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Curated some MONDO-MeSH mappings (sumir) #152

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merged 5 commits into from
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 @@ -897,6 +897,7 @@ 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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11 changes: 11 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 @@ -8966,6 +8966,7 @@ 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
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agreed

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
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 @@ -8978,11 +8979,13 @@ 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
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 @@ -8993,6 +8996,7 @@ 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
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agreed

mondo 0008738 aganglionosis, total intestinal skos:exactMatch mesh C538058 Aganglionosis, total intestinal semapv:ManualMappingCuration orcid:0000-0001-9439-5346
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agreed

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
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 @@ -9017,6 +9021,7 @@ 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
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 @@ -9027,6 +9032,7 @@ mondo 0010743 thrombocytopenia 1 skos:exactMatch mesh C564052 Thrombocytopenia 1
mondo 0010760 XH antigen skos:exactMatch mesh C009691 Xh antigen semapv:ManualMappingCuration orcid:0000-0001-9439-5346
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
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 @@ -9045,6 +9051,8 @@ 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
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 @@ -9104,6 +9112,7 @@ 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 @@ -9135,9 +9144,11 @@ 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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