Indra

Package structure and dependencies
- Protmapper and Gilda version requirements increased, PySB dependency restriction relaxed

Core assembly modules
- Ontology graph represents obsolete ID replacements in [`indra.ontology`](https://indra.readthedocs.io/en/latest/modules/ontology/ontology.html)
- Improved BioOntology graph which now includes MONDO, ECCODE, and improves OBO hierarchy import to avoid cycles [`indra.ontology.bio`](https://indra.readthedocs.io/en/latest/modules/ontology/bio_ontology.html)
- Identifier standardization now applies replaced IDs in [`indra.ontology.standardize`](https://indra.readthedocs.io/en/latest/modules/ontology/standardize.html)
- Refactor preassembler refinement finding to expose more endpoints in [`indra.preassembler.refinement`](https://indra.readthedocs.io/en/latest/modules/preassembler/preassembler.html#module-indra.preassembler.refinement)
- Refinement finding optimized when split index isn used in [`indra.preassembler.refinement`](https://indra.readthedocs.io/en/latest/modules/preassembler/preassembler.html#module-indra.preassembler.refinement)
- Grounding mapping disambiguation additional back-end options in [`indra.preassembler.grounding_mapper`](https://indra.readthedocs.io/en/latest/modules/preassembler/grounding_mapper.html)
- Ontology analysis extends to finding cycles [`indra.tools.analyze_ontology`](https://indra.readthedocs.io/en/latest/modules/tools/index.html#module-indra.tools.analyze_ontology)

Statement representation
- Additional functions for JSON (de)serialization of single Statements in [`indra.statements`](https://indra.readthedocs.io/en/latest/modules/statements.html#module-indra.statements.io)
- Validation: multiple validators supported, refactored to use classes [`indra.statements.validate`](https://indra.readthedocs.io/en/latest/modules/statements.html#module-indra.statements.validate)

Knowledge sources
- New API and processor for running the SemRep reading system and processing its outputs [`indra.sources.semrep`](https://indra.readthedocs.io/en/latest/modules/sources/semrep.html)
- New API and processor for CREEDS data in [`indra.sources.creeds`](https://indra.readthedocs.io/en/latest/modules/sources/creeds/index.html)
- New API and processor for UbiBrowser in [`indra.sources.ubibrowser`](https://indra.readthedocs.io/en/latest/modules/sources/ubibrowser.html)
- New API and processor for the ACSN database in [`indra.sources.acsn`](https://indra.readthedocs.io/en/latest/modules/sources/acsn.html)
- BEL processor now uses Selventa IDs instead of names in [`indra.sources.bel`](https://indra.readthedocs.io/en/latest/modules/sources/bel/index.html)
- Improved identifier extraction from BioPAX in [`indra.sources.biopax`](https://indra.readthedocs.io/en/latest/modules/sources/biopax/index.html)
- Eidos reader/CLI updated to work with the latest Eidos version in [`indra.sources.eidos`](https://indra.readthedocs.io/en/latest/modules/sources/eidos/index.html)
- Improved HPRD API with option to process compressed archive directly in [`indra.sources.hprd`](https://indra.readthedocs.io/en/latest/modules/sources/hprd/index.html)
- MINERVA client improved to process latest project automatically in [`indra.sources.minerva`](https://indra.readthedocs.io/en/latest/modules/sources/minerva/index.html)
- Improved OmniPath processing to decouple evidences among Statements in [`indra.sources.omnipath`](https://indra.readthedocs.io/en/latest/modules/sources/omnipath/index.html)
- Streamlined RLIMS-P API with improved identifier extraction in [`indra.sources.rlimsp`](https://indra.readthedocs.io/en/latest/modules/sources/rlimsp/index.html)
- SIGNOR processor is now compatible with latest data format [`indra.sources.signor`](https://indra.readthedocs.io/en/latest/modules/sources/signor/index.html)


Model assemblers
- Refactored (more options, better consistency) styling for the HTML Assembler in [`indra.assemblers.html`](https://indra.readthedocs.io/en/latest/modules/assemblers/html_assembler.html)
- New option in IndraNetAssembler to represent self loops [`indra.assemblers.indranet`](https://indra.readthedocs.io/en/latest/modules/assemblers/indranet_assembler.html)

