From e7957b83941eb1eca13c31d70d29624f964da0f6 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 18 Aug 2023 16:03:34 +0200 Subject: [PATCH 1/5] Improve trackability of committer (#148) --- src/biomappings/resources/__init__.py | 5 ++++- src/biomappings/testing.py | 5 ++++- src/biomappings/wsgi.py | 7 ++++--- 3 files changed, 12 insertions(+), 5 deletions(-) diff --git a/src/biomappings/resources/__init__.py b/src/biomappings/resources/__init__.py index 24208a16..47665fc2 100644 --- a/src/biomappings/resources/__init__.py +++ b/src/biomappings/resources/__init__.py @@ -477,9 +477,12 @@ def _standardize_mapping(mapping): return mapping +CURATORS_PATH = get_resource_file_path("curators.tsv") + + def load_curators(): """Load the curators table.""" - return _load_table(get_resource_file_path("curators.tsv")) + return _load_table(CURATORS_PATH) def filter_predictions(custom_filter: Mapping[str, Mapping[str, Mapping[str, str]]]) -> None: diff --git a/src/biomappings/testing.py b/src/biomappings/testing.py index 42d08cad..6e86550d 100644 --- a/src/biomappings/testing.py +++ b/src/biomappings/testing.py @@ -9,6 +9,7 @@ import bioregistry from biomappings.resources import ( + CURATORS_PATH, Mappings, MappingTuple, PredictionTuple, @@ -126,7 +127,9 @@ def test_contributors(self): for mapping in itt.chain(self.mappings, self.incorrect, self.unsure): source = mapping["source"] if not source.startswith("orcid:"): - continue + self.assertTrue(source.startswith("web-")) + ss = source[len("web-") :] + self.fail(msg=f'Add an entry with "{ss}" and your ORCID to {CURATORS_PATH}') self.assertIn(source[len("orcid:") :], contributor_orcids) def test_cross_redundancy(self): diff --git a/src/biomappings/wsgi.py b/src/biomappings/wsgi.py index 306e409f..6e44fa65 100644 --- a/src/biomappings/wsgi.py +++ b/src/biomappings/wsgi.py @@ -132,11 +132,12 @@ def get_app( KNOWN_USERS = {record["user"]: record["orcid"] for record in load_curators()} -def _manual_source(): - known_user = KNOWN_USERS.get(getpass.getuser()) +def _manual_source() -> str: + usr = getpass.getuser() + known_user = KNOWN_USERS.get(usr) if known_user: return f"orcid:{known_user}" - return "web" + return f"web-{usr}" class Controller: From 0523be109c6715883cae4c7a40328d6e1441124f Mon Sep 17 00:00:00 2001 From: Sangeetha Vempati Date: Mon, 14 Aug 2023 08:43:53 -0700 Subject: [PATCH 2/5] Curated 1 mapping (sangeethavempati) --- src/biomappings/resources/mappings.tsv | 1 + src/biomappings/resources/predictions.tsv | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biomappings/resources/mappings.tsv b/src/biomappings/resources/mappings.tsv index 9410f984..4c5a857d 100644 --- a/src/biomappings/resources/mappings.tsv +++ b/src/biomappings/resources/mappings.tsv @@ -4757,6 +4757,7 @@ mesh C535600 dopamine beta hydroxylase deficiency skos:exactMatch doid DOID:0090 mesh C535601 Dosage-sensitive sex reversal skos:exactMatch doid DOID:0111777 46,XY sex reversal 2 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535602 Doyne honeycomb retinal dystrophy skos:exactMatch doid DOID:0060745 Doyne honeycomb retinal dystrophy semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535607 Aicardi-Goutieres syndrome skos:exactMatch doid DOID:0050629 Aicardi-Goutieres syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +mesh C535618 Hairy elbows skos:exactMatch hp HP:0004780 Elbow hypertrichosis semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535627 Hand foot uterus syndrome skos:exactMatch doid DOID:0060739 hand-foot-genital syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535642 Growth retardation, Alopecia, Pseudoanodontia and Optic atrophy skos:exactMatch doid DOID:0112249 GAPO syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C535658 Acromesomelic dysplasia skos:exactMatch doid DOID:0080049 acromesomelic dysplasia semapv:ManualMappingCuration orcid:0000-0003-1307-2508 diff --git a/src/biomappings/resources/predictions.tsv b/src/biomappings/resources/predictions.tsv index 5878ea00..7bcbb8b7 100644 --- a/src/biomappings/resources/predictions.tsv +++ b/src/biomappings/resources/predictions.tsv @@ -24470,7 +24470,6 @@ mesh C535586 Carnevale syndrome skos:exactMatch efo 1001977 3MC syndrome 2 semap mesh C535588 Carnitine palmitoyl transferase 1A deficiency skos:exactMatch ncit C98871 Carnitine Palmitoyltransferase I Deficiency semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535598 Creatine deficiency, X-linked skos:exactMatch doid DOID:0050800 creatine transporter deficiency semapv:LexicalMatching 0.9 generate_doid_mesh_mappings.py mesh C535608 Aicardi-Goutieres syndrome 5 skos:exactMatch ncit C168564 Aicardi-Goutieres Syndrome 5 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh C535618 Hairy elbows skos:exactMatch hp HP:0004780 Elbow hypertrichosis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535648 Familial primary gastric lymphoma skos:exactMatch hp HP:0045038 Gastric lymphoma semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535658 Acromesomelic dysplasia skos:exactMatch doid DOID:0080051 acromesomelic dysplasia, Hunter-Thompson type semapv:LexicalMatching 0.9 generate_doid_mesh_mappings.py mesh C535683 Rigid spine syndrome skos:exactMatch ncit C126691 Rigid Spine Muscular Dystrophy 1 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py From 5e56d000596553f2321c673f4e35b0a67a07cf90 Mon Sep 17 00:00:00 2001 From: Sangeetha Vempati Date: Mon, 14 Aug 2023 09:05:11 -0700 Subject: [PATCH 3/5] Curated 2 mappings (sangeethavempati) --- src/biomappings/resources/mappings.tsv | 1 + src/biomappings/resources/predictions.tsv | 1 - 2 files changed, 1 insertion(+), 1 deletion(-) diff --git a/src/biomappings/resources/mappings.tsv b/src/biomappings/resources/mappings.tsv index 4c5a857d..e676b680 100644 --- a/src/biomappings/resources/mappings.tsv +++ b/src/biomappings/resources/mappings.tsv @@ -4760,6 +4760,7 @@ mesh C535607 Aicardi-Goutieres syndrome skos:exactMatch doid DOID:0050629 Aicard mesh C535618 Hairy elbows skos:exactMatch hp HP:0004780 Elbow hypertrichosis semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535627 Hand foot uterus syndrome skos:exactMatch doid DOID:0060739 hand-foot-genital syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535642 Growth retardation, Alopecia, Pseudoanodontia and Optic atrophy skos:exactMatch doid DOID:0112249 GAPO syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +mesh C535648 Familial primary gastric lymphoma skos:exactMatch hp HP:0045038 Gastric lymphoma semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535658 Acromesomelic dysplasia skos:exactMatch doid DOID:0080049 acromesomelic dysplasia semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535661 Acromesomelic dysplasia, Maroteaux type skos:exactMatch doid DOID:0080050 acromesomelic dysplasia, Maroteaux type semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535662 Acromicric dysplasia skos:exactMatch doid DOID:0111243 acromicric dysplasia semapv:ManualMappingCuration orcid:0000-0003-1307-2508 diff --git a/src/biomappings/resources/predictions.tsv b/src/biomappings/resources/predictions.tsv index 7bcbb8b7..f71100ed 100644 --- a/src/biomappings/resources/predictions.tsv +++ b/src/biomappings/resources/predictions.tsv @@ -24470,7 +24470,6 @@ mesh C535586 Carnevale syndrome skos:exactMatch efo 1001977 3MC syndrome 2 semap mesh C535588 Carnitine palmitoyl transferase 1A deficiency skos:exactMatch ncit C98871 Carnitine Palmitoyltransferase I Deficiency semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535598 Creatine deficiency, X-linked skos:exactMatch doid DOID:0050800 creatine transporter deficiency semapv:LexicalMatching 0.9 generate_doid_mesh_mappings.py mesh C535608 Aicardi-Goutieres syndrome 5 skos:exactMatch ncit C168564 Aicardi-Goutieres Syndrome 5 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh C535648 Familial primary gastric lymphoma skos:exactMatch hp HP:0045038 Gastric lymphoma semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535658 Acromesomelic dysplasia