Processors for knowledge input (indra.sources)

INDRA interfaces with and draws knowledge from many sources including reading systems (some that extract biological mechanisms, and some that extract general causal interactions from text) and also from structured databases, which are typically human-curated or derived from experimental data.

Reading Systems

• REACH (indra.sources.reach)
  • 1. INDRA communicating with a locally running REACH Server (indra.sources.reach.api)
  • 2. INDRA communicating with the UA REACH Server (indra.sources.reach.api)
  • 3. INDRA using a REACH JAR through a Python-Java bridge (indra.sources.reach.reader)
  • 4. Use REACH separately to produce output files and then process those with INDRA
  • REACH API (indra.sources.reach.api)
    • process_agents_from_entities()
    • process_fries_json_group()
    • process_json_file()
    • process_json_str()
    • process_nxml_file()
    • process_nxml_str()
    • process_pmc()
    • process_pubmed_abstract()
    • process_text()
  • REACH Processor (indra.sources.reach.processor)
    • ReachProcessor
    • Site
    • determine_reach_subtype()
    • prioritize_organism_grounding()
  • REACH reader (indra.sources.reach.reader)
    • ReachOfflineReadingError
    • ReachReader
• TRIPS (indra.sources.trips)
  • TRIPS API (indra.sources.trips.api)
    • process_text()
    • process_xml()
    • process_xml_file()
  • TRIPS Processor (indra.sources.trips.processor)
    • TripsProcessor
  • TRIPS Web-service Client (indra.sources.trips.client)
    • get_xml()
    • save_xml()
    • send_query()
  • TRIPS/DRUM Local Reader (indra.sources.trips.drum_reader)
    • DrumReader
• Sparser (indra.sources.sparser)
  • Sparser API (indra.sources.sparser.api)
    • get_version()
    • make_nxml_from_text()
    • process_json_dict()
    • process_nxml_file()
    • process_nxml_str()
    • process_sparser_output()
    • process_text()
    • process_xml()
    • run_sparser()
• MedScan (indra.sources.medscan)
  • MedScan API (indra.sources.medscan.api)
    • process_directory()
    • process_directory_statements_sorted_by_pmid()
    • process_file()
    • process_file_sorted_by_pmid()
  • MedScan Processor (indra.sources.medscan.processor)
    • MedscanEntity
    • MedscanProcessor
    • MedscanProperty
    • MedscanRelation
    • ProteinSiteInfo
    • normalize_medscan_name()
• TEES (indra.sources.tees)
  • TEES API (indra.sources.tees.api)
    • extract_output()
    • process_text()
    • run_on_text()
  • TEES Processor (indra.sources.tees.processor)
    • TEESProcessor
    • s2a()
• ISI (indra.sources.isi)
  • ISI API (indra.sources.isi.api)
    • process_json_file()
    • process_nxml()
    • process_output_folder()
    • process_preprocessed()
    • process_text()
  • ISI Processor (indra.sources.isi.processor)
    • IsiProcessor
• Geneways (indra.sources.geneways)
  • Geneways API (indra.sources.geneways.api)
    • process_geneways_files()
  • Geneways Processor (indra.sources.geneways.processor)
    • GenewaysProcessor
    • geneways_action_to_indra_statement_type()
• RLIMS-P (indra.sources.rlimsp)
  • RLIMS-P API (indra.sources.rlimsp.api)
    • process_from_json_file()
    • process_from_jsonish_str()
    • process_from_webservice()
    • process_jsonl_file()
    • process_jsonl_str()
  • RLIMSP-P Processor (indra.sources.rlimsp.processor)
    • RlimspParagraph
    • RlimspProcessor
    • get_agent_from_entity_info()
• Eidos (indra.sources.eidos)
  • 1. INDRA communicating with a separately running Eidos webapp (indra.sources.eidos.client)
  • 2. INDRA using an Eidos JAR directly through a Python-Java bridge (indra.sources.eidos.reader)
  • 3. INDRA using a Flask sever wrapping an Eidos JAR in a separate process (indra.sources.eidos.server)
  • 4. INDRA calling the Eidos CLI using java through the command line (indra.sources.eidos.cli)
  • 5. Use Eidos separately to produce output files and then process those with INDRA
  • Eidos API (indra.sources.eidos.api)
    • initialize_reader()
    • process_json_bio()
    • process_json_bio_entities()
    • process_text_bio()
    • process_text_bio_entities()
  • Eidos Processor (indra.sources.eidos.processor)
    • EidosProcessor
    • find_arg()
    • find_args()
  • Eidos Bio Processor (indra.sources.eidos.bio_processor)
    • EidosBioProcessor
  • Eidos Client (indra.sources.eidos.client)
    • process_text()
  • Eidos Reader (indra.sources.eidos.reader)
    • EidosReader
  • Eidos Webserver (indra.sources.eidos.server)
  • Eidos CLI (indra.sources.eidos.cli)
    • extract_and_process()
    • extract_from_directory()
    • run_eidos()
• GNBR (indra.sources.gnbr)
  • GNBR API (indra.sources.gnbr.api)
    • process_chemical_disease()
    • process_chemical_disease_from_web()
    • process_chemical_gene()
    • process_chemical_gene_from_web()
    • process_from_files()
    • process_from_web()
    • process_gene_disease()
    • process_gene_disease_from_web()
    • process_gene_gene()
    • process_gene_gene_from_web()
  • GNBR Processor (indra.sources.gnbr.processor)
    • GnbrProcessor
    • get_evidence()
    • get_std_chemical()
    • get_std_disease()
    • get_std_gene()
• SemRep (indra.sources.semrep)
  • SemRep API (indra.sources.semrep.api)
    • process_xml_file()
  • SemRep Processor (indra.sources.semrep.processor)
    • SemRepXmlProcessor

