Index

Symbols

--buffer indra-db-reading-run command line option indra-db-reading-run-local command line option --continuing indra-db-content-run command line option indra-db-dump-run-all command line option indra-db-dump-run-belief command line option indra-db-dump-run-end command line option indra-db-dump-run-full-pa-json command line option indra-db-dump-run-full-pa-stmts command line option indra-db-dump-run-mti-mesh-ids command line option indra-db-dump-run-principal-statistics command line option indra-db-dump-run-readonly command line option indra-db-dump-run-res-pos command line option indra-db-dump-run-sif command line option indra-db-dump-run-source-count command line option indra-db-dump-run-start command line option --date-stamp indra-db-dump-run-belief command line option indra-db-dump-run-end command line option indra-db-dump-run-full-pa-json command line option indra-db-dump-run-full-pa-stmts command line option indra-db-dump-run-mti-mesh-ids command line option indra-db-dump-run-principal-statistics command line option indra-db-dump-run-readonly command line option indra-db-dump-run-res-pos command line option indra-db-dump-run-sif command line option indra-db-dump-run-source-count command line option --debug indra-db-content-run command line option --delete-existing indra-db-dump-run-all command line option --dump-only indra-db-dump-run-all command line option --force indra-db-dump-run-belief command line option indra-db-dump-run-end command line option indra-db-dump-run-full-pa-json command line option indra-db-dump-run-full-pa-stmts command line option indra-db-dump-run-mti-mesh-ids command line option indra-db-dump-run-principal-statistics command line option indra-db-dump-run-readonly command line option indra-db-dump-run-res-pos command line option indra-db-dump-run-sif command line option indra-db-dump-run-source-count command line option --from-dump indra-db-dump-load-readonly command line option indra-db-dump-run-belief command line option indra-db-dump-run-end command line option indra-db-dump-run-full-pa-json command line option indra-db-dump-run-full-pa-stmts command line option indra-db-dump-run-mti-mesh-ids command line option indra-db-dump-run-principal-statistics command line option indra-db-dump-run-readonly command line option indra-db-dump-run-res-pos command line option indra-db-dump-run-sif command line option indra-db-dump-run-source-count command line option --load-only indra-db-dump-run-all command line option

--long indra-db-content-list command line option --no-redirect-to-principal indra-db-dump-load-readonly command line option indra-db-dump-run-all command line option --num-procs indra-db-reading-run-local command line option --project-name indra-db-reading-run command line option --with-raw indra-db-pa-list command line option -b indra-db-reading-run command line option indra-db-reading-run-local command line option -c indra-db-content-run command line option indra-db-dump-run-all command line option indra-db-dump-run-belief command line option indra-db-dump-run-end command line option indra-db-dump-run-full-pa-json command line option indra-db-dump-run-full-pa-stmts command line option indra-db-dump-run-mti-mesh-ids command line option indra-db-dump-run-principal-statistics command line option indra-db-dump-run-readonly command line option indra-db-dump-run-res-pos command line option indra-db-dump-run-sif command line option indra-db-dump-run-source-count command line option indra-db-dump-run-start command line option -d indra-db-content-run command line option indra-db-dump-run-all command line option indra-db-dump-run-belief command line option indra-db-dump-run-end command line option indra-db-dump-run-full-pa-json command line option indra-db-dump-run-full-pa-stmts command line option indra-db-dump-run-mti-mesh-ids command line option indra-db-dump-run-principal-statistics command line option indra-db-dump-run-readonly command line option indra-db-dump-run-res-pos command line option indra-db-dump-run-sif command line option indra-db-dump-run-source-count command line option -f indra-db-dump-run-belief command line option indra-db-dump-run-end command line option indra-db-dump-run-full-pa-json command line option indra-db-dump-run-full-pa-stmts command line option indra-db-dump-run-mti-mesh-ids command line option indra-db-dump-run-principal-statistics command line option indra-db-dump-run-readonly command line option indra-db-dump-run-res-pos command line option indra-db-dump-run-sif command line option indra-db-dump-run-source-count command line option -l indra-db-content-list command line option indra-db-dump-run-all command line option -n indra-db-reading-run-local command line option -r indra-db-pa-list command line option

