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OG-943. Revert and fix script, update dataset, fix output (#112)
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* Revert OG-943

* Bring back changes from OG-391, add check for existing mechanism

* OG-943. Fix script output, add comments

* Update Hallmarks of Aging and Go-terms in a dataset

* OG-943. Fix query where value were instead of id

* OG-943. Fix. Only select the result with an identical GO-term name

* OG-943. Fix. Consider GO-term children in SQL query for endpoint
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Constantine Rafikov authored Jan 11, 2023
1 parent d2336b5 commit 7783240
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9 changes: 5 additions & 4 deletions api/models/gene.py
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Expand Up @@ -154,10 +154,11 @@ class GeneCommon(BaseModel):
'name': 'coalesce(aging_mechanism.name_@LANG@,aging_mechanism.name_en)',
},
_from="""
FROM gene
LEFT JOIN gene_to_ontology ON gene.id = gene_to_ontology.gene_id
LEFT JOIN gene_ontology_to_aging_mechanism_visible ON gene_to_ontology.gene_ontology_id = gene_ontology_to_aging_mechanism_visible.gene_ontology_id
INNER JOIN aging_mechanism ON gene_ontology_to_aging_mechanism_visible.aging_mechanism_id = aging_mechanism.id AND aging_mechanism.name_en != ''
FROM gene
LEFT JOIN `gene_to_ontology` ON gene_to_ontology.gene_id = gene.id
LEFT JOIN `gene_ontology_relation` ON gene_to_ontology.gene_ontology_id = gene_ontology_parent_id
LEFT JOIN `gene_ontology_to_aging_mechanism_visible` ON gene_to_ontology.gene_ontology_id = gene_ontology_to_aging_mechanism_visible.gene_ontology_id
INNER JOIN `aging_mechanism` ON gene_ontology_to_aging_mechanism_visible.aging_mechanism_id = aging_mechanism.id AND aging_mechanism.name_en != ''
""",
)
]
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47 changes: 21 additions & 26 deletions scripts/aging_mechanisms/go_and_mechanisms.tsv
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@@ -1,27 +1,22 @@
go_terms name_en name_ru
['mitochondrial DNA replication', 'mitochondrial DNA catabolic process', 'mitochondrial genome maintenance', 'mitochondrial DNA repair', 'mitochondrial DNA packaging', 'mitochondrial DNA metabolic process', 'DNA synthesis involved in mitochondrial DNA replication'] mitochondrial DNA instability нестабильность митохондриальной ДНК
['nuclear DNA replication', 'nuclear DNA-directed RNA polymerase complex', 'DNA conformation change', 'chromosome organization', 'premeiotic DNA replication', 'apoptotic DNA fragmentation', 'regulation of nuclear cell cycle DNA replication', 'mitotic DNA replication', 'DNA double-strand break attachment to nuclear envelope', 'DNA repair', 'DNA repair complex', 'DNA damage response', 'detection of DNA damage'] nuclear DNA instability нестабильность ядерной ДНК
['nucleus', 'nucleus organization', 'nuclear envelope organization', 'nuclear migration', 'nuclear membrane disassembly'] nuclear architecture impairment нарушение ядерной архитектуры
['transposon integration', 'transposase activity', 'positive regulation of transposon integration', 'transposon integration involved in RNA-mediated transposition'] transposon activity транспозонная активность
['chromosome telomeric region', 'telomere maintenance via telomerase', 'telomere maintenance', 'telomere organization', 'telomere assembly', 'telomere localization', 'telomere single strand break repair', 'telomere-nuclear envelope anchor activity', 'telomere maintenance via base-excision repair', 'establishment of RNA localization to telomere', 'establishment of protein-containing complex localization to telomere', 'egulation of telomere maintenance in response to DNA damage', 'telomerase activity', 'interphase mitotic telomere clustering', 'meiotic telomere clustering', 'site-specific telomere resolvase activity', 'regulation of DNA recombination at telomere'] telomere attrition укорочение теломер
['histone modification'] alterations in histone modifications изменения модификаций гистонов
['chromatin remodeling'] chromatin remodeling ремоделирование хроматина