Model analysis
- Additional options added to ModelChecker to control explanation paths [`indra.explanation.model_checker`](https://indra.readthedocs.io/en/latest/modules/explanation/model_checker.html)

Tools
- Additional cases handled in validity fixing of identifiers [`indra.tools.fix_invalidities`](https://indra.readthedocs.io/en/latest/modules/tools/index.html#module-indra.tools.fix_invalidities)

Resources and database clients
- New client to access Bioregistry content in [`indra.databases.bioregistry_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.bioregistry_client)
- New client to access the Expasy enzyme (EC code) database in [`indra.databases.ec_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.ec_client)
- New client to interact with the Biolookup web service in [`indra.databases.biolookup_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.biolookup_client)
- Extended HGNC client to provide enzyme code mappings for genes in [`indra.databases.hgnc_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.hgnc_client)
- Extended MeSH client to access CAS mappings for compounds [`indra.databases.mesh_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.mesh_client)
- New client to interact with MONDO diseases [`indra.databases.mondo_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.mondo_client)
- Extended OBO client allowing access to more ontologies [`indra.databases.obo_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.obo_client)
- Extended PubChem client with additional functionalities [`indra.databases.pubchem_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.pubchem_client)
- Multiple resource files updated including for Biomappings, ChEBI, FamPlex, HGNC,
identifiers.org, MeSH, and Selventa entries

Literature clients
- PubMed client extended to provide substance-specific publications [`indra.literature.pubmed_client`](https://indra.readthedocs.io/en/latest/modules/literature/index.html#module-indra.literature.pubmed_client)
- New client to access COCI data from OpenCitations in [`indra.literature.coci_client`](https://indra.readthedocs.io/en/latest/modules/literature/index.html#module-indra.literature.coci_client)

Package structure and dependencies
- Multiple modules for the world modeling use case separated out into the INDRA World package (https://github.com/indralab/indra_world). For the specific modules affected, see [`#1278`](https://github.com/sorgerlab/indra/pull/1278) and [`#1283`](https://github.com/sorgerlab/indra/pull/1285).
- `rdflib` is no longer a requirement.
- Increased protmapper version (0.0.22) with updated protein resources.

Core assembly modules
- Multiple updates to the INDRA BioOntology (version incremented from 1.12 to 1.18) including adding entity types for nodes, UniProt-Entrez mappings for non-human proteins, chemical family relations from LSPCI in [`indra.ontology.bio`](https://indra.readthedocs.io/en/latest/modules/ontology/bio_ontology.html).
- Belief engine significantly refactored to allow more flexibility in statement scoring in [`indra.belief`](https://indra.readthedocs.io/en/latest/modules/belief/belief_engine.html).
- New belief scorer module added which learns and applies scorers using sklearn models based on curation data in [`indra.belief.skl`](https://indra.readthedocs.io/en/latest/modules/belief/skl_belief.html).

Statement representation
- Improved statement validation checking and exception messages in [`indra.statements.validate`](https://indra.readthedocs.io/en/latest/modules/statements.html#module-indra.statements.validate).

Knowledge sources
- New input API and processor for the GNBR reading system in [`indra.sources.gnbr`](https://indra.readthedocs.io/en/latest/modules/sources/gnbr/index.html).
- INDRA DB client module in [`indra.sources.indra_db_rest`](https://indra.readthedocs.io/en/latest/modules/sources/indra_db_rest/index.html) significantly refactored with changes to the API, improved control over e.g., limits and logging, and a new query module in [`indra.sources.indra_db_rest.query`](https://indra.readthedocs.io/en/latest/modules/sources/indra_db_rest/index.html#module-indra.sources.indra_db_rest.query) to allow complex query construction.
- Improved evidence extraction for CrOG in [`indra.sources.crog`](https://indra.readthedocs.io/en/latest/modules/sources/crog/index.html).
- Improved processing of statement polarities from CTD in [`indra.sources.ctd`](https://indra.readthedocs.io/en/latest/modules/sources/ctd/index.html).

