From 38780161bda80ac5898a9c66b25316a81302a7ee Mon Sep 17 00:00:00 2001 From: SumirHPandit <46551795+sumirp@users.noreply.github.com> Date: Wed, 6 Sep 2023 19:39:27 +0530 Subject: [PATCH 1/4] Curated 4 mappings (sumir) --- src/biomappings/resources/mappings.tsv | 4 ++++ src/biomappings/resources/predictions.tsv | 4 ---- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/biomappings/resources/mappings.tsv b/src/biomappings/resources/mappings.tsv index 8dacf6b6..61abf659 100644 --- a/src/biomappings/resources/mappings.tsv +++ b/src/biomappings/resources/mappings.tsv @@ -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 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 @@ -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 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 @@ -8987,6 +8990,7 @@ 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 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 diff --git a/src/biomappings/resources/predictions.tsv b/src/biomappings/resources/predictions.tsv index 3fc56124..4b003db9 100644 --- a/src/biomappings/resources/predictions.tsv +++ b/src/biomappings/resources/predictions.tsv @@ -38730,14 +38730,11 @@ mesh D066259 Betacellulin skos:exactMatch hgnc 1121 BTC semapv:LexicalMatching 0 mesh D066261 Epigen skos:exactMatch hgnc 17470 EPGN semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py mondo 0001115 familial polycythemia skos:exactMatch mesh C536842 Polycythemia, primary familial and congenital semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0002814 adrenal carcinoma skos:exactMatch mesh D018268 Adrenocortical Carcinoma semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0005594 severe cutaneous adverse reaction skos:exactMatch mesh D002921 Cicatrix semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0006209 fibroblastic neoplasm skos:exactMatch mesh D005354 Fibrosarcoma semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0007116 hereditary neurocutaneous angioma skos:exactMatch mesh C536364 Angioma hereditary neurocutaneous semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0007608 desmoid tumor skos:exactMatch mesh D018222 Fibromatosis, Aggressive semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0007614 congenital fibrosis of extraocular muscles skos:exactMatch mesh C580012 Congenital Fibrosis of the Extraocular Muscles semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0007794 hypogonadotropic hypogonadism 7 with or without anosmia skos:exactMatch mesh C562785 Idiopathic Hypogonadotropic Hypogonadism semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0007876 laryngeal abductor paralysis skos:exactMatch mesh C536354 Vocal cord dysfunction familial semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0008161 otodental syndrome skos:exactMatch mesh C563482 Otodental Dysplasia semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0008718 Morvan syndrome skos:exactMatch mesh D020385 Myokymia semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0008751 corticosterone methyloxidase type 1 deficiency skos:exactMatch mesh C537806 18-Hydroxylase deficiency semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0008888 Williams-Campbell syndrome skos:exactMatch mesh D055089 Tracheobronchomalacia semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py @@ -38754,7 +38751,6 @@ mondo 0010831 familial caudal dysgenesis skos:exactMatch mesh C535879 Rudd Klime mondo 0010880 telangiectasia, hereditary hemorrhagic, type 2 skos:exactMatch mesh C537139 Osler-rendu-weber syndrome 2 semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0011232 migraine, familial hemiplegic, 2 skos:exactMatch mesh C537246 Hemiplegic migraine, familial type 2 semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0011898 Charcot-Marie-Tooth disease, axonal, with vocal cord paresis, autosomal recessive skos:exactMatch mesh C539595 Charcot-Marie-Tooth disease, Type 4A, axonal form semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0012914 chromosome 1q21.1 deletion syndrome skos:exactMatch mesh C567291 Chromosome 1q21.1 Deletion Syndrome, 1.35-Mb semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0012937 Diamond-Blackfan anemia 6 skos:exactMatch mesh C538442 Aase Smith syndrome 2 semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0013996 focal facial dermal dysplasia type II skos:exactMatch mesh C536385 Facial ectodermal dysplasia semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0014945 myopathy, distal, with rimmed vacuoles skos:exactMatch mesh C536816 Distal myopathy, Nonaka type semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py From 8a25203dba7fa73e8727b92140164d251a26cc49 Mon Sep 17 00:00:00 2001 From: SumirHPandit <46551795+sumirp@users.noreply.github.com> Date: Thu, 14 Sep 2023 18:19:56 +0530 Subject: [PATCH 2/4] Curated 5 mappings (sumir) --- src/biomappings/resources/incorrect.tsv | 1 + src/biomappings/resources/mappings.tsv | 4 ++++ src/biomappings/resources/predictions.tsv | 5 ----- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/biomappings/resources/incorrect.tsv b/src/biomappings/resources/incorrect.tsv index