update HBA bridge mappings to nerves to point to nerve roots #3281

AvolaAmg · 2024-05-21T13:44:12Z

Fixes some #3264

@hkir-dev see if it fixes the issue on PCL

Fixes some #3264

src/ontology/uberon-edit.obo

src/ontology/imports/merged_import.owl

hkir-dev · 2024-05-23T16:00:23Z

I conducted some tests, and these updates resolved the inconsistencies mentioned in issue brain-bican/human_brain_atlas_ontology#2

…int-to-nerve-roots

github-actions · 2024-05-24T11:50:59Z

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

Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-base.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2024-05-24/uberon-base.owl
Loaded from: file:/__w/uberon/uberon/src/ontology/uberon-base-main.owl/uberon-base.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/uberon/uberon-base.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2024-05-24/uberon-base.owl
Loaded from: file:/__w/uberon/uberon/src/ontology/uberon-base-pr.owl/uberon-base.owl

Ontology imports

Ontology annotations

accessory XI nerve `http://purl.obolibrary.org/obo/UBERON_0002019`

Removed

accessory XI nerve hasDbXref "HBA:9340"

accessory nerve root `http://purl.obolibrary.org/obo/UBERON_0014615`

Added

accessory nerve root hasDbXref "HBA:9340"

cranial nerve `http://purl.obolibrary.org/obo/UBERON_0001785`

Removed

cranial nerve hasDbXref "HBA:9299"

glossopharyngeal nerve `http://purl.obolibrary.org/obo/UBERON_0001649`

Removed

glossopharyngeal nerve hasDbXref "HBA:9334"

glossopharyngeal nerve root `http://purl.obolibrary.org/obo/UBERON_0019310`

Added

glossopharyngeal nerve root hasDbXref "HBA:9334"

hypoglossal nerve `http://purl.obolibrary.org/obo/UBERON_0001650`

Removed

hypoglossal nerve hasDbXref "HBA:9343"

hypoglossal nerve root `http://purl.obolibrary.org/obo/UBERON_0004675`

Added

hypoglossal nerve root hasDbXref "HBA:9343"

root of cranial nerve `http://purl.obolibrary.org/obo/UBERON_0006843`

Added

root of cranial nerve hasDbXref "HBA:9299"

root of vagus nerve `http://purl.obolibrary.org/obo/UBERON_0011213`

Added

root of vagus nerve hasDbXref "HBA:9337"

trigeminal nerve `http://purl.obolibrary.org/obo/UBERON_0001645`

Removed

trigeminal nerve hasDbXref "HBA:9322"

trigeminal nerve root `http://purl.obolibrary.org/obo/UBERON_0004673`

Added

trigeminal nerve root hasDbXref "HBA:9322"

vagus nerve `http://purl.obolibrary.org/obo/UBERON_0001759`

Removed

vagus nerve hasDbXref "HBA:9337"

…int-to-nerve-roots

anitacaron · 2024-05-24T11:56:38Z

#gogoeditdiff

github-actions · 2024-05-24T12:06:37Z

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:/__w/uberon/uberon/master/src/ontology/uberon-edit.obo