['transcription', 'DNA-templated', 'antisense RNA transcription', 'DNA-templated transcription', 'elongation', 'DNA-templated transcription', 'initiation', 'DNA-templated transcription', 'termination', 'mRNA transcription', 'ncRNA transcription', 'negative regulation of transcription', 'DNA-templated', 'piRNA transcription', 'positive regulation of transcription', 'DNA-templated', 'promoter clearance during DNA-templated transcription', 'regulation of transcription', 'DNA-templated', 'telomeric repeat-containing RNA transcription', 'transcription by RNA polymerase I', 'transcription by RNA polymerase II', 'transcription by RNA polymerase III', 'transcription by RNA polymerase IV', 'transcription by RNA polymerase V', 'transcription regulator complex', 'transcription regulator activity', 'gene silencing', 'transcription elongation factor complex', 'RNA polymerase I transcription regulator complex', 'cyclin/CDK positive transcription elongation factor complex', 'positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response', 'regulation of mating-type specific transcription', 'DNA-templated', 'carbon catabolite regulation of transcription', 'regulation of transcription involved in meiotic cell cycle', 'regulation of DNA-binding transcription factor activity', 'negative regulation of transcription', 'DNA-templated'] transcriptional alterations транскрипционные изменения
['mRNA splicing', 'via endonucleolytic cleavage and ligation', 'mRNA splicing', 'via spliceosome', 'RNA splicing'] RNA splicing impairment нарушения сплайсинга РНК
['DNA methylation', 'DNA methylation on cytosine', 'DNA methylation on adenine', 'DNA methylation-dependent heterochromatin assembly', 'DNA methylation or demethylation', 'changes to DNA methylation involved in embryo development', 'gene silencing by RNA-directed DNA methylation', 'maintenance of DNA methylation', 'regulation of DNA methylation'] alterations in DNA methylation изменения метилирования ДНК
['protein folding chaperone', 'chaperone-mediated protein folding', 'regulation of chaperone-mediated protein folding', 'ATP-dependent protein folding chaperone'] impairment of proteins folding and stability нарушения фолдинга и стабильности белков
['proteolysis'] degradation of proteolytic systems деградация протеолитических систем
['TOR signaling', 'TOR complex', 'regulation of TOR signaling', 'negative regulation of TOR signaling', 'positive regulation of TOR signaling', 'negative regulation of macroautophagy by TORC1 signaling'] TOR pathway dysregulation дисрегуляция молекулярного пути TOR
['cAMP-dependent protein kinase activity', 'AMP-activated protein kinase activity', 'nucleotide-activated protein kinase complex', 'regulation of cAMP-dependent protein kinase activity', 'CAMKK-AMPK signaling cascade'] AMPK pathway dysregulation дисрегуляция молекулярного пути AMPK
['-'] SIRT pathway dysregulation дисрегуляция молекулярного пути SIRT
['insulin-like growth factor-activated receptor activity', 'insulin-like growth factor binding protein complex', 'insulin-like growth factor binding', 'insulin-like growth factor I binding', 'insulin-like growth factor receptor binding', 'insulin-like growth factor receptor signaling pathway', 'insulin-like growth factor binary complex', 'insulin-like growth factor ternary complex', 'regulation of insulin-like growth factor receptor signaling pathway'] INS/IGF-1 pathway dysregulation дисрегуляция молекулярного пути INS/IGF-1
['mitochondrial translation', 'mitochondrial transcription', 'mitochondrial RNA processing', 'mitochondrial gene expression', 'regulation of mitochondrial mRNA stability', 'mitochondrial ATP synthesis coupled electron transport', 'mitochondrial membrane organization', 'mitochondrial proliferation', 'mitochondrial protein catabolic process', 'mitochondrion organization'] impairment of the mitochondrial integrity and biogenesis нарушение целостности и биогенеза митохондрий
['oxidoreductase activity', 'oxidoreductase activity', 'cell redox homeostasis', 'reactive oxygen species metabolic process'] accumulation of reactive oxygen species накопление активных форм кислорода