_

_mesh_nums (indra_db.client.readonly.query.FromMeshIds attribute)

_mesh_type (indra_db.client.readonly.query.FromMeshIds attribute)

A

add_to_review() (indra_db.cli.content.ContentManager method)

agent_interactions() (indra_db.schemas.readonly_schema.ReadonlySchema method)

B

Belief (class in indra_db.cli.dump) belief() (indra_db.schemas.readonly_schema.ReadonlySchema method) BelLcManager (class in indra_db.cli.knowledgebase) BiogridManager (class in indra_db.cli.knowledgebase)

build_hash_query() (indra_db.client.readonly.query.Query method) BulkAwsReadingManager (class in indra_db.cli.reading) BulkLocalReadingManager (class in indra_db.cli.reading) BulkReadingManager (class in indra_db.cli.reading)

C

CBNManager (class in indra_db.cli.knowledgebase) commit() (indra_db.databases.DatabaseManager method) construct_readers() (in module indra_db.reading.read_db) ContentManager (class in indra_db.cli.content) copy() (indra_db.client.readonly.query.Query method) (indra_db.databases.DatabaseManager method) copy_detailed_report_lazy() (indra_db.databases.DatabaseManager method) copy_lazy() (indra_db.databases.DatabaseManager method) copy_push() (indra_db.databases.DatabaseManager method)

copy_report_lazy() (indra_db.databases.DatabaseManager method) copy_report_push() (indra_db.databases.DatabaseManager method) count() (indra_db.databases.DatabaseManager method) create_corpus() (indra_db.preassembly.preassemble_db.DbPreassembler method) create_instance() (indra_db.databases.DatabaseManager class method) create_schema() (indra_db.databases.DatabaseManager method) create_tables() (indra_db.databases.PrincipalDatabaseManager method) CTDManager (class in indra_db.cli.knowledgebase) curations() (indra_db.schemas.principal_schema.PrincipalSchema method)

D

DatabaseManager (class in indra_db.databases) DatabaseMeshRefData (class in indra_db.reading.read_db) DatabaseReader (class in indra_db.reading.read_db) DatabaseResultData (class in indra_db.reading.read_db) DatabaseStatementData (class in indra_db.reading.read_db) db_info() (indra_db.schemas.principal_schema.PrincipalSchema method) DbIndexError DbPreassembler (class in indra_db.preassembly.preassemble_db) delete_all() (indra_db.databases.DatabaseManager method) delete_raw_statements_by_id() (in module indra_db.util.distill_statements) discarded_statements() (indra_db.schemas.principal_schema.PrincipalSchema method) distill_stmts() (in module indra_db.util.distill_statements) doi_in() (indra_db.schemas.mixins.IndraDBRefTable class method) doi_notin() (indra_db.schemas.mixins.IndraDBRefTable class method)

download_archive() (indra_db.cli.content.PmcManager method) drop_schema() (indra_db.databases.DatabaseManager method) drop_tables() (indra_db.databases.PrincipalDatabaseManager method) DrugBankManager (class in indra_db.cli.knowledgebase) dump() (in module indra_db.cli.dump) dump_annotations() (indra_db.cli.content.Pubmed method) dump_readings_to_db() (indra_db.reading.read_db.DatabaseReader method) dump_readings_to_pickle() (indra_db.reading.read_db.DatabaseReader method) dump_readonly() (indra_db.databases.PrincipalDatabaseManager method) dump_results_to_db() (indra_db.reading.read_db.DatabaseReader method) dump_results_to_pickle() (indra_db.reading.read_db.DatabaseReader method) dump_sif() (in module indra_db.util.dump_sif) DumperChild (in module indra_db.cli.dump) DumpOrderError

