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.” |