Model assemblers
- Improved hub layout generation for CX networks in [`indra.assemblers.cx`](https://indra.readthedocs.io/en/latest/modules/assemblers/cx_assembler.html).
- HtmlAssembler extended to generate links out for database sources, display belief badges, and improve knowledge source badges in [`indra.assemblers.html`](https://indra.readthedocs.io/en/latest/modules/assemblers/html_assembler.html).
- IndraNet assembler extended to provide better aggregation logic for
Statements into network edges in [`indra.assemblers.indranet`](https://indra.readthedocs.io/en/latest/modules/assemblers/indranet_assembler.html).
- PyBEL assembler extended to include additional annotations on edges in [`indra.assemblers.pybel`](https://indra.readthedocs.io/en/latest/modules/assemblers/pybel_assembler.html).

Tools
- Assemble corpus extended with mechanism linking functions in [`indra.tools.assemble_corpus`](https://indra.readthedocs.io/en/latest/modules/tools/index.html#module-indra.tools.assemble_corpus).
- Validity fixing tools [`indra.tools.fix_invalidities`]().

Resources and database clients
- Expose GO namespaces for terms in [`indra.databases.go_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.go_client).
- Expose locus types in HGNC client in [`indra.databases.hgnc_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.hgnc_client).
- Improved prefix/id format handling in identifiers.org client [`indra.databases.identifiers`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.identifiers).
- New Infectious Disease Ontology client in [`indra.databases.ido_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.ido_client).
- MeSH client extended to provide supplementary concept mappings to primary terms and tree numbers for supplementary concepts in [`indra.databases.mesh_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.mesh_client).
- New client for ingesting OWL ontologies in [`indra.databases.owl_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.owl_client) and corresponding refactoring OBO client in [`indra.databases.obo_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.obo_client).
- Resource file content updates for FamPlex, HGNC and MeSH.

Package structure and dependencies
- INDRA is now tested with Python 3.9 (supports 3.6-3.9).
- Increased protmapper version (0.0.21) with updated protein resources.
- Moved out deprecated evaluation scripts ([`1283`](https://github.com/sorgerlab/indra/pull/1283)).

Core assembly modules
- Preassembler refactored to support refinement filter classes to enable incremental assembly [`indra.preassembler`](https://indra.readthedocs.io/en/latest/modules/preassembler/preassembler.html).
- Belief engine refactored to support incremental assembly [`indra.belief`](https://indra.readthedocs.io/en/latest/modules/belief/index.html).
- New function to get standard Agent from name and references in [`indra.ontology.standardize`](https://indra.readthedocs.io/en/latest/modules/ontology/standardize.html).
- Support for intermediate node annotations and local file parsing in YAML ontology [`indra.ontology.world`](https://indra.readthedocs.io/en/latest/modules/ontology/world_ontology.html).
- INDRA BioOntology updated from v1.7 to v1.12 with bug fixes and resource updates [`indra.ontology.bio`](https://indra.readthedocs.io/en/latest/modules/ontology/bio_ontology.html).
- New function to re-map DB refs within the same namespace in [`indra.tools.assemble_corpus`](https://indra.readthedocs.io/en/latest/modules/tools/index.html#module-indra.tools.assemble_corpus).

Statement representation
- New pretty print and statement statistics functions in [`indra.statements.io`](https://indra.readthedocs.io/en/latest/modules/statements.html#module-indra.statements.io).
- Fixes related to refinement finding and hash calculation in [`indra.statements`](https://indra.readthedocs.io/en/latest/modules/statements.html).
- Fixed refinement finding for multiple agents with the same name in bound conditions [`indra.statements.agent`](https://indra.readthedocs.io/en/latest/modules/statements.html#module-indra.statements.agent).