E

Elsevier (class in indra_db.cli.content) End (class in indra_db.cli.dump) enrich_textrefs() (indra_db.cli.content.Manuscripts method) ensure_indices() (indra_db.databases.ReadonlyDatabaseManager method) ev_filter() (indra_db.client.readonly.query.FromMeshIds method) (indra_db.client.readonly.query.Intersection method) (indra_db.client.readonly.query.Union method)

evidence_counts() (indra_db.schemas.readonly_schema.ReadonlySchema method) EvidenceFilter (class in indra_db.client.readonly.query) execute() (indra_db.databases.ReadonlyDatabaseManager method) export_relation_dict_to_tsv() (in module indra_db.client.datasets) extract_agent_data() (in module indra_db.util.insert)

F

fast_raw_pa_link() (indra_db.schemas.readonly_schema.ReadonlySchema method) filter_query() (indra_db.databases.DatabaseManager method) filter_text_content() (indra_db.cli.content.PmcManager method) filter_text_refs() (indra_db.cli.content.ContentManager method) find_all_missing_pmcids() (indra_db.cli.content.PmcOA method) fix_doi() (indra_db.cli.content.Pubmed static method)

from_date() (indra_db.cli.dump.Start class method) from_simple_json() (indra_db.client.readonly.query.Query class method) FromAgentJson (class in indra_db.client.readonly.query) FromMeshIds (class in indra_db.client.readonly.query) FromPapers (class in indra_db.client.readonly.query) FullPaJson (class in indra_db.cli.dump) FullPaStmts (class in indra_db.cli.dump)

G

generate_reading_id() (in module indra_db.reading.read_db) generate_readonly() (indra_db.databases.PrincipalDatabaseManager method) get_active_tables() (indra_db.databases.DatabaseManager method) (indra_db.databases.ReadonlyDatabaseManager method) get_agents() (indra_db.client.readonly.query.Query method) get_archives_after_date() (indra_db.cli.content.PmcOA method) get_cols() (indra_db.reading.read_db.DatabaseMeshRefData static method) (indra_db.reading.read_db.DatabaseStatementData static method) get_column_names() (indra_db.databases.DatabaseManager method) get_column_objects() (indra_db.databases.DatabaseManager method) get_config_string() (indra_db.databases.DatabaseManager method) (indra_db.databases.ReadonlyDatabaseManager method) get_content_by_refs() (in module indra_db.client.principal.content) get_copy_cursor() (indra_db.databases.DatabaseManager method) get_csv_files() (indra_db.cli.content.PmcManager method) get_curations() (in module indra_db.client.principal.curation) get_data_from_xml_str() (indra_db.cli.content.PmcManager method) get_db() (in module indra_db.util.constructors) get_env_string() (indra_db.databases.DatabaseManager method) get_evidence() (in module indra_db.client.statements) get_file_data() (indra_db.cli.content.Manuscripts method) (indra_db.cli.content.PmcOA method) get_filtered_db_stmts() (in module indra_db.util.distill_statements) get_filtered_rdg_stmts() (in module indra_db.util.distill_statements) get_grounding_curations() (in module indra_db.client.principal.curation) get_hashes() (indra_db.client.readonly.query.Query method) get_interactions() (indra_db.client.readonly.query.Query method) get_latest_dump_s3_path() (in module indra_db.cli.dump) get_latest_update() (indra_db.cli.content.ContentManager class method) get_latest_updates() (indra_db.cli.reading.ReadingManager static method) get_license() (indra_db.cli.content.Manuscripts method) (indra_db.cli.content.PmcManager method) (indra_db.cli.content.PmcOA method) get_missing_pmids() (indra_db.cli.content.PmcManager static method)

