Repositories list

• Knowtator-2.0

  Public
  A text annotation plugin for Protege 5+

  Java

  •

  MIT License

  •3•18•5•1•Updated Jul 12, 2025Jul 12, 2025

• translator-relation-extraction

  Public
  This repository catalogs manually annotated sentences, code, and models used to mine relations between ontology concepts from text.

  Java

  •

  MIT License

  •0•0•1•12•Updated Mar 19, 2025Mar 19, 2025

• bluebert

  Public
  BlueBERT, pre-trained on PubMed abstracts and clinical notes (MIMIC-III).

  Python

  •

  Other

  •82•1•0•0•Updated Mar 13, 2025Mar 13, 2025

• Cartoomics

  Public
  Python

  •0•0•39•3•Updated Jan 29, 2025Jan 29, 2025

• Translator-TM-Provider-Cooccurrence

  Public
  Java

  •

  MIT License

  •2•0•1•0•Updated Nov 14, 2024Nov 14, 2024

• DocumentMetadataAPI

  Public
  Python

  •3•0•7•1•Updated Oct 9, 2024Oct 9, 2024

• sentence-simplification-service

  Public
  MIT License

  •0•0•0•0•Updated Sep 3, 2024Sep 3, 2024

• text_mining_targeted_association

  Public
  Python

  •2•0•0•0•Updated Jul 9, 2024Jul 9, 2024

• kgx-export

  Public
  Python

  •1•0•0•0•Updated Jun 21, 2024Jun 21, 2024

• Translator-TM-Provider-UI

  Public
  UI for targeted assertion data

  HTML

  •1•0•1•0•Updated Mar 29, 2024Mar 29, 2024

• Translator-TM-Provider-Evidence

  Public
  Python

  •1•0•0•0•Updated Mar 26, 2024Mar 26, 2024

• biorxiv-aws

  Public
  AWS Lambda code for retrieving and extracting bioRxiv articles

  Python

  •1•0•0•0•Updated Mar 26, 2024Mar 26, 2024

• translator-api-registry

  Public
  This repo hosts the API metadata for the Translator project

  Jupyter Notebook

  •31•0•0•0•Updated Mar 8, 2024Mar 8, 2024

• Translator-TM-Provider-Pipelines

  Public
  A collection of Apache Beam pipelines used for building and maintaining the TM Provider knowledge graph.

  Java

  •

  MIT License

  •1•1•31•4•Updated Jan 5, 2024Jan 5, 2024

• CRAFT

  Public
  Clojure

  •

  Other

  •17•74•0•0•Updated Dec 20, 2023Dec 20, 2023

• ccp-nlp-pipelines

  Public
  A collection of NLP pipelines including pipelines that use the UIMA ConceptMapper to annotate text with concepts from the Open Biomedical Ontologies

  AMPL

  •

  BSD 3-Clause "New" or "Revised" License

  •8•9•0•0•Updated May 16, 2023May 16, 2023

• ccp-nlp

  Public
  A library of NLP related code

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •4•6•0•1•Updated Apr 16, 2023Apr 16, 2023

• pmc-xml-to-txt-docker

  Public
  Docker container for converting articles in the Pubmed Central XML format to plain text

  Dockerfile

  •

  MIT License

  •0•0•0•0•Updated Jan 3, 2023Jan 3, 2023

• common

  Public
  a library of utility code for a variety of "common" tasks

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •2•1•0•6•Updated Dec 6, 2022Dec 6, 2022

• Ignorance-Base

  Public
  Python

  •1•0•0•0•Updated Oct 13, 2022Oct 13, 2022

• Concept-Recognition-as-Translation

  Public
  Python

  •2•0•1•0•Updated Oct 11, 2022Oct 11, 2022

• Ignorance-Question-Work-Full-Corpus

  Public
  Python

  •1•0•0•0•Updated Oct 11, 2022Oct 11, 2022

• craft-shared-tasks

  Public
  This repository hosts evaluation scripts for evaluating annotations of various types against the CRAFT corpus.

  Clojure

  •

  Eclipse Public License 1.0

  •0•4•1•0•Updated Aug 10, 2022Aug 10, 2022

• obo-ci

  Public
  Continuous integration for the Open Biomedical Ontologies

  Shell

  •0•3•0•0•Updated Aug 9, 2022Aug 9, 2022

• translator-concept-recognition

  Public
  A repository dedicated to training and evaluating concept recognition pipelines and components that are used by the Text Mining Provider for the NCATS Biomedical Translator Program.

  Java

  •

  MIT License

  •0•0•6•0•Updated Aug 4, 2022Aug 4, 2022

• file-conversion

  Public
  Conversion utility for various NLP-related file types

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•1•Updated Jul 25, 2022Jul 25, 2022

• medline

  Public
  Code related to processing the leased content of Medline provided by NLM

  Java

  •0•0•0•0•Updated Feb 22, 2022Feb 22, 2022

• datasource

  Public
  A library of code for parsing (mostly biomedical) data source files and converting their contents to RDF

  Java

  •

  BSD 3-Clause "New" or "Revised" License

  •8•2•0•2•Updated Feb 22, 2022Feb 22, 2022

• brat-docker

  Public
  containerised brat (http://brat.nlplab.org/)

  Dockerfile

  •60•0•0•0•Updated Feb 5, 2022Feb 5, 2022

• Ignorance-Question-Work

  Public
  Epistemic/Questions corpus and classification information

  Python

  •1•5•0•0•Updated Jan 21, 2022Jan 21, 2022