skos:exactMatch doid DOID:0080051 acromesomelic dysplasia, Hunter-Thompson type semapv:LexicalMatching 0.9 generate_doid_mesh_mappings.py mesh C535683 Rigid spine syndrome skos:exactMatch ncit C126691 Rigid Spine Muscular Dystrophy 1 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535687 Roberts Syndrome skos:exactMatch ncit C126326 Roberts Syndrome semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py From 2cda2c5e71838826fbe459e8e0d5314b2e13a0e8 Mon Sep 17 00:00:00 2001 From: Sangeetha Vempati Date: Thu, 17 Aug 2023 10:53:56 -0700 Subject: [PATCH 4/5] Curated 15 mappings (sangeethavempati) --- src/biomappings/resources/incorrect.tsv | 8 ++++++++ src/biomappings/resources/mappings.tsv | 9 +++++++++ src/biomappings/resources/predictions.tsv | 17 ----------------- 3 files changed, 17 insertions(+), 17 deletions(-) diff --git a/src/biomappings/resources/incorrect.tsv b/src/biomappings/resources/incorrect.tsv index 7eb7d17f..1d62875f 100644 --- a/src/biomappings/resources/incorrect.tsv +++ b/src/biomappings/resources/incorrect.tsv @@ -599,10 +599,14 @@ mesh C477269 3 beta-hydroxy-delta 5-steroid dehydrogenase, rat skos:exactMatch g mesh C509674 marinocine protein, Marinomonas mediterranea skos:exactMatch go GO:0033736 L-lysine 6-oxidase activity semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C531673 Familial ependymoma skos:exactMatch doid DOID:5509 pediatric ependymoma semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C531763 Irritable heart skos:exactMatch doid DOID:0111154 postural orthostatic tachycardia syndrome semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +mesh C535425 Congenital torticollis skos:exactMatch hp HP:0005988 Congenital muscular torticollis semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535442 Bile acid synthesis defect, congenital, 1 skos:exactMatch doid DOID:0050674 congenital bile acid synthesis defect semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535536 Iridogoniodysgenesis, dominant type skos:exactMatch doid DOID:0050786 iridogoniodysgenesis syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +mesh C535568 Absent patella skos:exactMatch hp HP:0006443 Patellar aplasia semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535837 Pancreatic carcinoma, familial skos:exactMatch doid DOID:4905 pancreatic carcinoma semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535847 Hay-Wells syndrome skos:exactMatch doid DOID:0090119 ankyloblepharon-ectodermal defects-cleft lip/palate syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +mesh C535968 Hereditary macular coloboma skos:exactMatch hp HP:0001116 Macular coloboma semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C536021 Achromatopsia 1 skos:exactMatch hp HP:0011516 Achromatopsia semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C536133 Meckel syndrome type 1 skos:exactMatch doid DOID:0050778 Meckel syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C536192 Brittle cornea syndrome 1 skos:exactMatch doid DOID:14775 brittle cornea syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536277 Idiopathic dilation cardiomyopathy skos:exactMatch doid DOID:0110429 dilated cardiomyopathy 1H semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -632,11 +636,14 @@ mesh D000068256 Darbepoetin alfa skos:exactMatch hgnc 4392 GNAS semapv:ManualMap mesh D000068437 Pemetrexed skos:exactMatch chebi CHEBI:17509 5'-S-methyl-5'-thioadenosine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D000068800 Etanercept skos:exactMatch hgnc 11917 TNFRSF1B semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D000070636 Rotator Cuff Injuries skos:exactMatch efo 1001250 rotator cuff tear semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +mesh D000070636 Rotator Cuff Injuries skos:exactMatch hp HP:0032201 Rotator cuff tear semapv:ManualMappingCuration web semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 mesh D000071636 Protein Phosphatase 2C skos:exactMatch hgnc 9279 PDP1 semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D000074767 Diapause skos:exactMatch go GO:0030431 sleep semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +mesh D000075529 Solitary Kidney skos:exactMatch hp HP:0000122 Unilateral renal agenesis semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py 0.95 mesh D000077190 Interferon alpha-2 skos:exactMatch hgnc 5423 IFNA2 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D000077212 Ropivacaine skos:exactMatch chebi CHEBI:8890 (S)-ropivacaine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D000077324 Crystalloid Solutions skos:exactMatch go GO:0044312 crystalloid semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +mesh D000152 Acne Vulgaris skos:exactMatch hp HP:0001061 Acne semapv:ManualMappingCuration web semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 mesh D000203 Activities of Daily Living skos:exactMatch efo 0008451 activities of daily living score measurement semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D000309 Adrenal Insufficiency skos:exactMatch doid DOID:10493 adrenal cortical hypofunction semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh D000371 Agglutination skos:exactMatch go GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules semapv:ManualMappingCuration orcid:0000-0003-4423-4370 @@ -657,6 +664,7 @@ mesh D001661 Biliary Tract Neoplasms skos:exactMatch doid DOID:0050625 biliary t mesh D001731 Bisphosphoglycerate Mutase skos:exactMatch go GO:0004619 phosphoglycerate mutase activity semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D001749 Urinary Bladder Neoplasms skos:exactMatch doid DOID:4007 bladder carcinoma semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh D001761 Bleomycin skos:exactMatch chebi CHEBI:3139 bleomycin A2 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +mesh D001766 Blindness skos:exactMatch hp HP:0000572 Visual loss semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py 0.95 mesh D001792 Blood Platelets skos:exactMatch efo 0009237 Estimated Platelets Measurement semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D001859 Bone Neoplasms skos:exactMatch efo 1000350 Malignant Bone Neoplasm semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D001907 Boutonneuse Fever skos:exactMatch doid DOID:0050035 African tick-bite fever semapv:ManualMappingCuration orcid:0000-0003-1307-2508 diff --git a/src/biomappings/resources/mappings.tsv b/src/biomappings/resources/mappings.tsv index e676b680..a4aaa95c 100644 --- a/src/biomappings/resources/mappings.tsv +++ b/src/biomappings/resources/mappings.tsv @@ -4539,6 +4539,7 @@ mesh C486356 FGF12 protein, human skos:exactMatch uniprot P61328 FGF12 semapv:Ma mesh C486393 RAX protein, human skos:exactMatch uniprot Q9Y2V3 RAX semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C486593 PARVG protein, human skos:exactMatch uniprot Q9HBI0 PARVG semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C486655 BMF protein, human skos:exactMatch uniprot Q96LC9 BMF semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +mesh C487483 ANNA-2 antibody, human skos:exactMatch hp HP:5000030 Anti-Ri antibody semapv:ManualMappingCuration web semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 mesh C488098 NXNL1 protein, human skos:exactMatch uniprot Q96CM4 NXNL1 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C488261 ZW10 protein, human skos:exactMatch uniprot O43264 ZW10 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C488760 RAET1E protein, human skos:exactMatch uniprot Q8TD07 RAET1E semapv:ManualMappingCuration orcid:0000-0001-9439-5346 @@ -4719,6 +4720,7 @@ mesh C535419 Charcot-Marie-Tooth disease, Type 4A skos:exactMatch doid DOID:0110 mesh C535420 Charcot-Marie-Tooth disease, Type 4B1 skos:exactMatch doid DOID:0110191 Charcot-Marie-Tooth disease type 4B1 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535421 Charcot-Marie-Tooth disease, Type 4B2 skos:exactMatch doid DOID:0110190 Charcot-Marie-Tooth disease type 4B2 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535436 