bill-baumgartner Goto Github PK

annotegrate

Formal integration of biomedical text mining output using community-vetted ontologies

bh17

This repository catalogs work done at BioHackathon 2017

ccp-nlp

A library of NLP related code

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

commondatamodel

Definition and DDLs for the OMOP Common Data Model (CDM)

cqs

craft

datasource

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

docker-rdf4j

Docker image for RDF4J

gluon-nlp

NLP made easy

hanalyzer

A reboot of the Hanalyzer prototype using the KaBOB knowledge base as a backend.

ignorenet

identifying uncharacterized disease-associated genes

kabob

KaBOB (Knowledge Base Of Biomedicine)

kabob-base.docker

Build files for a KaBOB Docker image

kabob-query

kabob.app

Install, build, and run a KaBOB instance via Docker

kr

Clojure API for RDF and SPARQL - provides consistent access to APIs including Jena and Sesame

neuralcoref

✨Fast Coreference Resolution in spaCy with Neural Networks

nlp-pipelines.docker

Configuration for a Docker image to run nlp-pipelines over corpora and catalog their output

oger

owltools

OWLTools

pheknowlator

PheKnowLator: Automated Construction of Heterogeneous Biomedical Knowledge Graphs Under Alternative Semantic Models

phenotype-phebruary

pmc-metadata

Code creates RDF triples for PMC Open access articles

reasonerapi

NCATS Biomedical Translator Reasoners Standard API

reference-coreference-scorers

This is the reference implementation of commonly used coreference metrics.

relay

Autonomous relay system for NCATS Biomedical Data Translator

standoff2conll

Conversion from brat-flavored standoff to CoNLL format

translatorpm

Activities related to the overall project management for Translator

ucdenver-ccp-kabob-query