groups.yml 21.2 KB
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chembl_molecule:
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  download:
    default: ['molecule_chembl_id', 'pref_name', 'molecule_synonyms', 'molecule_type', 'max_phase',
    'molecule_properties.full_mwt', '_metadata.related_targets.count', '_metadata.related_activities.count',
    'molecule_properties.alogp', 'molecule_properties.psa', 'molecule_properties.hba', 'molecule_properties.hbd',
    'molecule_properties.num_ro5_violations', 'molecule_properties.rtb', 'molecule_properties.ro3_pass',
    'molecule_properties.qed_weighted', 'molecule_properties.cx_most_apka', 'molecule_properties.cx_most_bpka',
    'molecule_properties.cx_logp', 'molecule_properties.cx_logd', 'molecule_properties.aromatic_rings',
    'structure_type', 'inorganic_flag', 'molecule_properties.heavy_atoms', 'molecule_properties.hba_lipinski',
    'molecule_properties.hbd_lipinski', 'molecule_properties.num_lipinski_ro5_violations',
    'molecule_properties.mw_monoisotopic', 'molecule_properties.molecular_species',
    'molecule_properties.full_molformula', 'molecule_structures.canonical_smiles']
  browser_table:
    default: ['molecule_chembl_id', 'pref_name', 'molecule_synonyms', 'molecule_type', 'max_phase',
    'molecule_properties.full_mwt', '_metadata.related_targets.count', '_metadata.related_activities.count',
    'molecule_properties.alogp', 'molecule_properties.psa', 'molecule_properties.hba', 'molecule_properties.hbd',
    'molecule_properties.num_ro5_violations', 'molecule_properties.rtb', 'molecule_properties.ro3_pass',
    'molecule_properties.qed_weighted']
    optional: ['molecule_properties.cx_most_apka', 'molecule_properties.cx_most_bpka', 'molecule_properties.cx_logp',
    'molecule_properties.cx_logd', 'molecule_properties.aromatic_rings', 'structure_type', 'inorganic_flag',
    'molecule_properties.heavy_atoms', 'molecule_properties.hba_lipinski', 'molecule_properties.hbd_lipinski',
    'molecule_properties.num_lipinski_ro5_violations', 'molecule_properties.mw_monoisotopic',
    'molecule_properties.molecular_species', 'molecule_properties.full_molformula',
    'molecule_structures.canonical_smiles']
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  eubopen_browser_table:
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    default: [ 'molecule_chembl_id', 'pref_name', 'molecule_synonyms', 'molecule_type']
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  browser_cards:
    default: ['molecule_chembl_id', 'pref_name']
  alternate_forms_carousel:
    default: ['molecule_chembl_id']
  download_drugs:
    default: ['drug_parent_molecule_chembl_id', 'molecule_synonyms', 'research_codes', 'drug_phase',
    '_metadata.drug.drug_data.applicants', 'usan_stem', 'usan_year', 'usan_stem_definition',
    '_metadata.drug.drug_data.usan_stem_substem', 'first_approval', 'drug_atc_codes', 'drug_atc_codes_level_4',
    'drug_atc_codes_level_3', 'drug_atc_codes_level_2', 'drug_atc_codes_level_1',
    'indication_class', '_metadata.drug.drug_data.sc_patent', '_metadata.drug.drug_data.drug_type',
    '_metadata.drug.drug_data.rule_of_five', '_metadata.drug.drug_data.first_in_class',
    '_metadata.compound_generated.chirality_label', '_metadata.drug.drug_data.prodrug',
    '_metadata.drug.drug_data.oral', '_metadata.drug.drug_data.parenteral', '_metadata.drug.drug_data.topical',
    '_metadata.drug.drug_data.black_box', '_metadata.compound_generated.availability_type_label',
    '_metadata.drug.drug_data.withdrawn_year', '_metadata.drug.drug_data.withdrawn_reason',
    '_metadata.drug.drug_data.withdrawn_country', '_metadata.drug.drug_data.withdrawn_class',
    'molecule_structures.canonical_smiles']
  browser_cards_drugs:
    default: ['drug_parent_molecule_chembl_id', 'molecule_synonyms', 'research_codes', 'drug_phase']
  browser_table_drugs:
    default: ['drug_parent_molecule_chembl_id', 'molecule_synonyms', 'research_codes', 'drug_phase',
    '_metadata.drug.drug_data.applicants', 'usan_stem', 'usan_year', 'first_approval', 'drug_atc_codes', 'drug_icon']
    optional: ['usan_stem_definition', '_metadata.drug.drug_data.usan_stem_substem',  'drug_atc_codes_level_4',
