NAME
    similarity_match.pl

SYNOPSIS
    Compares a list of annotations to another ontology and suggests the best
    match based on some similarity metric (Levenshtein distance). It is also
    possible to align one ontology to another. Accepts ontologies in both
    OBO and OWL formats as well as MeSH ASCII.

    The script runs non-interactively and the results have to be manually
    inspected, although it can be expected that anything with a similarity
    score higher than ~80-90% will be a valid match.

USAGE
    similarity_match.pl (-w owlfile || -o obofile || -m meshfile) -t
    targetfile -r resultfile [--obotarget || --owltarget]

    Optional '--obotarget' setting specifies that the target file is an OBO
    ontology. Optional '--owltarget' setting specifies that the target file
    is an OWL ontology.

  INPUT FILES
    ontologies to map the targetfile against
        owlfile, obofile, meshfile are ontologies in OWL, OBO and MeSH ASCII
        formats. Only a single file needs to be specified.

    targetfile
        The script expects a single column text file with no headears.

  OUTPUT
    The script will produce a single tab-delimited file as set with the -r
    flag. The file will have four headers:

    ID  Accession of the term from the targetfile if the file was an
        ontology, otherwise OE_VALUE repeated.

    OE_VALUE
        Annotation from the supplied targetfile or a term label if the file
        was an ontology.

    ONTOLOGY_TERM
        Term label that was matched based on the highest similarity from the
        supplied onotlogy file.

    ACCESSION
        Accession of the ontology term that provided the best match.

    SIMILARITY%
        Similarity score of ONTOLOGY_TERM compared to OE_VALUE. This is the
        Levenshtein distance normalised by OE_VALUE length expressed in %.
        Higher is better.

AUTHORS
    Tomasz Adamusiak 2010