Knowledge sources
- New API and processor for the Drug Gene Interaction (DGI) database at [`indra.sources.dgi`](https://indra.readthedocs.io/en/latest/modules/sources/dgi/index.html).
- New API and processor for the Chemical Roles Graph (CRoG) at [`indra.sources.crog`](https://indra.readthedocs.io/en/latest/modules/sources/crog/index.html).
- New API and processor for MINERVA models at [`indra.sources.minerva`](https://indra.readthedocs.io/en/latest/modules/sources/minerva/index.html).
- New function to process a single BEL statement string in [`indra.sources.bel`](https://indra.readthedocs.io/en/latest/modules/sources/bel/index.html).
- Improved chemical grounding in BioPAX processor [`indra.sources.biopax`](https://indra.readthedocs.io/en/latest/modules/sources/biopax/index.html).
- New process from web function for DrugBank [`indra.sources.drugbank`](https://indra.readthedocs.io/en/latest/modules/sources/drugbank/index.html).
- EidosBioProcessor refactored into a separate class [`indra.sources.eidos`](https://indra.readthedocs.io/en/latest/modules/sources/eidos/index.html).
- Eidos processor allows using custom grounder when processing into bio statements [`indra.sources.eidos.bio_processor`](https://indra.readthedocs.io/en/latest/modules/sources/eidos/index.html#module-indra.sources.eidos.bio_processor).
- New feature to turn Statements into Hypothes.is annotations and upload them in [`indra.sources.hypothesis`](https://indra.readthedocs.io/en/latest/modules/sources/hypothesis/index.html).
- Support for processing BEL script annotations from Hypothes.is in [`indra.sources.hypothesis`](https://indra.readthedocs.io/en/latest/modules/sources/hypothesis/index.html).
- New processor to process remote INDRA JSON files [`indra.sources.utils`](https://indra.readthedocs.io/en/latest/modules/sources/index.html#module-indra.sources.utils).

Model assemblers
- Statement presentation refactored to support custom grouping and sorting [`indra.util.statement_presentation`](https://indra.readthedocs.io/en/latest/modules/util/index.html#module-indra.util.statement_presentation).
- HTML assembler builds on new statement presentation to support custom sorting [`indra.assemblers.html`](https://indra.readthedocs.io/en/latest/modules/assemblers/html_assembler.html).
- IndraNet assembler supports adding extra columns/properties to the output [`indra.assemblers.indranet`](https://indra.readthedocs.io/en/latest/modules/assemblers/indranet_assembler.html).
- PySB assembler allows reverse-engineering Agents from an assembled model [`indra.assemblers.pysb`](https://indra.readthedocs.io/en/latest/modules/assemblers/pysb_assembler.html).

Model analysis / explanation
- INDRA is now compatible with Kappy 4.1.2 (which changes the contact map format).
- New Kappa contact map analysis to diagnose cycles in [`indra.assemblers.pysb.kappa_util`](https://indra.readthedocs.io/en/latest/modules/assemblers/pysb_assembler.html#module-indra.assemblers.pysb.kappa_util).
- New NodeContainer class for model checking to carry node annotations in [`indra.explanation.model_checker`](https://indra.readthedocs.io/en/latest/modules/explanation/model_checker.html).
- Support for custom edge filters in path finding in [`indra.explanation.path_finding`](https://indra.readthedocs.io/en/latest/modules/explanation/pathfinding.html).
- Support for reporting refinement edges in path finding in [`indra.explanation.reporting`](https://indra.readthedocs.io/en/latest/modules/explanation/reporting.html).

Tools
- New tool to upload annotations to Hypothes.is from INDRA Statements in [`indra.tools.hypothesis_annotator`](https://indra.readthedocs.io/en/latest/modules/tools/index.html#module-indra.tools.hypothesis_annotator).

Resources and database clients
- Resource updates to Biomappings, ChEBI and EFO resources.
- Many new grounding curations added to grounding resources (mappings, misgrounding, ignores).
- Better handling for external namespaces in the OBO client [`indra.databases.obo_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.obo_client).

Literature clients
- The DART client was moved into the INDRA World package.
- New function to get titles for PMC articles in [`indra.literature.pmc_client`](https://indra.readthedocs.io/en/latest/modules/literature/index.html#module-indra.literature.pmc_client).

Package structure and dependencies
- Setup adjusted to require newer versions of PyBEL (0.15), PyBioPax (0.0.5), and Protmapper (0.0.19).
- Automated testing has been migrated from Travis CI to Github Actions.