get_pmcid_file_dict() (indra_db.cli.content.PmcManager method) get_primary_db() (in module indra_db.util.constructors) get_primary_key() (indra_db.databases.DatabaseManager method) get_raw_stmt_jsons() (in module indra_db.client.principal.raw_statements) get_raw_stmt_jsons_from_agents() (in module indra_db.client.principal.raw_statements) get_raw_stmt_jsons_from_papers() (in module indra_db.client.principal.raw_statements) get_raw_stmts_frm_db_list() (in module indra_db.util.helpers) get_reader_output() (in module indra_db.client.principal.content) get_reading_stmt_dict() (in module indra_db.util.distill_statements) get_readings() (indra_db.reading.read_db.DatabaseReader method) get_ref_dict() (indra_db.schemas.mixins.IndraDBRefTable method) get_relation_dict() (in module indra_db.client.datasets) get_relations() (indra_db.client.readonly.query.Query method) get_results() (indra_db.reading.read_db.DatabaseReader method) get_ro() (in module indra_db.util.constructors) get_ro_host() (in module indra_db.util.constructors) get_schemas() (indra_db.databases.DatabaseManager method) get_source_counts() (in module indra_db.util.dump_sif) get_source_names() (indra_db.databases.ReadonlyDatabaseManager method) get_statement_essentials() (in module indra_db.client.datasets) get_statement_object() (in module indra_db.util.helpers) get_statements() (in module indra_db.client.statements) (indra_db.client.readonly.query.Query method) get_statements_by_gene_role_type() (in module indra_db.client.statements) get_statements_by_paper() (in module indra_db.client.statements) get_statements_from_hashes() (in module indra_db.client.statements) get_stmts_with_agent_text_like() (in module indra_db.util.content_scripts) get_support() (in module indra_db.client.statements) get_tables() (indra_db.databases.DatabaseManager method) get_tarname_from_filename() (indra_db.cli.content.Manuscripts method) get_text() (in module indra_db.client.principal.content) get_text_content_from_stmt_ids() (in module indra_db.util.content_scripts) get_values() (indra_db.databases.DatabaseManager method) grab_session() (indra_db.databases.DatabaseManager method)

H

has_entry() (indra_db.databases.DatabaseManager method) has_ref() (indra_db.schemas.mixins.IndraDBRefTable class method) HasAgent (class in indra_db.client.readonly.query) HasDatabases (class in indra_db.client.readonly.query) HasEvidenceBound (class in indra_db.client.readonly.query) hash_pmid_counts() (indra_db.schemas.readonly_schema.ReadonlySchema method) HasHash (class in indra_db.client.readonly.query)

HasNumAgents (class in indra_db.client.readonly.query) HasNumEvidence (class in indra_db.client.readonly.query) HasOnlySource (class in indra_db.client.readonly.query) HasReadings (class in indra_db.client.readonly.query) HasSources (class in indra_db.client.readonly.query) HasType (class in indra_db.client.readonly.query) HPRDManager (class in indra_db.cli.knowledgebase)

I

indra-db-content-list command line option --long -l indra-db-content-run command line option --continuing --debug -c -d SOURCES TASK indra-db-dump-list command line option STATE indra-db-dump-load-readonly command line option --from-dump --no-redirect-to-principal indra-db-dump-run-all command line option --continuing --delete-existing --dump-only --load-only --no-redirect-to-principal -c -d -l indra-db-dump-run-belief command line option --continuing --date-stamp --force --from-dump -c -d -f indra-db-dump-run-end command line option --continuing --date-stamp --force --from-dump -c -d -f indra-db-dump-run-full-pa-json command line option --continuing --date-stamp --force --from-dump -c -d -f indra-db-dump-run-full-pa-stmts command line option --continuing --date-stamp --force --from-dump -c -d -f indra-db-dump-run-mti-mesh-ids command line option --continuing --date-stamp --force --from-dump -c -d -f indra-db-dump-run-principal-statistics command line option --continuing --date-stamp --force --from-dump -c -d -f indra-db-dump-run-readonly command line option --continuing --date-stamp --force --from-dump -c -d -f indra-db-dump-run-res-pos command line option --continuing --date-stamp --force --from-dump -c -d -f indra-db-dump-run-sif command line option --continuing --date-stamp --force --from-dump -c -d -f indra-db-dump-run-source-count command line option --continuing --date-stamp --force --from-dump -c -d -f

indra-db-dump-run-start command line option --continuing -c indra-db-kb-run command line option SOURCES TASK indra-db-pa-list command line option --with-raw -r indra-db-pa-run command line option PROJECT_NAME TASK indra-db-pipeline-stats command line option TASK indra-db-reading-run command line option --buffer --project-name -b TASK indra-db-reading-run-local command line option --buffer --num-procs -b -n TASK indra_db.belief module indra_db.cli.content module indra_db.cli.dump module indra_db.cli.knowledgebase module indra_db.cli.preassembly module indra_db.cli.reading module indra_db.client.datasets module indra_db.client.principal.content module indra_db.client.principal.curation module indra_db.client.principal.raw_statements module indra_db.client.readonly.query module indra_db.client.statements module indra_db.databases module indra_db.preassembly.preassemble_db module indra_db.preassembly.submitter module indra_db.reading.read_db module indra_db.reading.read_db_aws module indra_db.reading.submitter module indra_db.schemas.indexes module indra_db.schemas.mixins module indra_db.schemas.principal_schema module indra_db.schemas.readonly_schema module indra_db.util.constructors module indra_db.util.content_scripts module indra_db.util.distill_statements module indra_db.util.dump_sif module indra_db.util.helpers module indra_db.util.insert module IndraDbException IndraDBPreassemblyError IndraDBRefTable (class in indra_db.schemas.mixins) IndraDBTableMetaClass (class in indra_db.schemas.mixins) insert() (indra_db.databases.DatabaseManager method) insert_db_stmts() (in module indra_db.util.insert) insert_many() (indra_db.databases.DatabaseManager method) insert_pa_stmts() (in module indra_db.util.insert) insert_raw_agents() (in module indra_db.util.insert) Intersection (class in indra_db.client.readonly.query) IntrusiveQuery (class in indra_db.client.readonly.query) invert() (indra_db.client.readonly.query.Query method) is_inverse_of() (indra_db.client.readonly.query.Intersection method) (indra_db.client.readonly.query.Query method) (indra_db.client.readonly.query.SourceIntersection method) (indra_db.client.readonly.query.Union method) is_trips_datestring() (in module indra_db.reading.read_db_aws) item_type (indra_db.client.readonly.query.HasNumAgents attribute) (indra_db.client.readonly.query.HasNumEvidence attribute) (indra_db.client.readonly.query.HasType attribute) iter_contents() (indra_db.cli.content.PmcManager method) (indra_db.cli.content.Pubmed method) iter_xmls() (indra_db.cli.content.PmcManager method)

L

link() (indra_db.databases.DatabaseManager method) list_component_queries() (indra_db.client.readonly.query.Query method) list_dumps() (in module indra_db.cli.dump) list_last_updates() (in module indra_db.cli.preassembly) list_latest_raw_stmts() (in module indra_db.cli.preassembly) load() (indra_db.cli.dump.Start method) load_annotations() (indra_db.cli.content.Pubmed method)

load_db_content() (in module indra_db.util.dump_sif) load_dump() (indra_db.databases.ReadonlyDatabaseManager method) load_files() (indra_db.cli.content.Pubmed method) load_mock_statements() (in module indra_db.belief) load_res_pos() (in module indra_db.util.dump_sif) load_text_refs() (indra_db.cli.content.Pubmed method) LoadError

M

make_copy_batch_id() (indra_db.databases.DatabaseManager method) make_dataframe() (in module indra_db.util.dump_sif) make_graph() (in module indra_db.preassembly.preassemble_db) make_results() (indra_db.reading.read_db.DatabaseReader method) make_text_ref_str() (indra_db.cli.content.ContentManager method) make_tuple() (indra_db.reading.read_db.DatabaseMeshRefData method) (indra_db.reading.read_db.DatabaseStatementData method) Manuscripts (class in indra_db.cli.content) MergeQuery (class in indra_db.client.readonly.query) mesh_concept_meta() (indra_db.schemas.readonly_schema.ReadonlySchema method) mesh_concept_ref_counts() (indra_db.schemas.readonly_schema.ReadonlySchema method) mesh_concepts() (indra_db.schemas.readonly_schema.ReadonlySchema method) mesh_ids (indra_db.client.readonly.query.FromMeshIds attribute) mesh_ref_annotations() (indra_db.schemas.principal_schema.PrincipalSchema method) mesh_term_meta() (indra_db.schemas.readonly_schema.ReadonlySchema method) mesh_term_ref_counts() (indra_db.schemas.readonly_schema.ReadonlySchema method) mesh_terms() (indra_db.schemas.readonly_schema.ReadonlySchema method) MockEvidence (class in indra_db.belief) MockStatement (class in indra_db.belief) module indra_db.belief indra_db.cli.content indra_db.cli.dump indra_db.cli.knowledgebase indra_db.cli.preassembly indra_db.cli.reading indra_db.client.datasets indra_db.client.principal.content indra_db.client.principal.curation indra_db.client.principal.raw_statements indra_db.client.readonly.query indra_db.client.statements indra_db.databases indra_db.preassembly.preassemble_db indra_db.preassembly.submitter indra_db.reading.read_db indra_db.reading.read_db_aws indra_db.reading.submitter indra_db.schemas.indexes indra_db.schemas.mixins indra_db.schemas.principal_schema indra_db.schemas.readonly_schema indra_db.util.constructors indra_db.util.content_scripts indra_db.util.distill_statements indra_db.util.dump_sif indra_db.util.helpers indra_db.util.insert

mti_ref_annotaions_test() (indra_db.schemas.principal_schema.PrincipalSchema method)

N

name_meta() (indra_db.schemas.readonly_schema.ReadonlySchema method)

not_has_ref() (indra_db.schemas.mixins.IndraDBRefTable class method)

O

other_meta() (indra_db.schemas.readonly_schema.ReadonlySchema method)

P

pa_activity() (indra_db.schemas.principal_schema.PrincipalSchema method) pa_agent_counts() (indra_db.schemas.readonly_schema.ReadonlySchema method) pa_agents() (indra_db.schemas.principal_schema.PrincipalSchema method) pa_meta() (indra_db.schemas.readonly_schema.ReadonlySchema method) pa_mods() (indra_db.schemas.principal_schema.PrincipalSchema method) pa_muts() (indra_db.schemas.principal_schema.PrincipalSchema method) pa_ref_link() (indra_db.schemas.readonly_schema.ReadonlySchema method) pa_statements() (indra_db.schemas.principal_schema.PrincipalSchema method) pa_stmt_src() (indra_db.schemas.readonly_schema.ReadonlySchema method) pa_support_links() (indra_db.schemas.principal_schema.PrincipalSchema method) PathwayCommonsManager (class in indra_db.cli.knowledgebase) pg_dump() (indra_db.databases.DatabaseManager method) pg_restore() (indra_db.databases.DatabaseManager method) PhosphoElmManager (class in indra_db.cli.knowledgebase) PhosphositeManager (class in indra_db.cli.knowledgebase) pmcid_in() (indra_db.schemas.mixins.IndraDBRefTable class method) pmcid_notin() (indra_db.schemas.mixins.IndraDBRefTable class method)

PmcManager (class in indra_db.cli.content) PmcOA (class in indra_db.cli.content) pmid_in() (indra_db.schemas.mixins.IndraDBRefTable class method) pmid_notin() (indra_db.schemas.mixins.IndraDBRefTable class method) populate() (indra_db.cli.content.ContentManager method) (indra_db.cli.content.Elsevier method) (indra_db.cli.content.PmcManager method) (indra_db.cli.content.Pubmed method) populate_support() (in module indra_db.belief) preassembly_updates() (indra_db.schemas.principal_schema.PrincipalSchema method) PrincipalDatabaseManager (class in indra_db.databases) PrincipalSchema (class in indra_db.schemas.principal_schema) PrincipalStats (class in indra_db.cli.dump) process_content() (in module indra_db.reading.read_db) PROJECT_NAME indra-db-pa-run command line option Pubmed (class in indra_db.cli.content)

Q

Query (class in indra_db.client.readonly.query)

R

raw_activity() (indra_db.schemas.principal_schema.PrincipalSchema method) raw_agents() (indra_db.schemas.principal_schema.PrincipalSchema method) raw_mods() (indra_db.schemas.principal_schema.PrincipalSchema method) raw_muts() (indra_db.schemas.principal_schema.PrincipalSchema method) raw_statements() (indra_db.schemas.principal_schema.PrincipalSchema method) raw_stmt_mesh_concepts() (indra_db.schemas.readonly_schema.ReadonlySchema method) raw_stmt_mesh_terms() (indra_db.schemas.readonly_schema.ReadonlySchema method) raw_stmt_src() (indra_db.schemas.readonly_schema.ReadonlySchema method) raw_unique_links() (indra_db.schemas.principal_schema.PrincipalSchema method) read() (in module indra_db.reading.read_db) read_all() (indra_db.cli.reading.BulkReadingManager method) (indra_db.cli.reading.ReadingManager method) read_new() (indra_db.cli.reading.BulkReadingManager method) (indra_db.cli.reading.ReadingManager method) ReadDBError

reader_versions (in module indra_db.databases) readers (in module indra_db.databases) reading() (indra_db.schemas.principal_schema.PrincipalSchema method) reading_ref_link() (indra_db.schemas.readonly_schema.ReadonlySchema method) reading_updates() (indra_db.schemas.principal_schema.PrincipalSchema method) ReadingManager (class in indra_db.cli.reading) ReadingUpdateError Readonly (class in indra_db.cli.dump) ReadonlyDatabaseManager (class in indra_db.databases) ReadonlySchema (class in indra_db.schemas.readonly_schema) regularize_agent_id() (in module indra_db.util.insert) rejected_statements() (indra_db.schemas.principal_schema.PrincipalSchema method) ResiduePosition (class in indra_db.cli.dump) RlimspManager (class in indra_db.cli.knowledgebase) run_preassembly() (in module indra_db.cli.preassembly) run_reading() (in module indra_db.reading.read_db)

S

Schema (class in indra_db.schemas.mixins) select_all() (indra_db.databases.DatabaseManager method) select_all_batched() (indra_db.databases.DatabaseManager method) select_one() (indra_db.databases.DatabaseManager method) select_sample_from_table() (indra_db.databases.DatabaseManager method) set_print_only() (indra_db.client.readonly.query.Query method) shash() (in module indra_db.preassembly.preassemble_db) show_tables() (indra_db.databases.DatabaseManager method) Sif (class in indra_db.cli.dump) SignorManager (class in indra_db.cli.knowledgebase) source_file() (indra_db.schemas.principal_schema.PrincipalSchema method) source_meta() (indra_db.schemas.readonly_schema.ReadonlySchema method)

SourceCount (class in indra_db.cli.dump) SourceIntersection (class in indra_db.client.readonly.query) SourceQuery (class in indra_db.client.readonly.query) SOURCES indra-db-content-run command line option indra-db-kb-run command line option Start (class in indra_db.cli.dump) STATE indra-db-dump-list command line option StatementHashMeshId (class in indra_db.cli.dump) submit_curation() (in module indra_db.client.principal.curation) supplement_corpus() (indra_db.preassembly.preassemble_db.DbPreassembler method)

T

TASK indra-db-content-run command line option indra-db-kb-run command line option indra-db-pa-run command line option indra-db-pipeline-stats command line option indra-db-reading-run command line option indra-db-reading-run-local command line option

TasManager (class in indra_db.cli.knowledgebase) text_content() (indra_db.schemas.principal_schema.PrincipalSchema method) text_meta() (indra_db.schemas.readonly_schema.ReadonlySchema method) text_ref() (indra_db.schemas.principal_schema.PrincipalSchema method) to_json() (indra_db.client.readonly.query.Query method) TrrustManager (class in indra_db.cli.knowledgebase)

U

Union (class in indra_db.client.readonly.query) update() (indra_db.cli.content.ContentManager method) (indra_db.cli.content.Elsevier method) (indra_db.cli.content.Manuscripts method) (indra_db.cli.content.PmcManager method) (indra_db.cli.content.PmcOA method) (indra_db.cli.content.Pubmed method)

updates() (indra_db.schemas.principal_schema.PrincipalSchema method) upload_all_missing_pmcids() (indra_db.cli.content.PmcOA method) upload_archives() (indra_db.cli.content.PmcManager method) upload_batch() (indra_db.cli.content.PmcManager method) upload_text_content() (indra_db.cli.content.ContentManager method) UploadError UserQuit

V

VirHostNetManager (class in indra_db.cli.knowledgebase)

X

xdd_updates() (indra_db.schemas.principal_schema.PrincipalSchema method)