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PavlidisLab / Gemma

Genomics data re-analysis
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Category and terms with multiple labels #570

Open arteymix opened 1 year ago

arteymix commented 1 year ago 
select CATEGORY_URI, GROUP_CONCAT(distinct CATEGORY)
from CHARACTERISTIC
where CATEGORY_URI is not null
group by CATEGORY_URI
having count(distinct CATEGORY) > 1;
select VALUE_URI, GROUP_CONCAT(distinct VALUE)
from CHARACTERISTIC
where VALUE_URI is not null
group by VALUE_URI
having count(distinct VALUE) > 1;
Affected categories | CATEGORY\_URI | GROUP\_CONCAT\(distinct CATEGORY\) | | :--- | :--- | | http://purl.obolibrary.org/obo/CLO\_0000031 | ???,cell line,cell type | | http://purl.obolibrary.org/obo/GO\_0007610 | behavior,clinical history,phenotype | | http://purl.obolibrary.org/obo/GO\_0008150 | biological process,biological\_process | | http://purl.obolibrary.org/obo/OBI\_0000181 | age,population,strain | | http://purl.obolibrary.org/obo/OBI\_0000272 | genotype,protocol | | http://purl.obolibrary.org/obo/PATO\_0000047 | biological sex,sex | | http://www.ebi.ac.uk/efo/EFO\_0000246 | age,clinical history,developmental stage,timepoint | | http://www.ebi.ac.uk/efo/EFO\_0000322 | cell line,cell type,CellLine,genotype,obsolete\_cell line,organism part,strain | | http://www.ebi.ac.uk/efo/EFO\_0000324 | ,cell line,cell type,CellType,clinical history,collection of material,disease,genotype,growth condition,organism part,phenotype,timepoint,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000352 | behavior,clinical history,developmental stage,diet,disease,phenotype,timepoint,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000428 | dose,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000523 | growth condition,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000542 | disease,individual | | http://www.ebi.ac.uk/efo/EFO\_0000562 | LabelCompound,labelling | | http://www.ebi.ac.uk/efo/EFO\_0000635 | BioSource,cell type,collection of material,disease,disease staging,environmental history,genotype,organism part,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000727 | genotype,treatment | | http://www.ebi.ac.uk/efo/EFO\_0001426 | collection of material,study design | | http://www.ebi.ac.uk/efo/EFO\_0002571 | disease,medical procedure,treatment | | http://www.ebi.ac.uk/efo/EFO\_0002755 | diet,treatment | | http://www.ebi.ac.uk/efo/EFO\_0005066 | block,collection of material,treatment | | http://www.ebi.ac.uk/efo/EFO\_0005067 | block,collection of material,study design |
Affected terms | VALUE\_URI | GROUP\_CONCAT\(distinct VALUE\) | | :--- | :--- | | http://gemma.msl.ubc.ca/ont/TGEMO\_00001 | external stratum pyramidale,homozygous,Homozygous negative | | http://gemma.msl.ubc.ca/ont/TGEMO\_00003 | APP \(K670N/M671L\),Heterozygous | | http://gemma.msl.ubc.ca/ont/TGEMO\_00016 | C57BL/6,C57BL/6J | | http://gemma.msl.ubc.ca/ont/TGEMO\_00017 | C57BL/6 x DBA/2,DBA/2 | | http://gemma.msl.ubc.ca/ont/TGEMO\_00025 | CD1 mus strain,Crl:CD1\(ICR\) | | http://gemma.msl.ubc.ca/ont/TGEMO\_00027 | NOD,NOD mouse | | http://gemma.msl.ubc.ca/ont/TGEMO\_00035 | 129/Sv,129S/Sv | | http://gemma.msl.ubc.ca/ont/TGEMO\_00053 | C3H,Sprague Dawley | | http://gemma.msl.ubc.ca/ont/TGEMO\_00096 | E18,Wistar | | http://gemma.msl.ubc.ca/ont/TGEMO\_00099 | E18.5,P4,Sprague Dawley | | http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Age | Age,SamplingTimePoint | | http://purl.obolibrary.org/obo/CHEBI\_15379 | dioxygen,oxygen | | http://purl.obolibrary.org/obo/CHEBI\_16330 | 17beta-hydroxy-5alpha-androstan-3-one,2 d | | http://purl.obolibrary.org/obo/CHEBI\_17141 | 250 uM,cysteamine | | http://purl.obolibrary.org/obo/CHEBI\_17234 | Glucose,supernatant present | | http://purl.obolibrary.org/obo/CHEBI\_17747 | bis\(2-ethylhexyl\) phthalate,diethylhexyl phthalate | | http://purl.obolibrary.org/obo/CHEBI\_23367 | molecular entity,treatment | | http://purl.obolibrary.org/obo/CHEBI\_28262 | dimethyl sulfoxide,DMSO | | http://purl.obolibrary.org/obo/CHEBI\_35476 | aged,antipsychotic drug | | http://purl.obolibrary.org/obo/CHEBI\_80555 | 1000 nM,4-Hydroxy-N-desmethyltamoxifen | | http://purl.obolibrary.org/obo/CHEBI\_9168 | rapamycin,sirolimus | | http://purl.obolibrary.org/obo/CHEBI\_9288 | streptozocin,streptozotocin | | http://purl.obolibrary.org/obo/CLO\_0000031 | cell line,cell type | | http://purl.obolibrary.org/obo/CLO\_0037317 | embryonic stem cell,mouse embryonic stem cell line cell | | http://purl.obolibrary.org/obo/CLO\_0051536 | EP156T cell,RCB2143 cell | | http://purl.obolibrary.org/obo/CL\_0000025 | egg,egg cell | | http://purl.obolibrary.org/obo/CL\_0000057 | fibroblast,TIG107 | | http://purl.obolibrary.org/obo/CL\_0000129 | ADRc5,microglial cell | | http://purl.obolibrary.org/obo/CL\_0000134 | induced differentiation,mesenchymal cell,mesenchymal stem cell | | http://purl.obolibrary.org/obo/CL\_0000625 | CD8-positive, alpha beta T cell,CD8-positive, alpha-beta T cell | | http://purl.obolibrary.org/obo/CL\_0000738 | leukocyte,white blood cell | | http://purl.obolibrary.org/obo/CL\_0000837 | hematopoietic multipotent progenitor cell,hematopoietic progenitor cell | | http://purl.obolibrary.org/obo/CL\_0000842 | mononuclear cell,peripheral blood mononuclear cell | | http://purl.obolibrary.org/obo/CL\_0002322 | embryonic stem cell,embyronic stem cell | | http://purl.obolibrary.org/obo/CL\_0002540 | mesenchymal stem cell of the bone marrow,mesenchymal stem cell of the bone marrow | | http://purl.obolibrary.org/obo/CL\_0002553 | fibroblast of lung,lung fibroblast | | http://purl.obolibrary.org/obo/CL\_0002618 | endothelial cell of umbilical vein,endothelial cell of umbilical vein | | http://purl.obolibrary.org/obo/CL\_0011012 | neural crest cell,neural crest cell derived | | http://purl.obolibrary.org/obo/DOID\_0050430 | multiple endocrine neoplasia type 2A,Sipple syndrome | | http://purl.obolibrary.org/obo/DOID\_0050431 | arrhythmogenic right ventricular cardiomyopathy,arrhythmogenic right ventricular dysplasia | | http://purl.obolibrary.org/obo/DOID\_0050445 | X-linked hypophosphatemia,X-linked hypophosphatemic rickets | | http://purl.obolibrary.org/obo/DOID\_0060169 | benign familial infantile convulsion,benign familial infantile epilepsy | | http://purl.obolibrary.org/obo/DOID\_10017 | multiple endocrine neoplasia type 1,Wermer syndrome | | http://purl.obolibrary.org/obo/DOID\_10283 | malignant neoplasm of prostate,prostate cancer | | http://purl.obolibrary.org/obo/DOID\_104 | Bacterial Infections,bacterial infectious disease | | http://purl.obolibrary.org/obo/DOID\_1040 | chronic lymphocytic leukemia,Leukemia, Lymphocytic, Chronic | | http://purl.obolibrary.org/obo/DOID\_1059 | intellectual disability,Mental Retardation | | http://purl.obolibrary.org/obo/DOID\_11054 | malignant neoplasm of urinary bladder,urinary bladder cancer | | http://purl.obolibrary.org/obo/DOID\_1156 | chondrocalcinosis,pseudogout | | http://purl.obolibrary.org/obo/DOID\_11665 | Patau syndrome,Trisomy 13 | | http://purl.obolibrary.org/obo/DOID\_11722 | myotonic dystrophy,myotonic dystrophy type 1 | | http://purl.obolibrary.org/obo/DOID\_11723 | Duchenne muscular dystrophy,Muscular Dystrophy, Duchenne | | http://purl.obolibrary.org/obo/DOID\_11870 | Pick's disease,Pick's disease of the brain | | http://purl.obolibrary.org/obo/DOID\_11949 | Creutzfeldt-Jakob disease,Creutzfeldt-Jakob syndrome | | http://purl.obolibrary.org/obo/DOID\_11981 | morbid obesity,Obesity, Morbid | | http://purl.obolibrary.org/obo/DOID\_12010 | anterior ischemic optic neuropathy,ischemic optic neuropathy | | http://purl.obolibrary.org/obo/DOID\_1205 | allergy,Hypersensitivity,hypersensitivity reaction type I disease | | http://purl.obolibrary.org/obo/DOID\_12385 | Dysentery, Bacillary,shigellosis | | http://purl.obolibrary.org/obo/DOID\_12722 | Liver Metastases,liver metastasis | | http://purl.obolibrary.org/obo/DOID\_12803 | mucopolysaccharidosis VII,Sly syndrome | | http://purl.obolibrary.org/obo/DOID\_12849 | autism,autistic disorder | | http://purl.obolibrary.org/obo/DOID\_12858 | Huntington Disease,Huntington's disease | | http://purl.obolibrary.org/obo/DOID\_13809 | familial combined hyperlipidemia,Hyperlipidemia, Familial Combined | | http://purl.obolibrary.org/obo/DOID\_14069 | cerebral malaria,Malaria, Cerebral | | http://purl.obolibrary.org/obo/DOID\_14282 | osteoarthritis,Osteoarthritis, Knee | | http://purl.obolibrary.org/obo/DOID\_1441 | autosomal dominant cerebellar ataxia,spinocerebellar ataxia,Spinocerebellar Ataxias | | http://purl.obolibrary.org/obo/DOID\_14503 | neuronal ceroid lipofuscinosis,neuronal ceroid-lipofuscinosis | | http://purl.obolibrary.org/obo/DOID\_14557 | primary pulmonary hypertension,Pulmonary hypertension, primary | | http://purl.obolibrary.org/obo/DOID\_14777 | benign familial neonatal convulsion,benign familial neonatal epilepsy | | http://purl.obolibrary.org/obo/DOID\_1612 | breast cancer,mammary cancer | | http://purl.obolibrary.org/obo/DOID\_1682 | congenital heart defect,congenital heart disease | | http://purl.obolibrary.org/obo/DOID\_1826 | Epilepsy,epilepsy syndrome | | http://purl.obolibrary.org/obo/DOID\_1911 | endodermal sinus tumor,Yolk Sac carcinoma | | http://purl.obolibrary.org/obo/DOID\_2030 | anxiety disorder,anxiety disorders | | http://purl.obolibrary.org/obo/DOID\_2106 | myotonia congenita,Thomsen disease | | http://purl.obolibrary.org/obo/DOID\_235 | colonic benign neoplasm,colonic neoplasm,Colonic Neoplasms | | http://purl.obolibrary.org/obo/DOID\_2394 | Neoplasm, Ovarian,ovarian cancer,ovarian neoplasm | | http://purl.obolibrary.org/obo/DOID\_263 | kidney cancer,Kidney Neoplasms | | http://purl.obolibrary.org/obo/DOID\_2957 | pulmonary tuberculosis,Tuberculosis, Pulmonary | | http://purl.obolibrary.org/obo/DOID\_2975 | cystic kidney,cystic kidney disease | | http://purl.obolibrary.org/obo/DOID\_3007 | breast ductal carcinoma,ductal carcinoma | | http://purl.obolibrary.org/obo/DOID\_3008 | Ductal Breast Carcinoma,invasive ductal carcinoma | | http://purl.obolibrary.org/obo/DOID\_3068 | Glioblastoma,glioblastoma multiforme | | http://purl.obolibrary.org/obo/DOID\_3073 | brain glioblastoma multiforme,Glioblastoma Multiforme of Brain | | http://purl.obolibrary.org/obo/DOID\_3078 | anaplastic astrocytoma,grade III astrocytoma | | http://purl.obolibrary.org/obo/DOID\_3083 | chronic Obstructive Airway disease,chronic obstructive pulmonary disease | | http://purl.obolibrary.org/obo/DOID\_3165 | skin benign neoplasm,skin benign neoplasm | | http://purl.obolibrary.org/obo/DOID\_3211 | lysosomal storage disease,lysosomal storage metabolic disease | | http://purl.obolibrary.org/obo/DOID\_3310 | atopic dermatitis,Dermatitis, Atopic | | http://purl.obolibrary.org/obo/DOID\_3328 | Epilepsy, Temporal Lobe,temporal lobe epilepsy | | http://purl.obolibrary.org/obo/DOID\_3329 | benign epilepsy with centrotemporal spikes,rolandic epilepsy | | http://purl.obolibrary.org/obo/DOID\_3343 | glycoproteinosis,mucolipidosis | | http://purl.obolibrary.org/obo/DOID\_3369 | Ewing sarcoma,Ewings sarcoma,peripheral primitive neuroectodermal tumor | | http://purl.obolibrary.org/obo/DOID\_3393 | coronary artery disease,coronary heart disease | | http://purl.obolibrary.org/obo/DOID\_3491 | Turner syndrome,Turner's Syndrome | | http://purl.obolibrary.org/obo/DOID\_3507 | dermatofibrosarcoma,dermatofibrosarcoma protuberans | | http://purl.obolibrary.org/obo/DOID\_3620 | central nervous system cancer,Central Nervous System Neoplasms | | http://purl.obolibrary.org/obo/DOID\_3713 | Adenocarcinoma of the Ovary,ovary adenocarcinoma | | http://purl.obolibrary.org/obo/DOID\_3905 | Carcinoma of lung,lung carcinoma | | http://purl.obolibrary.org/obo/DOID\_3907 | lung squamous cell carcinoma,Squamous Cell Carcinoma of Lung | | http://purl.obolibrary.org/obo/DOID\_3910 | Adenocarcinoma of Lung,lung adenocarcinoma | | http://purl.obolibrary.org/obo/DOID\_4001 | Epithelial ovarian cancer,ovarian carcinoma | | http://purl.obolibrary.org/obo/DOID\_4006 | bladder transitional cell carcinoma,transitional cell carcinoma of bladder | | http://purl.obolibrary.org/obo/DOID\_417 | autoimmune disease,hypersensitivity reaction type II disease | | http://purl.obolibrary.org/obo/DOID\_4249 | Gerstmann-Straussler-Scheinker disease,Gerstmann-Straussler-Scheinker syndrome | | http://purl.obolibrary.org/obo/DOID\_4378 | peanut allergic reaction,peanut allergy | | http://purl.obolibrary.org/obo/DOID\_4467 | Clear Cell Carcinoma of Kidney,renal clear cell carcinoma | | http://purl.obolibrary.org/obo/DOID\_4556 | Large Cell Carcinoma of Lung,lung large cell carcinoma | | http://purl.obolibrary.org/obo/DOID\_4610 | intestinal benign neoplasm,intestinal neoplasm | | http://purl.obolibrary.org/obo/DOID\_4706 | infratentorial cancer,infratentorial neoplasm | | http://purl.obolibrary.org/obo/DOID\_480 | movement disease,Movement disorders | | http://purl.obolibrary.org/obo/DOID\_4844 | benign ependymoma,Ependymoma | | http://purl.obolibrary.org/obo/DOID\_4866 | adenoid cystic carcinoma,salivary gland adenoid cystic carcinoma | | http://purl.obolibrary.org/obo/DOID\_4874 | neurodegenerative disorder,Neurodegenerative disorders | | http://purl.obolibrary.org/obo/DOID\_4914 | Adenocarcinoma of Esophagus,esophagus adenocarcinoma | | http://purl.obolibrary.org/obo/DOID\_526 | HIV Infections,Human immunodeficiency virus infectious disease | | http://purl.obolibrary.org/obo/DOID\_5295 | intestinal disease,Intestinal diseases | | http://purl.obolibrary.org/obo/DOID\_5409 | lung small cell carcinoma,Small cell carcinoma of lung | | http://purl.obolibrary.org/obo/DOID\_5614 | eye disease,Eye diseases | | http://purl.obolibrary.org/obo/DOID\_5744 | ovary serous adenocarcinoma,serous adenocarcinoma of the ovary | | http://purl.obolibrary.org/obo/DOID\_5810 | ADA deficiency,adenosine deaminase deficiency | | http://purl.obolibrary.org/obo/DOID\_6000 | congestive heart failure,Heart failure | | http://purl.obolibrary.org/obo/DOID\_6039 | intraocular