Core assembly modules
- The statement refinement finding algorithm has been reimplemented for a speedup of multiple orders of magnitude depending on application in [`indra.preassembler`](https://indra.readthedocs.io/en/latest/modules/preassembler/preassembler.html).
- The Preassembler now supports a series of user-supplied filter functions to speed up refinement finding in a use case-specific way in [`indra.preassembler`](https://indra.readthedocs.io/en/latest/modules/preassembler/preassembler.html).
- The BioOntology's version has increased to 1.7 with many resource updates and new sources (e.g., [`Biomappings`](https://github.com/biomappings/biomappings) included in [`indra.ontology`](https://indra.readthedocs.io/en/latest/modules/ontology/ontology.html).
- The IndraOntology no longer contains connected component labels (faster initialization and loading), in [`indra.ontology`](https://indra.readthedocs.io/en/latest/modules/ontology/ontology.html).
- The grounding disambiguation code is refactored with improved prioritization in [`indra.preassembler.grounding_mapper`](https://indra.readthedocs.io/en/latest/modules/preassembler/grounding_mapper.html).
- Grounding disambiguation has been refactored into a separate module in [`indra.preassembler.grounding_mapper.disambiguate`](https://indra.readthedocs.io/en/latest/modules/preassembler/grounding_mapper.html#module-indra.preassembler.grounding_mapper.disambiguate).
- New Statement validation module for automated consistency checks of Statements, Agents, and their attributes in [`indra.statements.validate`](https://indra.readthedocs.io/en/latest/modules/statements.html#module-indra.statements.validate).
- Improvements to WorldOntology extension during runtime in [`indra.ontology.world`](https://indra.readthedocs.io/en/latest/modules/ontology/world_ontology.html).

Knowledge sources
- Structured meta-information on INDRA's sources is now available as a resource file in [`indra/resources/source_info.json`](https://github.com/sorgerlab/indra/blob/master/indra/resources/source_info.json).
- The deprecated LINCS Small Molecules (`indra.sources.lincs_drug`) source module has been removed; replaced by TAS in [`indra.sources.tas`](https://indra.readthedocs.io/en/latest/modules/sources/tas/index.html).
- The BEL processor is now compatible with PyBEL 0.15+ in [`indra.sources.bel`](https://indra.readthedocs.io/en/latest/modules/sources/bel/index.html).
- Updaed BioGRID processor, more extractions and compatibility with the TAB 3.0 format in [`indra.sources.biogrid`](https://indra.readthedocs.io/en/latest/modules/sources/biogrid/index.html).
- Improvements to BioPAX processing to support e.g., BioPAX from Reactome in [`indra.sources.biopax`](https://indra.readthedocs.io/en/latest/modules/sources/biopax/index.html).
- Support for compositional grounding from the [`CWMS`](https://indra.readthedocs.io/en/latest/modules/sources/cwms/index.html), [`Eidos`](https://indra.readthedocs.io/en/latest/modules/sources/eidos/index.html), [`Sofia`](https://indra.readthedocs.io/en/latest/modules/sources/sofia/index.html), and [`Hume`](https://indra.readthedocs.io/en/latest/modules/sources/hume/index.html) readers.
- Support for event type filter for the [`CWMS`](https://indra.readthedocs.io/en/latest/modules/sources/cwms/index.html), [`Eidos`](https://indra.readthedocs.io/en/latest/modules/sources/eidos/index.html), [`Sofia`](https://indra.readthedocs.io/en/latest/modules/sources/sofia/index.html), and [`Hume`](https://indra.readthedocs.io/en/latest/modules/sources/hume/index.html) readers.
- Grounding cache feature added for re-grounding in [`indra.sources.eidos`](https://indra.readthedocs.io/en/latest/modules/sources/eidos/index.html#indra.sources.eidos.client.reground_texts).
- Support for using obtained evidence counts in INDRA DB REST client and HTML assembler.
- Support for specifying organism priority for protein grounding in Reach processor in [`indra.sources.reach`](https://indra.readthedocs.io/en/latest/modules/sources/reach/index.html).
- Handle protein chain/fragment grounding in Reach processor in [`indra.sources.reach`](https://indra.readthedocs.io/en/latest/modules/sources/reach/index.html).
- Improvements to extracting some forms of regulation in Reach processor in [`indra.sources.reach`](https://indra.readthedocs.io/en/latest/modules/sources/reach/index.html)
- Many improvements to Signor processor in [`indra.sources.signor`](https://indra.readthedocs.io/en/latest/modules/sources/signor/index.html).
- New EKB forms extracted in TRIPS processor [`indra.sources.trips`](https://indra.readthedocs.io/en/latest/modules/sources/trips/index.html).

