Text Mining Schema

The results of the text mining will be wrapped in a container (Annotation Set). While the Annotation Set was one of the key elements of Annotation Ontology, it has not been standardized in any form in Open Annotation yet. Therefore, until the OA standard will not include the notion of set we are going to group the annotation in an Annotation Ontology wrapper for now:

Note that in this document we are using both the oa (Open Annotation) and the ao (Annotation Ontology) prefixes. Be extra careful.

  {
    "@id": "urn:annotopia:annotationset:uuid:FE213280-EA6E-46D5-804C-40527C89935B",
    "@type": "ao:AnnotationSet",
    // Label and descriptions for human/software consumption
    "rdfs:label": "",
    "rdfs:comment": "",
    // Detailed provenance
    "pav:importedFrom": "---text mining provider---",
    "pav:importedBy": "urn:annotopia:software:service:<ConnectorServiceName>:<Version>",
    "pav:importedOn": "2014-01-17 13:33:56 -0500",
    // Annotations
    "ao:item": [
        // Annotations in Open Annotation format
    ]
  }

Additional information can be provided in the same document so that the clients will have enough information to perform the basic taks without requiring for multiple calls to the back-end.

In particular:

    "annotopia:agents": [
        // Basic description of the agents involved in the transacion
        // These are mostly FOAF/PROV entities
    ],
    "annotopia:resources": [
        // Basic description of the resources involved in the transaction
    ]

  {
    "co:element": [
        {
            "oa:hasBody": {
                "@type": "oa:SemanticTag",
                "@id": "http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#sao1143333050"
            },
            "oa:hasTarget": {
                "@type": "oa:SpecificResource",
                "oa:hasSelector": {
                    "oa:suffix": "+protein+accumulation+is+not+good+for+humans.",
                    "oa:prefix": "",
                    "@type": "oa:TextQuoteSelector",
                    "@id": "urn:domeo:selector:uuid:470AE24F-CB3B-4FC4-96C6-269FEB975BA3",
                    "oa:exact": "APP",
                    "pav:createdOn": "2014-08-27 14:57:06 -0400"
                },
                "@id": "urn:domeo:specificresource:uuid:9D88B4BF-D96C-459D-BBF8-D71CD0CFB252",
                "oa:hasSource": "urn:domeo:contentsnippet:uuid:FB8DE577-4D80-4F65-9AD4-D8D03A8B0AD6"
            },
            "@type": "oa:Annotation",
            "@id": "urn:domeo:annotation:uuid:468FE80E-FDA3-4668-8B91-7E06B3C7C4DC"
        },
        {
            "oa:hasBody": {
                "@type": "oa:SemanticTag",
                "@id": "http://purl.obolibrary.org/obo/PR_000004168"
            },
            "oa:hasTarget": {
                "@type": "oa:SpecificResource",
                "oa:hasSelector": {
                    "oa:suffix": "+protein+accumulation+is+not+good+for+humans.",
                    "oa:prefix": "",
                    "@type": "oa:TextQuoteSelector",
                    "@id": "urn:domeo:selector:uuid:24A3F3E9-9EEC-4072-AF2B-527BB0D41C65",
                    "oa:exact": "APP",
                    "pav:createdOn": "2014-08-27 14:57:06 -0400"
                },
                "@id": "urn:domeo:specificresource:uuid:C8542F57-AC45-49C1-9F54-31070F8E4C61",
                "oa:hasSource": "urn:domeo:contentsnippet:uuid:FB8DE577-4D80-4F65-9AD4-D8D03A8B0AD6"
            },
            "@type": "oa:Annotation",
            "@id": "urn:domeo:annotation:uuid:E1AD7836-835D-4F7F-AAE0-C1A486BBCC07"
        }
    ],
    "ao:onResource": "urn:domeo:contentsnippet:uuid:FB8DE577-4D80-4F65-9AD4-D8D03A8B0AD6",
    "rdfs:label": "NCBO Annotator Results",
    "pav:importedOn": "2014-08-27 14:57:06 -0400",
    "dct:description": "NCBO Annotator Results",
    "@type": "ao:AnnotationSet",
    "pav:importedBy": "urn:domeo:software:service:ConnectorBioPortalService:0.1-001",
    "domeo:resource": [
        {
            "@type": "cnt:ContentAsText",
            "@id": "urn:domeo:contentsnippet:uuid:FB8DE577-4D80-4F65-9AD4-D8D03A8B0AD6",
            "cnt:chars": "APP+protein+accumulation+is+not+good+for+humans.",
            "pav:derivedFrom": "http://paolociccarese.info"
        }
    ],
    "domeo:agent": [
        {
            "rdfs:label": "BioPortalConnector",
            "@type": "foafx:Software",
            "foaf:name": "BioPortalConnector",
            "@id": "urn:domeo:software:service:ConnectorBioPortalService:0.1-001",
            "pav:version": "0.1 b001"
        },
        {
            "rdfs:label": "NCBO Annotator Web Service",
            "@type": "foafx:Software",
            "foaf:name": "NCBO Annotator Web Service",
            "@id": "http://www.bioontology.org/wiki/index.php/Annotator_Web_service",
            "pav:version": "1.0"
        }
    ],
    "@id": "urn:domeo:annotationset:uuid:1695EDCF-9B4B-4E99-8EFD-962C9200CC46",
    "pav:importedFrom": "http://www.bioontology.org/wiki/index.php/Annotator_Web_service"
    }