melanoma,uveal melanoma | | http://purl.obolibrary.org/obo/DOID\_6245 | oncocytoma of kidney,renal oncocytoma | | http://purl.obolibrary.org/obo/DOID\_6432 | hypertension, pulmonary,pulmonary hypertension | | http://purl.obolibrary.org/obo/DOID\_648 | kuru,kuru encephalopathy | | http://purl.obolibrary.org/obo/DOID\_684 | hepatocellular carcinoma,Primary carcinoma of the liver cells | | http://purl.obolibrary.org/obo/DOID\_686 | liver and intrahepatic biliary tract carcinoma,liver carcinoma | | http://purl.obolibrary.org/obo/DOID\_715 | Leukemia, T-Cell,T-cell leukemia | | http://purl.obolibrary.org/obo/DOID\_750 | peptic ulcer,peptic ulcer disease | | http://purl.obolibrary.org/obo/DOID\_7725 | epilepsy with generalized tonic-clonic seizures,tonic-clonic epilepsy | | http://purl.obolibrary.org/obo/DOID\_8354 | C3 deficiency,complement component 3 deficiency | | http://purl.obolibrary.org/obo/DOID\_8545 | anesthesia,malignant hyperthermia | | http://purl.obolibrary.org/obo/DOID\_8552 | chronic myeloid leukemia,Myeloid leukemia, chronic | | http://purl.obolibrary.org/obo/DOID\_8567 | Hodgkin's disease, unspecified type,Hodgkin's lymphoma | | http://purl.obolibrary.org/obo/DOID\_8584 | Burkitt lymphoma,Burkitt's lymphoma | | http://purl.obolibrary.org/obo/DOID\_891 | progressive myoclonic epilepsy,progressive myoclonus epilepsy | | http://purl.obolibrary.org/obo/DOID\_9119 | acute myeloid leukemia,Myeloid leukemia, acute | | http://purl.obolibrary.org/obo/DOID\_92 | speech disorder,speech disorders | | http://purl.obolibrary.org/obo/DOID\_9253 | gastrointestinal stromal tumor,Gastrointestinal Stromal Tumors | | http://purl.obolibrary.org/obo/DOID\_9261 | Carcinoma of Nasopharynx,nasopharynx carcinoma | | http://purl.obolibrary.org/obo/DOID\_9352 | diabetes mellitus type 2,Diabetes Mellitus, Non-Insulin-Dependent,type 2 diabetes mellitus | | http://purl.obolibrary.org/obo/DOID\_9452 | fatty liver,fatty liver disease | | http://purl.obolibrary.org/obo/DOID\_9744 | diabetes mellitus type 1,Diabetes Mellitus, Insulin-Dependent,type 1 diabetes mellitus | | http://purl.obolibrary.org/obo/DOID\_9884 | Muscular Dystrophies,muscular dystrophy | | http://purl.obolibrary.org/obo/DOID\_9975 | Cocaine Addiction,cocaine dependence | | http://purl.obolibrary.org/obo/GO\_0000080 | GO\_0000080,mitotic G1 phase | | http://purl.obolibrary.org/obo/GO\_0000086 | G2/M transition of mitotic cell cycle,GO\_0000086 | | http://purl.obolibrary.org/obo/GO\_0000237 | GO\_0000237,leptotene | | http://purl.obolibrary.org/obo/GO\_0000239 | GO\_0000239,pachytene | | http://purl.obolibrary.org/obo/GO\_0000340 | GO\_0000340,RNA 7-methylguanosine cap binding | | http://purl.obolibrary.org/obo/GO\_0000346 | GO\_0000346,transcription export complex | | http://purl.obolibrary.org/obo/GO\_0000380 | alternative mRNA splicing, via spliceosome,GO\_0000380 | | http://purl.obolibrary.org/obo/GO\_0000785 | chromatin,GO\_0000785 | | http://purl.obolibrary.org/obo/GO\_0000790 | GO\_0000790,nuclear chromatin | | http://purl.obolibrary.org/obo/GO\_0000987 | GO\_0000987,proximal promoter sequence-specific DNA binding | | http://purl.obolibrary.org/obo/GO\_0001503 | GO\_0001503,ossification | | http://purl.obolibrary.org/obo/GO\_0001508 | action potential,GO\_0001508 | | http://purl.obolibrary.org/obo/GO\_0001525 | angiogenesis,GO\_0001525 | | http://purl.obolibrary.org/obo/GO\_0001666 | GO\_0001666,response to hypoxia | | http://purl.obolibrary.org/obo/GO\_0001837 | epithelial to mesenchymal transition,GO\_0001837 | | http://purl.obolibrary.org/obo/GO\_0001939 | female pronucleus,GO\_0001939 | | http://purl.obolibrary.org/obo/GO\_0002024 | diet induced thermogenesis,GO\_0002024 | | http://purl.obolibrary.org/obo/GO\_0003824 | catalytic activity,GO\_0003824 | | http://purl.obolibrary.org/obo/GO\_0004029 | aldehyde dehydrogenase \(NAD\) activity,GO\_0004029 | | http://purl.obolibrary.org/obo/GO\_0004053 | arginase activity,GO\_0004053 | | http://purl.obolibrary.org/obo/GO\_0004532 | exoribonuclease activity,GO\_0004532 | | http://purl.obolibrary.org/obo/GO\_0004707 | GO\_0004707,MAP kinase activity | | http://purl.obolibrary.org/obo/GO\_0004708 | GO\_0004708,MAP kinase kinase activity | | http://purl.obolibrary.org/obo/GO\_0004784 | GO\_0004784,superoxide dismutase activity | | http://purl.obolibrary.org/obo/GO\_0004904 | GO\_0004904,interferon receptor activity | | http://purl.obolibrary.org/obo/GO\_0005152 | GO\_0005152,interleukin-1 receptor antagonist activity | | http://purl.obolibrary.org/obo/GO\_0005577 | fibrinogen complex,GO\_0005577 | | http://purl.obolibrary.org/obo/GO\_0005844 | GO\_0005844,polysome | | http://purl.obolibrary.org/obo/GO\_0005942 | GO\_0005942,phosphatidylinositol 3-kinase complex | | http://purl.obolibrary.org/obo/GO\_0006113 | fermentation,GO\_0006113 | | http://purl.obolibrary.org/obo/GO\_0006277 | DNA amplification,GO\_0006277 | | http://purl.obolibrary.org/obo/GO\_0006338 | chromatin remodeling,GO\_0006338 | | http://purl.obolibrary.org/obo/GO\_0006607 | GO\_0006607,NLS-bearing protein import into nucleus | | http://purl.obolibrary.org/obo/GO\_0006911 | GO\_0006911,phagocytosis, engulfment | | http://purl.obolibrary.org/obo/GO\_0006915 | apoliproprotein E3,GO\_0006915 | | http://purl.obolibrary.org/obo/GO\_0006937 | GO\_0006937,regulation of muscle contraction | | http://purl.obolibrary.org/obo/GO\_0006955 | GO\_0006955,immune response | | http://purl.obolibrary.org/obo/GO\_0007050 | cell cycle arrest,GO\_0007050 | | http://purl.obolibrary.org/obo/GO\_0007219 | GO\_0007219,Notch signaling pathway | | http://purl.obolibrary.org/obo/GO\_0007283 | GO\_0007283,spermatogenesis | | http://purl.obolibrary.org/obo/GO\_0007409 | axonogenesis,GO\_0007409 | | http://purl.obolibrary.org/obo/GO\_0007520 | GO\_0007520,myoblast fusion | | http://purl.obolibrary.org/obo/GO\_0007568 | aging,GO\_0007568 | | http://purl.obolibrary.org/obo/GO\_0007595 | GO\_0007595,lactation | | http://purl.obolibrary.org/obo/GO\_0007610 | behavior,GO\_0007610,phenotype | | http://purl.obolibrary.org/obo/GO\_0008150 | biological process,biological\_process | | http://purl.obolibrary.org/obo/GO\_0008278 | cohesin complex,GO\_0008278 | | http://purl.obolibrary.org/obo/GO\_0008283 | cell proliferation,GO\_0008283 | | http://purl.obolibrary.org/obo/GO\_0009408 | GO\_0009408,response to heat | | http://purl.obolibrary.org/obo/GO\_0009409 | GO\_0009409,response to cold | | http://purl.obolibrary.org/obo/GO\_0009566 | fertilization,GO\_0009566 | | http://purl.obolibrary.org/obo/GO\_0009609 | GO\_0009609,response to symbiotic bacterium | | http://purl.obolibrary.org/obo/GO\_0009629 | GO\_0009629,response to gravity | | http://purl.obolibrary.org/obo/GO\_0009644 | GO\_0009644,response to high light intensity | | http://purl.obolibrary.org/obo/GO\_0010452 | GO\_0010452,histone H3-K36 methylation | | http://purl.obolibrary.org/obo/GO\_0010467 | gene expression,GO\_0010467 | | http://purl.obolibrary.org/obo/GO\_0014065 | GO\_0014065,phosphatidylinositol 3-kinase signaling | | http://purl.obolibrary.org/obo/GO\_0014889 | GO\_0014889,muscle atrophy | | http://purl.obolibrary.org/obo/GO\_0014902 | GO\_0014902,myotube differentiation | | http://purl.obolibrary.org/obo/GO\_0015631 | GO\_0015631,tubulin binding | | http://purl.obolibrary.org/obo/GO\_0016246 | GO\_0016246,RNA interference | | http://purl.obolibrary.org/obo/GO\_0016458 | gene silencing,GO\_0016458 | | http://purl.obolibrary.org/obo/GO\_0016477 | cell migration,GO\_0016477 | | http://purl.obolibrary.org/obo/GO\_0018574 | 2,6-dichloro-p-hydroquinone 1,2-dioxygenase activity,GO\_0018574 | | http://purl.obolibrary.org/obo/GO\_0019933 | cAMP-mediated signaling,GO\_0019933 | | http://purl.obolibrary.org/obo/GO\_0021522 | GO\_0021522,spinal cord motor neuron differentiation | | http://purl.obolibrary.org/obo/GO\_0021861 | forebrain radial glial cell differentiation,GO\_0021861 | | http://purl.obolibrary.org/obo/GO\_0021892 | cerebral cortex GABAergic interneuron differentiation,GO\_0021892 | | http://purl.obolibrary.org/obo/GO\_0021894 | cerebral cortex GABAergic interneuron development,GO\_0021894 | | http://purl.obolibrary.org/obo/GO\_0021979 | GO\_0021979,hypothalamus cell differentiation | | http://purl.obolibrary.org/obo/GO\_0021987 | cerebral cortex development,GO\_0021987 | | http://purl.obolibrary.org/obo/GO\_0030097 | GO\_0030097,hemopoiesis | | http://purl.obolibrary.org/obo/GO\_0030154 | cell differentiation,GO\_0030154 | | http://purl.obolibrary.org/obo/GO\_0030177 | GO\_0030177,positive regulation of Wnt signaling pathway | | http://purl.obolibrary.org/obo/GO\_0030182 | GO\_0030182,neuron differentiation | | http://purl.obolibrary.org/obo/GO\_0030218 | erythrocyte differentiation,GO\_0030218 | | http://purl.obolibrary.org/obo/GO\_0030219 | GO\_0030219,megakaryocyte differentiation | | http://purl.obolibrary.org/obo/GO\_0030324 | GO\_0030324,lung development | | http://purl.obolibrary.org/obo/GO\_0030424 | axon,GO\_0030424 | | http://purl.obolibrary.org/obo/GO\_0030510 | GO\_0030510,regulation of BMP signaling pathway | | http://purl.obolibrary.org/obo/GO\_0031099 | GO\_0031099,regeneration | | http://purl.obolibrary.org/obo/GO\_0032259 | GO\_0032259,methylation | | http://purl.obolibrary.org/obo/GO\_0032609 | GO\_0032609,interferon-gamma production | | http://purl.obolibrary.org/obo/GO\_0033267 | axon part,GO\_0033267 | | http://purl.obolibrary.org/obo/GO\_0033523 | GO\_0033523,histone H2B ubiquitination | | http://purl.obolibrary.org/obo/GO\_0035073 | GO\_0035073,pupariation | | http://purl.obolibrary.org/obo/GO\_0035176 | GO\_0035176,social behavior | | http://purl.obolibrary.org/obo/GO\_0035301 | GO\_0035301,Hedgehog signaling complex | | http://purl.obolibrary.org/obo/GO\_0035330 | GO\_0035330,regulation of hippo signaling | | http://purl.obolibrary.org/obo/GO\_0035900 | GO\_0035900,response to isolation stress | | http://purl.obolibrary.org/obo/GO\_0036094 | GO\_0036094,small molecule binding | | http://purl.obolibrary.org/obo/GO\_0036119 | GO\_0036119,response to platelet-derived growth factor | | http://purl.obolibrary.org/obo/GO\_0036268 | GO\_0036268,swimming | | http://purl.obolibrary.org/obo/GO\_0036273 | GO\_0036273,response to statin | | http://purl.obolibrary.org/obo/GO\_0036363 | GO\_0036363,transforming growth factor beta activation | | http://purl.obolibrary.org/obo/GO\_0036367 | GO\_0036367,light adaption | | http://purl.obolibrary.org/obo/GO\_0036396 | GO\_0036396,RNA N6-methyladenosine methyltransferase complex | | http://purl.obolibrary.org/obo/GO\_0036477 | GO\_0036477,somatodendritic compartment | | http://purl.obolibrary.org/obo/GO\_0042101 | GO\_0042101,T cell receptor complex | | http://purl.obolibrary.org/obo/GO\_0042110 | GO\_0042110,T cell activation | | http://purl.obolibrary.org/obo/GO\_0042493 | GO\_0042493,response to drug | | http://purl.obolibrary.org/obo/GO\_0042637 | catagen,GO\_0042637 | | http://purl.obolibrary.org/obo/GO\_0042640 | anagen,GO\_0042640 | | http://purl.obolibrary.org/obo/GO\_0042697 | GO\_0042697,menopause | | http://purl.obolibrary.org/obo/GO\_0042746 | circadian sleep/wake cycle, wakefulness,GO\_0042746 | | http://purl.obolibrary.org/obo/GO\_0042749 | GO\_0042749,regulation of circadian sleep/wake cycle | | http://purl.obolibrary.org/obo/GO\_0043020 | GO\_0043020,NADPH oxidase complex | | http://purl.obolibrary.org/obo/GO\_0043402 | glucocorticoid mediated signaling pathway,GO\_0043402 | | http://purl.obolibrary.org/obo/GO\_0044297 | cell body,GO\_0044297 | | http://purl.obolibrary.org/obo/GO\_0044774 | GO\_0044774,Top2b antibody | | http://purl.obolibrary.org/obo/GO\_0044838 | cell quiescence,GO\_0044838 | | http://purl.obolibrary.org/obo/GO\_0044839 | cell cycle G2/M phase transition,GO\_0044839 | | http://purl.obolibrary.org/obo/GO\_0045120 | GO\_0045120,pronucleus | | http://purl.obolibrary.org/obo/GO\_0045190 | GO\_0045190,isotype switching | | http://purl.obolibrary.org/obo/GO\_0045444 | fat cell differentiation,GO\_0045444 | | http://purl.obolibrary.org/obo/GO\_0048008 | GO\_0048008,platelet-derived growth factor receptor signaling pathway | | http://purl.obolibrary.org/obo/GO\_0048143 | astrocyte activation,GO\_0048143 | | http://purl.obolibrary.org/obo/GO\_0048245 | eosinophil chemotaxis,GO\_0048245 | | http://purl.obolibrary.org/obo/GO\_0048674 | collateral sprouting of injured axon,GO\_0048674 | | http://purl.obolibrary.org/obo/GO\_0050802 | circadian sleep/wake cycle, sleep,GO\_0050802 | | http://purl.obolibrary.org/obo/GO\_0051568 | GO\_0051568,histone H3-K4 methylation | | http://purl.obolibrary.org/obo/GO\_0060290 | GO\_0060290,transdifferentiation | | http://purl.obolibrary.org/obo/GO\_0060395 | GO\_0060395,SMAD protein signal transduction | | http://purl.obolibrary.org/obo/GO\_0061564 | axon development,GO\_0061564 | | http://purl.obolibrary.org/obo/GO\_0061743 | GO\_0061743,motor learning | | http://purl.obolibrary.org/obo/GO\_0061771 | GO\_0061771,response to caloric restriction | | http://purl.obolibrary.org/obo/GO\_0070206 | GO\_0070206,protein trimerization | | http://purl.obolibrary.org/obo/GO\_0070365 | GO\_0070365,hepatocyte differentiation | | http://purl.obolibrary.org/obo/GO\_0070603 | GO\_0070603,SWI/SNF superfamily-type complex | | http://purl.obolibrary.org/obo/GO\_0070671 | GO\_0070671,response to interleukin-12 | | http://purl.obolibrary.org/obo/GO\_0070852 | cell body fiber,GO\_0070852 | | http://purl.obolibrary.org/obo/GO\_0070988 | demethylation,GO\_0070988 | | http://purl.obolibrary.org/obo/GO\_0071260 | cellular response to mechanical stimulus,GO\_0071260 | | http://purl.obolibrary.org/obo/GO\_0071339 | GO\_0071339,MLL1 complex | | http://purl.obolibrary.org/obo/GO\_0071492 | cellular response to UV-A,GO\_0071492 | | http://purl.obolibrary.org/obo/GO\_0071493 | cellular response to UV-B,GO\_0071493 | | http://purl.obolibrary.org/obo/GO\_0071542 | dopaminergic neuron differentiation,GO\_0071542 | | http://purl.obolibrary.org/obo/GO\_0071625 | GO\_0071625,vocalization behavior | | http://purl.obolibrary.org/obo/GO\_0071735 | GO\_0071735,IgG immunoglobulin complex | | http://purl.obolibrary.org/obo/GO\_0071742 | GO\_0071742,IgE immunoglobulin complex | | http://purl.obolibrary.org/obo/GO\_0071774 | GO\_0071774,response to fibroblast growth factor | | http://purl.obolibrary.org/obo/GO\_0080182 | GO\_0080182,histone H3-K4 trimethylation | | http://purl.obolibrary.org/obo/GO\_0090649 | GO\_0090649,response to oxygen-glucose deprivation | | http://purl.obolibrary.org/obo/GO\_0090650 | cellular response to oxygen-glucose deprivation,GO\_0090650 | | http://purl.obolibrary.org/obo/GO\_0097450 | astrocyte end-foot,GO\_0097450 | | http://purl.obolibrary.org/obo/GO\_0097719 | GO\_0097719,neural tissue regeneration | | http://purl.obolibrary.org/obo/GO\_0140041 | cellular detoxification of methylglyoxal,GO\_0140041 | | http://purl.obolibrary.org/obo/GO\_1901652 | GO\_1901652,response to peptide | | http://purl.obolibrary.org/obo/GO\_1902521 | GO\_1902521,response to etoposide | | http://purl.obolibrary.org/obo/GO\_1903561 | extracellular vesicle,GO\_1903561 | | http://purl.obolibrary.org/obo/GO\_1905217 | GO\_1905217,response to astaxanthin | | http://purl.obolibrary.org/obo/GO\_1990124 | GO\_1990124,messenger ribonucleoprotein complex | | http://purl.obolibrary.org/obo/GO\_1990265 | GO\_1990265,platelet-derived growth factor complex | | http://purl.obolibrary.org/obo/GO\_1990280 | GO\_1990280,RNA localization to chromatin | | http://purl.obolibrary.org/obo/GO\_1990478 | GO\_1990478,response to ultrasound | | http://purl.obolibrary.org/obo/GO\_1990603 | dark adaptation,GO\_1990603 | | http://purl.obolibrary.org/obo/GO\_1990742 | GO\_1990742,microvesicle | | http://purl.obolibrary.org/obo/GO\_1990928 | GO\_1990928,response to amino acid starvation | | http://purl.obolibrary.org/obo/HP\_0001263 | Developmental delay,Global developmental delay | | http://purl.obolibrary.org/obo/HP\_0100660 | Dyskinesia,Dyskinesis | | http://purl.obolibrary.org/obo/MP\_0002006 | neoplasm,tumorigenesis | | http://purl.obolibrary.org/obo/MP\_0005039 | hypoxia,hypoxic conditions | | http://purl.obolibrary.org/obo/NCBITaxon\_5811 | Toxoplasma gondii,Toxoplasma gondii type 2 | | http://purl.obolibrary.org/obo/OBI\_0000025 | Aspergillus pneumonia ,reference substance role | | http://purl.obolibrary.org/obo/OBI\_0000181 | age,population,strain | | http://purl.obolibrary.org/obo/OBI\_0000220 | afferent deprivation,reference subject role | | http://purl.obolibrary.org/obo/OBI\_0000272 | genotype,protocol | | http://purl.obolibrary.org/obo/OBI\_0000994 | intravenous injection,IV-hUMSC | | http://purl.obolibrary.org/obo/OBI\_0100060 | cell culture,cultured cell population | | http://purl.obolibrary.org/obo/OBI\_0500020 | Multivariate statistical method RLQ,time series design | | http://purl.obolibrary.org/obo/PATO\_0000047 | biological sex,sex | | http://purl.obolibrary.org/obo/PATO\_0000389 | acute,peak phase | | http://purl.obolibrary.org/obo/PATO\_0000469 | high,Ly6C-high,positive | | http://purl.obolibrary.org/obo/PATO\_0001706 | behavioural inactive,inactive | | http://purl.obolibrary.org/obo/PATO\_0002097 | malignant,neoplastic, malignant | | http://purl.obolibrary.org/obo/PATO\_0002098 | metastatic,neoplastic, metastatic | | http://purl.obolibrary.org/obo/SO\_0000234 | mRNA,ribosome-protected mRNA | | http://purl.obolibrary.org/obo/UBERON\_0000178 | blood,blood,peripheral blood | | http://purl.obolibrary.org/obo/UBERON\_0000922 | embryo,embryo | | http://purl.obolibrary.org/obo/UBERON\_0001003 | epidermis,skin epidermis | | http://purl.obolibrary.org/obo/UBERON\_0001134 | skeletal muscle,skeletal muscle tissue | | http://purl.obolibrary.org/obo/UBERON\_0001379 | vastus lateralis,vastus lateralis muscle | | http://purl.obolibrary.org/obo/UBERON\_0001384 | motor cortex,primary motor cortex | | http://purl.obolibrary.org/obo/UBERON\_0001897 | dorsal plus ventral thalamus,thalamus | | http://purl.obolibrary.org/obo/UBERON\_0002667 | lateral septal nucleus,lateral septal nucleus | | http://purl.obolibrary.org/obo/UBERON\_0002728 | entorhinal area,entorhinal cortex | | http://purl.obolibrary.org/obo/UBERON\_0009834 | dorsalateral prefrontal cortex,dorsolateral prefrontal cortex | | http://purl.org/commons/record/ncbi\_gene/107963955 | E2A-PBX1 breakpoint,LOC107963955 \[human\] BCR-ABL major-breakpoint cluster region | | http://purl.org/commons/record/ncbi\_gene/11820 | APP \(K595N/M596L\),APP \[human\] amyloid beta \(A4\) precursor protein,App \[mouse\] amyloid beta \(A4\) precursor protein | | http://purl.org/commons/record/ncbi\_gene/19122 | P100,Prnp \[mouse\] prion protein | | http://purl.org/commons/record/ncbi\_gene/20371 | 6 h,Foxp3 \[mouse\] forkhead box P3 | | http://purl.org/commons/record/ncbi\_gene/3456 | glatiramer acetate,IFNB1 \[human\] interferon, beta 1, fibroblast | | http://purl.org/commons/record/ncbi\_gene/4609 | MYC \[human\] v-myc avian myelocytomatosis viral oncogene homolog,MYC \[human\] v-myc myelocytomatosis viral oncogene homolog \(avian\) | | http://purl.org/commons/record/ncbi\_gene/68169 | Ndnf \[mouse\] neuron-derived neurotrophic factor,Ndnf-negative cell | | http://www.ebi.ac.uk/efo/EFO\_0000246 | age,clinical history,developmental stage,timepoint | | http://www.ebi.ac.uk/efo/EFO\_0000322 | cell line,cell type,genotype,organism part,strain | | http://www.ebi.ac.uk/efo/EFO\_0000324 | cell line,cell type,clinical history,collection of material,disease,genotype,growth condition,organism part,phenotype,timepoint,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000352 | behavior,clinical history,developmental stage,diet,disease,phenotype,timepoint,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000399 | age,cell type,developmental stage,organism part,timepoint,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000408 | cell line,cell type,collection of material,diet,disease,disease staging,genotype,organism part,phenotype,strain,timepoint,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000410 | disease,disease staging,phenotype,timepoint,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000428 | dose,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000470 | environmental stress,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000510 | cell type,genotype,phenotype,strain,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000513 | cell line,disease,genotype,strain,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000523 | growth condition,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000542 | disease,individual | | http://www.ebi.ac.uk/efo/EFO\_0000599 | 129,129/Sv | | http://www.ebi.ac.uk/efo/EFO\_0000601 | 129 x C57BL/6,129xC57BL/6 | | http://www.ebi.ac.uk/efo/EFO\_0000635 | cell type,collection of material,disease,disease staging,EFO\_0000635,environmental history,genotype,organism part,organismpart,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000651 | behavior,cell type,clinical history,collection of material,disease,genotype,phenotype,population,strain,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000724 | cell line,developmental stage,timepoint,treatment | | http://www.ebi.ac.uk/efo/EFO\_0000727 | cell type,collection of material,diet,disease,environmental history,genotype,growth condition,phenotype,strain,timepoint,treatment | | http://www.ebi.ac.uk/efo/EFO\_0001200 | MCF 10A,MCF 10A cell | | http://www.ebi.ac.uk/efo/EFO\_0001267 | biological sex,hermaphrodite | | http://www.ebi.ac.uk/efo/EFO\_0001272 | 6 weeks - 8 weeks,adult | | http://www.ebi.ac.uk/efo/EFO\_0001426 | collection of material,study design | | http://www.ebi.ac.uk/efo/EFO\_0002571 | disease,medical procedure,treatment | | http://www.ebi.ac.uk/efo/EFO\_0002755 | diet,treatment | | http://www.ebi.ac.uk/efo/EFO\_0003128 | HCC1359,HCC1438 cell | | http://www.ebi.ac.uk/efo/EFO\_0004425 | 24 h,41 h,6 h,initial time point,post surgery | | http://www.ebi.ac.uk/efo/EFO\_0004444 | behavior,clinical history,collection of material,disease,environmental history,treatment | | http://www.ebi.ac.uk/efo/EFO\_0004905 | induced pluripotent stem cel,induced pluripotent stem cell | | http://www.ebi.ac.uk/efo/EFO\_0005066 | block,collection of material,treatment | | http://www.ebi.ac.uk/efo/EFO\_0005067 | block,collection of material,study design | | http://www.ebi.ac.uk/efo/EFO\_0005135 | cell line,genotype,organism part,phenotype,strain | | http://www.ebi.ac.uk/efo/EFO\_0005371 | HCC1195,HCC1313 cell |
ppavlidis commented 1 year ago

The approach here would be to replace them with the current label based on the latest ontology. A bit of a pain but if we have code to do this we can run it periodically as these things tend to creep into the system (as discussed).

A related issue is that ontology terms that we use can become obsolete and finding and fixing those is the first step to taking action.

arteymix commented 1 year ago

With https://github.com/PavlidisLab/Gemma/commit/df8b10fb6c087f3ad1463b2155e3b1df492eccae, having terms with multiple labels does not duplicate groups.

However, the CATEGORY and VALUE that is picked is arbitrary, so we need to address the multiple labels in order to display accurate information in GemBrow.

arteymix commented 1 year ago

I'll focus on fixing the category first. Terms will need a more systematic approach.

arteymix commented 1 year ago

All the categories with multiple labels have been fixed now.