Skip to content

Commit

Permalink
More ChEBI-MeSH curations (#166)
Browse files Browse the repository at this point in the history 
Adding a few more CHEBI-MeSH equivalences that came up during Gilda
grounding.
  • Loading branch information
@bgyori
bgyori authored Jun 20, 2024
2 parents feb9c9b + 81ebbf6 commit 0f537af
Show file tree
Hide file tree
Showing 3 changed files with 14 additions and 14 deletions.
1 change: 1 addition & 0 deletions src/biomappings/resources/incorrect.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -106,6 +106,7 @@ chebi CHEBI:15367 all-trans-retinoic acid skos:exactMatch mesh D012160 Retina se
chebi CHEBI:15756 hexadecanoic acid skos:exactMatch mesh D010169 Palmitic Acids semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/indralab/panacea_indra/blob/master/panacea_indra/make_ctd_tests.py 0.9
chebi CHEBI:15940 nicotinic acid skos:exactMatch mesh D009539 Nicotinic Acids semapv:ManualMappingCuration orcid:0000-0003-4423-4370
chebi CHEBI:16543 N(2)-acetyl-L-ornithine skos:exactMatch mesh C021951 N(delta)-acetylornithine semapv:ManualMappingCuration orcid:0000-0003-4423-4370
chebi CHEBI:17221 beta-myrcene skos:exactMatch mesh C509595 myrcene semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:17544 hydrogencarbonate skos:exactMatch mesh D001639 Bicarbonates semapv:ManualMappingCuration orcid:0000-0003-4423-4370
chebi CHEBI:17883 hydrogen chloride skos:exactMatch mesh D007943 Leukemia, Hairy Cell semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:22927 bromine atom skos:exactMatch mesh D031724 Bromus semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
Expand Down
13 changes: 13 additions & 0 deletions src/biomappings/resources/mappings.tsv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2362,6 +2362,7 @@ chebi CHEBI:27770 nonanoyl-CoA skos:exactMatch mesh C057128 nonanoyl-coenzyme A
chebi CHEBI:27777 acetohydroxamic acid skos:exactMatch mesh C006358 acetohydroxamic acid semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:28179 benzamide skos:exactMatch mesh C037689 benzamide semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:28426 cyanidin 3-O-beta-D-glucoside skos:exactMatch mesh C114438 cyanidin 3-O-glucoside semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:28755 2,4,6-trichlorophenol skos:exactMatch mesh C024564 2,4,6-trichlorophenol semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:28777 liquiritigenin skos:exactMatch mesh C083152 liquiritigenin semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:28792 erucic acid skos:exactMatch mesh C049811 erucic acid semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:28821 piperine skos:exactMatch mesh C008922 piperine semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand All @@ -2377,6 +2378,7 @@ chebi CHEBI:2968 bacampicillin skos:exactMatch mesh C011674 bacampicillin semapv
chebi CHEBI:29688 telithromycin skos:exactMatch mesh C106791 telithromycin semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:2980 5,6,7-trimethoxyflavone skos:exactMatch mesh C107364 5,6,7-trimethoxyflavone semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:30222 neutron skos:exactMatch mesh D009502 Neutrons semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:30704 molybdenum disulfide skos:exactMatch mesh C082964 molybdenum disulfide semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:30746 benzoic acid skos:exactMatch mesh D019817 Benzoic Acid semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:3078 betamethasone sodium phosphate skos:exactMatch mesh C028994 betamethasone sodium phosphate semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:30805 dodecanoic acid skos:exactMatch mesh C030358 lauric acid semapv:ManualMappingCuration orcid:0000-0003-4423-4370
Expand Down Expand Up @@ -2447,6 +2449,7 @@ chebi CHEBI:3353 candoxatril skos:exactMatch mesh C062766 candoxatril semapv:Man
chebi CHEBI:3404 carboprost tromethamine skos:exactMatch mesh C062843 carboprost tromethamine semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:34339 3-Hydroxyestra-1,3,5(10),6-tetraen-17-one skos:exactMatch mesh C076348 3-hydroxyestra-1,3,5(10),6-tetraen-17-one semapv:ManualMappingCuration orcid:0000-0003-4423-4370
chebi CHEBI:34380 monobenzone skos:exactMatch mesh C006429 monobenzone semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:34399 4-Chloronitrobenzene skos:exactMatch mesh C010407 4-chloronitrobenzene semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:34545 Azimilide skos:exactMatch mesh C086123 azimilide semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:34762 Ferric gluconate skos:exactMatch mesh C035552 ferric gluconate semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:3481 cefamandole nafate skos:exactMatch mesh C012810 cefamandole nafate semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand All @@ -2457,6 +2460,7 @@ chebi CHEBI:34946 Reactive blue 2 skos:exactMatch mesh C012842 Cibacron Blue F 3
