mmusv: change TS to post-natal

[cmungall]

@tfhayamizu confirms:

We consider TS28 to mean postnatal, all the way through adulthood.

[ANiknejad]

Hi @cmungall currently in mmusdv.obo

[Term] id: MmusDv:0000092 name: postnatal stage namespace: mouse_developmental_stage def: "Mouse developmental stage that covers the period from birth until late adulthood." [Bgee:curator "Bgee"] xref: UBERON:0000066 is_a: MmusDv:0000000 ! mouse life cycle stage relationship: part_of MmusDv:0000001 ! mouse life cycle relationship: immediately_preceded_by MmusDv:0000042 ! prenatal stage property_value: start_dpc "19.0" xsd:float property_value: start_wpb "0.0" xsd:float

[Term] id: MmusDv:0000037 name: Theiler stage 28 namespace: mouse_developmental_stage def: "Postnatal development." [http://php.med.unsw.edu.au/embryology/index.php?title=Mouse_Stages#Theiler_Stage_28 "adapted from"] synonym: "TS28" RELATED [] xref: XUO:0000072 is_obsolete: true xref: EMAPA:TS28 ! TS28 (P0-Adult) consider: MmusDv:0000043 comment: This term was obsoleted as it is a broad term to describe the postnatal development, while in our ontology we use the immature stage preceding the mature stage to describe the postnatal development.

So we are correct, right? (sorry boring you) Anne

[tfhayamizu]

The GXD, as well EMAP/EMAGE and GUDMAP groups have given this a great deal of thought, specifically with respect to how the Theiler Stages can be used in a consistent standardized manner for the collection and integration of data by various resources.

Theiler makes a distinction between TS28, Postnatal Development, and TS27, Newborn Mouse. We consider "postnatal" to cover the period after the "newborn" stage and continuing to adulthood. Clearly this is somewhat problematic in that "newborn" has not been precisely defined.

Taking into account significant variation in the duration of gestation for different strains of mice, "birth" itself can occur over a range of embryonic ("post coitum") days. Thus, Theiler's description of "19 Days" has proved less that completely useful. Some mice are born prior to this time, and E19 and older mice may have not been born yet.

From extensive experience dealing with mouse data from a range of fields and data providers, we conclude there are many different views for what constitutes "newborn" as well. For practical purposes, we have adopted the convention of using TS26 for the period from embryonic day 18 up to birth itself. Furthermore, we decided to use TS27 for postnatal days 0 through 3. This is a somewhat arbitrary cut-off but seems to best fit the data we have encountered. TS28 is then used from postnatal day 4 onward.

Thus, different staging conventions are being used: MmusDv:00000035 - Theiler stage 26 - E18 (EMAPA/GXD/GUDMAP) TS 26 - E18 to birth MmusDv:0000036 - Theiler stage 27 (EMAPA) TS 27 - P0 to P3 - E19-20, P0 MmusDv:0000043 - immature stage (xref: EMAPA:TS28) MmusEv:0000044 - 1-7 days (EMAPA/GXD/GUDMAP) TS28 - P4 to adulthood

note: The GXD resource currently includes over 250K mouse gene expression results for the postnatal mice, including ~43K for the P0-P3 "newborn" period.

[cmungall]

Thanks!

@ANiknejad - do you want to make the necessary changes?

[ANiknejad]

Here a corrected version (mmusdv_correction.obo), could you please check/comments @cmungall @tfhayamizu

In summary:

• prenatal stage
• postpartum stage (new)
  • TS27 (P0-P3)
  • TS28 (P4 to adulthood) (='post-natal' but does not mean post-birth)
  • premature stage (new)
  • mature stage

[ANiknejad]

the ontology as is sounds to be accepted and is available here

https://raw.githubusercontent.com/obophenotype/developmental-stage-ontologies/master/src/mmusdv/mmusdv.obo