in 1.20218612 sec."]]
I, [2020-09-07T18:56:25.117186 #8073]  INFO -- : ["Page 58 of 58 cached in Annotator in 1.20218612 sec."]
I, [2020-09-07T18:56:25.224264 #8073]  INFO -- : [["Completed caching ontology: CHEBI (http://data.bioontology.org/ontologies/CHEBI/submissions/1) in 127.29543524500332 sec. 144649 classes."]]
I, [2020-09-07T18:56:25.224325 #8073]  INFO -- : ["Completed caching ontology: CHEBI (http://data.bioontology.org/ontologies/CHEBI/submissions/1) in 127.29543524500332 sec. 144649 classes."]
D, [2020-09-07T18:57:25.981082 #8073] DEBUG -- : ["Completed processing of http://data.bioontology.org/ontologies/CHEBI/submissions/1 in 188.47s"]
I, [2020-09-07T18:57:25.982870 #8073]  INFO -- : ["Running ontologies report for ontologies CHEBI...\n"]
I, [2020-09-07T18:57:25.982940 #8073]  INFO -- : ["Processing report for CHEBI - 1 of 1 ontologies."]
I, [2020-09-07T18:57:26.504996 #8073]  INFO -- : ["Finished report for CHEBI in 0.5218716039962601 sec."]
I, [2020-09-07T18:57:26.507349 #8073]  INFO -- : ["Finished updating report for ontologies CHEBI. Wrote report data to /srv/ontoportal/data/reports/ontologies_report.json.\n"]
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