a few xrefs that might need updating #1150

Closed
CatherineLeroy opened this Issue Sep 22, 2015 · 2 comments

Comments

Projects
None yet
2 participants
@CatherineLeroy

Hello,
Me again.
Still working on updating the cross reference in EFO ontology, I had a look through a tiny part of you terms (285).
I have put a list of changes I would suggest below. However, I might not have them all right. Let me know if you agree on some of them.

http://purl.obolibrary.org/obo/UBERON_0001772 corneal epithelium SNOMEDCT:15775008(Structure of corneal epithelium) to be replaced by SNOMEDCT:368825001(All corneal epithelium)

http://purl.obolibrary.org/obo/UBERON_0001621 uterine cervix SNOMEDCT:245494008(Entire cervical canal) to be replaced by SNOMEDCT:181453009 (Entire cervix uteri)

http://purl.obolibrary.org/obo/UBERON_0001691 external ear SNOMEDCT:181176000(COULD NOT FIND IT IN BIOPORTAL) to be replaced by SNOMEDCT:420893000(Entire external ear)

http://purl.obolibrary.org/obo/UBERON_0001870 frontal cortex SNOMEDCT:180920004(Entire frontal lobe) to be replaced by SNOMEDCT:314140006(Region of frontal cortex)

http://purl.obolibrary.org/obo/UBERON_0003894 liver primordium NCI_Thesaurus:Hepatic_Cord,NCI_Thesaurus:Primordium_of_the_Liver to be replaced by NCIt:C34277(Primordium of the Liver)
http://purl.obolibrary.org/obo/UBERON_0002028 hindbrain could add : SNOMEDCT/303456008 (Hindbrain structure)

http://purl.obolibrary.org/obo/UBERON_0000079 male reproductive system NCI_Thesaurus:Male_Genitalia,NCI_Thesaurus:Male_Reproductive_System to be replaced by NCIt:C12722(Male Reproductive System)

http://purl.obolibrary.org/obo/UBERON_0002374 metacarpal bone SNOMEDCT:425761003(Entire metacarpal of finger) to be replaced by SNOMEDCT:181977005(Entire metacarpal)

http://purl.obolibrary.org/obo/UBERON_0001211 Peyer's patch NCI_Thesaurus:Mouse_Peyer_s_Patches,NCI_Thesaurus:Peyer_s_Patch to be replaced by NCIt:C12771(Peyer Patch)
http://purl.obolibrary.org/obo/UBERON_0000004 remove EFO:0000828 which is now obsolete

http://purl.obolibrary.org/obo/UBERON_0001890 forebrain NCI_Thesaurus:Prosencephalon,NCI_Thesaurus:Fore-Brain to be replaced by NCIt:C40185(Forebrain)

http://purl.obolibrary.org/obo/UBERON_0002372 tonsil NCI_Thesaurus:Tonsilar_Tissue,NCI_Thesaurus:Tonsillar_Lymphoid_Tissue,NCI_Thesaurus:Tonsil to be replaced by NCIt:C12802(tonsil)

http://purl.obolibrary.org/obo/UBERON_0006860 swim bladder SNOMEDCT:64748009(not found in bioportal), so I would just drop this xref.

Thanks in advance for your time!
Catherine Leroy
cleroy@ebi.ac.uk

@cmungall cmungall closed this in 4f88546 Sep 22, 2015

@cmungall

This comment has been minimized.

Show comment
Hide comment
@cmungall

cmungall Sep 22, 2015

Member

http://purl.obolibrary.org/obo/UBERON_0001772 corneal epithelium SNOMEDCT:15775008 ! Structure of corneal epithelium to be replaced by SNOMEDCT:368825001 ! All corneal epithelium

Done, thanks!

http://purl.obolibrary.org/obo/UBERON_0001621 uterine cervix SNOMEDCT:245494008 ! Entire cervical canal to be replaced by SNOMEDCT:181453009 ! Entire cervix uteri

Done!

http://purl.obolibrary.org/obo/UBERON_0001691 external ear SNOMEDCT:181176000 ! COULD NOT FIND IT IN BIOPORTAL to be replaced by SNOMEDCT:420893000 ! Entire external ear

Ah yes, I see, marked as deprecated here:
http://www.snomedbrowser.com/Codes/Details/181176000 DEPRECATED

With the replacement you suggest

http://purl.obolibrary.org/obo/UBERON_0001870 frontal cortex SNOMEDCT:180920004 ! Entire frontal lobe to be replaced by SNOMEDCT:314140006 ! Region of frontal cortex

Hmm, a valid concept here:

http://www.snomedbrowser.com/Codes/Details/180920004

I really have no idea how term versioning works with SNOMED, and which version is where

It would be great to see a decent SNOMED browser in the new OLS but that may prove difficult with their annoying licensing

http://purl.obolibrary.org/obo/UBERON_0003894 liver primordium NCI_Thesaurus:Hepatic_Cord,NCI_Thesaurus:Primordium_of_the_Liver to be replaced by NCIt:C34277 ! Primordium of the Liver

Done!

http://purl.obolibrary.org/obo/UBERON_0002028 hindbrain could add : SNOMEDCT/303456008 ! Hindbrain structure

Done!

