Developmental stage ontologies

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.

Ontology development

For documentation about development of developmental stage ontologies, see https://github.com/obophenotype/developmental-stage-ontologies/wiki

life-stages-minimal

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.

Species-specific developmental stage ontologies

Namespaces

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/.

Source files

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")

Generated files

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.

External ontologies

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

Source files

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)

Generated files

In each subdirectory, the Makefile allows to generate the merge of the original ontology and of life-stages-minimal.obo.

Merge process

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