tisimpson

borb

borb is a library for reading, creating and manipulating PDF files in python.

biobert

Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining

goatools

Python library to handle Gene Ontology (GO) terms

corex_topic

Hierarchical unsupervised and semi-supervised topic models for sparse count data with CorEx

ontogpt

LLM-based ontological extraction tools, including SPIRES

MedCAT

Medical Concept Annotation Tool

movies-python-bolt

Neo4j Movies Example application with Flask backend using the neo4j-python-driver

linkml

Linked Open Data Modeling Language

SciGraph

A Neo4j backed ontology store

graph-data-science-client

A Python client for the Neo4j Graph Data Science (GDS) library

pymetamap

Python wraper for MetaMap

bio-lm

We evaluate many models used for biomedical and clinical nlp tasks, and train new models that perform much better.

machine-learning-with-ontologies

kgx

KGX is a Python library for exchanging Knowledge Graphs

OWL2Vec-Star

Embedding OWL ontologies

phenopacket-schema

Repository for the GA4GH phenopacket schema

megSAP

a Medical Genetics Sequence Analysis Pipeline

genepattern-notebook

Platform for integrating genomic analysis with Jupyter Notebooks.

TeamTat

Text annotation tool for team collaboration

komenti

Semantic query and text mining tool

CodeBuddy

CodeBuddy: A programming assignment management system for short-form exercises

neo2R

This R package provides simple connectors for querying neo4j graph databases.

phenopacket-python

komenti_guide

annodom

Javascript library for creating hovering annotation tags on text. Especially useful to show named entities.

PhDThesis

rb_vs_ode_model_of_darpp-32

Repository storing molecular rule-based models in Kappa language and Python-based figures published in PeerJ: https://doi.org/10.7717/peerj.14516

AnNet

Analysis of Networks

SFARI-Genes-and-where-to-find-them

PARADIGM