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Added morphology and related traits #214

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merged 10 commits into from
Feb 14, 2023
Merged

Added morphology and related traits #214

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a3f5b78
Added morphology and related traits
ar-ibrahim Feb 9, 2023
00dc56a
Update oba-efo.sssom.tsv
ar-ibrahim Feb 9, 2023
e492f32
Merge branch 'master' into issue_213
rays22 Feb 10, 2023
a3787f3
Update entity_attribute.tsv
ar-ibrahim Feb 14, 2023
fafe205
Update oba-efo.sssom.tsv
ar-ibrahim Feb 14, 2023
8f8e053
Refresh definitions
rays22 Feb 14, 2023
5e2f7fc
Restore mapping file to master version
rays22 Feb 14, 2023
feff0ed
Refresh merged import
rays22 Feb 14, 2023
2d1b920
Update dosdp patterns file
rays22 Feb 14, 2023
dabe4f0
Restore synonyms.tsv file to master version
rays22 Feb 14, 2023
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28 changes: 27 additions & 1 deletion src/mappings/oba-efo.sssom.tsv
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Expand Up @@ -146,4 +146,30 @@ GO:1903492 response to aspirin response to stimulus skos:relatedMatch OBA:204001
GO:1903493 response to clopidogrel response to stimulus skos:relatedMatch OBA:2040062 HumanCurated EFO OBA 2022-06-29 orcid:0000-0001-8314-2140
GO:1904014 response to serotonin response to stimulus skos:relatedMatch OBA:2040027 HumanCurated EFO OBA 2022-06-29 orcid:0000-0001-8314-2140
GO:1905119 response to haloperidol response to stimulus skos:relatedMatch OBA:2040092 HumanCurated EFO OBA 2022-06-29 orcid:0000-0001-8314-2140
GO:1990054 response to temozolomide response to stimulus skos:relatedMatch OBA:2040120 HumanCurated EFO OBA 2022-06-29 orcid:0000-0001-8314-2140
GO:1990054 response to temozolomide response to stimulus skos:relatedMatch OBA:2040120 HumanCurated EFO OBA 2022-06-29 orcid:0000-0001-8314-2140
EFO:0010076 femoral neck size measurement skos:exactMatch OBA:0002725 neck of femur size HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0010949 upper face morphology measurement measurement skos:broadMatch OBA:VT0003743 facial morphology trait HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0007824 hair shape measurement measurement skos:exactMatch OBA:0003493 strand of hair shape HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0004577 infant head circumference measurement skos:broadMatch OBA:VT0000047 head circumference HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0005852 Heschl's gyrus morphology measurement measurement skos:exactMatch OBA:VT0000803 transverse gyrus of Heschl morphology trait HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0005037 aortic root size measurement skos:exactMatch OBA:0005483 bulb of aorta size HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0007821 hair morphology measurement measurement skos:exactMatch OBA:VT0000367 coat/hair morphology trait HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0010948 lower face morphology measurement measurement skos:broadMatch OBA:VT0003743 facial morphology trait HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0004300 longevity measurement skos:exactMatch OBA:VT0005372 life span trait HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0004505 telomere length measurement skos:exactMatch OBA:2050100 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0007842 chin morphology measurement measurement skos:exactMatch OBA:2050101 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0009286 heart relative wall thickness measurement skos:broadMatch OBA:2050102 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0004844 hip bone size measurement skos:exactMatch OBA:2050103 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0600005 ganglion cell inner plexiform layer thickness measurement measurement skos:broadMatch OBA:2050104 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0009278 cranial vault morphology measurement measurement skos:exactMatch OBA:2050105 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0007844 forehead morphology measurement measurement skos:exactMatch OBA:2050106 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0005053 internal carotid intimal medial thickness measurement skos:broadMatch OBA:2050107 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0004860 common carotid intimal medial thickness measurement skos:broadMatch OBA:2050108 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0007739 left superior temporal gyrus thickness measurement measurement skos:broadMatch OBA:2050109 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0600002 retinal layer thickness measurement measurement skos:exactMatch OBA:2050110 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0600004 retinal nerve fibre layer thickness measurement measurement skos:exactMatch OBA:2050111 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0007823 facial hair thickness measurement measurement skos:exactMatch OBA:2050112 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0008593 ldl particle size measurement measurement skos:exactMatch OBA:2050113 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0008594 vldl particle size measurement measurement skos:exactMatch OBA:2050114 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0008592 hdl particle size measurement measurement skos:exactMatch OBA:2050115 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
EFO:0007117 carotid artery intima media thickness measurement skos:broadMatch OBA:2050108 HumanCurated EFO OBA 1 2023-02-09 orcid:0000-0001-6757-4744
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Please, remove thissrc/mappings/oba-efo.sssom.tsv version from the PR, because this version of the table has fewer lines than the OBA Ontology Development (GWAS, EFO, VT) gsheet.
Did you follow the 'Updating SSSOM mapping files' section of the Local development workflows with OBA?
This tsv should agree with the OBA Ontology Development (GWAS, EFO, VT) gsheet, but it does not.