Bethlem myopathy skos:exactMatch doid DOID:0050663 Bethlem myopathy semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +mesh C535438 Bidirectional tachycardia skos:exactMatch hp HP:0034040 Bidirectional ventricular tachycardia semapv:ManualMappingCuration web semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 mesh C535440 Bietti Crystalline Dystrophy skos:exactMatch doid DOID:0050664 Bietti crystalline corneoretinal dystrophy semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535441 Bifid nose skos:exactMatch hp HP:0011803 Bifid nose semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535443 Bile acid synthesis defect, congenital, 2 skos:exactMatch doid DOID:0111069 congenital bile acid synthesis defect 2 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -4752,6 +4754,7 @@ mesh C535566 Absent corpus callosum cataract immunodeficiency skos:exactMatch do mesh C535572 Cantu syndrome skos:exactMatch doid DOID:0060569 hypertrichotic osteochondrodysplasia Cantu type semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535579 Cardiofaciocutaneous syndrome skos:exactMatch doid DOID:0060233 cardiofaciocutaneous syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C535581 Cardiomyopathy dilated with Woolly hair and keratoderma skos:exactMatch doid DOID:0090128 Carvajal syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +mesh C535584 Cardiomyopathy, infantile histiocytoid skos:exactMatch hp HP:0005152 Histiocytoid cardiomyopathy semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535588 Carnitine palmitoyl transferase 1A deficiency skos:exactMatch doid DOID:0090129 carnitine palmitoyltransferase I deficiency semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C535600 dopamine beta hydroxylase deficiency skos:exactMatch doid DOID:0090145 dopamine beta-hydroxylase deficiency semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535601 Dosage-sensitive sex reversal skos:exactMatch doid DOID:0111777 46,XY sex reversal 2 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -4787,6 +4790,7 @@ mesh C535780 Spondylocarpotarsal synostosis skos:exactMatch doid DOID:0090116 sp mesh C535786 Spondyloepimetaphyseal dysplasia, sponastrime type skos:exactMatch doid DOID:5684 spondyloepimetaphyseal dysplasia, Sponastrime type semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535788 Spondyloepiphyseal dysplasia, congenita skos:exactMatch doid DOID:14789 spondyloepiphyseal dysplasia congenita semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535789 Spondyloepiphyseal dysplasia, Omani type skos:exactMatch doid DOID:0050813 spondyloepiphyseal dysplasia with congenital joint dislocations semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +mesh C535802 Sprengel deformity skos:exactMatch hp HP:0000912 Sprengel anomaly semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535803 succinic semialdehyde dehydrogenase deficiency skos:exactMatch doid DOID:0060175 succinic semialdehyde dehydrogenase deficiency semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535811 Molybdenum cofactor deficiency skos:exactMatch hp HP:0003570 Molybdenum cofactor deficiency semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535813 Neuropathy, hereditary motor and sensory, Russe type skos:exactMatch doid DOID:0110196 Charcot-Marie-Tooth disease type 4G semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -4841,6 +4845,7 @@ mesh C536096 Myoclonic dystonia skos:exactMatch doid DOID:0090033 myoclonic dyst mesh C536102 Myopathy, congenital nonprogressive with Moebius and Robin sequences skos:exactMatch doid DOID:0080194 Carey-Fineman-Ziter syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536106 Myostatin-related muscle hypertrophy skos:exactMatch doid DOID:0111072 myostatin-related muscle hypertrophy semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536108 N syndrome skos:exactMatch doid DOID:0050769 N syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +mesh C536111 Partial agenesis of corpus callosum skos:exactMatch hp HP:0001338 Partial agenesis of the corpus callosum semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C536123 Nivelon Nivelon Mabille syndrome skos:exactMatch doid DOID:0060644 chondrodysplasia-pseudohermaphroditism syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536129 Achromatopsia 3 skos:exactMatch doid DOID:0110008 achromatopsia 3 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536131 Meckel syndrome type 2 skos:exactMatch doid DOID:0070116 Meckel syndrome 2 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -4917,6 +4922,7 @@ mesh C536494 Uveal melanoma skos:exactMatch hp HP:0007716 Uveal melanoma semapv: mesh C536495 VACTERL association skos:exactMatch doid DOID:14679 VACTERL association semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536510 Thiamine responsive megaloblastic anemia syndrome skos:exactMatch doid DOID:0090117 thiamine-responsive megaloblastic anemia syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536512 Thiopurine S methyltranferase deficiency skos:exactMatch doid DOID:0080172 thiopurine S-methyltransferase deficiency semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +mesh C536524 Valinemia skos:exactMatch hp HP:0010910 Hypervalinemia semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C536525 Valproic acid antenatal infection skos:exactMatch doid DOID:0060471 fetal valproate syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536528 Van der Woude syndrome skos:exactMatch doid DOID:0060239 Van der Woude syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536530 Van Maldergem Wetzburger Verloes syndrome skos:exactMatch doid DOID:0060238 Van Maldergem syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -5235,6 +5241,7 @@ mesh C538344 Navajo neurohepatopathy skos:exactMatch doid DOID:0080125 mitochond mesh C538346 Naxos disease skos:exactMatch doid DOID:0080551 Naxos disease semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C538348 Nemaline myopathy 1 skos:exactMatch doid DOID:0110926 nemaline myopathy 1 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C538351 Nemaline myopathy 4 skos:exactMatch doid DOID:0110932 nemaline myopathy 4 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +mesh C538354 Potato nose skos:exactMatch hp HP:0000414 Bulbous nose semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C538355 Potocki-Lupski syndrome skos:exactMatch doid DOID:0060853 Potocki-Lupski syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C538356 Potocki-Shaffer syndrome skos:exactMatch doid DOID:0111687 Potocki-Shaffer syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C538361 Reticular dysgenesis skos:exactMatch doid DOID:0060020 reticular dysgenesis semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -5302,6 +5309,7 @@ mesh C562489 Lymphoid Interstitial Pneumonia skos:exactMatch doid DOID:0050159 l mesh C562509 Popliteal Pterygium Syndrome skos:exactMatch doid DOID:0060055 popliteal pterygium syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C562524 Fibrochondrogenesis skos:exactMatch doid DOID:0060465 fibrochondrogenesis semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C562538 Cerebrocostomandibular Syndrome skos:exactMatch doid DOID:0111248 cerebrocostomandibular syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 +mesh C562546 Megalodactyly skos:exactMatch hp HP:0004099 Macrodactyly semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C562562 Colonic Atresia skos:exactMatch hp HP:0010448 Colonic atresia semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C562563 Microcolon skos:exactMatch hp HP:0004388 Microcolon semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C562568 Cerebellar Hypoplasia skos:exactMatch doid DOID:0070338 cerebellar hypoplasia semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -6025,6 +6033,7 @@ mesh D000009 Abdominal Muscles skos:exactMatch ncit C32040 Abdominal Muscle sema mesh D000019 Abortifacient Agents skos:exactMatch chebi CHEBI:50691 abortifacient semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D000022 Abortion, Spontaneous skos:exactMatch ncit C34336 Spontaneous Abortion semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D000038 Abscess skos:exactMatch hp HP:0025615 Abscess semapv:ManualMappingCuration orcid:0000-0003-4423-4370 +mesh D000058 Accidental Falls skos:exactMatch hp HP:0002527 Falls semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh D000066450 Mouse Embryonic Stem Cells skos:exactMatch efo 0004038 mouse embryonic stem cell semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D000066530 Neurological Rehabilitation skos:exactMatch ncit C157934 Neurological Rehabilitation semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D000067128 Extracellular Vesicles skos:exactMatch go GO:1903561 extracellular vesicle semapv:ManualMappingCuration orcid:0000-0001-9439-5346 diff --git a/src/biomappings/resources/predictions.tsv b/src/biomappings/resources/predictions.tsv index f71100ed..4adccab7 100644 --- a/src/biomappings/resources/predictions.tsv +++ b/src/biomappings/resources/predictions.tsv @@ -20875,7 +20875,6 @@ mesh C487431 NMRK1 protein, human skos:exactMatch uniprot Q9NWW6 NMRK1 semapv:Le mesh C487434 BBS5 protein, human skos:exactMatch uniprot Q8N3I7 BBS5 semapv:LexicalMatching 0.999 https://github.com/biomappings/biomappings/blob/a840cf/scripts/generate_mesh_uniprot_mappings.py mesh C487464 SEC63 protein, human skos:exactMatch uniprot Q9UGP8 SEC63 semapv:LexicalMatching 0.999 https://github.com/biomappings/biomappings/blob/a840cf/scripts/generate_mesh_uniprot_mappings.py mesh C487465 NIPBL protein, human skos:exactMatch uniprot Q6KC79 NIPBL semapv:LexicalMatching 0.999 https://github.com/biomappings/biomappings/blob/a840cf/scripts/generate_mesh_uniprot_mappings.py -mesh C487483 ANNA-2 antibody, human skos:exactMatch hp HP:5000030 Anti-Ri antibody semapv:LexicalMatching 0.9 generate_hp_mesh_mappings.py mesh C487500 SLC25A24 protein, human skos:exactMatch uniprot Q6NUK1 SLC25A24 semapv:LexicalMatching 0.999 https://github.com/biomappings/biomappings/blob/a840cf/scripts/generate_mesh_uniprot_mappings.py mesh C487501 SLC25A25 protein, human skos:exactMatch uniprot Q6KCM7 SLC25A25 semapv:LexicalMatching 0.999 https://github.com/biomappings/biomappings/blob/a840cf/scripts/generate_mesh_uniprot_mappings.py mesh C487502 SLC25A26 protein, human skos:exactMatch uniprot Q70HW3 SLC25A26 semapv:LexicalMatching 0.999 https://github.com/biomappings/biomappings/blob/a840cf/scripts/generate_mesh_uniprot_mappings.py @@ -24454,8 +24453,6 @@ mesh C535361 Chromosome 1 ring skos:exactMatch ncit C36474 Ring Chromosome 1 sem mesh C535372 Chromosome 20, trisomy skos:exactMatch ncit C36397 Trisomy 20 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535378 Arthrogryposis multiplex congenita, distal type 1 skos:exactMatch ncit C115002 TPM2 wt Allele semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535408 Gamma-cystathionase deficiency skos:exactMatch hp HP:0003153 Cystathioninuria semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh C535425 Congenital torticollis skos:exactMatch hp HP:0005988 Congenital muscular torticollis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh C535438 Bidirectional tachycardia skos:exactMatch hp HP:0034040 Bidirectional ventricular tachycardia semapv:LexicalMatching 0.9 generate_hp_mesh_mappings.py mesh C535483 Freeman-Sheldon syndrome skos:exactMatch ncit C98931 Freeman-Sheldon Syndrome semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535484 13q deletion syndrome skos:exactMatch ncit C98993 Monosomy 13q Syndrome semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535488 Chromosome 14 trisomy skos:exactMatch ncit C116344 Trisomy 14 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py @@ -24464,8 +24461,6 @@ mesh C535494 Epidermolysis bullosa, pretibial skos:exactMatch hp HP:0012221 Pret mesh C535516 Hereditary leiomyomatosis and renal cell cancer skos:exactMatch ncit C51302 Hereditary Leiomyomatosis and Renal Cell Cancer semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535522 Infantile convulsions and paroxysmal choreoathetosis, familial skos:exactMatch ncit C126650 Infantile Convulsions and Paroxysmal Choreoathetosis, Familial semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535541 Isobutyryl-CoA dehydrogenase deficiency skos:exactMatch ncit C129975 Isobutyryl-CoA Dehydrogenase Deficiency semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh C535568 Absent patella skos:exactMatch hp HP:0006443 Patellar aplasia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh C535584 Cardiomyopathy, infantile histiocytoid skos:exactMatch hp HP:0005152 Histiocytoid cardiomyopathy semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535586 Carnevale syndrome skos:exactMatch efo 1001977 3MC syndrome 2 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535588 Carnitine palmitoyl transferase 1A deficiency skos:exactMatch ncit C98871 Carnitine Palmitoyltransferase I Deficiency semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535598 Creatine deficiency, X-linked skos:exactMatch doid DOID:0050800 creatine transporter deficiency semapv:LexicalMatching 0.9 generate_doid_mesh_mappings.py @@ -24482,7 +24477,6 @@ mesh C535736 Encephalocraniocutaneous lipomatosis skos:exactMatch ncit C4701 Enc mesh C535739 Congenital disorder of glycosylation type 1A skos:exactMatch ncit C126868 Congenital Disorder of Glycosylation Type Ia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535799 Spondyloperipheral dysplasia short ulna skos:exactMatch doid DOID:0112195 spondyloperipheral dysplasia semapv:LexicalMatching 0.9 generate_doid_mesh_mappings.py mesh C535799 Spondyloperipheral dysplasia short ulna skos:exactMatch ncit C135088 Spondyloperipheral Dysplasia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh C535802 Sprengel deformity skos:exactMatch hp HP:0000912 Sprengel anomaly semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535818 Pseudo-Zellweger syndrome skos:exactMatch ncit C119676 D-Bifunctional Protein Deficiency semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535819 Pseudoachondroplasia skos:exactMatch ncit C118635 Pseudoachondroplasia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535824 Pseudoangiomatous stromal hyperplasia skos:exactMatch ncit C104373 Pseudoangiomatous Stromal Hyperplasia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py @@ -24494,19 +24488,16 @@ mesh C535898 Limb-girdle muscular dystrophy, type 1B skos:exactMatch ncit C61149 mesh C535933 Cholestasis, progressive familial intrahepatic 1 skos:exactMatch doid DOID:0070221 progressive familial intrahepatic cholestasis semapv:LexicalMatching 0.9 generate_doid_mesh_mappings.py mesh C535952 Eosinophilic enteropathy skos:exactMatch hp HP:0032064 Gastrointestinal eosinophilia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535963 Cole Carpenter syndrome skos:exactMatch ncit C130985 Cole-Carpenter Syndrome semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh C535968 Hereditary macular coloboma skos:exactMatch hp HP:0001116 Macular coloboma semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535974 Complete atrioventricular septal defect skos:exactMatch hp HP:0001674 Complete atrioventricular canal defect semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535979 Congenital adrenal hyperplasia due to 21 hydroxylase deficiency skos:exactMatch ncit C131087 21-Hydroxylase Deficiency semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535981 Congenital alopecia X-linked skos:exactMatch ncit C35790 Congenital Alopecia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C535992 De Sanctis-Cacchione syndrome skos:exactMatch ncit C84666 De Sanctis-Cacchione Syndrome semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C536008 Achalasia Addisonianism Alacrimia syndrome skos:exactMatch ncit C35710 Triple A Syndrome semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh C536021 Achromatopsia 1 skos:exactMatch hp HP:0011516 Achromatopsia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C536038 