Molecular Pathway Databases

• BEL (indra.sources.bel)
  • BEL API (indra.sources.bel.api)
    • process_bel_stmt()
    • process_belscript()
    • process_cbn_jgif_file()
    • process_json_file()
    • process_large_corpus()
    • process_pybel_graph()
    • process_pybel_neighborhood()
    • process_pybel_network()
    • process_small_corpus()
  • PyBEL Processor (indra.sources.bel.processor)
    • PybelProcessor
    • get_agent()
• BioPAX (indra.sources.biopax)
  • BioPAX API (indra.sources.biopax.api)
    • process_model()
    • process_owl()
    • process_owl_gz()
    • process_owl_str()
    • process_pc_neighborhood()
    • process_pc_pathsbetween()
    • process_pc_pathsfromto()
  • BioPAX Processor (indra.sources.biopax.processor)
    • BiopaxProcessor
• SIGNOR (indra.sources.signor)
  • SIGNOR API (indra.sources.signor.api)
    • process_from_file()
    • process_from_web()
  • SIGNOR Processor (indra.sources.signor.processor)
    • SignorProcessor
    • process_uniprot_entry()
• BioGrid (indra.sources.biogrid)
  • BiogridProcessor
    • BiogridProcessor.statements
    • BiogridProcessor.physical_only
• Human Protein Reference Database (indra.sources.hprd)
  • HPRD API (indra.sources.hprd.api)
    • process_archive()
    • process_flat_files()
  • HPRD Processor (indra.sources.hprd.processor)
    • HprdProcessor
• TRRUST Database (indra.sources.trrust)
  • TRRUST API (indra.sources.trrust.api)
    • process_from_web()
  • TRRUST Processor (indra.sources.trrust.processor)
    • TrrustProcessor
    • get_grounded_agent()
    • make_stmt()
• Phospho.ELM (indra.sources.phosphoelm)
  • Phospho.ELM API (indra.sources.phosphoelm.api)
    • process_from_dump()
  • Phospho.ELM Processor (indra.sources.phosphoelm.processor)
    • PhosphoElmProcessor
• VirHostNet (indra.sources.virhostnet)
  • VirHostNet API (indra.sources.virhostnet.api)
    • process_df()
    • process_from_web()
    • process_tsv()
  • VirHostNet Processor (indra.sources.virhostnet.processor)
    • VirhostnetProcessor
    • get_agent_from_grounding()
    • parse_psi_mi()
    • parse_source_ids()
    • parse_text_refs()
    • process_row()
• OmniPath (indra.sources.omnipath)
  • OmniPath API (indra.sources.omnipath.api)
    • process_from_web()
  • OmniPath Processor (indra.sources.omnipath.processor)
    • OmniPathProcessor
• UbiBrowser Database (indra.sources.ubibrowser)
  • UbiBrowser API (indra.sources.ubibrowser.api)
    • process_df()
    • process_file()
    • process_from_web()
  • UbiBrowser Processor (indra.sources.ubibrowser.processor)
    • UbiBrowserProcessor
• ACSN Database (indra.sources.acsn)
  • ACSN API (indra.sources.acsn.api)
    • process_df()
    • process_files()
    • process_from_web()
  • ACSN Processor (indra.sources.acsn.processor)
    • AcsnProcessor
    • get_stmt_type()
• WormBase Database (indra.sources.wormbase)
  • WormBase API (indra.sources.wormbase.api)
    • process_from_files()
    • process_from_web()
  • WormBase Processor (indra.sources.wormbase.processor)
    • WormBaseProcessor

