BERVO - Biological and Environmental Research Variable Ontology

(Formerly the EcoSIM Ontology)

Browse

https://bioportal.bioontology.org/ontologies/BERVO (OLS coming soon)

Editing BERVO

The source of truth for BERVO is the repository on this branch.

Editors should update:

• src/ontology/bervo-src.csv for the ROBOT template that defines BERVO terms
• src/ontology/bervo-edit.owl for the ODK edit file that imports the generated component

All terms are preceded by the BERVO: prefix.

The Google Sheet is still available as a collaboration artifact:

https://docs.google.com/spreadsheets/d/1mS8VVtr-m24vZ7nQUtUbQrN8r-UBy3AwRzTfQsmwVL8/edit?usp=sharing

However, it is no longer the authoritative source for builds or pull requests. Changes should be proposed in this repository, ideally through a GitHub issue and pull request.

To rebuild the generated source component from the tracked CSV, run:

cd src/ontology
make components/bervo-src.owl

To prepare a CSV for uploading back into Google Sheets, run:

cd src/ontology
make export-google-sheet

Methods

See also this slide deck

Seeding of initial parameter list

chatgpt ADA was used to create a program to iterate through the bervo fortran codebase and generate an obo format file of all parameter codes plus their names.

IDs of the form BERVO:<CODE> were created

Note: in future these may be translated to numeric IDs but for now the codes are convenient

Generation of definitions

The OAK generate-definitions command was used to generate definitions for all terms

Generation of grouping classes

Each parameter was organized into a grouping class.

We used Claude due to the large context window. A csv of all CODE-label pairs were uploaded to Claude, Claude then suggested groupings for these. These were examined in text format, we then asked Claude to convert to OBO format.

Inferring linkages to other concepts

We curated a handful of OBO stanzas where we linked each parameter to other concepts.

This was loaded into a curategpt database, to serve as in-context examples.