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Curated some MONDO-MeSH mappings (sumir) #152

Merged
merged 5 commits into from
Mar 11, 2024
Merged

Curated some MONDO-MeSH mappings (sumir) #152

merged 5 commits into from
Mar 11, 2024

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sumirp
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@sumirp sumirp commented Sep 6, 2023

Hi I have curated 4 mappings. Kindly let me know if there are any errors. Thanks

cthoyt
cthoyt reviewed Sep 22, 2023
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src/biomappings/resources/incorrect.tsv
@@ -883,6 +883,7 @@ mondo 0007028 rotator cuff syndrome skos:exactMatch mesh D000070636 Rotator Cuff
mondo 0007323 Chondronectin skos:exactMatch mesh C029172 chondronectin protein, human semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mondo 0015053 hereditary angioedema type 1 skos:exactMatch mesh D056829 Hereditary Angioedema Types I and II semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0020320 acute myeloblastic leukemia with maturation skos:exactMatch mesh D000650 Amnion semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0021248 nervous system neoplasm skos:exactMatch mesh D009380 Neoplasms, Nerve Tissue semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
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agreed

cthoyt
cthoyt reviewed Sep 22, 2023
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src/biomappings/resources/mappings.tsv Outdated
@@ -8908,6 +8908,7 @@ mondo 0001688 toxic optic neuropathy skos:exactMatch mesh D000081028 Toxic Optic
mondo 0002012 methylmalonic acidemia skos:exactMatch mesh C537358 Methylmalonic acidemia semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0002648 mammary Paget disease skos:exactMatch mesh D010144 Paget's Disease, Mammary semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0005161 human papilloma virus infection skos:exactMatch mesh D030361 Papillomavirus Infections semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mondo 0005594 severe cutaneous adverse reaction skos:exactMatch mesh D002921 Cicatrix semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
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agreed

cthoyt
cthoyt reviewed Sep 22, 2023
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src/biomappings/resources/mappings.tsv Outdated
mondo 0007767 hyperparathyroidism 1 skos:exactMatch mesh C564166 Hyperparathyroidism 1 semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mondo 0007817 IgE responsiveness, atopic skos:exactMatch mesh C564133 Ige Responsiveness, Atopic semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0007909 familial multiple lipomatosis skos:exactMatch mesh D000071070 Familial Multiple Lipomatosis semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0007942 Mammastatin skos:exactMatch mesh C060120 mammastatin semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0008062 narcolepsy 1 skos:exactMatch mesh C563534 Narcolepsy 1 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0008161 otodental syndrome skos:exactMatch mesh C563482 Otodental Dysplasia semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
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agreed

cthoyt
cthoyt reviewed Sep 22, 2023
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src/biomappings/resources/mappings.tsv Outdated
@@ -8935,6 +8938,7 @@ mondo 0008597 trichorhinophalangeal syndrome, type III skos:exactMatch mesh C566
mondo 0008612 tuberous sclerosis 1 skos:exactMatch mesh C565346 Tuberous Sclerosis 1 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0008734 adrenocortical carcinoma, hereditary skos:exactMatch mesh C565972 Adrenocortical Carcinoma, Hereditary semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0008738 aganglionosis, total intestinal skos:exactMatch mesh C538058 Aganglionosis, total intestinal semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0008990 cleft larynx, posterior skos:exactMatch mesh C537851 Novak syndrome semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
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agreed

cthoyt
cthoyt reviewed Sep 22, 2023
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src/biomappings/resources/mappings.tsv
@@ -8959,6 +8963,7 @@ mondo 0010131 thyroid hormone resistance, generalized, autosomal recessive skos:
mondo 0010186 vitamin D-dependent rickets, type 2A skos:exactMatch mesh C562794 Vitamin D-Dependent Rickets, Type 2A semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0010201 Winchester syndrome skos:exactMatch mesh C536709 Winchester syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0010261 microphthalmia, syndromic 2 skos:exactMatch mesh C537465 Microphthalmia, syndromic 2 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0010323 Atkin-Flaitz syndrome skos:exactMatch mesh C538195 Atkin syndrome semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
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agreed

cthoyt
cthoyt reviewed Sep 22, 2023
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src/biomappings/resources/mappings.tsv Outdated
@@ -8967,8 +8972,10 @@ mondo 0010693 nystagmus 1, congenital, X-linked skos:exactMatch mesh C537853 Nys
mondo 0010717 pyruvate dehydrogenase E1-alpha deficiency skos:exactMatch mesh C564071 Pyruvate Dehydrogenase E1 Alpha Deficiency semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0010743 thrombocytopenia 1 skos:exactMatch mesh C564052 Thrombocytopenia 1 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0010760 XH antigen skos:exactMatch mesh C009691 Xh antigen semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0010778 cyclic vomiting syndrome skos:exactMatch mesh C536228 Familial cyclic vomiting syndrome semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
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it's not clear from the MONDO entry if these are an exact match, or if a "familial" variant is a narrower match

