Index

A

add_emmaa_annotations() (in module emmaa.statements) add_model_from_s3() (emmaa.db.manager.StatementDatabaseManager method) add_paper_ids() (emmaa.model.EmmaaModel method) add_result() (emmaa.model_tests.ModelManager method) add_statements() (emmaa.db.manager.StatementDatabaseManager method) (emmaa.model.EmmaaModel method) add_test() (emmaa.model_tests.ModelManager method) add_user() (emmaa.db.manager.QueryDatabaseManager method) agent_from_gene_name() (in module emmaa.priors.gene_list_prior) answer_dynamic_query() (emmaa.model_tests.ModelManager method) answer_immediate_query() (emmaa.answer_queries.QueryManager method) answer_intervention_query() (emmaa.model_tests.ModelManager method) answer_open_query() (emmaa.model_tests.ModelManager method) answer_path_query() (emmaa.model_tests.ModelManager method)

answer_queries() (emmaa.model_tests.ModelManager method) answer_queries_from_s3() (in module emmaa.answer_queries) answer_registered_queries() (emmaa.answer_queries.QueryManager method) applicable() (emmaa.model_tests.RefinementTestConnector static method) (emmaa.model_tests.ScopeTestConnector static method) (emmaa.model_tests.TestConnector static method) applicable_tests (emmaa.model_tests.ModelManager attribute) assemble_dynamic_pysb() (emmaa.model.EmmaaModel method) assemble_pybel() (emmaa.model.EmmaaModel method) assemble_pysb() (emmaa.model.EmmaaModel method) assemble_signed_graph() (emmaa.model.EmmaaModel method) assemble_unsigned_graph() (emmaa.model.EmmaaModel method) assembled_stmts (emmaa.model.EmmaaModel attribute) assembly_config (emmaa.model.EmmaaModel attribute)

B

build_from_s3() (emmaa.db.manager.StatementDatabaseManager method)

C

check() (emmaa.model_tests.StatementCheckingTest method) check_stmt() (in module emmaa.statements)

close_to_quota_max() (in module emmaa.subscription.email_service) ComparativeInterventionProperty (class in emmaa.queries) create_tables() (emmaa.db.manager.EmmaaDatabaseManager method)

D

date_str (emmaa.model_tests.ModelManager attribute) delete_statements() (emmaa.db.manager.StatementDatabaseManager method)

does_exist() (in module emmaa.util) drop_tables() (emmaa.db.manager.EmmaaDatabaseManager method) DynamicProperty (class in emmaa.queries)

E

eliminate_copies() (emmaa.model.EmmaaModel method) EmailHtmlBody (class in emmaa.subscription.notifications) emmaa.analyze_tests_results module emmaa.answer_queries module emmaa.aws_lambda_functions module emmaa.aws_lambda_functions.after_update module emmaa.aws_lambda_functions.model_manager_update module emmaa.aws_lambda_functions.model_updates module emmaa.aws_lambda_functions.update_lambda module emmaa.aws_lambda_functions.update_pipeline module emmaa.db module emmaa.db.manager module emmaa.db.schema module emmaa.filter_functions module emmaa.model module emmaa.model_tests module emmaa.priors module emmaa.priors.cancer_prior module emmaa.priors.gene_list_prior module emmaa.priors.literature_prior module

emmaa.priors.prior_stmts module emmaa.priors.reactome_prior module emmaa.queries module emmaa.readers module emmaa.readers.aws_reader module emmaa.readers.db_client_reader module emmaa.statements module emmaa.subscription module emmaa.subscription.email_service module emmaa.subscription.email_util module emmaa.subscription.notifications module emmaa.util module emmaa.xdd module emmaa.xdd.xdd_client module EmmaaDatabaseError EmmaaDatabaseManager (class in emmaa.db.manager) EmmaaModel (class in emmaa.model) EmmaaStatement (class in emmaa.statements) EmmaaTest (class in emmaa.model_tests) english_test_results (emmaa.analyze_tests_results.TestRound attribute) entities (emmaa.model_tests.ModelManager attribute) extend_unique() (emmaa.model.EmmaaModel method)