    'drug_atc_codes_level_3', 'drug_atc_codes_level_2', 'drug_atc_codes_level_1', 'indication_class',
    '_metadata.drug.drug_data.sc_patent', 'withdrawn_year', 'withdrawn_reason', 'withdrawn_country',
    'withdrawn_class', 'molecule_structures.canonical_smiles']
  download_similarity:
    default: ['similarity', 'molecule_chembl_id', 'pref_name', 'molecule_synonyms', 'molecule_type', 'max_phase',
    'molecule_properties.full_mwt', '_metadata.related_targets.count', '_metadata.related_activities.count',
    'molecule_properties.alogp', 'molecule_properties.psa', 'molecule_properties.hba', 'molecule_properties.hbd',
    'molecule_properties.num_ro5_violations', 'molecule_properties.rtb', 'molecule_properties.ro3_pass',
    'molecule_properties.qed_weighted', 'molecule_properties.cx_most_apka', 'molecule_properties.cx_most_bpka',
    'molecule_properties.cx_logp', 'molecule_properties.cx_logd', 'molecule_properties.aromatic_rings',
    'structure_type', 'inorganic_flag', 'molecule_properties.heavy_atoms', 'molecule_properties.hba_lipinski',
    'molecule_properties.hbd_lipinski', 'molecule_properties.num_lipinski_ro5_violations',
    'molecule_properties.mw_monoisotopic', 'molecule_properties.molecular_species',
    'molecule_properties.full_molformula', 'molecule_structures.canonical_smiles']
  browser_cards_similarity:
    default: ['molecule_chembl_id', 'pref_name', 'similarity']
  browser_table_similarity:
    default: ['similarity', 'molecule_chembl_id', 'pref_name', 'molecule_synonyms', 'molecule_type', 'max_phase',
    'molecule_properties.full_mwt', '_metadata.related_targets.count', '_metadata.related_activities.count',
    'molecule_properties.alogp', 'molecule_properties.psa', 'molecule_properties.hba', 'molecule_properties.hbd',
    'molecule_properties.num_ro5_violations', 'molecule_properties.rtb', 'molecule_properties.ro3_pass',
    'molecule_properties.qed_weighted']
    optional: ['molecule_properties.cx_most_apka', 'molecule_properties.cx_most_bpka', 'molecule_properties.cx_logp',
    'molecule_properties.cx_logd', 'molecule_properties.aromatic_rings', 'structure_type', 'inorganic_flag',
    'molecule_properties.heavy_atoms', 'molecule_properties.hba_lipinski', 'molecule_properties.hbd_lipinski',
    'molecule_properties.num_lipinski_ro5_violations', 'molecule_properties.mw_monoisotopic',
    'molecule_properties.molecular_species', 'molecule_properties.full_molformula',
    'molecule_structures.canonical_smiles']
  compound_sources:
    default: ['sources_list', 'additional_sources_list']
  withdrawal_info:
   default: ['withdrawn_year', 'withdrawn_reason', 'withdrawn_country', 'withdrawn_class']
  clinical_data:
    default: ['clinical_trials_terms', 'chochrane_terms']
  helm_notation:
    default: ['helm_notation']
  biocomponents:
    default: ['molecule_chembl_id', 'biotherapeutic.biocomponents']
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  sdf_data:
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    default: ['molecule_structures.molfile']
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  querystring:
    default: [ 'molecule_chembl_id', 'pref_name', 'molecule_synonyms', 'molecule_type', 'max_phase',
     'molecule_properties.full_mwt', '_metadata.related_targets.count', '_metadata.related_activities.count',
     'molecule_properties.alogp', 'molecule_properties.psa', 'molecule_properties.hba', 'molecule_properties.hbd',
     'molecule_properties.num_ro5_violations', 'molecule_properties.rtb', 'molecule_properties.ro3_pass',
     'molecule_properties.qed_weighted', 'molecule_properties.cx_most_apka', 'molecule_properties.cx_most_bpka',
     'molecule_properties.cx_logp', 'molecule_properties.cx_logd', 'molecule_properties.aromatic_rings',
     'structure_type', 'inorganic_flag', 'molecule_properties.heavy_atoms', 'molecule_properties.hba_lipinski',
     'molecule_properties.hbd_lipinski', 'molecule_properties.num_lipinski_ro5_violations',
     'molecule_properties.mw_monoisotopic', 'molecule_properties.molecular_species',
     'molecule_properties.full_molformula', 'molecule_structures.canonical_smiles' ]
