fixes #2912 add dorsal iris #2913

paulacalipho · 2023-06-06T08:29:02Z

cmungall · 2023-06-07T04:15:11Z

This should be failing qc checks due to missing isa

On Tue, Jun 6, 2023 at 4:29 AM PaulaDRoggli ***@***.***> wrote: fixes #2912 <#2912> ------------------------------ You can view, comment on, or merge this pull request online at: #2913 Commit Summary - 1ff3286 <1ff3286> fixes #2912 File Changes (1 file <https://github.com/obophenotype/uberon/pull/2913/files>) - *M* src/ontology/uberon-edit.obo <https://github.com/obophenotype/uberon/pull/2913/files#diff-7dde9e81f71ce11962436529956798fa723e49d1bc8d188cc399d8009c2f72b4> (8) Patch Links: - https://github.com/obophenotype/uberon/pull/2913.patch - https://github.com/obophenotype/uberon/pull/2913.diff — Reply to this email directly, view it on GitHub <#2913>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMONQIJR4B7EZFDTW6UTXJ3S5TANCNFSM6AAAAAAY4BXCLA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

paulacalipho · 2023-06-07T07:03:39Z

Hi @cmungall I do not know how to model this term:

is_a multi-tissue structure UBERON:0000481 and remove part_of iris UBERON:0001769 (iris is_a multi-tissue structure UBERON:0000481)
is_a organ part UBERON:0000064 (but iris is not an organ) and keep part_of iris UBERON:0001769
is_a iris UBERON:0001769

anitacaron · 2023-06-07T09:31:00Z

@cmungall, checking the profile.txt, the level of QC for missing_superclass is INFO.

anitacaron · 2023-06-07T09:31:45Z

#gogoeditdiff

github-actions · 2023-06-07T10:15:49Z

Here's a diff of how these changes impact the classified ontology (on -simple file):

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2023-06-07/uberon-simple.owl
Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-simple.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-simple.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2023-06-07/uberon-simple.owl
Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

dorsal iris `http://purl.obolibrary.org/obo/UBERON_8480063`

Added

dorsal iris contributor 0000-0002-0819-0473
dorsal iris has_obo_namespace "uberon"
dorsal iris id "UBERON:8480063"
dorsal iris label "dorsal iris"
dorsal iris definition "The dorsal part of the iris. This region is involved in lens regeneration in urodeles (newts and salamanders) in a process named Wolffian lens regeneration. In these species, lens regeneration proceeds through two steps. The first step involves the entire circumference of the iris pigmented epithelium. The second step is confined to the pigmented epithelial cells located along the dorsal rim of the iris and involves dorsal-specific activation of the Wnt signaling pathway."
- database_cross_reference "PMID:17030116"
- database_cross_reference "PMID:29579253"
dorsal iris date "2023-06-06T08:06:04Z"^^dateTime
Class: dorsal iris
dorsal iris SubClassOf part_of some iris

github-actions · 2023-06-07T10:15:52Z

Here's a diff of your edit file (unreasoned)

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
Version IRI: None
Loaded from: file:/work/src/ontology/../../master/src/ontology/uberon-edit.obo

Right

Ontology IRI: http://purl.obolibrary.org/obo/uberon/core.owl
Version IRI: None
Loaded from: file:/work/src/ontology/uberon-edit.obo

Ontology imports

Ontology annotations

dorsal iris `http://purl.obolibrary.org/obo/UBERON_8480063`

Added

dorsal iris contributor 0000-0002-0819-0473
dorsal iris has_obo_namespace "uberon"^^string
dorsal iris id "UBERON:8480063"^^string
dorsal iris label "dorsal iris"^^string
dorsal iris definition "The dorsal part of the iris. This region is involved in lens regeneration in urodeles (newts and salamanders) in a process named Wolffian lens regeneration. In these species, lens regeneration proceeds through two steps. The first step involves the entire circumference of the iris pigmented epithelium. The second step is confined to the pigmented epithelial cells located along the dorsal rim of the iris and involves dorsal-specific activation of the Wnt signaling pathway."^^string
- database_cross_reference "PMID:29579253"^^string
- database_cross_reference "PMID:17030116"^^string
dorsal iris date "2023-06-06T08:06:04Z"^^dateTime
Class: dorsal iris
dorsal iris SubClassOf part_of some iris

matentzn · 2023-06-07T17:03:28Z

robot report MISSING_SUPERCLASS is too general. We would need something more bespoke, like "if it starts with UBERON: it needs to be an UBERON:anatomical entity" SPARQL thing.