Medium chain acyl CoA dehydrogenase deficiency skos:exactMatch ncit C84538 Medium-Chain Acyl-CoA Dehydrogenase Deficiency semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C536058 Osteopetrosis with renal tubular acidosis skos:exactMatch ncit C118438 Osteopetrosis with Renal Tubular Acidosis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C536068 Hoyeraal Hreidarsson syndrome skos:exactMatch ncit C126352 X-Linked Dyskeratosis Congenita semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C536075 Hyaloideoretinal degeneration of Wagner skos:exactMatch hp HP:0030673 Erosive vitreoretinopathy semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C536109 N-acetyl glutamate synthetase deficiency skos:exactMatch ncit C129307 N-Acetylglutamate Synthase Deficiency semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh C536111 Partial agenesis of corpus callosum skos:exactMatch hp HP:0001338 Partial agenesis of the corpus callosum semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C536112 Partial atrioventricular canal skos:exactMatch hp HP:0010445 Primum atrial septal defect semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C536119 Niemann-Pick disease, type C2 skos:exactMatch ncit C126865 Niemann-Pick Disease, Type C2 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C536122 Night blindness, congenital stationary skos:exactMatch hp HP:0007642 Congenital stationary night blindness semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py @@ -24550,7 +24541,6 @@ mesh C536475 Urachal cancer skos:exactMatch ncit C39842 Bladder Urachal Carcinom mesh C536498 Tetra-amelia autosomal recessive skos:exactMatch doid DOID:0112191 tetraamelia syndrome semapv:LexicalMatching 0.9 generate_doid_mesh_mappings.py mesh C536508 Thanatophoric dysplasia, type 2 skos:exactMatch ncit C98584 Type 2 Thanatophoric Dysplasia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C536519 Thrombocytopenia chromosome breakage skos:exactMatch ncit C129035 Thrombocytopenia 2 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh C536524 Valinemia skos:exactMatch hp HP:0010910 Hypervalinemia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C536534 VATER association skos:exactMatch ncit C99105 VACTERL Association semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C536535 Vein of Galen aneurysm skos:exactMatch hp HP:0030713 Vein of Galen aneurysmal malformation semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C536553 Trichofolliculoma skos:exactMatch ncit C4112 Trichofolliculoma semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py @@ -24705,7 +24695,6 @@ mesh C538320 Histidinemia skos:exactMatch hp HP:0010906 Hyperhistidinemia semapv mesh C538324 3-Hydroxy-3-Methylglutaryl-CoA Lyase Deficiency skos:exactMatch ncit C84523 HMG-CoA Lyase Deficiency semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C538349 Nemaline Myopathy 2 skos:exactMatch ncit C118784 Nemaline Myopathy 2 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C538353 Potassium aggravated myotonia skos:exactMatch ncit C122788 Potassium Aggravated Myotonia semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh C538354 Potato nose skos:exactMatch hp HP:0000414 Bulbous nose semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C538371 Revesz Debuse syndrome skos:exactMatch doid DOID:0070026 Revesz syndrome semapv:LexicalMatching 0.9 generate_doid_mesh_mappings.py mesh C538371 Revesz Debuse syndrome skos:exactMatch ncit C152064 Revesz Syndrome semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C538387 Hypertelorism with esophageal abnormality and hypospadias skos:exactMatch doid DOID:0080697 Opitz GBBB syndrome semapv:LexicalMatching 0.9 generate_doid_mesh_mappings.py @@ -25637,7 +25626,6 @@ mesh C562463 Pancreatic Carcinoma skos:exactMatch ncit C3850 Pancreatic Carcinom mesh C562487 Eosinophilic Fasciitis skos:exactMatch ncit C112116 Eosinophilic Fasciitis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C562492 Robinow Syndrome skos:exactMatch ncit C85048 Robinow Syndrome semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C562503 Otocephaly skos:exactMatch ncit C124568 Otocephaly semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh C562546 Megalodactyly skos:exactMatch hp HP:0004099 Macrodactyly semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C562557 Polythelia, Familial skos:exactMatch hp HP:0002558 Supernumerary nipple semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh C562573 cyclopia sequence skos:exactMatch doid DOID:0110881 holoprosencephaly 1 semapv:LexicalMatching 0.9 generate_doid_mesh_mappings.py mesh C562590 Xeroderma Pigmentosum, Complementation Group B skos:exactMatch ncit C3966 Xeroderma Pigmentosum, Complementation Group B semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py @@ -26644,7 +26632,6 @@ mesh D000050 Acanthocytes skos:exactMatch ncit C12523 Acanthocytes semapv:Lexica mesh D000051 Acantholysis skos:exactMatch ncit C54252 Acantholysis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000052 Acanthosis Nigricans skos:exactMatch ncit C26687 Acanthosis Nigricans semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000055 Accessory Nerve skos:exactMatch ncit C32041 Spinal Accessory Nerve semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh D000058 Accidental Falls skos:exactMatch hp HP:0002527 Falls semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000059 Accidents skos:exactMatch ncit C34340 Accident semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000064 Acclimatization skos:exactMatch ncit C68767 Acclimatization semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000066502 Grandparents skos:exactMatch ncit C71385 Grandparent semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py @@ -26809,7 +26796,6 @@ mesh D000070589 Talipes Cavus skos:exactMatch hp HP:0001761 Pes cavus semapv:Lex mesh D000070606 Aponeurosis skos:exactMatch ncit C32133 Aponeurosis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000070621 Cystography skos:exactMatch ncit C38049 Cystography semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000070633 Hamstring Muscles skos:exactMatch ncit C53042 Hamstring semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh D000070636 Rotator Cuff Injuries skos:exactMatch hp HP:0032201 Rotator cuff tear semapv:LexicalMatching 0.9 generate_hp_mesh_mappings.py mesh D000070642 Brain Injuries, Traumatic skos:exactMatch ncit C35542 Traumatic Encephalopathy semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000070696 Buttermilk skos:exactMatch ncit C72059 Buttermilk semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000070778 Perilipin-1 skos:exactMatch hgnc 9076 PLIN1 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py @@ -27240,7 +27226,6 @@ mesh D000075388 Netrin-1 skos:exactMatch ncit C33982 Netrin-1 semapv:LexicalMatc mesh D000075389 DCC Receptor skos:exactMatch hgnc 2701 DCC semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py mesh D000075389 DCC Receptor skos:exactMatch ncit C17908 Netrin Receptor DCC semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000075462 Serum Albumin, Human skos:exactMatch ncit C65218 Albumin (Human) semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh D000075529 Solitary Kidney skos:exactMatch hp HP:0000122 Unilateral renal agenesis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py mesh D000075529 Solitary Kidney skos:exactMatch ncit C101220 Unilateral Renal Agenesis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000075684 T-Lymphoma Invasion and Metastasis-inducing Protein 1 skos:exactMatch hgnc 11805 TIAM1 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000075687 NEDD8 Protein skos:exactMatch hgnc 7732 NEDD8 semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py @@ -27517,7 +27502,6 @@ mesh D000136 Acid-Base Equilibrium skos:exactMatch ncit C29644 pH Homeostasis se mesh D000140 Acidosis, Lactic skos:exactMatch ncit C98969 Lactic Acidosis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000141 