chebi CHEBI:34953 Ro 61-8048 skos:exactMatch mesh C110196 Ro 61-8048 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:34956 ruthenium red skos:exactMatch mesh D012430 Ruthenium Red semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:34973 Selfotel skos:exactMatch mesh C053672 selfotel semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:35028 Trimethylolpropane triacrylate skos:exactMatch mesh C027993 trimethylolpropane triacrylate semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:35036 fentin chloride skos:exactMatch mesh C012594 triphenyltin chloride semapv:ManualMappingCuration orcid:0000-0003-4423-4370
chebi CHEBI:3504 cefpodoxime skos:exactMatch mesh C053268 cefpodoxime semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:3505 cefpodoxime proxetil skos:exactMatch mesh C053267 cefpodoxime proxetil semapv:ManualMappingCuration orcid:0000-0003-4423-4370
Expand Down Expand Up @@ -2573,6 +2577,7 @@ chebi CHEBI:46050 docosane skos:exactMatch mesh C470023 docosane semapv:ManualMa
chebi CHEBI:46149 picric acid skos:exactMatch mesh C005858 picric acid semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:46245 coenzyme Q10 skos:exactMatch mesh C024989 coenzyme Q10 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:46557 zoledronic acid skos:exactMatch mesh D000077211 Zoledronic Acid semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:46643 isobutyl nitrite skos:exactMatch mesh C018086 isobutyl nitrite semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:46742 Nutlin-3 skos:exactMatch mesh C482205 nutlin 3 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:4682 dolasetron skos:exactMatch mesh C060344 dolasetron semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:469 1'-acetoxychavicol acetate skos:exactMatch mesh C047948 1'-acetoxychavicol acetate semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand Down Expand Up @@ -2627,6 +2632,7 @@ chebi CHEBI:51451 endothelin receptor antagonist skos:exactMatch mesh D065128 En
chebi CHEBI:52221 isothiocyanate skos:exactMatch mesh D017879 Isothiocyanates semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:52233 tin-116 atom skos:exactMatch mesh C000615562 Tin-116 semapv:ManualMappingCuration orcid:0000-0003-4423-4370
chebi CHEBI:52593 nanowire skos:exactMatch mesh D053770 Nanowires semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:52633 molybdenum-95 skos:exactMatch mesh C000615511 Molybdenum-95 semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:53078 N(6)-(2,4-dinitrophenyl)lysine skos:exactMatch mesh C007493 epsilon-dinitrophenyllysine semapv:ManualMappingCuration orcid:0000-0003-4423-4370
chebi CHEBI:53175 13-apo-beta-carotenone skos:exactMatch mesh C071310 beta-apo-13-carotenone semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:53457 glucuronoxylomannan skos:exactMatch mesh C027478 glucuronoxylomannan semapv:ManualMappingCuration orcid:0000-0003-4423-4370
Expand Down Expand Up @@ -2774,6 +2780,7 @@ chebi CHEBI:7611 nonacosan-10-ol skos:exactMatch mesh C468854 10-nonacosanol sem
chebi CHEBI:76114 benoxaprofen skos:exactMatch mesh C011677 benoxaprofen semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:76274 SC560 skos:exactMatch mesh C115461 SC 560 semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:76308 tetradecanedioic acid skos:exactMatch mesh C441251 1,14-tetradecanedioic acid semapv:ManualMappingCuration orcid:0000-0003-4423-4370
chebi CHEBI:76601 2-(chloromethyl)pyridine skos:exactMatch mesh C091423 2-chloromethylpyridine semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:76607 macitentan skos:exactMatch mesh C533860 macitentan semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:76617 EC 2.7.10.2 (non-specific protein-tyrosine kinase) inhibitor skos:exactMatch mesh D000075242 Janus Kinase Inhibitors semapv:ManualMappingCuration orcid:0000-0003-4423-4370
chebi CHEBI:76749 bopindolol skos:exactMatch mesh C036007 bopindolol semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand Down Expand Up @@ -2824,6 +2831,7 @@ chebi CHEBI:82220 atraton skos:exactMatch mesh C017035 atratone semapv:ManualMap
chebi CHEBI:82357 N-Nitrosodiethanolamine skos:exactMatch mesh C014129 N-nitrosodiethanolamine semapv:ManualMappingCuration orcid:0000-0003-4423-4370
chebi CHEBI:82392 Arsenobetaine skos:exactMatch mesh C038992 arsenobetaine semapv:ManualMappingCuration orcid:0000-0003-4423-4370
chebi CHEBI:82469 Glycidyl oleate skos:exactMatch mesh C013542 glycidyl oleate semapv:ManualMappingCuration orcid:0000-0003-4423-4370
chebi CHEBI:82482 Methyl acrylate skos:exactMatch mesh C035956 methyl acrylate semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching generate_chebi_mesh_mappings.py 0.95
chebi CHEBI:8256 Plantamajoside skos:exactMatch mesh C421173 plantamajoside semapv:ManualMappingCuration orcid:0000-0003-4423-4370
chebi CHEBI:82621 monascin skos:exactMatch mesh C517880 monascin semapv:ManualMappingCuration orcid:0000-0001-9439-5346
chebi CHEBI:82699 oritavancin skos:exactMatch mesh C100708 oritavancin semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand Down Expand Up @@ -4455,6 +4463,7 @@ mesh C019919 CoA-synthesizing protein complex skos:exactMatch go GO:1990143 CoA-
