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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:
The following stage ontologies maintain their source in separate repositories:
- FBdv (Drosophila) - browse
- WBls (C elegans) - browse
- plants - see http://www.plantontology.org - browse
- Xenopus (stages are part of anatomy ontology XAO) browse
These stages are primarily used to connect anatomical structures to start/end stages
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:
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:
- http://purl.obolibrary.org/obo/uberon/subsets/life-stages-core.obo
- http://purl.obolibrary.org/obo/uberon/subsets/life-stages-core.owl
- http://purl.obolibrary.org/obo/uberon/subsets/life-stages-composite.obo (OWL available soon)
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:
See Timings
See Relations
- RCN presentation on stages in PO
- Osumi-Sutherland, et al. The Drosophila phenotype ontology. Journal of biomedical semantics 4.1 (2013): 30. (this paper describes use of FBdv to classify embryonic lethal phenotypes)