['senescence-associated heterochromatin focus', 'negative regulation of replicative senescence', 'negative regulation of cellular senescence', 'positive regulation of cell aging', 'positive regulation of cellular senescence', 'positive regulation of replicative senescence', 'animal organ senescence', 'cellular senescence', 'cell aging', 'negative regulation of cellular senescence', 'oncogene-induced cell senescence', 'positive regulation of cellular senescence', 'regulation of cellular senescence', 'negative regulation of cellular senescence', 'positive regulation of cellular senescence', 'stress-induced premature senescence', 'oxidative stress-induced premature senescence', 'negative regulation of cell aging', 'negative regulation of cellular senescence', 'negative regulation of replicative senescence', 'nucleolar fragmentation', 'positive regulation of cell aging', 'positive regulation of cell aging', 'positive regulation of replicative senescence', 'progressive alteration of chromatin involved in cell aging', 'extrachromosomal circular DNA accumulation involved in cell aging', 'extrachromosomal circular DNA localization involved in cell aging', 'regulation of cell aging', 'negative regulation of cell aging', 'negative regulation of cellular senescence', 'negative regulation of replicative senescence', 'positive regulation of cell aging', 'positive regulation of cellular senescence', 'positive regulation of replicative senescence', 'regulation of cellular senescence', 'negative regulation of cellular senescence', 'positive regulation of cellular senescence', 'regulation of replicative senescence', 'negative regulation of replicative senescence', 'positive regulation of replicative senescence', 'replicative senescence'] senescent cells accumulation накопление сенесцентных клеток
['stem cell differentiation', 'stem cell division', 'stem cell population maintenance'] stem cell exhaustion истощение пула стволовых клеток
['inflammatory response', 'production of molecular mediator involved in inflammatory response'] sterile inflammation стерильное воспаление
['cell communication'] intercellular communication impairment нарушения межклеточного взаимодействия
['cell-matrix adhesion mediator activity', 'protein complex involved in cell-matrix adhesion', 'extracellular matrix assembly', 'mesangial cell-matrix adhesion', 'cellular response to cell-matrix adhesion', 'cell-matrix adhesion involved in mesendodermal cell migration', 'cell-matrix adhesion involved in ameboidal cell migration', 'extracellular matrix disassembly', 'extracellular matrix constituent secretion', 'dentin extracellular matrix secretion', 'ell adhesion molecule binding', 'extracellular matrix structural constituent'] changes in the extracellular matrix structure изменения структуры межклеточного матрикса
['cap-independent translational initiation of circular RNA'] circular RNAs accumulation накопление кольцевых РНК
['immune system process'] immune system impairment нарушения иммунной системы
['mRNA metabolic process', 'regulation of mRNA stability'] messenger RNA damage повреждение матричной РНК
['mitochondrial DNA replication', 'mitochondrial DNA catabolic process', 'mitochondrial genome maintenance', 'mitochondrial DNA repair', 'mitochondrial DNA packaging', 'DNA synthesis involved in mitochondrial DNA replication'] mitochondrial DNA instability нестабильность митохондриальной ДНК
['nuclear DNA replication', 'nuclear DNA-directed RNA polymerase complex', 'DNA conformation change', 'chromosome organization', 'premeiotic DNA replication', 'apoptotic DNA fragmentation', 'regulation of nuclear cell cycle DNA replication', 'mitotic DNA replication', 'DNA double-strand break attachment to nuclear envelope', 'DNA repair', 'DNA repair complex', 'DNA damage response', 'detection of DNA damage', 'DNA protection'] nuclear DNA instability нестабильность ядерной ДНК
['nucleus organization', 'nuclear envelope organization', 'nuclear migration', 'nuclear membrane disassembly'] nuclear architecture impairment нарушение ядерной архитектуры
['telomere maintenance'] telomere attrition укорочение теломер
['histone modification'] alterations in histone modifications изменения модификаций гистонов
['chromatin remodeling'] chromatin remodeling ремоделирование хроматина
['DNA-templated transcription'] transcriptional alterations транскрипционные изменения
['DNA methylation', 'DNA methylation on cytosine', 'DNA methylation on adenine', 'DNA methylation-dependent heterochromatin assembly', 'DNA methylation or demethylation', 'changes to DNA methylation involved in embryo development', 'gene silencing by RNA-directed DNA methylation', 'maintenance of DNA methylation', 'regulation of DNA methylation'] alterations in DNA methylation изменения метилирования ДНК
