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Chris Mungall edited this page Apr 5, 2017 · 8 revisions
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This repository is for the collection of species-specific stage ontologies.

NOTE - some of the links below will not work until purls are registered

This repository is primarily for the developers of these ontologies. End-users should access these ontologies via their standard purls; for example:

You can see the full metadata and list of files on the OBO page for that ontology:

Or via dedicated web interfaces (e.g. ZFIN) or OntoBee (e.g. http://purl.obolibrary.org/obo/ZFS_0000044 )

Currently this repository is the source for the following stage ontologies:

  • MmusDv (mouse)
  • HsapDv (human)
  • OlatDv (medaka) (purl not yet registered)
  • ZFS (zebrafish) - Browse

The following stage ontologies maintain their source in separate repositories:

Uses of Staging Ontologies

These stages are primarily used to connect anatomical structures to start/end stages

Note on mammalian stage ontologies

Currently EMAPA and EHDAA2 uses stages without an explicit namespace (they follow the form TSnn or CSnn). These will be mapped to mmusdv and hsapdv.

We also provide a combined mammalian stage ontology that includes uberon core stages, mmusdv and hsapdv:

Multi-species stage ontologies

Uberon includes a generic staging ontology (building on work by BILA and Bgee)

Documentation: http://purl.obolibrary.org/obo/uberon/docs/Modeling-developmental-stages

Two versions are available here:

The core includes only high-level grouping classes (zygote stage, gastrula stage, embryonic stage, etc).

The composite version includes species-specific stages hanging off as leaf nodes from the generic stages. No attempt is made to map stages at a more granular level (e.g. between human Carnegie and mouse Theiler).

These ontologies are described here:

Guidelines for contributors of stage ontologies

See ContributorGuidelines

Recording Timing Information

See Timings

Stage Relations

See Relations

Papers and Presentations