F

filter_chem_mesh_go() (in module emmaa.filter_functions) filter_emmaa_stmts_by_metadata() (in module emmaa.statements) filter_indra_stmts_by_metadata() (in module emmaa.statements) filter_to_internal_edges() (in module emmaa.filter_functions) find_delta_hashes() (emmaa.analyze_tests_results.Round method) find_drugs_for_genes() (emmaa.priors.cancer_prior.TcgaCancerPrior static method) (in module emmaa.priors.reactome_prior)

find_latest_emails() (in module emmaa.util) find_latest_s3_file() (in module emmaa.util) find_latest_s3_files() (in module emmaa.util) find_nth_latest_s3_file() (in module emmaa.util) format_results() (in module emmaa.answer_queries) from_json() (emmaa.priors.SearchTerm class method) function_mapping (emmaa.analyze_tests_results.Round attribute)

G

GeneListPrior (class in emmaa.priors.gene_list_prior) generate_signature() (in module emmaa.subscription.email_util) generate_stats_on_s3() (in module emmaa.analyze_tests_results) generate_unsubscribe_link() (in module emmaa.subscription.email_util) generate_unsubscribe_qs() (in module emmaa.subscription.email_util) get_agent_distribution() (emmaa.analyze_tests_results.ModelRound method) get_agent_from_gilda() (in module emmaa.queries) get_agent_from_text() (in module emmaa.queries) get_agent_from_trips() (in module emmaa.queries) get_all_raw_paper_ids() (emmaa.analyze_tests_results.ModelRound method) get_all_result_hashes() (emmaa.db.manager.QueryDatabaseManager method) get_all_stats() (in module emmaa.subscription.notifications) get_all_update_messages() (in module emmaa.subscription.notifications) get_applied_test_hashes() (emmaa.analyze_tests_results.TestRound method) get_assembled_entities() (emmaa.model.EmmaaModel method) get_assembled_statements() (in module emmaa.model) get_assembled_stmts_by_paper() (emmaa.analyze_tests_results.ModelRound method) get_document_figures() (in module emmaa.xdd.xdd_client) get_document_objects() (in module emmaa.xdd.xdd_client) get_drugs_for_gene() (in module emmaa.priors) get_email_subscriptions() (in module emmaa.subscription.email_util) get_english_statements_by_hash() (emmaa.analyze_tests_results.ModelRound method) get_entities() (emmaa.model.EmmaaModel method) (emmaa.model_tests.EmmaaTest method) (emmaa.model_tests.StatementCheckingTest method) (emmaa.queries.PathProperty method) get_figures_from_objects() (in module emmaa.xdd.xdd_client) get_figures_from_query() (in module emmaa.xdd.xdd_client) get_genes_contained_in_pathway() (in module emmaa.priors.reactome_prior) get_indra_stmts() (emmaa.model.EmmaaModel method) get_latest_date() (emmaa.db.manager.StatementDatabaseManager method) get_model_deltas() (in module emmaa.subscription.notifications) get_model_stats() (in module emmaa.model) get_model_users() (emmaa.db.manager.QueryDatabaseManager method) get_models() (in module emmaa.model)