Right

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

Ontology imports

Ontology annotations

accessory XI nerve `http://purl.obolibrary.org/obo/UBERON_0002019`

Removed

accessory XI nerve database_cross_reference "HBA:9340"^^string

accessory nerve root `http://purl.obolibrary.org/obo/UBERON_0014615`

Added

accessory nerve root database_cross_reference "HBA:9340"^^string

cranial nerve `http://purl.obolibrary.org/obo/UBERON_0001785`

Removed

cranial nerve database_cross_reference "HBA:9299"^^string

glossopharyngeal nerve `http://purl.obolibrary.org/obo/UBERON_0001649`

Removed

glossopharyngeal nerve database_cross_reference "HBA:9334"^^string

glossopharyngeal nerve root `http://purl.obolibrary.org/obo/UBERON_0019310`

Added

glossopharyngeal nerve root database_cross_reference "HBA:9334"^^string

hypoglossal nerve `http://purl.obolibrary.org/obo/UBERON_0001650`

Removed

hypoglossal nerve database_cross_reference "HBA:9343"^^string

hypoglossal nerve root `http://purl.obolibrary.org/obo/UBERON_0004675`

Added

hypoglossal nerve root database_cross_reference "HBA:9343"^^string

root of cranial nerve `http://purl.obolibrary.org/obo/UBERON_0006843`

Added

root of cranial nerve database_cross_reference "HBA:9299"^^string

root of vagus nerve `http://purl.obolibrary.org/obo/UBERON_0011213`

Added

root of vagus nerve database_cross_reference "HBA:9337"^^string

trigeminal nerve `http://purl.obolibrary.org/obo/UBERON_0001645`

Removed

trigeminal nerve database_cross_reference "HBA:9322"^^string

trigeminal nerve root `http://purl.obolibrary.org/obo/UBERON_0004673`

Added

trigeminal nerve root database_cross_reference "HBA:9322"^^string

vagus nerve `http://purl.obolibrary.org/obo/UBERON_0001759`

Removed

vagus nerve database_cross_reference "HBA:9337"^^string

…int-to-nerve-roots

anitacaron · 2024-06-10T13:47:28Z

I'll merge it because Alida is away, and we need a UBERON release soon.

update HBA bridge mappings to nerves to point to nerve roots

a193375

Fixes some #3264

AvolaAmg requested review from dosumis and hkir-dev May 21, 2024 13:44

AvolaAmg self-assigned this May 21, 2024

AvolaAmg requested a review from anitacaron as a code owner May 21, 2024 13:44

anitacaron requested changes May 21, 2024

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src/ontology/uberon-edit.obo Outdated Show resolved Hide resolved

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Update uberon-edit.obo

4f186e3

AvolaAmg requested a review from anitacaron May 23, 2024 10:39

AvolaAmg and others added 4 commits May 23, 2024 12:27

Update uberon-edit.obo

85ce1c2

Update merged_import.owl

adcb58e

revert changes on merged_import.owl

55d1c29

remove GO classification from uberon-edit.obo

2d6ed23

Anita Caron added 2 commits May 24, 2024 10:14

Merge branch 'master' into update-HBA-bridge-mappings-to-nerves-to-po…

048757a

…int-to-nerve-roots

Merge branch 'master' into update-HBA-bridge-mappings-to-nerves-to-po…

faf82b0

…int-to-nerve-roots

Merge branch 'master' into update-HBA-bridge-mappings-to-nerves-to-po…

1bff21d

…int-to-nerve-roots

Merge branch 'master' into update-HBA-bridge-mappings-to-nerves-to-po…

fd9c1ec

…int-to-nerve-roots

anitacaron linked an issue Jun 10, 2024 that may be closed by this pull request

update HBA bridge mappings to nerves to point to nerve roots #3264

Closed

anitacaron approved these changes Jun 10, 2024

View reviewed changes

anitacaron merged commit 86f815a into master Jun 10, 2024
1 check passed

anitacaron deleted the update-HBA-bridge-mappings-to-nerves-to-point-to-nerve-roots branch July 5, 2024 16:10

anitacaron mentioned this pull request Jul 10, 2024

HBA bridge unsatisfiable classes #2903

Closed

update HBA bridge mappings to nerves to point to nerve roots #3281

update HBA bridge mappings to nerves to point to nerve roots #3281

Conversation

AvolaAmg commented May 21, 2024

hkir-dev commented May 23, 2024

github-actions bot commented May 24, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