Model assemblers
- New HTML look implemented (with support for old/simplified view) in the HTML Assembler in [`indra.assemblers.html`](https://indra.readthedocs.io/en/latest/modules/assemblers/html_assembler.html).

Model analysis / explanation
- Many new path finding algorithms implemented in [`indra.explanation.pathfinding`](https://indra.readthedocs.io/en/latest/modules/explanation/pathfinding.html).
- Support for semantic filters on paths implemented for model checking in [`indra.explanation.model_checker`](https://indra.readthedocs.io/en/latest/modules/explanation/model_checker.html).

Resources and database clients
- [`indra.resources`](https://indra.readthedocs.io/en/latest/modules/resources.html) is now a proper module with helper functions to load resource files.
- New client for interacting with identifiers.org namespaces, IDs and URLs in [`indra.databases.identifiers`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.identifiers).
- Many resources have been updated (e.g., HGNC entries, FamPlex, new grounding mappings) in `indra.resources`.

Literature clients
- Better MeSH annotation extraction, including supplementary concepts in PubMed client [`indra.literature.pubmed_client`](https://indra.readthedocs.io/en/latest/modules/literature/index.html#module-indra.literature.pubmed_client).
- Local storage feature for DART client in [`indra.literature.dart_client`](https://indra.readthedocs.io/en/latest/modules/literature/index.html#module-indra.literature.dart_client).

Package structure and dependencies
- Starting with this release, INDRA supports Python 3.6+ only.
- The live curation service for the World Modelers use case is now in a separate repository at https://github.com/indralab/indra_wm_service.
- New dependencies for this release include `obonet`, `tqdm` and `pybiopax`.
- Pyjnius is no longer a necessary requirement for any INDRA module (though it can still be optionally used for local JAR-based reading with Eidos and Reach).

Core assembly modules
- A major change in the current release is the introduction of the [`indra.ontology`](https://indra.readthedocs.io/en/latest/modules/ontology/index.html) module which replaces the `indra.preassembler.hierarchy_manager` module, for more details, see #1100.
- New BioOntology at [`indra.ontology.bio`](https://indra.readthedocs.io/en/latest/modules/ontology/bio_ontology.html) which implements naming, identifier mapping and hierarchical relationships among 2.1 million relevant entities (up from 250k in the previous release). The BioOntology also subsumes the old cellular component hierarchy, activity hierarchy, and modification hierarchy, which has now been removed.
- New WorldOntology at [`indra.ontology.world`](https://indra.readthedocs.io/en/latest/modules/ontology/world_ontology.html) which replaces multiple reader-specific ontologies for the WorldModelers use case.
- New ontology web service in [`indra.ontology.app`](https://indra.readthedocs.io/en/latest/modules/ontology/ontology_service.html) which allows using the IndraOntology as a service for ID mapping, isa/partof queries, name lookups, etc.
- New VirtualOntology [`indra.ontology.virtual`](https://indra.readthedocs.io/en/latest/modules/ontology/virtual_ontology.html) which acts as a client for the ontology web service.
- The name standardization and grounding standardization code has been reimplemented to use the IndraOntology, and is now under the [`indra.ontology.standardize`](https://indra.readthedocs.io/en/latest/modules/ontology/standardize.html) module with significantly extended mapping capabilities, and many new functions.
- The Preassembler has been adapted to use the IndraOntology and is extended with new options in [`indra.preassembler`](https://indra.readthedocs.io/en/latest/modules/preassembler/index.html).
- The `indra.preassembler.ontology_mapper` module along with a host of other scripts for making hierarchies (all replaced by the new IndraOntology) have been deprecated and removed.
- Improved grounding mapping and disambiguation logic when multiple texts are available for an agent in [`indra.preassembler.grounding_mapper`](https://indra.readthedocs.io/en/latest/modules/preassembler/grounding_mapper.html).
- Many extensions to grounding mapping resources in `indra.resources.grounding`.
- Bug fixes in [`indra.pipeline`](https://indra.readthedocs.io/en/latest/modules/pipeline.html) for handling some corner cases.

