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[bioontology-support] Formula used by Bioportal Recommender to compute a Coverage

John Graybeal jbgmeta1 at stanford.edu
Tue Apr 26 19:45:06 PDT 2016


Hello Lamine,

Thanks for your question. I give a brief answer here about the Coverage score. In due course we expect to document other facets of the formula in a publication.

The total coverage score for each ontology is the sum of the annotation score for all the selected annotations (normalized to the range 0:1).

The selected annotations are those that are found by the Annotator, not including any overlapping annotations with lower or equal scores.

The annotation score for a single annotation multiples the number of annotated words in that annotation by a scale factor. The scale factor is higher for class preferred names (scale=10) than for class synonyms (scale=5), and higher still for multi-word annotations (add 6 to the previous scale). So, a 3-word annotation match to a preferred name of a class is worth 3 * (10+6) = 48.

John


On Apr 22, 2016, at 3:02 AM, Lamine Traore <laminet at gmail.com<mailto:laminet at gmail.com>> wrote:

Hi,

Apart from the following definition in Bioportal Help:

"Coverage<http://bioportal.bioontology.org/help#Recommender_Tab>: At what extent the ontology represents the input? The Recommender invokes the NCBO Annotator service to obtain all the annotations for the input and then uses those annotations to compute a coverage score for each ontology."

Do you have more information related to the formula used by Recommender to compute a coverage score for an ontology ?

Thanks in advance

--
Lamine TRAORE
Doctorant, PhD Candidate
INSERM U1142 - LIMICS<http://www.limics.fr/fr/accueil>
CNRS UMR7371 INSERM UMRS 1146 - LIB<https://www.lib.upmc.fr/>
Tel : +33 07 60 37 70 54



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========================
John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632
skype: graybealski


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