get_mutated_genes() (emmaa.priors.cancer_prior.TcgaCancerPrior method) get_new_readings() (emmaa.model.EmmaaModel method) get_number_of_dates() (emmaa.db.manager.StatementDatabaseManager method) get_number_of_statements() (emmaa.db.manager.StatementDatabaseManager method) get_number_passed_tests() (emmaa.analyze_tests_results.TestRound method) get_number_raw_papers() (emmaa.analyze_tests_results.ModelRound method) get_oldest_date() (emmaa.db.manager.StatementDatabaseManager method) get_paper_ids_from_stmts() (emmaa.model.EmmaaModel method) get_paper_titles_and_links() (emmaa.analyze_tests_results.ModelRound method) get_papers_distribution() (emmaa.analyze_tests_results.ModelRound method) get_passed_test_hashes() (emmaa.analyze_tests_results.TestRound method) get_path_counts() (emmaa.db.manager.StatementDatabaseManager method) get_pathways_containing_gene() (in module emmaa.priors.reactome_prior) get_queries() (emmaa.db.manager.QueryDatabaseManager method) get_raw_statements_for_pmids() (in module emmaa.priors.literature_prior) get_registered_queries() (emmaa.answer_queries.QueryManager method) get_relevant_nodes() (emmaa.priors.cancer_prior.TcgaCancerPrior method) get_results() (emmaa.db.manager.QueryDatabaseManager method) get_s3_client() (in module emmaa.util) get_send_statistics() (in module emmaa.subscription.email_service) get_statement_types() (emmaa.analyze_tests_results.ModelRound method) get_statements() (emmaa.db.manager.StatementDatabaseManager method) get_statements_by_evidence() (emmaa.analyze_tests_results.ModelRound method) get_statements_by_hash() (emmaa.db.manager.StatementDatabaseManager method) get_stmt_hashes() (emmaa.analyze_tests_results.ModelRound method) get_stmts_for_gene() (in module emmaa.priors.prior_stmts) get_stmts_for_gene_list() (in module emmaa.priors.prior_stmts) get_subscribed_queries() (emmaa.db.manager.QueryDatabaseManager method) get_subscribed_users() (emmaa.db.manager.QueryDatabaseManager method) get_temporal_pattern() (emmaa.queries.DynamicProperty method) get_total_applied_tests() (emmaa.analyze_tests_results.TestRound method) get_total_statements() (emmaa.analyze_tests_results.ModelRound method) get_updated_mc() (emmaa.model_tests.ModelManager method) get_user_models() (emmaa.db.manager.QueryDatabaseManager method) get_user_query_delta() (in module emmaa.subscription.notifications) GroundingError

H

hash_response_list() (emmaa.model_tests.ModelManager method)

I

is_internal() (in module emmaa.statements)

J

json_stats (emmaa.analyze_tests_results.ModelStatsGenerator attribute) (emmaa.analyze_tests_results.StatsGenerator attribute) (emmaa.analyze_tests_results.TestStatsGenerator attribute)

L

lambda_handler() (in module emmaa.aws_lambda_functions.after_update) (in module emmaa.aws_lambda_functions.model_manager_update) (in module emmaa.aws_lambda_functions.model_updates) (in module emmaa.aws_lambda_functions.update_pipeline) last_updated_date() (in module emmaa.model)

load_config_from_s3() (in module emmaa.model) load_extra_evidence() (in module emmaa.model) load_from_s3() (emmaa.model.EmmaaModel class method) load_sif_prior() (emmaa.priors.cancer_prior.TcgaCancerPrior method) load_stmts_from_s3() (in module emmaa.model) load_tests_from_s3() (in module emmaa.model_tests)