Odd that SNOMED doesn't have an E for this. Ah, gotta love the SEP pattern

http://purl.obolibrary.org/obo/UBERON_0000079 male reproductive system NCI_Thesaurus:Male_Genitalia,NCI_Thesaurus:Male_Reproductive_System to be replaced by NCIt:C12722 ! Male Reproductive System

Done!

http://purl.obolibrary.org/obo/UBERON_0002374 metacarpal bone SNOMEDCT:425761003 ! Entire metacarpal of finger to be replaced by SNOMEDCT:181977005 ! Entire metacarpal

I prefer to keep both and implicitly merge the concepts.

i.e. keep

xref: SCTID:181977005 ! Entire metacarpal
xref: SCTID:425761003 ! Entire metacarpal of finger

This must be a mistake in SCTID:
http://www.snomedbrowser.com/Codes/Details/181977005

all metacarpals are finger-associated. Maybe the more general one is intendend to be metapodium?

http://purl.obolibrary.org/obo/UBERON_0001211 Peyer's patch NCI_Thesaurus:Mouse_Peyer_s_Patches,NCI_Thesaurus:Peyer_s_Patch to be replaced by NCIt:C12771 ! Peyer Patch

Done!

http://purl.obolibrary.org/obo/UBERON_0000004 remove EFO:0000828 which is now obsolete

Done!

What, EFO has no nose? How does it smell?

http://purl.obolibrary.org/obo/UBERON_0001890 forebrain NCI_Thesaurus:Prosencephalon,NCI_Thesaurus:Fore-Brain to be replaced by NCIt:C40185 ! Forebrain

Done!

http://purl.obolibrary.org/obo/UBERON_0002372 tonsil NCI_Thesaurus:Tonsilar_Tissue,NCI_Thesaurus:Tonsillar_Lymphoid_Tissue,NCI_Thesaurus:Tonsil to be replaced by NCIt:C12802 ! tonsil

Done!

Member

cmungall commented Sep 22, 2015

http://purl.obolibrary.org/obo/UBERON_0001772 corneal epithelium SNOMEDCT:15775008 ! Structure of corneal epithelium to be replaced by SNOMEDCT:368825001 ! All corneal epithelium

Done, thanks!

http://purl.obolibrary.org/obo/UBERON_0001621 uterine cervix SNOMEDCT:245494008 ! Entire cervical canal to be replaced by SNOMEDCT:181453009 ! Entire cervix uteri

Done!

http://purl.obolibrary.org/obo/UBERON_0001691 external ear SNOMEDCT:181176000 ! COULD NOT FIND IT IN BIOPORTAL to be replaced by SNOMEDCT:420893000 ! Entire external ear

Ah yes, I see, marked as deprecated here:
http://www.snomedbrowser.com/Codes/Details/181176000 DEPRECATED

With the replacement you suggest

http://purl.obolibrary.org/obo/UBERON_0001870 frontal cortex SNOMEDCT:180920004 ! Entire frontal lobe to be replaced by SNOMEDCT:314140006 ! Region of frontal cortex

Hmm, a valid concept here:

http://www.snomedbrowser.com/Codes/Details/180920004

I really have no idea how term versioning works with SNOMED, and which version is where

It would be great to see a decent SNOMED browser in the new OLS but that may prove difficult with their annoying licensing

http://purl.obolibrary.org/obo/UBERON_0003894 liver primordium NCI_Thesaurus:Hepatic_Cord,NCI_Thesaurus:Primordium_of_the_Liver to be replaced by NCIt:C34277 ! Primordium of the Liver

Done!

http://purl.obolibrary.org/obo/UBERON_0002028 hindbrain could add : SNOMEDCT/303456008 ! Hindbrain structure

Done!

Odd that SNOMED doesn't have an E for this. Ah, gotta love the SEP pattern

http://purl.obolibrary.org/obo/UBERON_0000079 male reproductive system NCI_Thesaurus:Male_Genitalia,NCI_Thesaurus:Male_Reproductive_System to be replaced by NCIt:C12722 ! Male Reproductive System

Done!

http://purl.obolibrary.org/obo/UBERON_0002374 metacarpal bone SNOMEDCT:425761003 ! Entire metacarpal of finger to be replaced by SNOMEDCT:181977005 ! Entire metacarpal

I prefer to keep both and implicitly merge the concepts.

i.e. keep

xref: SCTID:181977005 ! Entire metacarpal
xref: SCTID:425761003 ! Entire metacarpal of finger

This must be a mistake in SCTID:
http://www.snomedbrowser.com/Codes/Details/181977005

all metacarpals are finger-associated. Maybe the more general one is intendend to be metapodium?

http://purl.obolibrary.org/obo/UBERON_0001211 Peyer's patch NCI_Thesaurus:Mouse_Peyer_s_Patches,NCI_Thesaurus:Peyer_s_Patch to be replaced by NCIt:C12771 ! Peyer Patch

Done!

http://purl.obolibrary.org/obo/UBERON_0000004 remove EFO:0000828 which is now obsolete

Done!

