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INDRA v1.17.0
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@bgyori bgyori released this 19 May 14:21
· 3070 commits to master since this release
1.17.0
13918aa

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.
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