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  calculated_properties:
    default: ['molecule_properties.mw_freebase', 'molecule_properties.mw_monoisotopic', 'molecule_properties.alogp',
              'molecule_properties.rtb', 'molecule_properties.psa', 'molecule_properties.molecular_species',
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              'molecule_properties.hba', 'molecule_properties.hbd', 'molecule_properties.num_ro5_violations',
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              'molecule_properties.hba_lipinski', 'molecule_properties.hbd_lipinski',
              'molecule_properties.num_lipinski_ro5_violations',
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              'molecule_properties.cx_most_apka', 'molecule_properties.cx_most_bpka', 'molecule_properties.cx_logp',
              'molecule_properties.cx_logd', 'molecule_properties.aromatic_rings', 'molecule_properties.heavy_atoms',
              'molecule_properties.qed_weighted']
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  eubopen_search_results:
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    default: ['pref_name', 'molecule_synonyms']
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    sticky: ['molecule_chembl_id']
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chembl_assay:
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  download:
    default: ['assay_chembl_id', 'assay_type', 'description', 'assay_organism', '_metadata.related_compounds.count',
    '_metadata.related_activities.count', 'bao_format', 'bao_label', 'confidence_score',
    '_metadata.assay_generated.confidence_label','assay_strain', '_metadata.source.src_description',
    'assay_tax_id', 'assay_type', 'tissue_chembl_id', 'assay_tissue', 'assay_cell_type', 'assay_subcellular_fraction',
    'document_chembl_id', '_metadata.document_data.pubmed_id', '_metadata.document_data.doi',
    '_metadata.document_data.year', '_metadata.document_data.journal', '_metadata.document_data.volume',
    '_metadata.document_data.first_page','_metadata.document_data.last_page', 'assay_parameters',
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    'assay_classifications_level1', 'assay_classifications_level2', 'assay_classifications_level3',
    'variant_sequence.accession', 'variant_sequence.mutation'
    ]
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  browser_table:
    default: ['assay_chembl_id', 'assay_type', 'description', 'assay_organism', '_metadata.related_compounds.count',
    'document_chembl_id', 'bao_label', '_metadata.source.src_description']
    optional: ['_metadata.related_activities.count', 'bao_format', 'confidence_score',
    '_metadata.assay_generated.confidence_label', 'assay_strain', 'assay_tax_id', 'assay_type', 'tissue_chembl_id',
    'assay_tissue', 'assay_cell_type', 'assay_subcellular_fraction', '_metadata.document_data.pubmed_id',
    '_metadata.document_data.doi', '_metadata.document_data.year', '_metadata.document_data.journal',
    '_metadata.document_data.volume', '_metadata.document_data.first_page','_metadata.document_data.last_page',
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    'assay_parameters', 'assay_classifications_level1', 'assay_classifications_level2', 'assay_classifications_level3',
    'variant_sequence.accession', 'variant_sequence.mutation']
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  assay_parameters:
    default: ['assay_parameters_report_card_rows']
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chembl_target:
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  download:
    default: ['target_chembl_id', 'pref_name', 'uniprot_accessions', 'target_type', 'organism',
    '_metadata.related_compounds.count', '_metadata.related_activities.count', 'tax_id', 'species_group_flag']
  download_blast:
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    default: ['best_expectation', 'best_positives', 'best_identities', 'best_score_bits', 'best_score', 'length',
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    'target_chembl_id', 'pref_name', 'uniprot_accessions', 'target_type', 'organism',