Acidosis, Renal Tubular skos:exactMatch ncit C28129 Renal Tubular Acidosis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000150 Acinetobacter skos:exactMatch ncit C76200 Acinetobacter semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh D000152 Acne Vulgaris skos:exactMatch hp HP:0001061 Acne semapv:LexicalMatching 0.9 generate_hp_mesh_mappings.py mesh D000153 Acne Keloid skos:exactMatch ncit C34346 Acne Keloid semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000162 Acoustics skos:exactMatch ncit C16256 Acoustic semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D000164 Acremonium skos:exactMatch ncit C118935 Acremonium semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py @@ -28110,7 +28094,6 @@ mesh D001760 Bleeding Time skos:exactMatch ncit C89775 Bleeding Time semapv:Lexi mesh D001762 Blepharitis skos:exactMatch ncit C112183 Blepharitis semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D001764 Blepharospasm skos:exactMatch ncit C118723 Blepharospasm semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D001765 Blind Loop Syndrome skos:exactMatch ncit C34431 Blind Loop Syndrome semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py -mesh D001766 Blindness skos:exactMatch hp HP:0000572 Visual loss semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py mesh D001766 Blindness skos:exactMatch ncit C97109 Blindness semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D001771 Blood Banks skos:exactMatch ncit C51963 Blood Bank semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py mesh D001772 Blood Cell Count skos:exactMatch efo 0004586 complete blood cell count semapv:LexicalMatching 0.95 https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py From 76968b7c37964c296d08d4492b845e93d78de11c Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Fri, 18 Aug 2023 17:00:28 +0200 Subject: [PATCH 5/5] Update provenance --- src/biomappings/resources/curators.tsv | 1 + src/biomappings/resources/incorrect.tsv | 16 ++++++++-------- src/biomappings/resources/mappings.tsv | 24 ++++++++++++------------ 3 files changed, 21 insertions(+), 20 deletions(-) diff --git a/src/biomappings/resources/curators.tsv b/src/biomappings/resources/curators.tsv index c912c64b..16ec0ff0 100644 --- a/src/biomappings/resources/curators.tsv +++ b/src/biomappings/resources/curators.tsv @@ -5,3 +5,4 @@ hoytfamily 0000-0003-1307-2508 Amelia Hoyt ddomingof 0000-0002-2046-6145 Daniel Domingo-Fernandez cmungall 0000-0002-6601-2165 Christopher Mungall KrishnaTO 0000-0002-2627-0696 Krishna Udaiwal +sangeethavempati 0009-0006-0654-7594 Sangeetha Vempati diff --git a/src/biomappings/resources/incorrect.tsv b/src/biomappings/resources/incorrect.tsv index 1d62875f..d49fd361 100644 --- a/src/biomappings/resources/incorrect.tsv +++ b/src/biomappings/resources/incorrect.tsv @@ -599,14 +599,14 @@ mesh C477269 3 beta-hydroxy-delta 5-steroid dehydrogenase, rat skos:exactMatch g mesh C509674 marinocine protein, Marinomonas mediterranea skos:exactMatch go GO:0033736 L-lysine 6-oxidase activity semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C531673 Familial ependymoma skos:exactMatch doid DOID:5509 pediatric ependymoma semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C531763 Irritable heart skos:exactMatch doid DOID:0111154 postural orthostatic tachycardia syndrome semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -mesh C535425 Congenital torticollis skos:exactMatch hp HP:0005988 Congenital muscular torticollis semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C535425 Congenital torticollis skos:exactMatch hp HP:0005988 Congenital muscular torticollis semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535442 Bile acid synthesis defect, congenital, 1 skos:exactMatch doid DOID:0050674 congenital bile acid synthesis defect semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535536 Iridogoniodysgenesis, dominant type skos:exactMatch doid DOID:0050786 iridogoniodysgenesis syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 -mesh C535568 Absent patella skos:exactMatch hp HP:0006443 Patellar aplasia semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C535568 Absent patella skos:exactMatch hp HP:0006443 Patellar aplasia semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535837 Pancreatic carcinoma, familial skos:exactMatch doid DOID:4905 pancreatic carcinoma semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535847 Hay-Wells syndrome skos:exactMatch doid DOID:0090119 ankyloblepharon-ectodermal defects-cleft lip/palate syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 -mesh C535968 Hereditary macular coloboma skos:exactMatch hp HP:0001116 Macular coloboma semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 -mesh C536021 Achromatopsia 1 skos:exactMatch hp HP:0011516 Achromatopsia semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C535968 Hereditary macular coloboma skos:exactMatch hp HP:0001116 Macular coloboma semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C536021 Achromatopsia 1 skos:exactMatch hp HP:0011516 Achromatopsia semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C536133 Meckel syndrome type 1 skos:exactMatch doid DOID:0050778 Meckel syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C536192 Brittle cornea syndrome 1 skos:exactMatch doid DOID:14775 brittle cornea syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536277 Idiopathic dilation cardiomyopathy skos:exactMatch doid DOID:0110429 dilated cardiomyopathy 1H semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -636,14 +636,14 @@ mesh D000068256 Darbepoetin alfa skos:exactMatch hgnc 4392 GNAS semapv:ManualMap mesh D000068437 Pemetrexed skos:exactMatch chebi CHEBI:17509 5'-S-methyl-5'-thioadenosine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D000068800 Etanercept skos:exactMatch hgnc 11917 TNFRSF1B semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D000070636 Rotator Cuff Injuries skos:exactMatch efo 1001250 rotator cuff tear semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -mesh D000070636 Rotator Cuff Injuries skos:exactMatch hp HP:0032201 Rotator cuff tear semapv:ManualMappingCuration web semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 +mesh D000070636 Rotator Cuff Injuries skos:exactMatch hp HP:0032201 Rotator cuff tear semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 mesh D000071636 Protein Phosphatase 2C skos:exactMatch hgnc 9279 PDP1 semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D000074767 Diapause skos:exactMatch go GO:0030431 sleep semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -mesh D000075529 Solitary Kidney skos:exactMatch hp HP:0000122 Unilateral renal agenesis semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py 0.95 +mesh D000075529 Solitary Kidney skos:exactMatch hp HP:0000122 Unilateral renal agenesis semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py 0.95 mesh D000077190 Interferon alpha-2 skos:exactMatch hgnc 5423 IFNA2 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D000077212 Ropivacaine skos:exactMatch chebi CHEBI:8890 (S)-ropivacaine semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D000077324 Crystalloid Solutions skos:exactMatch go GO:0044312 crystalloid semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -mesh D000152 Acne Vulgaris skos:exactMatch hp HP:0001061 Acne semapv:ManualMappingCuration web semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 +mesh D000152 Acne Vulgaris skos:exactMatch hp HP:0001061 Acne semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 mesh D000203 Activities of Daily Living skos:exactMatch efo 0008451 activities of daily living score measurement semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D000309 Adrenal Insufficiency skos:exactMatch doid DOID:10493 adrenal cortical hypofunction semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh D000371 Agglutination skos:exactMatch go GO:0007157 heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules semapv:ManualMappingCuration