['protein folding chaperone', 'chaperone-mediated protein folding', 'regulation of chaperone-mediated protein folding', 'ATP-dependent protein folding chaperone'] impairment of proteins folding and stability нарушения фолдинга и стабильности белков
['proteolysis'] degradation of proteolytic systems деградация протеолитических систем
['TOR signaling', 'TOR complex', 'regulation of TOR signaling', 'negative regulation of TOR signaling', 'positive regulation of TOR signaling', 'negative regulation of macroautophagy by TORC1 signaling'] TOR pathway dysregulation дисрегуляция молекулярного пути TOR
['cAMP-dependent protein kinase activity', 'AMP-activated protein kinase activity', 'nucleotide-activated protein kinase complex', 'regulation of cAMP-dependent protein kinase activity', 'CAMKK-AMPK signaling cascade'] AMPK pathway dysregulation дисрегуляция молекулярного пути AMPK
['insulin-like growth factor-activated receptor activity', 'insulin-like growth factor binding protein complex', 'insulin-like growth factor binding', 'insulin-like growth factor I binding', 'insulin-like growth factor receptor binding', 'insulin-like growth factor receptor signaling pathway', 'insulin-like growth factor binary complex', 'insulin-like growth factor ternary complex', 'regulation of insulin-like growth factor receptor signaling pathway', 'insulin receptor signaling pathway'] INS/IGF-1 pathway dysregulation дисрегуляция молекулярного пути INS/IGF-1
['mitochondrial translation', 'mitochondrial transcription', 'mitochondrial RNA processing', 'mitochondrial gene expression', 'regulation of mitochondrial mRNA stability', 'mitochondrial ATP synthesis coupled electron transport', 'mitochondrial DNA metabolic process', 'mitochondrial membrane organization', 'mitochondrial proliferation', 'mitochondrial protein catabolic process', 'mitochondrion organization'] impairment of the mitochondrial integrity and biogenesis нарушение целостности и биогенеза митохондрий
['oxidoreductase activity', 'cell redox homeostasis', 'reactive oxygen species metabolic process'] accumulation of reactive oxygen species накопление активных форм кислорода
['regulation of replicative senescence', 'replicative senescence', 'negative regulation of replicative senescence', 'positive regulation of replicative senescence', 'cellular senescence', 'regulation of cellular senescence', 'positive regulation of cellular senescence', 'negative regulation of cellular senescence', 'cell aging', 'regulation of cell aging', 'negative regulation of cell aging', 'positive regulation of cell aging', 'oncogene-induced cell senescence', 'stress-induced premature senescence', 'oxidative stress-induced premature senescence', 'progressive alteration of chromatin involved in cell aging', 'extrachromosomal circular DNA accumulation involved in cell aging', 'extrachromosomal circular DNA localization involved in cell aging'] senescent cells accumulation накопление сенесцентных клеток
['stem cell differentiation', 'stem cell division', 'stem cell population maintenance'] stem cell exhaustion истощение пула стволовых клеток
['transposition'] transposon activity транспозонная активность
['inflammatory response', 'production of molecular mediator involved in inflammatory response'] sterile inflammation стерильное воспаление
['cell communication'] intercellular communication impairment нарушения межклеточного взаимодействия
['cell-matrix adhesion', 'cell-matrix adhesion mediator activity', 'protein complex involved in cell-matrix adhesion', 'extracellular matrix assembly', 'mesangial cell-matrix adhesion', 'cellular response to cell-matrix adhesion', 'cell-matrix adhesion involved in mesendodermal cell migration', 'cell-matrix adhesion involved in ameboidal cell migration', 'extracellular matrix disassembly', 'extracellular matrix constituent secretion', 'dentin extracellular matrix secretion', 'cell adhesion molecule binding', 'extracellular matrix structural constituent'] changes in the extracellular matrix structure изменения структуры межклеточного матрикса
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