UC Denver Anschutz CCP

CRAFT

Knowtator-2.0

A text annotation plugin for Protege 5+

ccp-nlp-pipelines

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

ccp-nlp

A library of NLP related code

Ignorance-Question-Work

Epistemic/Questions corpus and classification information

craft-shared-tasks

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

obo-ci

Continuous integration for the Open Biomedical Ontologies

datasource

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

bluebert

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

common

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

Translator-TM-Provider-Pipelines

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

Translator-TM-Provider-Cooccurrence

biorxiv-aws

AWS Lambda code for retrieving and extracting bioRxiv articles

brat-docker

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

Cartoomics

Concept-Recognition-as-Translation

DocumentMetadataAPI

file-conversion

Conversion utility for various NLP-related file types

Ignorance-Base

Ignorance-Question-Work-Full-Corpus

kgx-export

medline

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

pmc-xml-to-txt-docker

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

text_mining_cooccurrence_kp

text_mining_targeted_association

translator-api-registry

This repo hosts the API metadata for the Translator project

translator-concept-recognition

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.

translator-relation-extraction

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

Translator-TM-Provider-Evidence

Translator-TM-Provider-UI

UI for targeted assertion data