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DBMI, University of Pittsburgh (@dbmi-pitt)

dbmi-pitt

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Java
28.1 %

Python
18.8 %

HTML
15.6 %

Jupyter Notebook
12.5 %

R
9.4 %

Web Ontology Language 3.1 %

CSS
3.1 %

JavaScript
3.1 %

PostScript 3.1 %

Common Lisp
3.1 %

public-PDDI-analysis

migrates from swat-4-med-safety/SW-DDI-catalog/drug-drug-interactions

SocialMediaDataScience

Data Science module - text analytics, Natural Language Processing, and Machine Learning on Social Media (twitter) data

Jupyter Notebook

UMLS-Graph

UMLS Graph database for semantic queries

Jupyter Notebook

bioinf_teachingNLP

NLP education notebooks for biomedical informatics students

Jupyter Notebook

DIKB-Micropublication

Micropublication and Open Data Annotation for drug-drug interaction evidence synthesis

pk-ddi-role-identifier

A pipeline for deriving a classifier that tags the drugs mentioned within a potential drug-drug interaction statement as having the precipitant or object role.

dbmi-annotator

based on annotator.js, an annotation framework enable user account and annotation permission management and templating annotation plugin in biomedical domain.

ddi-cds

All drug-drug interaction CDS rules written in Drools from the AHRQ funded projects

Merged-PDDI

Code to prototype the new Drug Interaction Knowledge Base

DIKB-Evidence-analytics

A suite of programs that implement the DIKB principals of representing drug drug interaction evidence and knowledge.

Web Ontology Language

ACT-Network

ACT - Accrual to Clinical Trials Network Repository

ubkg

The Unified Biomedical Knowledge Graph

iDIA_Rules

This repository contains the Java and Drools files necessary to work with the "Individualized Drug Interaction Alerts (iDIA)" project.

NER-pddi-table-parsing

COMRADEdb

xmeso

Information Extraction for National Mesothelioma Virtual Bank

docker-proteus

Dockerized version of Proteus data characterization suite

CCRI-Data-Characterization

Data characterization tools used across multiple CCRI projects

EvidenceType-Calculator

Serve form of evidence type related questions for various type of high level types (ex. DDI clinical trial, Experiments, Case Report, etc))

np-terminology-imports

A natural product terminology that maps botanical natural product Latin binomials to chemical constituents (e.g., metabolites), common names, and spelling variations. The vocabulary is represented using the OMOP vocabulary schema but is not dependent on OMOP/OHDSI tools.

np_name_finder

A project to use different computational approaches to identify natural product mentions in unstructured character strings.

Jupyter Notebook

slideviewer

SlideViwer is a high level java API that describes the behaviour of a generic digital slide image viewer.

annotator.js

docker-dbmi-annotator

CCRI-402

Center for Clinical Research Informatics

TCRN

TIES Cancer Research Network (TCRN)

u-of-pitt-spl-ddi-v2.0

Drug drug interaction NLP program migrated from google code swat-4-med-safety

scrubber-evaluation

Supports evaluation of de-identification software for clinical notes

mBiasPrevention

u-of-pitt-SPL-drug-NER

drools-ohdsi-test

test for using drools rules

openslideserver

OpenSlide Whole Slide Image Server

ODIE

The Ontology Development and Information Extraction(ODIE) framework is a NLP workbench to run various UIMA pipelines coupled with different ontologies and terminologies.

ocelot

Ocelot - obtain census tract and Walk Score data (walk, bike, and transit scores) based on geocoordinates