a535dc31..5ccf84b9 100644 --- a/src/biomappings/resources/incorrect.tsv +++ b/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 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 diff --git a/src/biomappings/resources/mappings.tsv b/src/biomappings/resources/mappings.tsv index 61abf659..9f4a3c93 100644 --- a/src/biomappings/resources/mappings.tsv +++ b/src/biomappings/resources/mappings.tsv @@ -9041,6 +9041,7 @@ 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 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 @@ -9050,6 +9051,7 @@ 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 @@ -9081,9 +9083,11 @@ 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 diff --git a/src/biomappings/resources/predictions.tsv b/src/biomappings/resources/predictions.tsv index 4b003db9..4c255dc5 100644 --- a/src/biomappings/resources/predictions.tsv +++ b/src/biomappings/resources/predictions.tsv @@ -38784,16 +38784,11 @@ mondo 0018951 distal myopathy with vocal cord weakness skos:exactMatch mesh C565 mondo 0019203 acute interstitial pneumonia skos:exactMatch mesh D000080203 Hamman-Rich Syndrome semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0019308 junctional epidermolysis bullosa inversa skos:exactMatch mesh C535958 Epidermolysis bullosa inversa dystrophica semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0019518 Waardenburg-Shah syndrome skos:exactMatch mesh C536467 Waardenburg syndrome, type 4 semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0019636 renal agenesis, unilateral skos:exactMatch mesh D000075529 Solitary Kidney semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0020506 ovarioleukodystrophy skos:exactMatch mesh C565836 Vanishing White Matter Leukodystrophy with Ovarian Failure semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0021053 carotid body paraganglioma skos:exactMatch mesh D002345 Carotid Body Tumor semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0021248 nervous system neoplasm skos:exactMatch mesh D009380 Neoplasms, Nerve Tissue semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0024685 Philadelphia-positive myelogenous leukemia skos:exactMatch mesh D015466 Leukemia, Myeloid, Chronic-Phase semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0030639 Teebi hypertelorism syndrome skos:exactMatch mesh C536951 Teebi syndrome semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0031169 odontochondrodysplasia skos:exactMatch mesh C535792 Spondylometaphyseal dysplasia with dentinogenesis imperfecta semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0044746 zoonotic bacterial infection skos:exactMatch mesh D000086966 Bacterial Zoonoses semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0100001 alpha-gal syndrome skos:exactMatch mesh C000655084 red meat allergy semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0100064 tyrosine hydroxylase deficiency skos:exactMatch mesh C537537 Segawa syndrome, autosomal recessive semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0100089 GATA1-Related X-Linked Cytopenia skos:exactMatch mesh C564525 Dyserythropoietic Anemia with Thrombocytopenia semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0100184 GTP cyclohydrolase I deficiency skos:exactMatch mesh C562656 Hyperphenylalaninemia, BH4-Deficient, B semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0100234 paroxysmal familial ventricular fibrillation skos:exactMatch mesh C537182 Paroxysmal ventricular fibrillation semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py From bf08a4ff49b3932d292cd030caa2585e7127682c Mon Sep 17 00:00:00 2001 From: SumirHPandit <46551795+sumirp@users.noreply.github.com> Date: Mon, 18 Sep 2023 16:19:15 +0530 Subject: [PATCH 3/4] Curated 5 mappings (sumir) --- src/biomappings/resources/mappings.tsv | 5 +++++ src/biomappings/resources/predictions.tsv | 5 ----- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/src/biomappings/resources/mappings.tsv b/src/biomappings/resources/mappings.tsv index 9f4a3c93..07f2536f 100644 --- a/src/biomappings/resources/mappings.tsv +++ b/src/biomappings/resources/mappings.tsv @@ -8938,6 +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 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 @@ -8962,6 +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 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 @@ -8970,8 +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 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 @@ -8991,6 +8995,7 @@ mondo 0012484 prosopagnosia, hereditary skos:exactMatch mesh C537242 Prosopagnos 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 diff --git a/src/biomappings/resources/predictions.tsv b/src/biomappings/resources/predictions.tsv index 4c255dc5..ad8e26e5 100644 --- a/src/biomappings/resources/predictions.tsv +++ b/src/biomappings/resources/predictions.tsv @@ -38738,20 +38738,15 @@ mondo 0007876 laryngeal abductor paralysis skos:exactMatch mesh C536354 Vocal co mondo 0008718 Morvan syndrome skos:exactMatch mesh D020385 Myokymia semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0008751 corticosterone methyloxidase type 1 deficiency