HsapDv:0000005 Carnegie stage 02 and HsapDv:0000004 cleavage stage

[fbastian]

Can these two be merged? HsapDv:0000005 is the only child of HsapDv:0000004

[ANiknejad]

@fbastian

yes, we could, but which one to conserve?

currently Uberon displays:

[Term] id: HsapDv:0000005 name: Carnegie stage 02 (human) name: CS02 namespace: human_developmental_stage def: "Embryonic stage during which cell division occurs with reduction in cytoplasmic volume, and formation of inner and outer cell mass." [http://embryology.med.unsw.edu.au/embryology/index.php?title=Carnegie_stage_table] comment: Usually starts between day 2 and day 3 post-fertilization. synonym: "CS02" EXACT [EHDAA2:CS02] xref: EHDAA2:CS02 xref: FMA:295884 xref: XUO:0000131 is_a: CS:0 ! Carnegie stage is_a: UBERON:0000067 ! embryo stage part relationship: only_in_taxon NCBITaxon:9606 ! Homo sapiens relationship: part_of UBERON:0000107 ! cleavage stage property_value: IAO:0000589 "Carnegie stage 02 (human)" xsd:string property_value: start_dpf "2.5" xsd:float

and HsapDv:0000004 cleavage stage does not appear in Uberon, neither as a class nor a xref

So maybe we only have to obsolete HsapDv:0000004 cleavage stage in hsapdv.obo ?

This means, we then have to do the following changes below, do you agree?

[Term] id: HsapDv:0000005 name: Carnegie stage 02 namespace: human_developmental_stage def: "Embryonic stage during which cell division occurs with reduction in cytoplasmic volume, and formation of inner and outer cell mass." [http://embryology.med.unsw.edu.au/embryology/index.php?title=Carnegie_stage_table "adapted from"] comment: Usually starts between day 2 and day 3 post-fertilization. is_a: HsapDv:0000000 ! human life cycle stage relationship: part_of HsapDv:0000004 ! cleavage stage xref: XUO:0000131 relationship: preceded_by HsapDv:0000003 ! Carnegie stage 01 xref: EHDAA2:CS02 ! CS02 synonym: "CS02" EXACT [EHDAA2:CS02] property_value: start_dpf "2.5" xsd:float xref: FMA:295884 ! carnegie stage 2

by

[Term] id: HsapDv:0000005 name: Carnegie stage 02 namespace: human_developmental_stage def: "Embryonic stage during which cell division occurs with reduction in cytoplasmic volume, and formation of inner and outer cell mass." [http://embryology.med.unsw.edu.au/embryology/index.php?title=Carnegie_stage_table "adapted from"] comment: Usually starts between day 2 and day 3 post-fertilization. is_a: HsapDv:0000000 ! human life cycle stage xref: UBERON:0000107 xref: XUO:0000131 relationship: preceded_by HsapDv:0000003 ! Carnegie stage 01 xref: EHDAA2:CS02 ! CS02 synonym: "CS02" EXACT [EHDAA2:CS02] property_value: start_dpf "2.5" xsd:float xref: FMA:295884 ! carnegie stage 2

Means also to change: (remove a line into:)

[Term] id: HsapDv:0000205 name: morula stage namespace: human_developmental_stage def: "The morula stage is the later part of Carnegie stage 02 when the cells have coalesced into a mass but the blastocystic cavity has not formed. Formation of the cavity marks the beginning of Carnegie stage 03." [Bgee:curator "adapted from DrJohnCork"] is_a: HsapDv:0000000 ! human life cycle stage relationship: part_of HsapDv:0000005 ! Carnegie stage 02 relationship: immediately_preceded_by HsapDv:0000004 ! cleavage stage

by

[Term] id: HsapDv:0000205 name: morula stage namespace: human_developmental_stage def: "The morula stage is the later part of Carnegie stage 02 when the cells have coalesced into a mass but the blastocystic cavity has not formed. Formation of the cavity marks the beginning of Carnegie stage 03." [Bgee:curator "adapted from DrJohnCork"] is_a: HsapDv:0000000 ! human life cycle stage relationship: part_of HsapDv:0000005 ! Carnegie stage 02

[ANiknejad]

Merge and changes DONE in hsapdv_4_hpoOxford.obo (local file)

[ANiknejad]

closed because commited on /develop branch now