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@cthoyt in this case although the OMIM entry is mentioned in both Mondo and Mesh, but because of the lack of clarity it would be advisable to put this in the unsure group.

cthoyt
cthoyt reviewed Sep 22, 2023
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src/biomappings/resources/mappings.tsv Outdated
mondo 0011042 Martinez-Frias syndrome skos:exactMatch mesh C563346 Martinez-Frias Syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0011120 neural tube defects, folate-sensitive skos:exactMatch mesh C536409 Neural tube defect, folate-sensitive semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0011232 migraine, familial hemiplegic, 2 skos:exactMatch mesh C537246 Hemiplegic migraine, familial type 2 semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
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agreed

cthoyt
cthoyt reviewed Sep 22, 2023
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src/biomappings/resources/mappings.tsv
@@ -8987,6 +8994,8 @@ mondo 0012425 corneal dystrophy, fuchs endothelial, 2 skos:exactMatch mesh C5354
mondo 0012484 prosopagnosia, hereditary skos:exactMatch mesh C537242 Prosopagnosia, hereditary semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0012522 diabetes mellitus, transient neonatal, 3 skos:exactMatch mesh C566432 Diabetes Mellitus, Transient Neonatal, 3 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0012548 Kostmann syndrome skos:exactMatch mesh C537592 Neutropenia, Severe Congenital, Autosomal Recessive 3 semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mondo 0012914 chromosome 1q21.1 deletion syndrome skos:exactMatch mesh C567291 Chromosome 1q21.1 Deletion Syndrome, 1.35-Mb semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
mondo 0012937 Diamond-Blackfan anemia 6 skos:exactMatch mesh C538442 Aase Smith syndrome 2 semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
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agreed

cthoyt
cthoyt reviewed Sep 22, 2023
View reviewed changes
src/biomappings/resources/mappings.tsv
@@ -8987,6 +8994,8 @@ mondo 0012425 corneal dystrophy, fuchs endothelial, 2 skos:exactMatch mesh C5354
mondo 0012484 prosopagnosia, hereditary skos:exactMatch mesh C537242 Prosopagnosia, hereditary semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0012522 diabetes mellitus, transient neonatal, 3 skos:exactMatch mesh C566432 Diabetes Mellitus, Transient Neonatal, 3 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0012548 Kostmann syndrome skos:exactMatch mesh C537592 Neutropenia, Severe Congenital, Autosomal Recessive 3 semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mondo 0012914 chromosome 1q21.1 deletion syndrome skos:exactMatch mesh C567291 Chromosome 1q21.1 Deletion Syndrome, 1.35-Mb semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
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agreed

cthoyt
cthoyt reviewed Sep 22, 2023
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src/biomappings/resources/mappings.tsv Outdated
@@ -9037,6 +9046,7 @@ mondo 0019107 Rh deficiency syndrome skos:exactMatch mesh C562717 Rh Deficiency
mondo 0019155 Leydig cell hypoplasia skos:exactMatch mesh C562567 Leydig Cell Hypoplasia semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0019169 pyruvate dehydrogenase deficiency skos:exactMatch mesh D015325 Pyruvate Dehydrogenase Complex Deficiency Disease semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0019353 Stargardt disease skos:exactMatch mesh D000080362 Stargardt Disease semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0019636 renal agenesis, unilateral skos:exactMatch mesh D000075529 Solitary Kidney semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
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the MONDO term appears to be specific towards the developmental condition whereas the MeSH term appears to be more about the effect

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@sumirp will you look into this?

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@cthoyt yes i agree this is not an exact match as you mentioned.

sumirp
sumirp commented Oct 11, 2023
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src/biomappings/resources/mappings.tsv
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@cthoyt I have checked the rest and it looks fine to me except for zoonotic bacterial infection, which I cannot seem to find in Mondo.

cthoyt
cthoyt approved these changes Mar 11, 2024
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Just made 2 small fixes for the mappings we decided weren't exact. Will merge after tests pass, thanks @sumirp

@cthoyt cthoyt changed the title Curated 4 mappings (sumir) Curated some MONDO-MeSH mappings (sumir) Mar 11, 2024
@cthoyt cthoyt merged commit 826cd08 into biopragmatics:master Mar 11, 2024
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sumirp commented Mar 11, 2024

@cthoyt Thank you

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@sumirp @cthoyt