AGATHA: Automatic Graph-mining And Transformer based Hypothesis generation Approach

ANN Search through the COVID CORD-19 Dataset using SBERT.

Build a knowledge graph from UMLS Knowledge Sources (2022) with load, visualize and query with Neo4j and Scispacy

🏥 Clinical NER with UMLS lookup 🏥

MedGraph is a project focused to construct biomedical knowledge graph. It harnesses the power of pubMed for data retrieval, spaCy for NLP, Mondo Ontology for semantic enrichment, and pywikibot for integrating external knowledge. The final step involves deploying the graph onto the Neo4j database, creating a platform to explore medical information.

A Biomedically Oriented automatically annotated Twitter COVID-19 Dataset

Collection of bio-medical and clinical ner models in spacy, stanza, flair with some utility files

Analyzing medical concept distribution of clinical text with Snomed ontology.

spaCy & scispacy wrappers

Use SciSpacy to retrieve medical knowledge from PubMed and build a real-time platform for disease-therapy associations.

Generating Candidate Entities with ScispaCy

muddy_db - mud volcano database

Scispacy Entity Linker

An NLP approach to extract useful data from medical case studies

NLP on biology paper abstracts

Matching patient profiles with clinical trials

COVID19-Entity-Recognition uses scispaCy to locate symptoms and medications in the CORD-19 corpus.

muddy_mine - mining pipeline

An end-to-end Python app that generates professional HTML and PDF patient documentation quality improvement reports. QuICR produces patient chart reviews, traditionally time-consuming and labor-intensive, using generative AI, NLP, and strict formatting techniques.

Using scispaCy extracting and identifying entities in medical text data and generate network and sub-networks for visualizations