Develop a BioPortal endpoint to retrieve all ontologies (remove ontologies cache in CEDAR)

[marcosmro]

Each ontology should include: id (acronym), name, isFlat?, description, number of classes, number of properties.

This task was originally part of metadatacenter/cedar-terminology-server#28

[mdorf]

Adding an endpoint /ontologies_full, which will have the following structure:

[{
    "ontology": {
        "administeredBy": [
            "http://localhost:9393/users/linikujp",
            "http://localhost:9393/users/yongqunh%40med.umich.edu"
        ],
        "acronym": "ICO",
        "name": "Informed Consent Ontology",
        "summaryOnly": null,
        "flat": null,
        "ontologyType": "http://localhost:9393/ontology_types/ONTOLOGY",
        "@id": "http://localhost:9393/ontologies/ICO",
        "@type": "http://data.bioontology.org/metadata/Ontology"
    },
    "latest_submission": {
        "contact": [ ],
        "ontology": null,
        "hasOntologyLanguage": "OWL",
        "released": "2017-05-11T18:04:40-07:00",
        "creationDate": "2017-05-11T18:04:40-07:00",
        "homepage": "https://github.com/ICO-ontology",
        "publication": null,
        "documentation": "https://github.com/ICO-ontology",
        "version": "Arbor version; 1.0.72",
        "description": null,
        "status": null,
        "submissionId": 11,
        "@id": "http://localhost:9393/ontologies/ICO/submissions/11",
        "@type": "http://data.bioontology.org/metadata/OntologySubmission"
    },
    "metrics": null
},
{
    "ontology": {
        "administeredBy": [
            "http://localhost:9393/users/pjd"
        ],
        "acronym": "GEOSPECIES",
        "name": "GeoSpecies Ontology",
        "summaryOnly": false,
        "flat": false,
        "ontologyType": "http://localhost:9393/ontology_types/ONTOLOGY",
        "@id": "http://localhost:9393/ontologies/GEOSPECIES",
        "@type": "http://data.bioontology.org/metadata/Ontology"
    },
    "latest_submission": {
        "contact": [
            {
                "id": "http://localhost:9393/contacts/e88c2f70-0300-0131-abbd-001ec9b0ea92",
                "name": "Peter J. DeVries",
                "email": "pdevries@wisc.edu"
            }
        ],
        "ontology": null,
        "hasOntologyLanguage": "OWL",
        "released": "2012-10-02T00:00:00+00:00",
        "creationDate": "2017-12-13T13:51:09-08:00",
        "homepage": "http://lod.geospecies.org/",
        "publication": "http://about.geospecies.org/",
        "documentation": "http://lod.geospecies.org/ontology/doc/index.html",
        "version": "2012-10-02",
        "description": "This ontology was designed to help integrate species concepts with species occurrences, gene sequences, images, references and geographical information. See also Taxonconcept.org",
        "status": "alpha",
        "submissionId": 2,
        "@id": "http://localhost:9393/ontologies/GEOSPECIES/submissions/2",
        "@type": "http://data.bioontology.org/metadata/OntologySubmission"
    },
    "metrics": {
        "id": "http://localhost:9393/ontologies/GEOSPECIES/submissions/2/metrics",
        "created": "2017-12-13T13:53:36-08:00",
        "classes": 86,
        "individuals": 204,
        "properties": 116,
        "maxDepth": 3,
        "maxChildCount": 18,
        "averageChildCount": 5,
        "classesWithOneChild": 2,
        "classesWithMoreThan25Children": 0,
        "classesWithNoDefinition": 82,
        "submission": [
            "http://localhost:9393/ontologies/GEOSPECIES/submissions/2"
        ],
        "@id": "http://localhost:9393/ontologies/GEOSPECIES/submissions/2/metrics",
        "@type": "http://data.bioontology.org/metadata/Metrics"
    }
}]

The call to reproduce this output would be:

http://data.bioontology.org/ontologies_full?include_links=false&include_context=false