orcid:0000-0003-4423-4370 @@ -664,7 +664,7 @@ mesh D001661 Biliary Tract Neoplasms skos:exactMatch doid DOID:0050625 biliary t mesh D001731 Bisphosphoglycerate Mutase skos:exactMatch go GO:0004619 phosphoglycerate mutase activity semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D001749 Urinary Bladder Neoplasms skos:exactMatch doid DOID:4007 bladder carcinoma semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh D001761 Bleomycin skos:exactMatch chebi CHEBI:3139 bleomycin A2 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -mesh D001766 Blindness skos:exactMatch hp HP:0000572 Visual loss semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py 0.95 +mesh D001766 Blindness skos:exactMatch hp HP:0000572 Visual loss semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py 0.95 mesh D001792 Blood Platelets skos:exactMatch efo 0009237 Estimated Platelets Measurement semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D001859 Bone Neoplasms skos:exactMatch efo 1000350 Malignant Bone Neoplasm semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D001907 Boutonneuse Fever skos:exactMatch doid DOID:0050035 African tick-bite fever semapv:ManualMappingCuration orcid:0000-0003-1307-2508 diff --git a/src/biomappings/resources/mappings.tsv b/src/biomappings/resources/mappings.tsv index a4aaa95c..92144d04 100644 --- a/src/biomappings/resources/mappings.tsv +++ b/src/biomappings/resources/mappings.tsv @@ -4539,7 +4539,7 @@ mesh C486356 FGF12 protein, human skos:exactMatch uniprot P61328 FGF12 semapv:Ma mesh C486393 RAX protein, human skos:exactMatch uniprot Q9Y2V3 RAX semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C486593 PARVG protein, human skos:exactMatch uniprot Q9HBI0 PARVG semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C486655 BMF protein, human skos:exactMatch uniprot Q96LC9 BMF semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -mesh C487483 ANNA-2 antibody, human skos:exactMatch hp HP:5000030 Anti-Ri antibody semapv:ManualMappingCuration web semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 +mesh C487483 ANNA-2 antibody, human skos:exactMatch hp HP:5000030 Anti-Ri antibody semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 mesh C488098 NXNL1 protein, human skos:exactMatch uniprot Q96CM4 NXNL1 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C488261 ZW10 protein, human skos:exactMatch uniprot O43264 ZW10 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C488760 RAET1E protein, human skos:exactMatch uniprot Q8TD07 RAET1E semapv:ManualMappingCuration orcid:0000-0001-9439-5346 @@ -4720,7 +4720,7 @@ mesh C535419 Charcot-Marie-Tooth disease, Type 4A skos:exactMatch doid DOID:0110 mesh C535420 Charcot-Marie-Tooth disease, Type 4B1 skos:exactMatch doid DOID:0110191 Charcot-Marie-Tooth disease type 4B1 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535421 Charcot-Marie-Tooth disease, Type 4B2 skos:exactMatch doid DOID:0110190 Charcot-Marie-Tooth disease type 4B2 semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535436 Bethlem myopathy skos:exactMatch doid DOID:0050663 Bethlem myopathy semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -mesh C535438 Bidirectional tachycardia skos:exactMatch hp HP:0034040 Bidirectional ventricular tachycardia semapv:ManualMappingCuration web semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 +mesh C535438 Bidirectional tachycardia skos:exactMatch hp HP:0034040 Bidirectional ventricular tachycardia semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9 mesh C535440 Bietti Crystalline Dystrophy skos:exactMatch doid DOID:0050664 Bietti crystalline corneoretinal dystrophy semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535441 Bifid nose skos:exactMatch hp HP:0011803 Bifid nose semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535443 Bile acid synthesis defect, congenital, 2 skos:exactMatch doid DOID:0111069 congenital bile acid synthesis defect 2 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -4754,16 +4754,16 @@ mesh C535566 Absent corpus callosum cataract immunodeficiency skos:exactMatch do mesh C535572 Cantu syndrome skos:exactMatch doid DOID:0060569 hypertrichotic osteochondrodysplasia Cantu type semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535579 Cardiofaciocutaneous syndrome skos:exactMatch doid DOID:0060233 cardiofaciocutaneous syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C535581 Cardiomyopathy dilated with Woolly hair and keratoderma skos:exactMatch doid DOID:0090128 Carvajal syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 -mesh C535584 Cardiomyopathy, infantile histiocytoid skos:exactMatch hp HP:0005152 Histiocytoid cardiomyopathy semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C535584 Cardiomyopathy, infantile histiocytoid skos:exactMatch hp HP:0005152 Histiocytoid cardiomyopathy semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535588 Carnitine palmitoyl transferase 1A deficiency skos:exactMatch doid DOID:0090129 carnitine palmitoyltransferase I deficiency semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C535600 dopamine beta hydroxylase deficiency skos:exactMatch doid DOID:0090145 dopamine beta-hydroxylase deficiency semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535601 Dosage-sensitive sex reversal skos:exactMatch doid DOID:0111777 46,XY sex reversal 2 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535602 Doyne honeycomb retinal dystrophy skos:exactMatch doid DOID:0060745 Doyne honeycomb retinal dystrophy semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535607 Aicardi-Goutieres syndrome skos:exactMatch doid DOID:0050629 Aicardi-Goutieres syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 -mesh C535618 Hairy elbows skos:exactMatch hp HP:0004780 Elbow hypertrichosis semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C535618 Hairy elbows skos:exactMatch hp HP:0004780 Elbow hypertrichosis semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535627 Hand foot uterus syndrome skos:exactMatch doid DOID:0060739 hand-foot-genital syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535642 Growth retardation, Alopecia, Pseudoanodontia and Optic atrophy skos:exactMatch doid DOID:0112249 GAPO syndrome semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -mesh C535648 Familial primary gastric lymphoma skos:exactMatch hp HP:0045038 Gastric lymphoma semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C535648 Familial primary gastric lymphoma skos:exactMatch hp HP:0045038 Gastric lymphoma semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535658 Acromesomelic dysplasia skos:exactMatch doid DOID:0080049 acromesomelic dysplasia semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535661 Acromesomelic dysplasia, Maroteaux type skos:exactMatch doid DOID:0080050 acromesomelic dysplasia, Maroteaux type semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535662 Acromicric dysplasia skos:exactMatch doid DOID:0111243 acromicric dysplasia semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -4790,7 +4790,7 @@ mesh C535780 Spondylocarpotarsal synostosis skos:exactMatch doid DOID:0090116 sp mesh C535786 Spondyloepimetaphyseal dysplasia, sponastrime type skos:exactMatch doid DOID:5684 spondyloepimetaphyseal dysplasia, Sponastrime type semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535788 Spondyloepiphyseal dysplasia, congenita skos:exactMatch doid DOID:14789 spondyloepiphyseal dysplasia congenita semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535789 Spondyloepiphyseal dysplasia, Omani type skos:exactMatch doid DOID:0050813 spondyloepiphyseal dysplasia with congenital joint dislocations semapv:ManualMappingCuration orcid:0000-0003-1307-2508 -mesh C535802 Sprengel deformity skos:exactMatch hp HP:0000912 Sprengel anomaly semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C535802 Sprengel deformity skos:exactMatch hp HP:0000912 Sprengel anomaly semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C535803 succinic semialdehyde