    '_metadata.related_compounds.count', '_metadata.related_activities.count', 'tax_id', 'species_group_flag']
  browser_table:
    default: [ 'target_chembl_id', 'pref_name', 'uniprot_accessions', 'target_type', 'organism',
    '_metadata.related_compounds.count', '_metadata.related_activities.count']
    optional: ['tax_id', 'species_group_flag']
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  eubopen_browser_table:
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    default: [ 'target_chembl_id', 'pref_name', 'target_synonyms', 'target_type', 'organism']
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  browser_table_blast:
    default: ['best_expectation', 'best_positives', 'best_identities', 'best_score_bits', 'best_score', 'length',
    'target_chembl_id', 'pref_name', 'uniprot_accessions', 'target_type', 'organism',
    '_metadata.related_compounds.count', '_metadata.related_activities.count']
    optional: ['tax_id', 'species_group_flag']
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  references:
    default: ['cross_references']
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  querystring:
    default: [ 'target_chembl_id', 'pref_name', 'uniprot_accessions', 'target_type', 'organism',
               '_metadata.related_compounds.count', '_metadata.related_activities.count', 'tax_id', 'species_group_flag' ]
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  eubopen_search_results:
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    default: ['pref_name', 'target_synonyms', 'target_type', 'organism']
    sticky: ['target_chembl_id']
    highlight: ['pref_name', 'target_synonyms', 'target_type', 'organism']
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chembl_document:
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  download:
    default: ['document_chembl_id', 'journal_full_title', 'src_id', '_metadata.source', 'title', 'pubmed_id', 'doi',
    'patent_id', 'authors', 'year', 'volume', 'issue', 'first_page', 'last_page', 'doc_type', 'abstract',
    '_metadata.related_compounds.count', '_metadata.related_targets.count', '_metadata.related_activities.count']
  browser_table:
    default: ['document_chembl_id', 'journal_full_title', '_metadata.source', 'title', 'pubmed_id', 'doi', 'patent_id',
    'authors', 'year', 'volume', 'issue', 'first_page', 'last_page', '_metadata.related_activities.count']
    optional: ['src_id', 'abstract', '_metadata.related_compounds.count', '_metadata.related_targets.count']
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chembl_cell_line:
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  download:
    default: ['cell_chembl_id', 'cell_name', 'cell_description', 'cell_source_organism', 'cell_source_tissue',
    'cell_source_tax_id', 'clo_id', 'efo_id', 'cellosaurus_id', 'cl_lincs_id', '_metadata.related_compounds.count',
    '_metadata.related_activities.count']
  browser_table:
    default: ['cell_chembl_id', 'cell_name', 'cell_description', 'cell_source_organism', 'cell_source_tissue',
    '_metadata.related_activities.count']
    optional: ['cell_source_tax_id', 'clo_id', 'efo_id', 'cellosaurus_id', 'cl_lincs_id',
    '_metadata.related_compounds.count']
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chembl_tissue:
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  download:
    default: ['tissue_chembl_id', 'pref_name', 'uberon_id', 'efo_id', 'bto_id', 'caloha_id',
    '_metadata.related_compounds.count', '_metadata.related_activities.count']
  browser_table:
    default: ['tissue_chembl_id', 'pref_name', 'uberon_id', 'efo_id', '_metadata.related_activities.count']
    optional: ['bto_id', 'caloha_id', '_metadata.related_compounds.count']
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chembl_drug_indication_by_parent:
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  download:
    default: ['parent_molecule.molecule_chembl_id', 'parent_molecule.pref_name', 'parent_molecule.molecule_type',
    'drug_indication.max_phase_for_ind', 'parent_molecule.first_approval', 'drug_indication.mesh_id',
    'drug_indication.mesh_heading', 'efo_ids', 'efo_terms', 'drug_indication.indication_refs',