M

make_changes_over_time() (emmaa.analyze_tests_results.ModelStatsGenerator method) (emmaa.analyze_tests_results.StatsGenerator method) (emmaa.analyze_tests_results.TestStatsGenerator method) make_config() (emmaa.priors.gene_list_prior.GeneListPrior method) make_curation_summary() (emmaa.analyze_tests_results.ModelStatsGenerator method) make_date_str() (in module emmaa.util) make_gene_statements() (emmaa.priors.gene_list_prior.GeneListPrior method) make_html_report_per_user() (in module emmaa.subscription.notifications) make_model() (emmaa.priors.gene_list_prior.GeneListPrior method) make_model_delta() (emmaa.analyze_tests_results.ModelStatsGenerator method) make_model_html_email() (in module emmaa.subscription.notifications) make_model_summary() (emmaa.analyze_tests_results.ModelStatsGenerator method) make_paper_delta() (emmaa.analyze_tests_results.ModelStatsGenerator method) make_paper_summary() (emmaa.analyze_tests_results.ModelStatsGenerator method) make_prior() (emmaa.priors.cancer_prior.TcgaCancerPrior method) make_prior_from_genes() (in module emmaa.priors.reactome_prior) make_reports_from_results() (in module emmaa.subscription.notifications) make_search_terms() (emmaa.priors.gene_list_prior.GeneListPrior method) (in module emmaa.priors.literature_prior) make_stats() (emmaa.analyze_tests_results.ModelStatsGenerator method) (emmaa.analyze_tests_results.TestStatsGenerator method) make_str_report_per_user() (in module emmaa.subscription.notifications) make_test_summary() (emmaa.analyze_tests_results.TestStatsGenerator method) make_tests() (emmaa.model_tests.TestManager method) make_tests_delta() (emmaa.analyze_tests_results.TestStatsGenerator method) mc_mapping (emmaa.model_tests.ModelManager attribute) mc_types (emmaa.model_tests.ModelManager attribute) mc_types_results (emmaa.analyze_tests_results.TestRound attribute) model_to_tests() (in module emmaa.model_tests) model_update_notify() (in module emmaa.subscription.notifications) ModelDeltaEmailHtmlBody (class in emmaa.subscription.notifications) ModelManager (class in emmaa.model_tests) ModelRound (class in emmaa.analyze_tests_results)

ModelStatsGenerator (class in emmaa.analyze_tests_results) module emmaa.analyze_tests_results emmaa.answer_queries emmaa.aws_lambda_functions emmaa.aws_lambda_functions.after_update emmaa.aws_lambda_functions.model_manager_update emmaa.aws_lambda_functions.model_updates emmaa.aws_lambda_functions.update_lambda emmaa.aws_lambda_functions.update_pipeline emmaa.db emmaa.db.manager emmaa.db.schema emmaa.filter_functions emmaa.model emmaa.model_tests emmaa.priors emmaa.priors.cancer_prior emmaa.priors.gene_list_prior emmaa.priors.literature_prior emmaa.priors.prior_stmts emmaa.priors.reactome_prior emmaa.queries emmaa.readers emmaa.readers.aws_reader emmaa.readers.db_client_reader emmaa.statements emmaa.subscription emmaa.subscription.email_service emmaa.subscription.email_util emmaa.subscription.notifications emmaa.util emmaa.xdd emmaa.xdd.xdd_client

N

ndex_network (emmaa.model.EmmaaModel attribute)

NotAClassName

O

OpenSearchQuery (class in emmaa.queries)

P

passed_over_total() (emmaa.analyze_tests_results.TestRound method) path_stmt (emmaa.queries.OpenSearchQuery attribute) path_stmt_types (emmaa.model_tests.ModelManager attribute) PathProperty (class in emmaa.queries)

process_response() (emmaa.model_tests.ModelManager method) put_queries() (emmaa.db.manager.QueryDatabaseManager method) put_results() (emmaa.db.manager.QueryDatabaseManager method) pysb_to_gromet() (in module emmaa.model)

Q

Query (class in emmaa.db.schema) (class in emmaa.queries) query_config (emmaa.model.EmmaaModel attribute)

QueryDatabaseManager (class in emmaa.db.manager) QueryEmailHtmlBody (class in emmaa.subscription.notifications) QueryManager (class in emmaa.answer_queries)

R

read_db_doi_search_terms() (in module emmaa.readers.db_client_reader) read_db_ids_search_terms() (in module emmaa.readers.db_client_reader) read_db_pmid_search_terms() (in module emmaa.readers.db_client_reader) read_pmid_search_terms() (in module emmaa.readers.aws_reader) read_pmids() (in module emmaa.readers.aws_reader) reading_config (emmaa.model.EmmaaModel attribute) RefinementTestConnector (class in emmaa.model_tests) register_email_unsubscribe() (in module emmaa.subscription.email_util) register_filter() (in module emmaa.filter_functions) render() (emmaa.subscription.notifications.ModelDeltaEmailHtmlBody method) (emmaa.subscription.notifications.QueryEmailHtmlBody method)

