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Curated some MONDO-MeSH mappings (sumir) #152

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Mar 11, 2024
Merged

Curated some MONDO-MeSH mappings (sumir) #152

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3878016
Curated 4 mappings (sumir)
sumirp Sep 6, 2023
8a25203
Curated 5 mappings (sumir)
sumirp Sep 14, 2023
bf08a4f
Curated 5 mappings (sumir)
sumirp Sep 18, 2023
145ceaf
Merge branch 'master' into pr/152
cthoyt Mar 11, 2024
59fcb82
Fix some
cthoyt Mar 11, 2024
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1 change: 1 addition & 0 deletions src/biomappings/resources/incorrect.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -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

mondo 0021661 coronary atherosclerosis skos:exactMatch mesh D003324 Coronary Artery Disease semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0044346 echinococcus granulosus infectious disease skos:exactMatch mesh D048209 Echinococcus granulosus semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0100073 methicillin-resistant staphylococcus aureus infectious disease skos:exactMatch mesh D055624 Methicillin-Resistant Staphylococcus aureus semapv:ManualMappingCuration orcid:0000-0001-9439-5346
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13 changes: 13 additions & 0 deletions 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.

Original file line number Diff line number Diff line change
Expand Up @@ -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

mondo 0005607 chronic bronchitis skos:exactMatch mesh D029481 Bronchitis, Chronic semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0006033 diffuse intrinsic pontine glioma skos:exactMatch mesh D000080443 Diffuse Intrinsic Pontine Glioma semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0006094 Askin tumor skos:exactMatch mesh C563168 Askin Tumor semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand All @@ -8920,11 +8921,13 @@ mondo 0007440 major affective disorder 1 skos:exactMatch mesh C565111 Major Affe
mondo 0007459 dilution, pigmentary skos:exactMatch mesh C566872 Dilution, Pigmentary semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0007547 epidermoid cysts skos:exactMatch mesh D004814 Epidermal Cyst semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0007578 esterase B skos:exactMatch mesh C049262 esterase B semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0007608 desmoid tumor skos:exactMatch mesh D018222 Fibromatosis, Aggressive semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
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

mondo 0008163 otofaciocervical syndrome skos:exactMatch mesh C563481 Otofaciocervical Syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0008197 parietal foramina 1 skos:exactMatch mesh C566827 Parietal Foramina 1 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0008273 actinic prurigo skos:exactMatch mesh C566780 Actinic Prurigo semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand All @@ -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

mondo 0009003 achromatopsia 2 skos:exactMatch mesh C536128 Achromatopsia 2 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0009097 persistent hyperplastic primary vitreous, autosomal recessive skos:exactMatch mesh C566966 Persistent Hyperplastic Primary Vitreous, Autosomal Recessive semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mondo 0009130 Dyggve-Melchior-Clausen disease skos:exactMatch mesh C535726 Dyggve-Melchior-Clausen syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand All @@ -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

mondo 0010391 angioma serpiginosum, X-linked skos:exactMatch mesh C536366 Angioma serpiginosum, X-linked semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0010535 Bazex-Dupre-Christol syndrome skos:exactMatch mesh C537663 Bazex-Dupre-Christol syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0010623 ichthyosis and male hypogonadism skos:exactMatch mesh C537365 Ichthyosis and male hypogonadism semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand All @@ -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.

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

mondo 0011544 paragangliomas 3 skos:exactMatch mesh C565335 Paragangliomas 3 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0011713 melanoma-pancreatic cancer syndrome skos:exactMatch mesh C563985 Melanoma-Pancreatic Cancer Syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0011826 glucocorticoid deficiency 2 skos:exactMatch mesh C564577 Glucocorticoid Deficiency 2 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand All @@ -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

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

mondo 0013129 cone dystrophy 4 skos:exactMatch mesh C567758 Cone Dystrophy 4 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0013199 tuberous sclerosis 2 skos:exactMatch mesh C566021 Tuberous Sclerosis 2 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0013203 corneal dystrophy, Fuchs endothelial, 3 skos:exactMatch mesh C567678 Corneal Dystrophy, Fuchs Endothelial, 3 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand Down Expand Up @@ -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.

mondo 0019669 hypochondrogenesis skos:exactMatch mesh C563007 Hypochondrogenesis semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0019760 terminal transverse defects of arm skos:exactMatch mesh C565681 Terminal Transverse Defects of Arm semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0019804 tracheomalacia skos:exactMatch mesh D055090 Tracheomalacia semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand All @@ -9046,6 +9056,7 @@ mondo 0020540 ovarian gynandroblastoma skos:exactMatch mesh C538459 Ovarian gyna
mondo 0020756 migraine, familial hemiplegic, 1 skos:exactMatch mesh C536890 Hemiplegic migraine, familial type 1 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0020792 dwarfism with tall vertebrae skos:exactMatch mesh C535725 Dwarfism tall vertebrae semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0020806 sinoatrial block skos:exactMatch mesh D012848 Sinoatrial Block semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0021053 carotid body paraganglioma skos:exactMatch mesh D002345 Carotid Body Tumor semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
mondo 0021065 pleural neoplasm skos:exactMatch mesh D010997 Pleural Neoplasms semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0021092 fallopian tube neoplasm skos:exactMatch mesh D005185 Fallopian Tube Neoplasms semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0021106 laminopathy skos:exactMatch mesh D000083083 Laminopathies semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand Down Expand Up @@ -9077,9 +9088,11 @@ mondo 0041161 endometrial hyperplasia skos:exactMatch mesh D004714 Endometrial H
mondo 0041656 ST-elevation myocardial infarction skos:exactMatch mesh D000072657 ST Elevation Myocardial Infarction semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0041751 multibacillary leprosy skos:exactMatch mesh D056006 Leprosy, Multibacillary semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0041752 paucibacillary leprosy skos:exactMatch mesh D056005 Leprosy, Paucibacillary semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0044746 zoonotic bacterial infection skos:exactMatch mesh D000086966 Bacterial Zoonoses semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
mondo 0044877 paraneoplastic cerebellar degeneration skos:exactMatch mesh D020362 Paraneoplastic Cerebellar Degeneration semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0054868 meconium ileus skos:exactMatch mesh D000074270 Meconium Ileus semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0100053 anaphylaxis skos:exactMatch mesh D000707 Anaphylaxis semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0100064 tyrosine hydroxylase deficiency skos:exactMatch mesh C537537 Segawa syndrome, autosomal recessive semapv:ManualMappingCuration orcid:0000-0002-1216-4761 semapv:LexicalMatching generate_mondo_mesh_mappings.py 0.9
mondo 0100075 jaw fracture skos:exactMatch mesh D007572 Jaw Fractures semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0100115 acute flaccid myelitis skos:exactMatch mesh C000629404 acute flaccid myelitis semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mondo 0100120 vector-borne disease skos:exactMatch mesh D000079426 Vector Borne Diseases semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand Down
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