skos:exactMatch mesh C537806 18-Hydroxylase deficiency semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0008888 Williams-Campbell syndrome skos:exactMatch mesh D055089 Tracheobronchomalacia semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0008990 cleft larynx, posterior skos:exactMatch mesh C537851 Novak syndrome semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0009336 hemosiderosis, pulmonary, with deficiency of gamma-a globulin skos:exactMatch mesh C536281 Idiopathic pulmonary hemosiderosis semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0009349 holoprosencephaly 1 skos:exactMatch mesh C562573 cyclopia sequence semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0009606 methemoglobinemia due to deficiency of methemoglobin reductase skos:exactMatch mesh C537841 NADH cytochrome B5 reductase deficiency semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0009622 Jawad syndrome skos:exactMatch mesh C567101 Microcephaly with Mental Retardation and Digital Anomalies semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0009809 multicentric osteolysis, nodulosis, and arthropathy skos:exactMatch mesh C536051 Osteolysis hereditary multicentric semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0010323 Atkin-Flaitz syndrome skos:exactMatch mesh C538195 Atkin syndrome semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0010746 thumbs, congenital Clasped skos:exactMatch mesh C562949 Adducted Thumbs Syndrome semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0010778 cyclic vomiting syndrome skos:exactMatch mesh C536228 Familial cyclic vomiting syndrome semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0010831 familial caudal dysgenesis skos:exactMatch mesh C535879 Rudd Klimek syndrome semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0010880 telangiectasia, hereditary hemorrhagic, type 2 skos:exactMatch mesh C537139 Osler-rendu-weber syndrome 2 semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0011232 migraine, familial hemiplegic, 2 skos:exactMatch mesh C537246 Hemiplegic migraine, familial type 2 semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0011898 Charcot-Marie-Tooth disease, axonal, with vocal cord paresis, autosomal recessive skos:exactMatch mesh C539595 Charcot-Marie-Tooth disease, Type 4A, axonal form semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py -mondo 0012937 Diamond-Blackfan anemia 6 skos:exactMatch mesh C538442 Aase Smith syndrome 2 semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0013996 focal facial dermal dysplasia type II skos:exactMatch mesh C536385 Facial ectodermal dysplasia semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0014945 myopathy, distal, with rimmed vacuoles skos:exactMatch mesh C536816 Distal myopathy, Nonaka type semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py mondo 0015450 triatrial heart skos:exactMatch mesh D003310 Cor Triatriatum semapv:LexicalMatching 0.9 generate_mondo_mesh_mappings.py From 59fcb82bda014fa511aa584f036f657b9e070537 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Mon, 11 Mar 2024 14:18:13 +0100 Subject: [PATCH 4/4] Fix some --- src/biomappings/resources/mappings.tsv | 2 -- src/biomappings/resources/unsure.tsv | 2 ++ 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/src/biomappings/resources/mappings.tsv b/src/biomappings/resources/mappings.tsv index a71a621c..abad42ce 100644 --- a/src/biomappings/resources/mappings.tsv +++ b/src/biomappings/resources/mappings.tsv @@ -9030,7 +9030,6 @@ 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 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 @@ -9104,7 +9103,6 @@ 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 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 diff --git a/src/biomappings/resources/unsure.tsv b/src/biomappings/resources/unsure.tsv index 85bfb790..fe9d13e0 100644 --- a/src/biomappings/resources/unsure.tsv +++ b/src/biomappings/resources/unsure.tsv @@ -82,6 +82,8 @@ mesh D021581 Active Transport, Cell Nucleus skos:exactMatch go GO:0051169 nuclea mesh D051716 Replication Protein A skos:exactMatch go GO:0005662 DNA replication factor A complex semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D059268 Atrophic Vaginitis skos:exactMatch doid DOID:11968 postmenopausal atrophic vaginitis semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh D063306 Mitochondrial Degradation skos:exactMatch go GO:0000423 mitophagy semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +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 +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 obi OBI:0000430 plasmid skos:exactMatch ncbitaxon 45202 unidentified plasmid semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching kestrel-mappings 0.778 obi OBI:0000737 cloning vector skos:exactMatch ncbitaxon 45196 unidentified cloning vector semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching kestrel-mappings 0.778 uberon UBERON:0002397 maxilla skos:exactMatch bto BTO:0006516 invertebrate maxilla semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/530a1b/scripts/generate_uberon_bto_mappings.py 0.556