ghost · 2023-06-13T14:22:18Z

src/ontology/uberon-edit.obo

+[Term]
+id: UBERON:8480063
+name: dorsal iris
+def: "The dorsal part of the iris. This region is involved in lens regeneration in urodeles (newts and salamanders) in a process named Wolffian lens regeneration. In these species, lens regeneration proceeds through two steps. The first step involves the entire circumference of the iris pigmented epithelium. The second step is confined to the pigmented epithelial cells located along the dorsal rim of the iris and involves dorsal-specific activation of the Wnt signaling pathway." [PMID:17030116, PMID:29579253]


Consider keeping the first two sentences in the text definition and relegating the rest to a comment.

Also consider if a new GO term 'Wolffian lens regeneration' is warranted.

Indeed this term does not exist in GO. Should I make a NTR to GO?

ghost · 2023-06-13T14:23:39Z

src/ontology/uberon-edit.obo

@@ -224055,6 +224055,14 @@ relationship: dc-contributor https://orcid.org/0000-0002-0819-0473
 relationship: part_of UBERON:0006767 ! head of femur
 property_value: dcterms-date "2023-05-30T06:34:18Z" xsd:dateTime

+[Term]
+id: UBERON:8480063
+name: dorsal iris


If "dorsal rim of the iris" is an exact synonym, consider adding (dbxref PMID:29579253).

ghost · 2023-06-13T14:25:41Z

This should be failing qc checks due to missing isa

Since 'anatomical entity' (CARO:0000000) is inferred, should this still fail?

paulacalipho · 2023-06-13T14:44:49Z

@bvarner-ebi thanks for the input. I will make the changes in the definition and add the synonym. Should I try is_a "anatomical entity"?

ghost · 2023-06-13T14:57:05Z

@bvarner-ebi thanks for the input. I will make the changes in the definition and add the synonym. Should I try is_a "anatomical entity"?

'anatomical entity' (CARO:0000000) is already inferred, so I don't think it needs to be manually asserted. I think adding superclass 'anatomical structure' would be reasonable.

uberon · 2023-06-13T15:12:09Z

It needs a more specific term asserted. I suggest UBERON:0000064 ! organ part This isn't in the guide but it should be, sorry...

…

On Tue, Jun 13, 2023 at 7:57 AM bvarner-ebi ***@***.***> wrote: @bvarner-ebi <https://github.com/bvarner-ebi> thanks for the input. I will make the changes in the definition and add the synonym. Should I try is_a "anatomical entity"? 'anatomical entity' (CARO:0000000) is already inferred, so I don't think it needs to be manually asserted. I think adding superclass 'anatomical structure' would be reasonable. — Reply to this email directly, view it on GitHub <#2913 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGZRCGUUV66OK5X2IQVI6TXLB5U3ANCNFSM6AAAAAAY4BXCLA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

paulacalipho · 2023-06-13T15:15:25Z

@bvarner-ebi I should add is_a organ part UBERON:0000064 instead of anatomical structure?

ghost · 2023-06-13T15:30:29Z

@bvarner-ebi I should add is_a organ part UBERON:0000064 instead of anatomical structure?

Uberon considers eye to be a 'sense organ', which is an organ, and the text definition of 'organ part' is "A multicellular structure that is a part of an organ", so it seems reasonable.

