RNCBO

Mapping ontology terms using NCBO recommender

eNanoMapper Developers | [eNanoMapper Project] (http://www.enanomapper.net/)

The script is using RCurl and rjson in order to map a list of words to ontology terms using the scores from [NCBO recommender] (http://bioportal.bioontology.org/recommender).

You should add your API KEY into the script in order obtain results!

The script flow:

Reading the terms to be mapped from input CSV file (one column) and a list of possible ontologies
Use of NCBO REST Recommender to obtain the list of ontologies (ordered by score, filtered for errors)
Use of NCBO REST Search to obtain detailed information about the mappings
CSV output with results for mapped terms: Term, Score, Acronym, Ontology, ID, Notation, Description, Synonyms
CSV list with non mapped terms

The R script is presented with examples of files for terms and possible ontologies. Please check the main R script.

Other example using different languages (Python, Java, bash, etc.): [https://github.com/ncbo/ncbo_rest_sample_code] (https://github.com/ncbo/ncbo_rest_sample_code). The recommender algorithm is presented into publication with [DOI: 10.1186/2041-1480-1-S1-S1] (http://www.ncbi.nlm.nih.gov/pubmed/20626921) (PMID: 20626921, PMCID: PMC2903720).

Thank you for the help of Marcos Martinez-Romero from University of Coruña, RNASA-IMEDIR group.

This version corresponds to the new NCBO APIs and it was updated by Manfred Kohler.

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