Knowledge sources
- With the relase of PyBioPAX (https://github.com/indralab/pybiopax), the BioPAX processor has been fully reimplemented, and is now a pure-Python module that no longer requires `pyjnius` to operate. See [`indra.sources.biopax`](https://indra.readthedocs.io/en/latest/modules/sources/biopax/index.html).
- New API and processor for the Comparative Toxicogenomics Database (CTD) at [`indra.sources.ctd`](https://indra.readthedocs.io/en/latest/modules/sources/ctd/index.html).
- Improved extraction of grounding from PyBEL models in [`indra.sources.bel`](https://indra.readthedocs.io/en/latest/modules/sources/bel/index.html).
- New API and processor for the DrugBank database at [`indra.sources.drugbank`](https://indra.readthedocs.io/en/latest/modules/sources/drugbank/index.html).
- New API and processor for the OmniPath web service at [`indra.sources.omnipath`](https://indra.readthedocs.io/en/latest/modules/sources/omnipath/index.html).
- New API and processor for Biofactoid at [`indra.sources.biofactoid`](https://indra.readthedocs.io/en/latest/modules/sources/biofactoid/index.html).
- Overhauled API and processor for the Target Affinity Spectrum in [`indra.sources.tas`](https://indra.readthedocs.io/en/latest/modules/sources/tas/index.html) with significantly extended content and improved naming and grounding.
- The BEL RDF processor has been deprecated and removed with the PyBEL processor continuing to serve as the entrypoint for processing BEL content in [`indra.sources.bel`](https://indra.readthedocs.io/en/latest/modules/sources/bel/index.html).
- Multiple new biology-oriented endpoints in the Eidos API in [`indra.sources.eidos`](https://indra.readthedocs.io/en/latest/modules/sources/eidos/index.html).
- The CWMS RDF processor has been removed in factor of the EKB/XML processor which continues to operate at [`indra.sources.cwms`](https://indra.readthedocs.io/en/latest/modules/sources/cwms/index.html).

Model assemblers
- Extended support for knowledge sources and simplified support for evidence count and source count annotations in the HtmlAssembler in [`indra.assemblers.html`](https://indra.readthedocs.io/en/latest/modules/assemblers/html_assembler.html). There are also several bug fixes in handling some statement types in this module, as well as improved links out to literature content.
- Extended support for knowledge source annotations in the CX assembler in [`indra.assemblers.cx`](https://indra.readthedocs.io/en/latest/modules/assemblers/cx_assembler.html).
- Handling negative modification conditions in the EnglishAssembler [`indra.assemblers.english`](https://indra.readthedocs.io/en/latest/modules/assemblers/english_assembler.html).
- Improved signed graph assembly from BEL graphs in [`indra.assemblers.pybel`](https://indra.readthedocs.io/en/latest/modules/assemblers/pybel_assembler.html).

Model analysis / explanation
- New dedicated module for causal path finding methods in [`indra.explanation.pathfinding`](https://indra.readthedocs.io/en/latest/modules/explanation/pathfinding.html).
- Generalized and improved statement checking in all submodules of [`indra.explanation.model_checker`](https://indra.readthedocs.io/en/latest/modules/explanation/model_checker.html)
with support for open-ended search.

Resources and database clients
- New Taxonomy client in [`indra.databases.taxonomy_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.taxonomy_client)
- New DrugBank client in [`indra.databases.drugbank_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.drugbank_client)
- Reimplemented ChEBI client based on OBO in [`indra.databases.chebi_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.chebi_client).
- Extended ChEBML client with naming information in [`indra.databases.chembl_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.chembl_client).
- Extended LINCS client with more naming and mapping information in [`indra.databases.lincs_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.lincs_client).
- The BioGRID client has been removed from `indra.databases.biogrid_client` since it has become redundant with `indra.sources.biogrid`.
- Support for the PubChem JSON web service endpoint in [`indra.databases.pubchem_client`](https://indra.readthedocs.io/en/latest/modules/databases/index.html#module-indra.databases.pubchem_client).
- The network relevance client has been removed from `indra.databases.relevance_client` since it relied on a web service that is no longer operational.
- Many extensions to mapping and naming resources, in particular for chemicals.