mesh C021240 tissue-factor-pathway inhibitor 2 skos:exactMatch ncit C111846 Tissue Factor Pathway Inhibitor 2 semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh C022052 placental ribonuclease inhibitor skos:exactMatch ncit C101604 Ribonuclease Inhibitor semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh C024352 fludarabine skos:exactMatch ncit C1094 Fludarabine semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh C024564 2,4,6-trichlorophenol skos:exactMatch ncit C44304 2,4,6-Trichlorophenol semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
mesh C025026 sodium sulfite skos:exactMatch ncit C28205 Sodium Sulfite semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh C025462 sulindac sulfide skos:exactMatch ncit C29854 Sulindac Sulfide semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh C026452 messenger ribonucleoprotein skos:exactMatch go GO:1990124 messenger ribonucleoprotein complex semapv:ManualMappingCuration orcid:0000-0003-4423-4370
Expand Down Expand Up @@ -7458,6 +7467,7 @@ mesh D008934 Mitogens skos:exactMatch chebi CHEBI:52290 mitogen semapv:ManualMap
mesh D008937 Mitomycins skos:exactMatch chebi CHEBI:25357 mitomycin semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D008942 Mitoxantrone skos:exactMatch chebi CHEBI:50729 mitoxantrone semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D008976 Molluscum Contagiosum skos:exactMatch hp HP:0032163 Molluscum contagiosum semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9
mesh D008982 Molybdenum skos:exactMatch chebi CHEBI:28685 molybdenum atom semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
mesh D009020 Morphine skos:exactMatch chebi CHEBI:17303 morphine semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D009026 Mortality skos:exactMatch efo 0004352 mortality semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D009026 Mortality skos:exactMatch ncit C16880 Mortality semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand Down Expand Up @@ -7742,6 +7752,7 @@ mesh D013405 Suicide skos:exactMatch efo 0007624 suicide semapv:ManualMappingCur
mesh D013405 Suicide skos:exactMatch ncit C3394 Suicide semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D013413 Sulfadoxine skos:exactMatch chebi CHEBI:9329 sulfadoxine semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D013420 Sulfamethoxazole skos:exactMatch chebi CHEBI:9332 sulfamethoxazole semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D013427 Sulfapyridine skos:exactMatch chebi CHEBI:132842 sulfapyridine semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py 0.95
mesh D013547 Sweating, Gustatory skos:exactMatch hp HP:0025277 Gustatory sweating semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching generate_hp_mesh_mappings.py 0.9
mesh D013550 Swimming skos:exactMatch go GO:0036268 swimming semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D013559 Symbiosis skos:exactMatch go GO:0044403 symbiotic process semapv:ManualMappingCuration orcid:0000-0001-9439-5346
Expand Down Expand Up @@ -7851,13 +7862,15 @@ mesh D015530 Nuclear Matrix skos:exactMatch go GO:0016363 nuclear matrix semapv:
mesh D015539 Platelet Activation skos:exactMatch go GO:0030168 platelet activation semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D015570 Josamycin skos:exactMatch chebi CHEBI:31739 josamycin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/492ede/scripts/import_gilda_mappings.py 0.95
mesh D015570 Josamycin skos:exactMatch ncit C83851 Josamycin semapv:ManualMappingCuration orcid:0000-0003-4423-4370 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
mesh D015632 1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine skos:exactMatch chebi CHEBI:17963 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
mesh D015636 Magnesium Chloride skos:exactMatch chebi CHEBI:6636 magnesium dichloride semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D015636 Magnesium Chloride skos:exactMatch ncit C29240 Magnesium Chloride semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D015662 Trimethoprim, Sulfamethoxazole Drug Combination skos:exactMatch chebi CHEBI:3770 co-trimoxazole semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D015715 Corneal Edema skos:exactMatch ncit C50508 Corneal Edema semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D015725 Fluconazole skos:exactMatch chebi CHEBI:46081 fluconazole semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D015735 Mifepristone skos:exactMatch chebi CHEBI:50692 mifepristone semapv:ManualMappingCuration orcid:0000-0003-4423-4370
mesh D015742 Propofol skos:exactMatch chebi CHEBI:44915 propofol semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D015761 4-Aminopyridine skos:exactMatch chebi CHEBI:34385 4-aminopyridine semapv:ManualMappingCuration orcid:0000-0001-9439-5346 semapv:LexicalMatching https://github.com/biomappings/biomappings/blob/a80ed2/scripts/import_gilda_mappings.py 0.95
mesh D015774 Ganciclovir skos:exactMatch chebi CHEBI:465284 ganciclovir semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D015775 Fractures, Stress skos:exactMatch ncit C26779 Stress Fracture semapv:ManualMappingCuration orcid:0000-0001-9439-5346
mesh D015831 Osteochondroma skos:exactMatch efo 1000411 Osteochondroma semapv:ManualMappingCuration orcid:0000-0003-4423-4370
Expand Down
Loading

0 comments on commit 0f537af

Please sign in to comment.