Bio-LarK

Bio-LarK CR is a Human Phenotype Ontology (HPO) concept recognition tool. It uses a two-step approach to index and retrieve HPO concepts, combined with a series of language techniques to enable term normalization. In addition to standard CR, Bio-LarK CR is able to decompose and align conjunctive terms, of the form 'short and broad fingers', as well as recognise and process non-canonical phenotypes - e.g., 'fingers are short and broad'.

Bio-LarK CR is available via a REST API at: http://bio-lark.org:8080/biolark/annotate

Input parameters:

• text - the text to be annotated.
• dataSource - currently only Human Phenotype Ontology is supported.
• Example: http://bio-lark.org:8080/biolark/annotate?text=The long bones are shortened, the metaphyses flared,
cupped and irregular but the density and structure of the bones is grossly normal.&dataSource=Human Phenotype Ontology

Response: A JSON-formatted list of concepts:

• dataSource - currently only Human Phenotype Ontology
• startOffset - absolute start index of the annotated text span.
• endOffset - absolute end index of the annotated text span.
• originalSpan - the actual text span being annotated.
• uri - the HPO concept assigned to the annotated text span.

The call listed above will result in the following reponse:

[
    {
        "dataSource": "Human Phenotype Ontology",
        "startOffset": "34",
        "endOffset": "51",
        "originalSpan": "metaphyses flared",
        "uri": "http://purl.obolibrary.org/obo/HP_0003015"
    },
    {
        "dataSource": "Human Phenotype Ontology",
        "startOffset": "4",
        "endOffset": "28",
        "originalSpan": "long bones shortened",
        "uri": "http://purl.obolibrary.org/obo/HP_0003026"
    },
    {
        "dataSource": "Human Phenotype Ontology",
        "startOffset": "143",
        "endOffset": "152",
        "originalSpan": "back pain",
        "uri": "http://purl.obolibrary.org/obo/HP_0003418"
    },
    {
        "dataSource": "Human Phenotype Ontology",
        "startOffset": "148",
        "endOffset": "152",
        "originalSpan": "pain",
        "uri": "http://purl.obolibrary.org/obo/HP_0012531"
    }
]