accessory XI nerve http://purl.obolibrary.org/obo/UBERON_0002019

Removed

accessory nerve root http://purl.obolibrary.org/obo/UBERON_0014615

Added

cranial nerve http://purl.obolibrary.org/obo/UBERON_0001785

Removed

glossopharyngeal nerve http://purl.obolibrary.org/obo/UBERON_0001649

Removed

glossopharyngeal nerve root http://purl.obolibrary.org/obo/UBERON_0019310

Added

hypoglossal nerve http://purl.obolibrary.org/obo/UBERON_0001650

Removed

hypoglossal nerve root http://purl.obolibrary.org/obo/UBERON_0004675

Added

root of cranial nerve http://purl.obolibrary.org/obo/UBERON_0006843

Added

root of vagus nerve http://purl.obolibrary.org/obo/UBERON_0011213

Added

trigeminal nerve http://purl.obolibrary.org/obo/UBERON_0001645

Removed

trigeminal nerve root http://purl.obolibrary.org/obo/UBERON_0004673

Added

vagus nerve http://purl.obolibrary.org/obo/UBERON_0001759

Removed

anitacaron commented May 24, 2024

github-actions bot commented May 24, 2024

Ontology comparison

Left

Right

Ontology imports

Ontology annotations

accessory XI nerve http://purl.obolibrary.org/obo/UBERON_0002019

Removed

accessory nerve root http://purl.obolibrary.org/obo/UBERON_0014615

Added

cranial nerve http://purl.obolibrary.org/obo/UBERON_0001785

Removed

glossopharyngeal nerve http://purl.obolibrary.org/obo/UBERON_0001649

Removed

glossopharyngeal nerve root http://purl.obolibrary.org/obo/UBERON_0019310

Added

hypoglossal nerve http://purl.obolibrary.org/obo/UBERON_0001650

Removed

hypoglossal nerve root http://purl.obolibrary.org/obo/UBERON_0004675

Added

root of cranial nerve http://purl.obolibrary.org/obo/UBERON_0006843

Added

root of vagus nerve http://purl.obolibrary.org/obo/UBERON_0011213

Added

trigeminal nerve http://purl.obolibrary.org/obo/UBERON_0001645

Removed

trigeminal nerve root http://purl.obolibrary.org/obo/UBERON_0004673

Added

vagus nerve http://purl.obolibrary.org/obo/UBERON_0001759

Removed

anitacaron commented Jun 10, 2024

accessory XI nerve `http://purl.obolibrary.org/obo/UBERON_0002019`

accessory nerve root `http://purl.obolibrary.org/obo/UBERON_0014615`

cranial nerve `http://purl.obolibrary.org/obo/UBERON_0001785`

glossopharyngeal nerve `http://purl.obolibrary.org/obo/UBERON_0001649`

glossopharyngeal nerve root `http://purl.obolibrary.org/obo/UBERON_0019310`

hypoglossal nerve `http://purl.obolibrary.org/obo/UBERON_0001650`

hypoglossal nerve root `http://purl.obolibrary.org/obo/UBERON_0004675`

root of cranial nerve `http://purl.obolibrary.org/obo/UBERON_0006843`

root of vagus nerve `http://purl.obolibrary.org/obo/UBERON_0011213`

trigeminal nerve `http://purl.obolibrary.org/obo/UBERON_0001645`

trigeminal nerve root `http://purl.obolibrary.org/obo/UBERON_0004673`

vagus nerve `http://purl.obolibrary.org/obo/UBERON_0001759`

accessory XI nerve `http://purl.obolibrary.org/obo/UBERON_0002019`

accessory nerve root `http://purl.obolibrary.org/obo/UBERON_0014615`

cranial nerve `http://purl.obolibrary.org/obo/UBERON_0001785`

glossopharyngeal nerve `http://purl.obolibrary.org/obo/UBERON_0001649`

glossopharyngeal nerve root `http://purl.obolibrary.org/obo/UBERON_0019310`

hypoglossal nerve `http://purl.obolibrary.org/obo/UBERON_0001650`

hypoglossal nerve root `http://purl.obolibrary.org/obo/UBERON_0004675`

root of cranial nerve `http://purl.obolibrary.org/obo/UBERON_0006843`

root of vagus nerve `http://purl.obolibrary.org/obo/UBERON_0011213`

trigeminal nerve `http://purl.obolibrary.org/obo/UBERON_0001645`

trigeminal nerve root `http://purl.obolibrary.org/obo/UBERON_0004673`

vagus nerve `http://purl.obolibrary.org/obo/UBERON_0001759`