Evolve development_stage_ontology_term_id to support multiple species

[brianraymor]

Per November 13 2024 call with @ambrosejcarr, @jahilton, @BAevermann, @SESDNA :

1. CELLxGENE schema will continue to use taxon specific development stage ontologies when available; otherwise, will default to UBERON.
2. STRONGLY RECOMMENDED development stage terms will be removed from the schema.

---

Available from developmental-stage-ontologies

prefix	namespace	format
acardv (AcarDv)	lizard	owl
btaudv (BtauDv)	cow	owl
cfamdv (CfamDv)	dog	owl
cpordv (CporDv)	cavy (Caviidae)	owl
danadv (DanaDv)	Drosophila ananassae	obo
dmojdv (DmojDv)	Drosophila mojavensis	obo
dpsedv (DpseDv)	Drosophila pseudobscura	obo
dsimdv (DsimDv)	Drosophila simulans	owl
dvirdv (DvirDv)	Drosophila virilis	obo
dyakdv (DyakDv)	Drosophila yakuba	obo
ecabdv (EcabDv)	Horse	owl
eeurdv (EeurDv)	Hedgehog	obo
fcatdv (FcatDv)	Cat	owl
ggaldv (GgalDv)	Chicken	owl
ggordv (GgorDv)	Gorilla	owl
mdomdv (MdomDv)	Opossum	owl
metadv	-	-
mmuldv (MmulDv)	Rhesus Macaque	owl
oanadv (OanaDv)	Platypus	owl
oaridv (OariDv)	Sheep	owl
ocundv (OcunDv)	Rabbit	owl
olatdv (OlatDv)	Medaka adapted from MFO by Thorsten Henrich	owl
pdumdv (PdumDv)	Platynereis	owl
ppandv (PpanDv)	Bonobo	owl
ppygdv (PpygDv)	Orangutan	obo
ptrodv (PtroDv)	Chimpanzee	owl
rnordv (RnorDv)	Rat	owl
ssaldv (SsalDv)	Atlantic Salmon	obo
sscrdv (SscrDv)	Pig	owl
tnigdv (TnigDv)	Pufferfish	obo not in release

[BAevermann]

For cases where there is a species specific development stages ontology, why not consider there usage as "REQUIRED"? I am specifically thinking about human and mouse as the terms in UBERON are clear downgrade as compared to the curation currently available.

[brianraymor]

We depend on the kindness of curators to define the most accurate development stage terms. For example, the schema only requires

If organism_ontolology_term_id is "NCBITaxon:9606" for Homo sapiens, this MUST be the most accurate descendant of HsapDv:0000001 for life cycle with the following STRONGLY RECOMMENDED: ... followed by a list of HsapDv terms.

There's nothing preventing a submitter from selecting a high-level HsapDv term such as embyronic stage.

Further, the development stage ontologies duplicate the UBERON high-level hierarchical terms for stages such as blastula stage. For example, HsapDv vs UBERON.

The schema could certainly define tables per species with REQUIRED and STRONGLY RECOMMENDED UBERON and species specific ontology terms.

For	Use
UBERON stage	A term from the set of Carnegie stages 1-23 (up to 8 weeks after conception; e.g. HsapDv:0000003)
UBERON stage	A term from the set of 9 to 38 week post-fertilization human stages (9 weeks after conception and before birth; e.g. HsapDv:0000046)

If @jahilton and @jychien believe that we could strengthen the requirements for development stages to block high-level stages, then that's another possibility - MUST USE A term from the set of Carnegie stages 1-23

Currently, we're in the middle of the multiple species and relaxed schema experiment - but if multiple species begin to surface in the CELLxGENE Discover UX, then I'd expect that @niknak33 and @hthomas-czi may prefer to simplify the Development Stages UX Filter to be species neutral and rely more on the UBERON terms. The current design was based on constraints that are no longer valid.

[jahilton]

I would support requiring the species-specific Dv ontology to be used, like we currently do for human & mouse, "For cases where species specific development stages ontologies...exist". I don't see any reason to allow an UBERON term in those cases.