Literature clients
- New client for the DART document infrastructure used in the World Modelers use case in [`indra.literature.dart`](https://indra.readthedocs.io/en/latest/modules/literature/index.html#module-indra.literature.dart_client).
- Better search by MeSH terms in the PubMed client in [`indra.literature.pubmed_client`](https://indra.readthedocs.io/en/latest/modules/literature/index.html#module-indra.literature.pubmed_client).

REST API
- The INDRA REST API has been completely reimplemented in a new framework, and has been extended significantly in its functionalities. It also comes with improved Swagger documentation with a public instance
running at `http://api.indra.bio:8000`.

Package structure and dependencies
- The high-throughput reading tools in `indra.tools.reading` have been
moved into an independent repository at
`https://github.com/indralab/indra_reading`.
- The `obonet` package is now a required dependency.

Input processors
- New VirHostNet API and processor in `indra.sources.virhostnet`.
- New Hypothes.is API and processor allowing processing
annotations into INDRA Statements in `indra.sources.hypothesis`.
- Integrated new version of Sparser reader with improved and adapted
processor in `indra.sources.sparser`.
- Refactored Eidos API into separate reader, client and server with
significantly extended usage instructions in `indra.sources.eidos`.
- New endpoints in Eidos API implementing biology-oriented processing, as
well as regrounding with respect to a user-supplied ontology in
`indra.sources.eidos`.
- Overhauled Reach API supporting the latest Reach version and prioritizing
using Reach as a (local) web service over JAR-based reading
in `indra.sources.reach`, also with significantly extended usage
instructions.
- Support for extracting Conversion statements from Reach output in
`indra.sources.reach`.
- ISI reader processor in `indra.sources.isi` no longer requires a Python 2
runtime and the separate nxml2text tool.
- Updated RLIMS-P API in `indra.sources.rlimsp` to work with latest web service at
`https://research.bioinformatics.udel.edu/itextmine/api/data/rlims/`.

Resources and clients
- Overhauled GO resources and client to be based on OBO in
`indra.databases.go_client`.
- MeSH tree numbers, `isa` relationships and determination of
subtree implemented in `indra.databases.mesh_client`.
- Extended mappings added between MeSH and GO, ChEBI, EFO, DOID, HP.
- All resource files updated to latest version in `indra.resources`.

Core assembly modules
- New Pipeline module in `indra.pipeline` allowing building
and running custom assembly pipelines programmatically or from a JSON file.
- UniProt protein features and EFO, DOID, HP ontologies
integrated with name/grounding standardization.
- Overhauled integration of `Gilda` (https://github.com/indralab/gilda) with
`indra.preassembler.grounding_mapper` allowing selective re-grounding
of statements as well as disambiguation.
- New one-statement-per-line JSON output mode in `indra.statements.io` to
support streaming large INDRA Statement JSONs.

Literature
- New bioRxiv/medRxiv client to monitor collections and download PDF/XML/text
content in `indra.literature.biorxiv_client`.
- Significantly improved text extraction from PMC NXML in
`indra.literature.pmc_client`.

Output assemblers
- Refactoried English assembler to allow keeping track of
entity coordinates within each assembled sentence in
`indra.assemblers.english`.
- Improved construction of entity links in HTML assembler
in `indra.assemblers.html`.
- More annotations propagated into PyBEL graph in
`indra.assemblers.pybel`.
- Made the upload and update of CX networks more robust in
`indra.assemblers.cx`.


Explanation
- Improvements to finding all paths of a given length in
`indra.explanation`.

Tools
- Refactored LiveCuration service into a separate module in
`indra.tools.live_curation`.
- Updated outdated assembly approach in GeneNetwork tool in
`indra.tools.gene_network`.

Other
- Updated and extended README, usage examples and tutorials.