Chemical Information Databases

• CTD (indra.sources.ctd)
  • CTD API (indra.sources.ctd.api)
    • process_dataframe()
    • process_from_web()
    • process_tsv()
  • CTD Processor (indra.sources.ctd.processor)
    • CTDChemicalDiseaseProcessor
    • CTDChemicalGeneProcessor
    • CTDGeneDiseaseProcessor
    • CTDProcessor
• DrugBank (indra.sources.drugbank)
  • DrugBank API (indra.sources.drugbank.api)
    • process_element_tree()
    • process_from_web()
    • process_xml()
  • DrugBank Processor (indra.sources.drugbank.processor)
    • DrugbankProcessor
• Drug Gene Interaction (DGI) Database (indra.sources.dgi)
  • DGI API (indra.sources.dgi.api)
    • get_version_df()
    • process_df()
    • process_version()
  • DGI Processor (indra.sources.dgi.processor)
    • DGIProcessor
• Target Affinity Spectrum (indra.sources.tas)
  • TAS API (indra.sources.tas.api)
    • process_csv()
    • process_from_web()
  • TAS Processor (indra.sources.tas.processor)
    • TasProcessor
• CRoG (indra.sources.crog)
  • CRoG API (indra.sources.crog.api)
    • process_from_web()
  • CRoG Processor (indra.sources.crog.processor)
    • CrogProcessor
• CREEDS (indra.sources.creeds)
  • CREEDS API (indra.sources.creeds.api)
    • process_from_file()
    • process_from_web()
  • CREEDS Processor (indra.sources.creeds.processor)
    • CREEDSChemicalProcessor
    • CREEDSDiseaseProcessor
    • CREEDSGeneProcessor

Custom Knowledge Bases

• NDEx CX API (indra.sources.ndex_cx.api)
  • process_cx()
  • process_cx_file()
  • process_ndex_network()
  • NDEx CX Processor (indra.sources.ndex_cx.processor)
    • NdexCxProcessor
• INDRA Database REST Client (indra.sources.indra_db_rest)
  • API to the INDRA Database REST Service (indra.sources.indra_db_rest.api)
    • Limits, timeouts and threading
    • Using the Query Language
    • Evidence Filtering
    • Curation Submission
    • get_statements()
    • get_statements_for_papers()
    • get_statements_by_hash()
    • get_statements_from_query()
    • submit_curation()
    • get_curations()
  • Advanced Query Construction (indra.sources.indra_db_rest.query)
    • Query Classes (the building blocks)
    • Building Nontrivial Queries (how to put the blocks together)
    • Query
    • And
    • Or
    • HasAgent
    • FromMeshIds
    • HasHash
    • HasSources
    • HasOnlySource
    • HasReadings
    • HasDatabases
    • HasType
    • HasNumAgents
    • HasNumEvidence
    • HasEvidenceBound
    • FromPapers
    • EmptyQuery
  • INDRA Database REST Processor (indra.sources.indra_db_rest.processor)
    • IndraDBQueryProcessor
    • DBQueryStatementProcessor
    • DBQueryHashProcessor
• Hypothes.is (indra.sources.hypothesis)
  • Curation tutorial
    • Curating Statements
    • Curating grounding
  • Hypothes.is API (indra.sources.hypothesis.api)
    • get_annotations()
    • process_annotations()
    • upload_annotation()
    • upload_statement_annotation()
  • Hypothes.is Processor (indra.sources.hypothesis.processor)
    • HypothesisProcessor
    • get_text_refs()
    • parse_context_entry()
    • parse_grounding_entry()
• Biofactoid (indra.sources.biofactoid)
  • Biofactoid API (indra.sources.biofactoid.api)
    • process_from_web()
    • process_json()
  • Biofactoid Processor (indra.sources.biofactoid.processor)
    • BioFactoidProcessor
• MINERVA (indra.sources.minerva)
  • MINERVA Source API (indra.sources.minerva.api)
    • process_file()
    • process_files()
    • process_from_web()
  • MINERVA SIF Processor (indra.sources.minerva.processor)
    • SifProcessor
    • get_agent()
    • get_agent_from_refs()
    • get_family()

Utilities

Processor for remote INDRA JSON files.

class indra.sources.utils.Processor

A base class for processors.

classmethod cli()

Run the CLI for this processor.

Return type:

None

extract_statements()

Extract statements from the remote JSON file.

Return type:

List[Statement]

classmethod get_cli()

Get the CLI for this processor.

Return type:

Command

class indra.sources.utils.RemoteProcessor(url)

A processor for INDRA JSON file to be retrieved by URL.

Parameters:

url (str) – The URL of the INDRA JSON file to load

extract_statements()

Extract statements from the remote JSON file.

Return type:

List[Statement]

print_summary()

Print a summary of the statements.

Return type:

None

property statements: List[Statement]

The extracted statements.

url: str

The URL of the data