What, EFO has no nose? How does it smell?

http://purl.obolibrary.org/obo/UBERON_0001890 forebrain NCI_Thesaurus:Prosencephalon,NCI_Thesaurus:Fore-Brain to be replaced by NCIt:C40185 ! Forebrain

Done!

http://purl.obolibrary.org/obo/UBERON_0002372 tonsil NCI_Thesaurus:Tonsilar_Tissue,NCI_Thesaurus:Tonsillar_Lymphoid_Tissue,NCI_Thesaurus:Tonsil to be replaced by NCIt:C12802 ! tonsil

Done!

@CatherineLeroy

This comment has been minimized.

Show comment
Hide comment
@CatherineLeroy

CatherineLeroy Sep 23, 2015

I really have no idea how term versioning works with SNOMED, and which version is where

It would be great to see a decent SNOMED browser in the new OLS but that may prove difficult with their annoying licensing

Might be difficult!

http://purl.obolibrary.org/obo/UBERON_0002374 metacarpal bone SNOMEDCT:425761003 ! Entire metacarpal of finger to be replaced by SNOMEDCT:181977005 ! Entire metacarpal

I prefer to keep both and implicitly merge the concepts.

i.e. keep

xref: SCTID:181977005 ! Entire metacarpal
xref: SCTID:425761003 ! Entire metacarpal of finger
This must be a mistake in SCTID:
http://www.snomedbrowser.com/Codes/Details/181977005

all metacarpals are finger-associated. Maybe the more general one is intendend to be metapodium?

Metacarpe is used in mammals (porc, horses) too and those don’t have ‘fingers’. Maybe finger metacarpe is more specific to humans?
http://purl.obolibrary.org/obo/UBERON_0001211 Peyer's patch NCI_Thesaurus:Mouse_Peyer_s_Patches,NCI_Thesaurus:Peyer_s_Patch to be replaced by NCIt:C12771 ! Peyer Patch

Done!

http://purl.obolibrary.org/obo/UBERON_0000004 remove EFO:0000828 which is now obsolete

Done!

What, EFO has no nose? How does it smell?

;-) We smell thanks to Uberon. (we import your term)

Thanks for the update!
Cheers,
Catherine

http://purl.obolibrary.org/obo/UBERON_0001890 forebrain NCI_Thesaurus:Prosencephalon,NCI_Thesaurus:Fore-Brain to be replaced by NCIt:C40185 ! Forebrain

Done!

http://purl.obolibrary.org/obo/UBERON_0002372 tonsil NCI_Thesaurus:Tonsilar_Tissue,NCI_Thesaurus:Tonsillar_Lymphoid_Tissue,NCI_Thesaurus:Tonsil to be replaced by NCIt:C12802 ! tonsil

Done!


Reply to this email directly or view it on GitHub.

I really have no idea how term versioning works with SNOMED, and which version is where

It would be great to see a decent SNOMED browser in the new OLS but that may prove difficult with their annoying licensing

Might be difficult!

http://purl.obolibrary.org/obo/UBERON_0002374 metacarpal bone SNOMEDCT:425761003 ! Entire metacarpal of finger to be replaced by SNOMEDCT:181977005 ! Entire metacarpal

I prefer to keep both and implicitly merge the concepts.

i.e. keep

xref: SCTID:181977005 ! Entire metacarpal
xref: SCTID:425761003 ! Entire metacarpal of finger
This must be a mistake in SCTID:
http://www.snomedbrowser.com/Codes/Details/181977005

all metacarpals are finger-associated. Maybe the more general one is intendend to be metapodium?

Metacarpe is used in mammals (porc, horses) too and those don’t have ‘fingers’. Maybe finger metacarpe is more specific to humans?
http://purl.obolibrary.org/obo/UBERON_0001211 Peyer's patch NCI_Thesaurus:Mouse_Peyer_s_Patches,NCI_Thesaurus:Peyer_s_Patch to be replaced by NCIt:C12771 ! Peyer Patch

Done!

http://purl.obolibrary.org/obo/UBERON_0000004 remove EFO:0000828 which is now obsolete

Done!

What, EFO has no nose? How does it smell?

;-) We smell thanks to Uberon. (we import your term)

Thanks for the update!
Cheers,
Catherine

http://purl.obolibrary.org/obo/UBERON_0001890 forebrain NCI_Thesaurus:Prosencephalon,NCI_Thesaurus:Fore-Brain to be replaced by NCIt:C40185 ! Forebrain

Done!

http://purl.obolibrary.org/obo/UBERON_0002372 tonsil NCI_Thesaurus:Tonsilar_Tissue,NCI_Thesaurus:Tonsillar_Lymphoid_Tissue,NCI_Thesaurus:Tonsil to be replaced by NCIt:C12802 ! tonsil

Done!


Reply to this email directly or view it on GitHub.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment