Added tuberal nucleus for rodents and fish by shawntanzk · Pull Request #2441 · obophenotype/uberon

shawntanzk · 2022-04-29T08:00:16Z

Fixes #2439

Tagging @patrick-lloyd-ray

…system (sensu Teleostei) Fixes #2439

shawntanzk · 2022-04-29T13:19:39Z

hmm seems like adding primate taxon breaks something - will figure this out

Seems like it was added to the wrong term - hopefully everything will work now :)

This reverts commit 52cc421.

github-actions · 2022-04-29T14:54:29Z

Here's a diff of your human-view

# Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/uberon/subsets/human-view.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-04-29/subsets/human-view.owl
Loaded from: file:/work/src/ontology/../../master/src/ontology/subsets/human-view.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/uberon/subsets/human-view.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-04-29/subsets/human-view.owl
Loaded from: file:/work/src/ontology/subsets/human-view.owl

Ontology imports

Ontology annotations

_:genid2147483648

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_:genid2147483648 database_cross_reference "FBC:VH"

_:genid2147483649

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_:genid2147483649 database_cross_reference "PHENOSCAPE:alex"

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_:genid2147483650 database_cross_reference "UBERON:CL_meeting_20110725"

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_:genid2147483651 database_cross_reference "ISBN:0073040584"

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_:genid2147483652 database_cross_reference "GO:0021728"

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_:genid2147483654 database_cross_reference "GO:0061214"

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_:genid2147483655 database_cross_reference "HP:0003832"

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_:genid2147483656 database_cross_reference "FBC:VH"
_:genid2147483656 database_cross_reference "FBC:DOS"

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_:genid2147483657 database_cross_reference "MP:0009993"

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_:genid2147483658 database_cross_reference "GO:0003226"

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_:genid2147483659 database_cross_reference "FBC:VH"
_:genid2147483659 database_cross_reference "FBC:DOS"

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_:genid2147483660 database_cross_reference "GO:0060682"

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_:genid2147483661 database_cross_reference "FBC:VH"
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_:genid2147483665 database_cross_reference "FlyBase:FBrf0002482"
_:genid2147483665 database_cross_reference "FlyBase:FBrf0007196"
_:genid2147483665 database_cross_reference "FlyBase:FBrf0007735"
_:genid2147483665 database_cross_reference "FlyBase:FBrf0034076"

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_:genid2147483666 database_cross_reference "MP:0010002"

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_:genid2147483667 database_cross_reference "HP:0000606"

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_:genid2147483668 database_cross_reference "GO_REF:0000021"
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_:genid2147483681 database_cross_reference "HP:0005289"

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_:genid2147483682 database_cross_reference "MP:0009997"

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_:genid2147483683 database_cross_reference "FBC:DOS"

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_:genid2147483684 database_cross_reference "BIRNLEX:1755"

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_:genid2147483687 database_cross_reference "MP:0009999"

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_:genid2147483688 database_cross_reference "ISBN:0073040584"

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_:genid2147483690 database_cross_reference "PHENOSCAPE:Wasila"

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_:genid2147483691 database_cross_reference "ISBN:0073040584"

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_:genid2147483710 database_cross_reference "BIRNLEX:1732"

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_:genid2147483711 database_cross_reference "GO:0003224"

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_:genid2147483712 database_cross_reference "FlyBase:FBrf0089570"

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_:genid2147483713 database_cross_reference "MP:0009993"

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_:genid2147483714 database_cross_reference "UBERON:CL_meeting_20110725"

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_:genid2147483715 database_cross_reference "MP:0009997"

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_:genid2147483716 database_cross_reference "HP:0000864"

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_:genid2147483719 database_cross_reference "PHENOSCAPE:alex"

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_:genid2147483720 database_cross_reference "GO:0003227"

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_:genid2147483721 database_cross_reference "GO:0003225"

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_:genid2147483722 database_cross_reference "BIRNLEX:1734"

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_:genid2147483723 database_cross_reference "MP:0009999"

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_:genid2147483724 database_cross_reference "PMCID:PMC2093943"

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_:genid2147483725 database_cross_reference "ISBN:0073040584"

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_:genid2147483726 database_cross_reference "MP:0009989"

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_:genid2147483727 database_cross_reference "GO:0021729"
_:genid2147483727 database_cross_reference "GO_REF:0000021"

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_:genid2147483728 database_cross_reference "GO:0061249"

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_:genid2147483729 database_cross_reference "MP:0009996"

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_:genid2147483730 database_cross_reference "GO:0021729"

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_:genid2147483731 database_cross_reference "GO:0003226"

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_:genid2147483732 database_cross_reference "FBC:DOS"

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_:genid2147483734 database_cross_reference "FBC:DOS"

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_:genid2147483735 database_cross_reference "PHENOSCAPE:alex"

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_:genid2147483736 database_cross_reference "GO:0072003"

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_:genid2147483737 database_cross_reference "FBC:VH"

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_:genid2147483738 database_cross_reference "FBC:DOS"

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_:genid2147483739 database_cross_reference "FlyBase:FBrf0007735"
_:genid2147483739 database_cross_reference "FlyBase:FBrf0034076"
_:genid2147483739 database_cross_reference "FlyBase:FBrf0007196"
_:genid2147483739 database_cross_reference "FlyBase:FBrf0002482"

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_:genid2147483740 database_cross_reference "GO:0021751"

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_:genid2147483741 database_cross_reference "GO:0003285"

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_:genid2147483742 database_cross_reference "ISBN:0073040584"

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_:genid2147483743 database_cross_reference "GO:0003291"

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_:genid2147483744 database_cross_reference "HP:0003350"

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_:genid2147483745 database_cross_reference "GO:0072166"

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_:genid2147483746 database_cross_reference "GO:0061214"

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_:genid2147483747 database_cross_reference "HP:0000606"

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_:genid2147483748 database_cross_reference "FlyBase:FBrf0006943"

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_:genid2147483749 database_cross_reference "EFO:0000240"

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_:genid2147483750 database_cross_reference "FBC:VH"
_:genid2147483750 database_cross_reference "FBC:DOS"

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_:genid2147483751 database_cross_reference "ZFIN:cvs"
_:genid2147483751 database_cross_reference "GO:dph"

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_:genid2147483752 database_cross_reference "ISBN:0073040584"

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_:genid2147483753 database_cross_reference "FlyBase:FBrf0007733"
_:genid2147483753 database_cross_reference "FlyBase:FBrf0064792"

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_:genid2147483754 database_cross_reference "GO:0021728"

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_:genid2147483755 database_cross_reference "MP:0009994"

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_:genid2147483756 database_cross_reference "BIRNLEX:1755"

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_:genid2147483757 database_cross_reference "MP:0009988"

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_:genid2147483758 database_cross_reference "FBC:VH"
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_:genid2147483759 database_cross_reference "FBC:DOS"

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_:genid2147483760 database_cross_reference "GO:0060682"

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_:genid2147483761 database_cross_reference "HP:0005289"

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_:genid2147483762 database_cross_reference "GO:0072165"

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_:genid2147483763 database_cross_reference "MP:0009990"

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_:genid2147483764 database_cross_reference "MP:0009364"

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_:genid2147483765 database_cross_reference "FBC:VH"

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_:genid2147483766 database_cross_reference "MP:0010002"

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_:genid2147483767 database_cross_reference "ISBN:0073040584"

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_:genid2147483768 database_cross_reference "PHENOSCAPE:Wasila"

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_:genid2147483769 database_cross_reference "FBC:VH"
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_:genid2147483770 database_cross_reference "HP:0003832"

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_:genid2147483771 database_cross_reference "MP:0010003"

lateral tuberal nucleus `http://purl.obolibrary.org/obo/UBERON_0000435`

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lateral tuberal nucleus database_cross_reference "MBA:614"
lateral tuberal nucleus database_cross_reference "DMBA:16271"

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lateral tuberal nucleus comment "The lateral tuberal nucleus is specific to humans and higher primates, however, this term is sometimes used loosely. If using for rodents, please use tuberal nucleus (sensu Rodentia) instead. If refering to the nucleus lateralis tuberis of fish, please use nucleus lateralis tuberis system (sensu Teleostei)"

Here's a diff of your mouse-view

# Ontology comparison

Left

Ontology IRI: http://purl.obolibrary.org/obo/uberon/subsets/mouse-view.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-04-29/subsets/mouse-view.owl
Loaded from: file:/work/src/ontology/../../master/src/ontology/subsets/mouse-view.owl

Right

Ontology IRI: http://purl.obolibrary.org/obo/uberon/subsets/mouse-view.owl
Version IRI: http://purl.obolibrary.org/obo/uberon/releases/2022-04-29/subsets/mouse-view.owl
Loaded from: file:/work/src/ontology/subsets/mouse-view.owl

Ontology imports

Ontology annotations

UBERON_8440007 `http://purl.obolibrary.org/obo/UBERON_8440007`

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UBERON_8440007 has_broad_synonym "lateral tuberal nucleus (sensu Rodentia)"
- database_cross_reference centraldirectory.aspx?ID=1890
UBERON_8440007 contributor 0000-0001-7258-9596
UBERON_8440007 curator notes "Lateral tuberal nucleus is listed as both an exact synonym and related synonym as the term has been used in both ways. See lateral tuberal nucleus is specific to humans and primates #2439 for more details. No homology links has been made as this is unclear from the literature."
UBERON_8440007 id "UBERON:8440007"
UBERON_8440007 has_obo_namespace "uberon"
UBERON_8440007 label "tuberal nucleus (sensu Rodentia)"
UBERON_8440007 database_cross_reference "MBA:614"
UBERON_8440007 database_cross_reference "DMBA:16271"
UBERON_8440007 has_exact_synonym "lateral tuberal nucleus (sensu Rodentia)"
- database_cross_reference 29976812
UBERON_8440007 definition "A hypothalamic region in rodents that is homologous to the lateral tuberal nucleus in humans and higher primates and is involved in energy homeostasis."
- database_cross_reference 29976812
- database_cross_reference 29976824
UBERON_8440007 comment "While lateral tuberal nucleus is often used interchangeably with tuberal nucleus in rodents, lateral tuberal nucleus is specific to humans and higher primates. In some cases, lateral tuberal nucleus is thought to be part of the tuberal nucleus in rodents, and could possibly be homologous to human tuberal region instead."
Class: UBERON_8440007
UBERON_8440007 SubClassOf hypothalamic nucleus

_:genid2147483648

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_:genid2147483648 database_cross_reference "UBERON:CL_meeting_20110725"

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_:genid2147483649 database_cross_reference "MP:0009990"

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_:genid2147483650 database_cross_reference "GO:0003227"

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_:genid2147483652 database_cross_reference "GO:0060682"

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_:genid2147483659 database_cross_reference "FlyBase:FBrf0064792"

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_:genid2147483662 database_cross_reference "PHENOSCAPE:alex"

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_:genid2147483671 database_cross_reference "BIRNLEX:1734"

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_:genid2147483672 database_cross_reference "ISBN:0073040584"

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_:genid2147483675 database_cross_reference "HP:0003350"

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_:genid2147483676 database_cross_reference "FBC:VH"
_:genid2147483676 database_cross_reference "FBC:DOS"

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_:genid2147483677 database_cross_reference "MP:0009996"

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_:genid2147483678 database_cross_reference "HP:0005289"

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_:genid2147483679 database_cross_reference "FBC:DOS"

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_:genid2147483680 database_cross_reference "FBC:DOS"

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_:genid2147483681 database_cross_reference "PHENOSCAPE:Wasila"

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_:genid2147483682 database_cross_reference "GO:0003224"

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_:genid2147483683 database_cross_reference "GO:0003291"

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_:genid2147483684 database_cross_reference "ISBN:0073040584"

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_:genid2147483685 database_cross_reference "GO:0072003"

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_:genid2147483686 database_cross_reference "HP:0003832"

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_:genid2147483687 database_cross_reference "PHENOSCAPE:alex"

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_:genid2147483688 database_cross_reference "ISBN:0073040584"

_:genid2147483689

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_:genid2147483689 database_cross_reference "FBC:DOS"

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_:genid2147483690 database_cross_reference "GO:0061249"

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_:genid2147483691 database_cross_reference "ISBN:0073040584"

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_:genid2147483692 database_cross_reference "GO:0072166"

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_:genid2147483693 database_cross_reference "BIRNLEX:1755"

_:genid2147483694

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_:genid2147483694 database_cross_reference "GO:dph"
_:genid2147483694 database_cross_reference "ZFIN:cvs"

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_:genid2147483695 database_cross_reference "MP:0009994"

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_:genid2147483696 database_cross_reference "MP:0009988"

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_:genid2147483697 database_cross_reference "GO_REF:0000021"
_:genid2147483697 database_cross_reference "GO:0021729"

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_:genid2147483698 database_cross_reference "PMCID:PMC2093943"

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_:genid2147483699 database_cross_reference "FBC:VH"

_:genid2147483700

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_:genid2147483700 database_cross_reference "FBC:DOS"

_:genid2147483701

Removed

_:genid2147483701 database_cross_reference "FlyBase:FBrf0007196"
_:genid2147483701 database_cross_reference "FlyBase:FBrf0002482"
_:genid2147483701 database_cross_reference "FlyBase:FBrf0034076"
_:genid2147483701 database_cross_reference "FlyBase:FBrf0007735"

_:genid2147483702

Removed

_:genid2147483702 database_cross_reference "GO:0021728"

_:genid2147483703

Removed

_:genid2147483703 database_cross_reference "MP:0010003"

_:genid2147483704

Removed

_:genid2147483704 database_cross_reference "MP:0009997"

_:genid2147483705

Removed

_:genid2147483705 database_cross_reference "GO:0072165"

_:genid2147483706

Removed

_:genid2147483706 database_cross_reference "MP:0009989"

_:genid2147483707

Removed

_:genid2147483707 database_cross_reference "FBC:VH"

_:genid2147483708

Removed

_:genid2147483708 database_cross_reference "FBC:VH"
_:genid2147483708 database_cross_reference "FBC:DOS"

_:genid2147483709

Removed

_:genid2147483709 database_cross_reference "FBC:VH"

_:genid2147483710

Added

_:genid2147483710 database_cross_reference "GO:0003291"

_:genid2147483711

Added

_:genid2147483711 database_cross_reference "GO:0021751"

_:genid2147483712

Added

_:genid2147483712 database_cross_reference "GO:0072166"

_:genid2147483713

Added

_:genid2147483713 database_cross_reference "MP:0009988"

_:genid2147483714

Added

_:genid2147483714 database_cross_reference "MP:0010003"

_:genid2147483715

Added

_:genid2147483715 database_cross_reference "ISBN:0073040584"

_:genid2147483716

Added

_:genid2147483716 database_cross_reference "MP:0010002"

_:genid2147483717

Added

_:genid2147483717 database_cross_reference "GO:0003285"

_:genid2147483718

Added

_:genid2147483718 database_cross_reference "FBC:VH"
_:genid2147483718 database_cross_reference "FBC:DOS"

_:genid2147483719

Added

_:genid2147483719 database_cross_reference "ISBN:0073040584"

_:genid2147483720

Added

_:genid2147483720 database_cross_reference "PHENOSCAPE:alex"

_:genid2147483721

Added

_:genid2147483721 database_cross_reference "MP:0009990"

_:genid2147483722

Added

_:genid2147483722 database_cross_reference "GO:0060682"

_:genid2147483723

Added

_:genid2147483723 database_cross_reference "GO:0072165"

_:genid2147483724

Added

_:genid2147483724 database_cross_reference "FBC:VH"

_:genid2147483725

Added

_:genid2147483725 database_cross_reference "GO:0021729"
_:genid2147483725 database_cross_reference "GO_REF:0000021"

_:genid2147483726

Added

_:genid2147483726 database_cross_reference "BIRNLEX:1734"

_:genid2147483727

Added

_:genid2147483727 database_cross_reference "MP:0009946"

_:genid2147483728

Added

_:genid2147483728 database_cross_reference "GO:0021729"

_:genid2147483729

Added

_:genid2147483729 database_cross_reference "GO:0021728"

_:genid2147483730

Added

_:genid2147483730 database_cross_reference "BIRNLEX:1755"

_:genid2147483731

Added

_:genid2147483731 database_cross_reference "GO:0061249"

_:genid2147483732

Added

_:genid2147483732 database_cross_reference "FlyBase:FBrf0006943"

_:genid2147483733

Added

_:genid2147483733 database_cross_reference "FBC:VH"
_:genid2147483733 database_cross_reference "FBC:DOS"

_:genid2147483734

Added

_:genid2147483734 database_cross_reference "FlyBase:FBrf0089570"

_:genid2147483735

Added

_:genid2147483735 database_cross_reference "PHENOSCAPE:Wasila"

_:genid2147483736

Added

_:genid2147483736 database_cross_reference "HP:0003832"

_:genid2147483737

Added

_:genid2147483737 database_cross_reference "HP:0003350"

_:genid2147483738

Added

_:genid2147483738 database_cross_reference "GO:0061214"

_:genid2147483739

Added

_:genid2147483739 database_cross_reference "GO:0072003"

_:genid2147483740

Added

_:genid2147483740 database_cross_reference "GO:0003225"

_:genid2147483741

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_:genid2147483741 database_cross_reference "MP:0009997"

_:genid2147483742

Added

_:genid2147483742 database_cross_reference "MP:0009996"

_:genid2147483743

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_:genid2147483743 database_cross_reference "FBC:VH"

_:genid2147483744

Added

_:genid2147483744 database_cross_reference "FlyBase:FBrf0034076"
_:genid2147483744 database_cross_reference "FlyBase:FBrf0007196"
_:genid2147483744 database_cross_reference "FlyBase:FBrf0002482"
_:genid2147483744 database_cross_reference "FlyBase:FBrf0007735"

_:genid2147483745

Added

_:genid2147483745 database_cross_reference "FBC:VH"

_:genid2147483746

Added

_:genid2147483746 database_cross_reference "PMCID:PMC2093943"

_:genid2147483747

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_:genid2147483747 database_cross_reference "GO:0003224"

_:genid2147483748

Added

_:genid2147483748 database_cross_reference "FlyBase:FBrf0064792"
_:genid2147483748 database_cross_reference "FlyBase:FBrf0007733"

_:genid2147483749

Added

_:genid2147483749 database_cross_reference "FBC:DOS"

_:genid2147483750

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_:genid2147483750 database_cross_reference "BIRNLEX:1732"

_:genid2147483751

Added

_:genid2147483751 database_cross_reference "HP:0000864"

_:genid2147483752

Added

_:genid2147483752 database_cross_reference "HP:0000606"

_:genid2147483753

Added

_:genid2147483753 database_cross_reference "GO:0003226"

_:genid2147483754

Added

_:genid2147483754 database_cross_reference "EFO:0000240"

_:genid2147483755

Added

_:genid2147483755 database_cross_reference "MP:0009994"

_:genid2147483756

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_:genid2147483756 database_cross_reference "FBC:VH"

_:genid2147483757

Added

_:genid2147483757 database_cross_reference "PHENOSCAPE:alex"

_:genid2147483758

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_:genid2147483758 database_cross_reference "HP:0005289"

_:genid2147483759

Added

_:genid2147483759 database_cross_reference "FBC:DOS"

_:genid2147483760

Added

_:genid2147483760 database_cross_reference "ISBN:0073040584"

_:genid2147483761

Added

_:genid2147483761 database_cross_reference "MP:0009364"

_:genid2147483762

Added

_:genid2147483762 database_cross_reference "MP:0009989"

_:genid2147483763

Added

_:genid2147483763 database_cross_reference "GO:0003227"

_:genid2147483764

Added

_:genid2147483764 database_cross_reference "FBC:DOS"

_:genid2147483765

Added

_:genid2147483765 database_cross_reference "FBC:DOS"
_:genid2147483765 database_cross_reference "FBC:VH"

_:genid2147483766

Added

_:genid2147483766 database_cross_reference "GO:dph"
_:genid2147483766 database_cross_reference "ZFIN:cvs"

_:genid2147483767

Added

_:genid2147483767 database_cross_reference "MP:0009999"

_:genid2147483768

Added

_:genid2147483768 database_cross_reference "ISBN:0073040584"

_:genid2147483769

Added

_:genid2147483769 database_cross_reference "FBC:DOS"

_:genid2147483770

Added

_:genid2147483770 database_cross_reference "MP:0009993"

_:genid2147483771

Added

_:genid2147483771 database_cross_reference "UBERON:CL_meeting_20110725"

lateral tuberal nucleus `http://purl.obolibrary.org/obo/UBERON_0000435`

Removed

lateral tuberal nucleus database_cross_reference "MBA:614"
lateral tuberal nucleus has_exact_synonym "lateral tuberal hypothalamic nuclei"
- database_cross_reference "FMA:62336"
lateral tuberal nucleus database_cross_reference "BIRNLEX:1206"
lateral tuberal nucleus database_cross_reference "BAMS:LTu"
lateral tuberal nucleus database_cross_reference "DMBA:16271"
lateral tuberal nucleus database_cross_reference C0086527
lateral tuberal nucleus database_cross_reference "DHBA:10493"
lateral tuberal nucleus has_obo_namespace "uberon"
lateral tuberal nucleus definition "Nerve cell nuclei situated ventrally in the intermediate hypothalamic region, mainly in the lateral hypothalamic area."
- database_cross_reference "BTO:0002481"
lateral tuberal nucleus database_cross_reference centraldirectory.aspx?ID=428
lateral tuberal nucleus database_cross_reference "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=428"
- source "BIRNLEX:1206"
lateral tuberal nucleus has_exact_synonym "lateral tuberal nuclei"
- database_cross_reference "FMA:62336"
lateral tuberal nucleus label "lateral tuberal nucleus"
lateral tuberal nucleus database_cross_reference "FMA:62336"
lateral tuberal nucleus database_cross_reference "BM:TU"
lateral tuberal nucleus has_exact_synonym "lateral tuberal nuclear complex"
- database_cross_reference "BIRNLEX:1206"
lateral tuberal nucleus has_related_synonym "nucleus tuberis"
- has_synonym_type latin term
- database_cross_reference "NeuroNames:428"
lateral tuberal nucleus has_broad_synonym "LTu"
- database_cross_reference "BIRNLEX:1206"
- has_synonym_type abbreviation
- database_cross_reference "NIFSTD:NeuroNames_abbrevSource"
lateral tuberal nucleus database_cross_reference "UMLS:C0086527"
- source "BIRNLEX:1206"
lateral tuberal nucleus database_cross_reference "EV:0100240"
lateral tuberal nucleus has_related_synonym "nuclei tuberales laterales"
- database_cross_reference "BTO:0002481"
lateral tuberal nucleus database_cross_reference "BTO:0002481"
lateral tuberal nucleus has_related_synonym "nucleus tuberis lateralis"
- has_synonym_type latin term
- database_cross_reference "NeuroNames:428"
lateral tuberal nucleus has_related_synonym "nucleus tuberis hypothalami"
- has_synonym_type latin term
- database_cross_reference "NeuroNames:428"
lateral tuberal nucleus id "UBERON:0000435"
lateral tuberal nucleus database_cross_reference "HBA:12915"
Class: lateral tuberal nucleus
lateral tuberal nucleus SubClassOf hypothalamic nucleus
lateral tuberal nucleus SubClassOf part_of some lateral hypothalamic area

github-actions · 2022-05-30T03:05:30Z

This PR has not seen any activity in the past month; if nobody comments or reviews it in the next week, the PR editor will be allowed to proceed with merging without explicit approval, should they wish to do so.

This reverts commit 1b44f3d.

This reverts commit b635bd5.

github-actions · 2022-05-30T08:17:36Z

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/2022-06-09/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/2022-06-09/uberon-simple.owl
Loaded from: file:/work/src/ontology/uberon-simple.owl

Ontology imports

Ontology annotations

UBERON_8440041 `http://purl.obolibrary.org/obo/UBERON_8440041`

Added

UBERON_8440041 definition "A hypothalamic region in rodents that is homologous to the lateral tuberal nucleus in humans and higher primates and is involved in energy homeostasis."
- database_cross_reference "PMID:29976812"
- database_cross_reference "PMID:29976824"
UBERON_8440041 has_broad_synonym "lateral tuberal nucleus (sensu Rodentia)"
- database_cross_reference "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1890"
UBERON_8440041 database_cross_reference "MBA:614"
UBERON_8440041 curator notes "Lateral tuberal nucleus is listed as both an exact synonym and related synonym as the term has been used in both ways. See lateral tuberal nucleus is specific to humans and primates #2439 for more details. No homology links has been made as this is unclear from the literature."
UBERON_8440041 label "tuberal nucleus (sensu Rodentia)"
UBERON_8440041 database_cross_reference "DMBA:16271"
UBERON_8440041 id "UBERON:8440041"
UBERON_8440041 contributor 0000-0001-7258-9596
UBERON_8440041 has_exact_synonym "lateral tuberal nucleus (sensu Rodentia)"
- database_cross_reference "PMID:29976812"
UBERON_8440041 has_obo_namespace "uberon"
UBERON_8440041 comment "While lateral tuberal nucleus is often used interchangeably with tuberal nucleus in rodents, lateral tuberal nucleus is specific to humans and higher primates. In some cases, lateral tuberal nucleus is thought to be part of the tuberal nucleus in rodents, and could possibly be homologous to human tuberal region instead."
- database_cross_reference "PMID:1362279"
- database_cross_reference "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1890"
- database_cross_reference "PMID:29976824"
Class: UBERON_8440041
UBERON_8440041 SubClassOf hypothalamic nucleus

UBERON_8440042 `http://purl.obolibrary.org/obo/UBERON_8440042`

Added

UBERON_8440042 comment "This term is used specifically for fish (or Teleostei in general) as lateral tuberal nucleus (UBERON:0000435) refers to a structure that is specific to humans and higher primates. See lateral tuberal nucleus is specific to humans and primates #2439 for more details."
- database_cross_reference "PMID:1362279"
UBERON_8440042 label "nucleus lateralis tuberis system (sensu Teleostei)"
UBERON_8440042 definition "A prominent nucleus located in the ventral tuberal area of Teleostei that is anatomically homologous to the hypothalamic arcuate (infundibular)-median eminence (ME) system of tetrpods."
- database_cross_reference "PMID:25205931"
- database_cross_reference "DOI:10.1016/0016-6480(71)90165-1"
UBERON_8440042 has_obo_namespace "uberon"
UBERON_8440042 has_exact_synonym "NLT system (sensu Teleostei)"
- database_cross_reference "DOI:10.1016/0016-6480(71)90165-1"
UBERON_8440042 contributor 0000-0001-7258-9596
UBERON_8440042 id "UBERON:8440042"
Class: UBERON_8440042
UBERON_8440042 SubClassOf lateral hypothalamic nucleus

lateral tuberal nucleus `http://purl.obolibrary.org/obo/UBERON_0000435`

Removed

lateral tuberal nucleus database_cross_reference "MBA:614"
lateral tuberal nucleus database_cross_reference "DMBA:16271"

Added

lateral tuberal nucleus comment "The lateral tuberal nucleus is specific to humans and higher primates, however, this term is sometimes used loosely. If using for rodents, please use tuberal nucleus (sensu Rodentia) instead. If refering to the nucleus lateralis tuberis of fish, please use nucleus lateralis tuberis system (sensu Teleostei)"
- database_cross_reference "PMID:1362279"
- database_cross_reference "PMID:29976812"
- database_cross_reference "DOI:10.1016/0016-6480(71)90165-1"
- database_cross_reference "PMID:29976824"

github-actions · 2022-05-30T08:17:40Z

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/uberon-edit.obo

Right

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

Ontology imports

Ontology annotations

lateral tuberal nucleus `http://purl.obolibrary.org/obo/UBERON_0000435`

Removed

lateral tuberal nucleus comment "The lateral tuberal nucleus is specific to humans and higher primates, however, this term is sometimes used loosely. If using for rodents, please use tuberal nucleus (sensu Rodentia) instead. If refering to the nucleus lateralis tuberis of fish, please use nucleus lateralis tuberis system (sensu Teleostei)"^^string
- database_cross_reference "DOI:10.1016/0016-6480(71)90165-1"^^string
- database_cross_reference "PMID:29976824"^^string
- database_cross_reference "PMID:1362279"^^string
- database_cross_reference "PMID:29976812"^^string
lateral tuberal nucleus SubClassOf in taxon some Primates

Added

lateral tuberal nucleus database_cross_reference "DMBA:16271"^^string
lateral tuberal nucleus database_cross_reference "MBA:614"^^string

nucleus lateralis tuberis system (sensu Teleostei) `http://purl.obolibrary.org/obo/UBERON_8440042`

Removed

nucleus lateralis tuberis system (sensu Teleostei) definition "A prominent nucleus located in the ventral tuberal area of Teleostei that is anatomically homologous to the hypothalamic arcuate (infundibular)-median eminence (ME) system of tetrpods."^^string
- database_cross_reference "DOI:10.1016/0016-6480(71)90165-1"^^string
- database_cross_reference "PMID:25205931"^^string
nucleus lateralis tuberis system (sensu Teleostei) has_obo_namespace "uberon"^^string
nucleus lateralis tuberis system (sensu Teleostei) id "UBERON:8440042"^^string
nucleus lateralis tuberis system (sensu Teleostei) contributor 0000-0001-7258-9596
nucleus lateralis tuberis system (sensu Teleostei) has_exact_synonym "NLT system (sensu Teleostei)"^^string
- database_cross_reference "DOI:10.1016/0016-6480(71)90165-1"^^string
nucleus lateralis tuberis system (sensu Teleostei) label "nucleus lateralis tuberis system (sensu Teleostei)"^^string
nucleus lateralis tuberis system (sensu Teleostei) comment "This term is used specifically for fish (or Teleostei in general) as lateral tuberal nucleus (UBERON:0000435) refers to a structure that is specific to humans and higher primates. See lateral tuberal nucleus is specific to humans and primates #2439 for more details."^^string
- database_cross_reference "PMID:1362279"^^string
Class: nucleus lateralis tuberis system (sensu Teleostei)
nucleus lateralis tuberis system (sensu Teleostei) SubClassOf lateral hypothalamic nucleus
nucleus lateralis tuberis system (sensu Teleostei) SubClassOf in taxon some Teleostei

tuberal nucleus (sensu Rodentia) `http://purl.obolibrary.org/obo/UBERON_8440041`

Removed

tuberal nucleus (sensu Rodentia) has_broad_synonym "lateral tuberal nucleus (sensu Rodentia)"^^string
- database_cross_reference "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1890"^^[string](http://www.w3.org/2001/XMLSchema#string)
tuberal nucleus (sensu Rodentia) contributor 0000-0001-7258-9596
tuberal nucleus (sensu Rodentia) id "UBERON:8440041"^^string
tuberal nucleus (sensu Rodentia) label "tuberal nucleus (sensu Rodentia)"^^string
tuberal nucleus (sensu Rodentia) comment "While lateral tuberal nucleus is often used interchangeably with tuberal nucleus in rodents, lateral tuberal nucleus is specific to humans and higher primates. In some cases, lateral tuberal nucleus is thought to be part of the tuberal nucleus in rodents, and could possibly be homologous to human tuberal region instead."^^string
- database_cross_reference "PMID:29976824"^^string
- database_cross_reference "PMID:1362279"^^string
- database_cross_reference "http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=1890"^^[string](http://www.w3.org/2001/XMLSchema#string)
tuberal nucleus (sensu Rodentia) database_cross_reference "DMBA:16271"^^string
tuberal nucleus (sensu Rodentia) curator notes "Lateral tuberal nucleus is listed as both an exact synonym and related synonym as the term has been used in both ways. See lateral tuberal nucleus is specific to humans and primates #2439 for more details. No homology links has been made as this is unclear from the literature."^^string
tuberal nucleus (sensu Rodentia) definition "A hypothalamic region in rodents that is homologous to the lateral tuberal nucleus in humans and higher primates and is involved in energy homeostasis."^^string
- database_cross_reference "PMID:29976824"^^string
- database_cross_reference "PMID:29976812"^^string
tuberal nucleus (sensu Rodentia) database_cross_reference "MBA:614"^^string
tuberal nucleus (sensu Rodentia) has_obo_namespace "uberon"^^string
tuberal nucleus (sensu Rodentia) has_exact_synonym "lateral tuberal nucleus (sensu Rodentia)"^^string
- database_cross_reference "PMID:29976812"^^string
Class: tuberal nucleus (sensu Rodentia)
tuberal nucleus (sensu Rodentia) SubClassOf part of some hypothalamus
tuberal nucleus (sensu Rodentia) SubClassOf in taxon some Rodentia
tuberal nucleus (sensu Rodentia) SubClassOf nucleus of brain

This reverts commit eae85b0.

Added tuberal nucleus (sensu Rodentia) and nucleus lateralis tuberis …

a4d6ba6

…system (sensu Teleostei) Fixes #2439

shawntanzk requested review from dosumis and tgbugs April 29, 2022 08:00

shawntanzk self-assigned this Apr 29, 2022

Update uberon-edit.obo

52cc421

shawntanzk marked this pull request as draft April 29, 2022 13:20

shawntanzk added 2 commits April 29, 2022 14:22

Revert "Update uberon-edit.obo"

517fa22

This reverts commit 52cc421.

Update uberon-edit.obo

c2ed6e8

shawntanzk marked this pull request as ready for review April 29, 2022 13:25

patrick-lloyd-ray reviewed Apr 29, 2022

View reviewed changes

Comment thread src/ontology/uberon-edit.obo Outdated

patrick-lloyd-ray reviewed Apr 29, 2022

View reviewed changes

Comment thread src/ontology/uberon-edit.obo

Update uberon-edit.obo

c890075

github-actions Bot added the unreviewed label May 30, 2022

shawntanzk added 3 commits May 30, 2022 14:20

fix clashing ID

1b44f3d

Revert "fix clashing ID"

b635bd5

This reverts commit 1b44f3d.

Revert "Revert "fix clashing ID""

b870799

This reverts commit b635bd5.

Merge branch 'master' into add-tuberal-nucleus-for-rodent-and-fish

684d56c

shawntanzk removed the unreviewed label Jun 9, 2022

shawntanzk added 3 commits June 9, 2022 13:14

remove primate restriction

eae85b0

Update uberon-edit.obo

aed4f78

Revert "remove primate restriction"

6742019

This reverts commit eae85b0.

shawntanzk merged commit cccc162 into master Jun 9, 2022

shawntanzk deleted the add-tuberal-nucleus-for-rodent-and-fish branch June 9, 2022 06:51

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shawntanzk commented Apr 29, 2022

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Ontology imports

Ontology annotations

_:genid2147483648

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shawntanzk commented Apr 29, 2022 •

edited

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