    'parent_molecule._metadata.drug.drug_data.synonyms', 'parent_molecule._metadata.drug.drug_data.usan_stem',
    'parent_molecule._metadata.drug.drug_data.usan_year']
  browser_table:
    default: ['parent_molecule.molecule_chembl_id', 'parent_molecule.pref_name', 'parent_molecule.molecule_type',
    'drug_indication.max_phase_for_ind', 'parent_molecule.first_approval', 'drug_indication.mesh_id',
    'drug_indication.mesh_heading', 'efo_ids', 'efo_terms', 'drug_indication.indication_refs']
    optional: ['parent_molecule._metadata.drug.drug_data.synonyms',
    'parent_molecule._metadata.drug.drug_data.usan_stem', 'parent_molecule._metadata.drug.drug_data.usan_year']
  report_card_table:
    default: ['drug_indication.mesh_id', 'drug_indication.mesh_heading', 'efo_ids', 'efo_terms',
    'drug_indication.max_phase_for_ind', 'parent_molecule.first_approval', 'drug_indication.indication_refs']
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chembl_mechanism_by_parent_target:
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  download:
    default: ['parent_molecule.molecule_chembl_id', 'parent_molecule.pref_name', 'parent_molecule.molecule_type',
    'mechanism_of_action.max_phase', 'parent_molecule.first_approval', 'parent_molecule.usan_stem',
    'parent_molecule.molecule_structures.canonical_smiles', 'mechanism_of_action.mechanism_of_action',
    'mechanism_of_action.mechanism_comment', 'mechanism_of_action.selectivity_comment', 'target.target_chembl_id',
    'target.pref_name', 'mechanism_of_action.action_type', 'target.target_type', 'target.organism',
    'binding_site.site_name', 'mechanism_of_action.binding_site_comment', 'mechanism_of_action.mechanism_refs',
    'parent_molecule._metadata.drug.drug_data.synonyms', 'drug_atc_codes', 'drug_atc_codes_level_4',
    'drug_atc_codes_level_3', 'drug_atc_codes_level_2', 'drug_atc_codes_level_1', 'parent_molecule.molecule_chembl_id']
  browser_table:
    default: ['parent_molecule.molecule_chembl_id', 'parent_molecule.pref_name', 'parent_molecule.molecule_type',
    'mechanism_of_action.max_phase', 'parent_molecule.first_approval', 'parent_molecule.usan_stem',
    'target.target_chembl_id', 'target.pref_name', 'mechanism_of_action.action_type', 'target.target_type',
    'target.organism', 'binding_site.site_name', 'mechanism_of_action.mechanism_refs']
    optional: ['mechanism_of_action.mechanism_comment', 'mechanism_of_action.selectivity_comment',
    'mechanism_of_action.binding_site_comment', 'parent_molecule._metadata.drug.drug_data.synonyms',
    'drug_atc_codes', 'drug_atc_codes_level_4', 'drug_atc_codes_level_3', 'drug_atc_codes_level_2',
    'drug_atc_codes_level_1']
  report_card_table:
    default: ['mechanism_of_action.action_type', 'target.target_chembl_id', 'target.pref_name', 'target.target_type',
    'target.organism', 'binding_site.site_name', 'mechanism_of_action.mechanism_refs']
  target_report_card_table:
    default: ['parent_molecule.molecule_chembl_id', 'parent_molecule.pref_name', 'parent_molecule.molecule_type',
    'mechanism_of_action.max_phase', 'parent_molecule.first_approval', 'parent_molecule.usan_stem',
    'mechanism_of_action.mechanism_refs']
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chembl_activity:
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  download:
    default: ['molecule_chembl_id', 'molecule_pref_name', '_metadata.parent_molecule_data.max_phase',
    '_metadata.parent_molecule_data.full_mwt', '_metadata.parent_molecule_data.num_ro5_violations',
    '_metadata.parent_molecule_data.alogp', '_metadata.parent_molecule_data.compound_key', 'canonical_smiles',
    'standard_type', 'standard_relation', 'standard_value', 'standard_units', 'pchembl_value', 'data_validity_comment',
    'activity_comment', 'uo_units', 'ligand_efficiency.bei', 'ligand_efficiency.le', 'ligand_efficiency.lle',
    'ligand_efficiency.sei', 'potential_duplicate', 'assay_chembl_id', 'assay_description',
    'assay_type', 'bao_format', 'bao_label', '_metadata.assay_data.assay_organism',
    '_metadata.assay_data.tissue_chembl_id', '_metadata.assay_data.assay_tissue',