Also consider if adding 'has part' some 'iris epithelium' is appropriate.

cmungall · 2023-06-13T15:49:12Z

has part or overlaps? in organisms where dorsal iris is a meaningful subdivisions, are there parts of the iris epithelium that lie outside the dorsal iris?

paulacalipho · 2023-06-14T06:01:36Z

@cmungall @bvarner-ebi I don't think that there are parts of the dorsal iris epithelium that lie outside the dorsal iris

ghost · 2023-06-14T07:58:39Z

@cmungall @bvarner-ebi I don't think that there are parts of the dorsal iris epithelium that lie outside the dorsal iris

@paulacalipho, if there is 'iris epithelium' that exists outside the 'dorsal iris', overlaps would be appropriate.

ghost · 2023-06-15T12:08:46Z

@matentzn, can you kindly advise- did QC fail due to memory constraints? Any advice on how to proceed?

HTTP request sent, awaiting response... 200 OK
Length: 97201 (95K) [text/plain]
Saving to: ‘tmp/GO.xrf_abbs’

     0K .......... .......... .......... .......... .......... 52% 9.07M 0s
    50K .......... .......... .......... .......... ....      100% 9.19M=0.01s

2023-06-15 11:51:36 (9.12 MB/s) - ‘tmp/GO.xrf_abbs’ saved [97201/97201]

Replaced: 0
Killed
make: *** [uberon.Makefile:1136: reports/basic-allcycles] Error 137

Last few rows of QC report:

annotate -V http://purl.obolibrary.org/obo/uberon/releases/2023-06-15/uberon-basic.owl --annotation owl:versionInfo 2023-06-15 --output uberon-basic.owl.tmp.owl && mv uberon-basic.owl.tmp.owl uberon-basic.owl
robot --catalog catalog-v001.xml merge -i uberon-basic.owl annotate --ontology-iri http://purl.obolibrary.org/obo/uberon/basic.owl annotate -V http://purl.obolibrary.org/obo/uberon/releases/2023-06-15/basic.owl --annotation owl:versionInfo 2023-06-15 -o basic.owl
OWLTOOLS_MEMORY=20G owltools --use-catalog --no-debug basic.owl --list-cycles -f > reports/basic-allcycles

anitacaron · 2023-06-15T12:50:34Z

@bvarner-ebi, Sometimes, if you run again it works :)

fixes #2912

1ff3286

paulacalipho self-assigned this Jun 6, 2023

ghost reviewed Jun 13, 2023

View reviewed changes

Update uberon-edit.obo

a20d8c1

paulacalipho added 2 commits June 14, 2023 10:21

Update uberon-edit.obo

534747b

Update uberon-edit.obo

c82a6c2

ghost approved these changes Jun 15, 2023

View reviewed changes

ghost merged commit 6dabbf1 into master Jun 15, 2023
1 check passed

ghost deleted the #2912-NTR-dorsal-iris branch June 15, 2023 13:00

This pull request was closed.

fixes #2912 add dorsal iris #2913

fixes #2912 add dorsal iris #2913

Conversation

paulacalipho commented Jun 6, 2023

cmungall commented Jun 7, 2023 via email

paulacalipho commented Jun 7, 2023

anitacaron commented Jun 7, 2023

anitacaron commented Jun 7, 2023

github-actions bot commented Jun 7, 2023

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

dorsal iris http://purl.obolibrary.org/obo/UBERON_8480063

Added

github-actions bot commented Jun 7, 2023

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

dorsal iris http://purl.obolibrary.org/obo/UBERON_8480063

Added

matentzn commented Jun 7, 2023

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ghost commented Jun 13, 2023

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uberon commented Jun 13, 2023 via email

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ghost commented Jun 13, 2023

cmungall commented Jun 13, 2023

paulacalipho commented Jun 14, 2023 • edited Loading

ghost commented Jun 14, 2023

ghost commented Jun 15, 2023 • edited by ghost Loading

anitacaron commented Jun 15, 2023

dorsal iris `http://purl.obolibrary.org/obo/UBERON_8480063`

dorsal iris `http://purl.obolibrary.org/obo/UBERON_8480063`

paulacalipho commented Jun 14, 2023 •

edited

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ghost commented Jun 15, 2023 •

edited by ghost

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