Result (class in emmaa.db.schema) results_to_json() (emmaa.model_tests.ModelManager method) retrieve_results_from_hashes() (emmaa.answer_queries.QueryManager method) Round (class in emmaa.analyze_tests_results) run_all_tests() (emmaa.model_tests.ModelManager method) run_assembly() (emmaa.model.EmmaaModel method) run_model_tests_from_s3() (in module emmaa.model_tests) run_tests() (emmaa.model_tests.TestManager method) run_tests_per_mc() (emmaa.model_tests.ModelManager method) rx_id_from_up_id() (in module emmaa.priors.reactome_prior)

S

s3_put() (in module emmaa.util) save_assembled_statements() (emmaa.model_tests.ModelManager method) save_config_to_s3() (in module emmaa.model) save_tests_to_s3() (in module emmaa.model_tests) save_to_s3() (emmaa.model.EmmaaModel method) ScopeTestConnector (class in emmaa.model_tests) search_biorxiv() (emmaa.model.EmmaaModel static method) search_elsevier() (emmaa.model.EmmaaModel static method) search_literature() (emmaa.model.EmmaaModel method) search_pubmed() (emmaa.model.EmmaaModel static method) search_terms (emmaa.model.EmmaaModel attribute) search_terms_from_nodes() (emmaa.priors.cancer_prior.TcgaCancerPrior static method) SearchTerm (class in emmaa.priors) send_document_search_request() (in module emmaa.xdd.xdd_client)

send_email() (in module emmaa.subscription.email_service) send_query_search_request() (in module emmaa.xdd.xdd_client) send_request() (in module emmaa.xdd.xdd_client) SimpleInterventionProperty (class in emmaa.queries) sort_s3_files_by_date_str() (in module emmaa.util) sort_s3_files_by_last_mod() (in module emmaa.util) Statement (class in emmaa.db.schema) StatementCheckingTest (class in emmaa.model_tests) StatementDatabaseManager (class in emmaa.db.manager) StatsGenerator (class in emmaa.analyze_tests_results) stmts (emmaa.model.EmmaaModel attribute) stmts_by_papers (emmaa.analyze_tests_results.ModelRound attribute) strip_out_date() (in module emmaa.util) StructuralProperty (class in emmaa.queries) subscribe_to_model() (emmaa.db.manager.QueryDatabaseManager method)

T

TcgaCancerPrior (class in emmaa.priors.cancer_prior) test_config (emmaa.model.EmmaaModel attribute) TestConnector (class in emmaa.model_tests) TestManager (class in emmaa.model_tests) TestRound (class in emmaa.analyze_tests_results)

tests (emmaa.analyze_tests_results.TestRound attribute) TestStatsGenerator (class in emmaa.analyze_tests_results) to_emmaa_stmts() (in module emmaa.statements) to_json() (emmaa.model.EmmaaModel method) (emmaa.priors.SearchTerm method) tweet_deltas() (in module emmaa.subscription.notifications)

U

up_id_from_rx_id() (in module emmaa.priors.reactome_prior) update_email_subscription() (emmaa.db.manager.QueryDatabaseManager method) update_from_disease_map() (emmaa.model.EmmaaModel method) update_from_files() (emmaa.model.EmmaaModel method) update_path_counts() (in module emmaa.subscription.notifications) update_statements_path_counts() (emmaa.db.manager.StatementDatabaseManager method) update_to_ndex() (emmaa.model.EmmaaModel method)

update_with_cord19() (emmaa.model.EmmaaModel method) upload_function() (in module emmaa.aws_lambda_functions.update_lambda) upload_results() (emmaa.model_tests.ModelManager method) upload_to_ndex() (emmaa.model.EmmaaModel method) User (class in emmaa.db.schema) UserModel (class in emmaa.db.schema) UserQuery (class in emmaa.db.schema)

V

verify_email_signature() (in module emmaa.subscription.email_util)