16 changes: 16 additions & 0 deletions src/patterns/data/default/entity_attribute.tsv
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Expand Up @@ -4167,6 +4167,22 @@ OBA:2040170 GO:0030431 sleep PATO:0000001 quality
OBA:2040171 sleep duration trait GO:0030431 sleep PATO:0001309 duration
OBA:2040172 GO:0030431 sleep PATO:0001005 latency
OBA:2040173 GO:0030431 sleep PATO:0002325 onset quality
OBA:2050100 telomere length GO:0000781 chromosome, telomeric region PATO:0000122 length
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Suggested change
OBA:2050100 telomere length GO:0000781 chromosome, telomeric region PATO:0000122 length

There is already a term OBA:0003784 that has the same logical definition, so please drop OBA:2050100 from the table.

OBA:2050101 chin morphology trait UBERON:0008199 chin PATO:0000051 morphology
OBA:2050102 heart wall thickness UBERON:0037144 wall of heart PATO:0000915 thickness
OBA:2050103 hip bone size UBERON:0008202 bone of hip region PATO:0000117 size
OBA:2050104 ganglion thickness UBERON:0000045 ganglion PATO:0000915 thickness
OBA:2050105 cranial vault morphology trait UBERON:0004339 vault of skull PATO:0000051 morphology
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Suggested change
OBA:2050105 cranial vault morphology trait UBERON:0004339 vault of skull PATO:0000051 morphology

There is already a term OBA:VT0000076 that has the same logical definition, so please drop OBA:2050105 from the table.

OBA:2050106 forehead morphology trait UBERON:0008200 forehead PATO:0000051 morphology
OBA:2050107 internal carotid artery thickness UBERON:0001532 internal carotid artery PATO:0000915 thickness
OBA:2050108 carotid artery thickness UBERON:0005396 carotid artery segment PATO:0000915 thickness
OBA:2050109 superior temporal gyrus thickness UBERON:0002769 superior temporal gyrus PATO:0000915 thickness
OBA:2050110 retinal layer thickness UBERON:0001781 layer of retina PATO:0000915 thickness
OBA:2050111 retinal nerve fibre layer thickness UBERON:0001793 nerve fiber layer of retina PATO:0000915 thickness
OBA:2050112 facial hair thickness UBERON:0010171 strand of hair of face PATO:0000915 thickness
OBA:2050113 LDL particle size GO:0034362 low-density lipoprotein particle PATO:0000117 size low-density lipoprotein particle size
OBA:2050114 VLDL particle size GO:0034361 very-low-density lipoprotein particle PATO:0000117 size very-low-density lipoprotein particle size
OBA:2050115 HDL particle size GO:0034364 high-density lipoprotein particle PATO:0000117 size high-density lipoprotein particle size
OBA:2060179 body coordination efficacy NBO:0000351 body coordination PATO:0015002 process efficacy
OBA:2060180 limb coordination efficacy NBO:0000342 limb coordination PATO:0015002 process efficacy
OBA:2060181 upper limb coordination efficacy NBO:0000346 upper limb coordination PATO:0015002 process efficacy
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