This repository hosts developmental stage ontologies developed for many animal species, as well as a merge of all these ontologies into the structure of Uberon. This notably includes hsapdv.obo for human, and mmusdv.obo for mouse.
For documentation about development of developmental stage ontologies, see https://github.com/obophenotype/developmental-stage-ontologies/wiki
life-stages-minimal.obo is the core structure of developmental stages in Uberon. It is in this structure that all species-specific developmental stage ontologies will be merged.
All species-specific developmental stage ontologies developed as part of this project are present in the src folder, each in a subdirectory. The nomenclature for naming these ontologies is: first letter of genus name + three first letters of species name + 'dv' suffix. For example, for Homo sapiens, the corresponding namespace is hsapdv, and files related to this ontology are present in src/hsapdv/.
In each species-specific ontology folder, there are two files used to generate the necessary downstream files:
For each of this directory, the Makefile will generate several downstream files:
Some ontologies are not developed as part of this project, but are merged within Uberon nevertheless. The necessary files are present in src/external_ontologies/, with one subdirectory for each ontology:
In each subdirectory, a bridge file is provided (for instance, uberon-bridge-to-zfs.obo), allowing the merge into the structure of life-stages-minimal.obo.
Note: in some cases, an adaptation of this bridge file has been necessary and is provided as uberon-bridge-to-xxx-modified.obo ((for instance, uberon-bridge-to-zfs-modified.obo)
In each subdirectory, the Makefile allows to generate the merge of the original ontology and of life-stages-minimal.obo.
Once a merged ontology has been generated for each species, the Makefile allows to produced merges of all of them: