Our obo2json converter is written in Java and can be obtained from our GitHub repository.

In a digital bibliography, entries must have values for specific fields such as title, author and type. For Phenotero, each ontology class is defined as an “entry-dictionary” type, to better distinguish it from articles, books, etc. This reference-type is rarely used in biomedical articles and should hence not interfere with other Zotero capabilities. The ontology IDs are stored in the container-title field and the synonyms under author, as this field allows to have multiple entries per item. The exact mapping between OBO fields and JSON-format for Zotero is described in the following Table:

Bibliography field Value of ontology class Example value
type always “entry-dictionary” entry-dictionary
title primary label Abnormality of the kidney
container-title OBO-ID HP:0000077
id PURL http://purl.obolibrary.org/obo/HP_0000077
author List of synonyms and definition (one author per item) “renal anomaly”, “kidney disease”, “An abnormality of the kidney.”