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:
- namespace.obo (for instance, hsapdv.obo): the source ontology file in OBO format
- in this ontology, each term has an ID corresponding to the namespace.
- Terms that are mappable to Uberon terms present in life-stages-minimal.obo have an xref to the corresponding Uberon term.
- namespace-bridge-params.tsv (for instance, hsapdv-bridge-params.tsv): a file with one row and two columns separated by a tab, where the first column contains the species common name (for instance, "human"), and the second column contains the NCBI Taxon ID (for instance, "NCBITaxon:9606")
For each of this directory, the Makefile will generate several downstream files:
- namespace.owl (for instance, hsapdv.owl): the source ontology in OWL format
- namespace-bridge-to-uberon.obo (for instance, hsapdv-bridge-to-uberon.obo): a bridge file allowing to merge the species-specific ontology within the structure of life-stages-minimal.obo. For ontologies developed as part of this project, this bridge is automatically produced using the xrefs in the source ontology, while for external ontologies this bridge is generated probably manually.
- namespace-uberon.obo (for instance, hsapdv-uberon.obo): the species-specific ontology merged within the structure of life-stages-minimal.obo.
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:
- src/external_ontologies/fbdv/ for Drosophila melanogaster
- src/external_ontologies/wbls/ for C. elegans
- src/external_ontologies/xao/ for Xenopus
- src/external_ontologies/zfs/ for zebrafish
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:
- ssso-merged.obo: it is the union of all the unmerged species-specific ontologies and of life-stages-minimal.obo
- ssso-merged-uberon.obo: it is the merge of the merged species-specific ontologies within the structure of life-stages-minimal.obo