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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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Suggested xrefs (or new terms) to add #439

Closed fbastian closed 10 years ago

fbastian commented 10 years ago

While tracking the "future" terms used in vHOG to detect missing transformation_of relations (see #438), we identified some xrefs that could be added to terms corresponding to fully-formed structures, or that could correspond to missing "future" structures (although I'm not a fan of such structures, the choice is up to you). From @ANiknejad. Note that this is not required for the next release of Bgee, we report only for completeness.

EHDAA:2211 primitive trachea from VHOG:0000371 (trachea), xref of UBERON:0003126 trachea

EHDAA:3408 primitive pericardium from VHOG:0001280, xref of UBERON:0002407 pericardium

EMAPA:19177 primitive Sertoli cells from VHOG:0001348, xref of CL:0000216 Sertoli cell

EHDAA:280 primitive allantois from VHOG:0000738, xref of UBERON:0004340 allantois

EMAPA:18330 primitive seminiferous tubules from VHOG:0001363, xref of UBERON:0001343 seminiferous tubule of testis (note that EMAPA:18685 (primitive seminiferous tubules) is xref of UBERON:0001343)

EHDAA:6997 primitive ureter EHDAA:8089 primitive ureter from VHOG:0000605, xref of UBERON:0000056 ureter

EHDAA:5011 primitive pelvis of ureter EHDAA:8087 primitive pelvis of ureter from VHOG:0000945, xref of UBERON:0005249 metanephric renal pelvis

EHDAA:6401 primitive aortic arch from VHOG:0001196, xref of UBERON:0001508 arch of aorta

EHDAA:10439 primitive nephrons from VHOG:0000719 (metanephric nephron), xref of UBERON:0005110 metanephric nephron

EHDAA:4741 primitive cornea from VHOG:0000164, xref of UBERON:0000964 But: UBERON:0000964 develops_from UBERON:0005427 ! corneal primordium => Should EHDAA:4741 (primitive cornea) be xref of UBERON:0005427 corneal primordium ?

EHDAA:1003 future respiratory system from VHOG:0000202, xref of UBERON:0001004

EHDAA:4318 future basilar artery from VHOG:0000237, xref of UBERON:0001633

EHDAA:6938 future pars anterior from VHOG:0000244, xref of UBERON:0006964

cmungall commented 10 years ago

Thx!

EHDAA

I'm thinking of archiving the EHDAA xrefs - superseded by EHDAA2 the only data annotated to EHDAA is older Bgee releases.

EMAPA, gross anatomy

Where did this come from? EMAPA:18330 primitive seminiferous tubules

There used to be multiple copies of EMAPA floating around - there is now a canonical publication version, it has no record of any EMAPA:18330 (but may well have been in a previous version used by Bgee for annotation).

I suggest I mark them both as xrefs for now for data migration purposes?

Ideally EMAPA would include a record of historic IDs, either as alt_ids or obsoleted terms (with consider/replaced by links). cc @thayamizu

EMAPA, cell type

There is only a handful of these. I suggest that we put these in CL. However, primitive sertoli cell would not be an exact equiv - I think we add a new class for the progenitor. @dosumis @mellybelly

fbastian commented 10 years ago

EHDAA

No problem for archiving them, we have already transfered our human annotations.

EMAPA

Indeed we used a different version, from Aitken: http://www.aiai.ed.ac.uk/resources/bioinf/context-plus-mouse.obo Yes please, keep both xrefs, I still have a few annotations to transfer for mouse.

cmungall commented 10 years ago

Can we mark this as done?

For EMAPA we use the dev version from @obophenotype/mouse-anatomy-ontology which is up to date and is xreffed from MA. A recent push should snure this is up to date.

fbastian commented 10 years ago

Not 100% sure, but I think it is safe to close this.