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    '_metadata.assay_data.assay_cell_type', '_metadata.assay_data.assay_subcellular_fraction',
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    '_metadata.assay_data.assay_parameters', 'assay_variant_accession', 'assay_variant_mutation', 'target_chembl_id',
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    'target_pref_name', 'target_organism', '_metadata.target_data.target_type', 'document_chembl_id', 'src_id',
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    '_metadata.source.src_description', 'document_journal', 'document_year', '_metadata.assay_data.cell_chembl_id',
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    'activity_properties']
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  browser_table:
    default: ['molecule_chembl_id', '_metadata.parent_molecule_data.compound_key', 'standard_type', 'standard_relation',
     'standard_value', 'standard_units', 'pchembl_value', 'activity_comment', 'assay_chembl_id', 'assay_description',
     'bao_label', '_metadata.assay_data.assay_organism', 'target_chembl_id', 'target_pref_name', 'target_organism',
     '_metadata.target_data.target_type', 'document_chembl_id', '_metadata.source.src_description',
     '_metadata.assay_data.cell_chembl_id']
    optional: ['molecule_pref_name', '_metadata.parent_molecule_data.max_phase',
    '_metadata.parent_molecule_data.full_mwt', '_metadata.parent_molecule_data.num_ro5_violations',
    '_metadata.parent_molecule_data.alogp', 'canonical_smiles', 'data_validity_comment', 'uo_units',
    'ligand_efficiency.bei', 'ligand_efficiency.le', 'ligand_efficiency.lle', 'ligand_efficiency.sei',
    'potential_duplicate', 'assay_type', 'bao_format', '_metadata.assay_data.tissue_chembl_id',
    '_metadata.assay_data.assay_tissue', '_metadata.assay_data.assay_cell_type',
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    '_metadata.assay_data.assay_subcellular_fraction', '_metadata.assay_data.assay_parameters',
    'assay_variant_accession', 'assay_variant_mutation', 'src_id',
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    'document_journal', 'document_year', 'activity_properties']
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chembl_drug_warning_by_parent:
  report_card_table:
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    default: ['drug_warning.warning_type', 'drug_warning.warning_class', 'drug_warning.warning_description',
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              'drug_warning.where', 'drug_warning.warning_refs']
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  browser_table:
    default: [ 'drug_warning.molecule_chembl_id', 'drug_warning.parent_molecule_chembl_id', 'drug_warning.warning_type',
               'drug_warning.warning_class', 'drug_warning.warning_description',
               'drug_warning.where', 'drug_warning.warning_refs' ]
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  download:
    default: [ 'drug_warning.molecule_chembl_id', 'drug_warning.parent_molecule_chembl_id', 'drug_warning.warning_type',
               'drug_warning.warning_class', 'drug_warning.warning_description',
               'drug_warning.where', 'drug_warning.warning_refs' ]
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  querystring:
    default: [ 'drug_warning.molecule_chembl_id', 'drug_warning.parent_molecule_chembl_id', 'drug_warning.warning_type',
               'drug_warning.warning_class', 'drug_warning.warning_description',
               'drug_warning.where.country', 'drug_warning.where.year', 'drug_warning.warning_refs.ref_url',
               'drug_warning.warning_refs.ref_type', 'drug_warning.warning_refs.ref_id']
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chembl_eubopen_molecule:
  eubopen_search_results:
    default: ['pref_name']
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  eubopen_browser_table:
    default: ['pref_name']
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chembl_eubopen_target:
  eubopen_search_results:
    default: [ 'pref_name', 'organism' ]
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  eubopen_browser_table:
    default: [ 'pref_name' ]