dehydrogenase deficiency skos:exactMatch doid DOID:0060175 succinic semialdehyde dehydrogenase deficiency semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C535811 Molybdenum cofactor deficiency skos:exactMatch hp HP:0003570 Molybdenum cofactor deficiency semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C535813 Neuropathy, hereditary motor and sensory, Russe type skos:exactMatch doid DOID:0110196 Charcot-Marie-Tooth disease type 4G semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -4845,7 +4845,7 @@ mesh C536096 Myoclonic dystonia skos:exactMatch doid DOID:0090033 myoclonic dyst mesh C536102 Myopathy, congenital nonprogressive with Moebius and Robin sequences skos:exactMatch doid DOID:0080194 Carey-Fineman-Ziter syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536106 Myostatin-related muscle hypertrophy skos:exactMatch doid DOID:0111072 myostatin-related muscle hypertrophy semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536108 N syndrome skos:exactMatch doid DOID:0050769 N syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 -mesh C536111 Partial agenesis of corpus callosum skos:exactMatch hp HP:0001338 Partial agenesis of the corpus callosum semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C536111 Partial agenesis of corpus callosum skos:exactMatch hp HP:0001338 Partial agenesis of the corpus callosum semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C536123 Nivelon Nivelon Mabille syndrome skos:exactMatch doid DOID:0060644 chondrodysplasia-pseudohermaphroditism syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536129 Achromatopsia 3 skos:exactMatch doid DOID:0110008 achromatopsia 3 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536131 Meckel syndrome type 2 skos:exactMatch doid DOID:0070116 Meckel syndrome 2 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -4922,7 +4922,7 @@ mesh C536494 Uveal melanoma skos:exactMatch hp HP:0007716 Uveal melanoma semapv: mesh C536495 VACTERL association skos:exactMatch doid DOID:14679 VACTERL association semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536510 Thiamine responsive megaloblastic anemia syndrome skos:exactMatch doid DOID:0090117 thiamine-responsive megaloblastic anemia syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536512 Thiopurine S methyltranferase deficiency skos:exactMatch doid DOID:0080172 thiopurine S-methyltransferase deficiency semapv:ManualMappingCuration orcid:0000-0003-1307-2508 -mesh C536524 Valinemia skos:exactMatch hp HP:0010910 Hypervalinemia semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C536524 Valinemia skos:exactMatch hp HP:0010910 Hypervalinemia semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C536525 Valproic acid antenatal infection skos:exactMatch doid DOID:0060471 fetal valproate syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536528 Van der Woude syndrome skos:exactMatch doid DOID:0060239 Van der Woude syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C536530 Van Maldergem Wetzburger Verloes syndrome skos:exactMatch doid DOID:0060238 Van Maldergem syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -5241,7 +5241,7 @@ mesh C538344 Navajo neurohepatopathy skos:exactMatch doid DOID:0080125 mitochond mesh C538346 Naxos disease skos:exactMatch doid DOID:0080551 Naxos disease semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C538348 Nemaline myopathy 1 skos:exactMatch doid DOID:0110926 nemaline myopathy 1 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C538351 Nemaline myopathy 4 skos:exactMatch doid DOID:0110932 nemaline myopathy 4 semapv:ManualMappingCuration orcid:0000-0003-1307-2508 -mesh C538354 Potato nose skos:exactMatch hp HP:0000414 Bulbous nose semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C538354 Potato nose skos:exactMatch hp HP:0000414 Bulbous nose semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C538355 Potocki-Lupski syndrome skos:exactMatch doid DOID:0060853 Potocki-Lupski syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C538356 Potocki-Shaffer syndrome skos:exactMatch doid DOID:0111687 Potocki-Shaffer syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C538361 Reticular dysgenesis skos:exactMatch doid DOID:0060020 reticular dysgenesis semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -5309,7 +5309,7 @@ mesh C562489 Lymphoid Interstitial Pneumonia skos:exactMatch doid DOID:0050159 l mesh C562509 Popliteal Pterygium Syndrome skos:exactMatch doid DOID:0060055 popliteal pterygium syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C562524 Fibrochondrogenesis skos:exactMatch doid DOID:0060465 fibrochondrogenesis semapv:ManualMappingCuration orcid:0000-0003-1307-2508 mesh C562538 Cerebrocostomandibular Syndrome skos:exactMatch doid DOID:0111248 cerebrocostomandibular syndrome semapv:ManualMappingCuration orcid:0000-0003-1307-2508 -mesh C562546 Megalodactyly skos:exactMatch hp HP:0004099 Macrodactyly semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh C562546 Megalodactyly skos:exactMatch hp HP:0004099 Macrodactyly semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh C562562 Colonic Atresia skos:exactMatch hp HP:0010448 Colonic atresia semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh C562563 Microcolon skos:exactMatch hp HP:0004388 Microcolon semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh C562568 Cerebellar Hypoplasia skos:exactMatch doid DOID:0070338 cerebellar hypoplasia semapv:ManualMappingCuration orcid:0000-0003-1307-2508 @@ -6033,7 +6033,7 @@ mesh D000009 Abdominal Muscles skos:exactMatch ncit C32040 Abdominal Muscle sema mesh D000019 Abortifacient Agents skos:exactMatch chebi CHEBI:50691 abortifacient semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D000022 Abortion, Spontaneous skos:exactMatch ncit C34336 Spontaneous Abortion semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D000038 Abscess skos:exactMatch hp HP:0025615 Abscess semapv:ManualMappingCuration orcid:0000-0003-4423-4370 -mesh D000058 Accidental Falls skos:exactMatch hp HP:0002527 Falls semapv:ManualMappingCuration web semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 +mesh D000058 Accidental Falls skos:exactMatch hp HP:0002527 Falls semapv:ManualMappingCuration orcid:0009-0006-0654-7594 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95 mesh D000066450 Mouse Embryonic Stem Cells skos:exactMatch efo 0004038 mouse embryonic stem cell semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D000066530 Neurological Rehabilitation skos:exactMatch ncit C157934 Neurological Rehabilitation semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D000067128 Extracellular Vesicles skos:exactMatch go GO:1903561 extracellular vesicle semapv:ManualMappingCuration orcid:0000-0001-9439-5346 @@ -8789,7 +8789,7 @@ mesh D064794 Lorajmine skos:exactMatch chebi CHEBI:135646 lorajmine semapv:Manua mesh D064800 Prolyl-Hydroxylase Inhibitors skos:exactMatch chebi CHEBI:132365 EC 1.14.11.2 (procollagen-proline dioxygenase) inhibitor semapv:ManualMappingCuration orcid:0000-0003-4423-4370 mesh D064801 Phospholipase A2 Inhibitors skos:exactMatch chebi CHEBI:50469 EC 3.1.1.4 (phospholipase A2) inhibitor semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D064847 Multimodal Imaging skos:exactMatch ncit C19341 Multimodal Imaging semapv:ManualMappingCuration orcid:0000-0001-9439-5346 -mesh D064878 Web Browser skos:exactMatch ncit C142748 Web Browser semapv:ManualMappingCuration orcid:0000-0001-9439-5346 +mesh D064878 orcid:0009-0006-0654-7594 Browser skos:exactMatch ncit C142748 orcid:0009-0006-0654-7594 Browser semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D064886 Dataset skos:exactMatch ncit C47824 Data Set semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D064888 Observational Study skos:exactMatch ncit C16084 Observational Study semapv:ManualMappingCuration orcid:0000-0001-9439-5346 mesh D064890 Social Determinants of Health skos:exactMatch ncit C171586 Social Determinants of Health semapv:ManualMappingCuration orcid:0000-0001-9439-5346