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

🏥 Clinical NER with UMLS lookup 🏥

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

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

A Biomedically Oriented automatically annotated Twitter COVID-19 Dataset

Analyzing medical concept distribution of clinical text with Snomed ontology.

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.

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

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

muddy_mine - mining pipeline

Matching patient profiles with clinical trials

Scispacy Entity Linker

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

NLP on biology paper abstracts

An NLP approach to extract useful data from medical case studies

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

Generating Candidate Entities with ScispaCy

spaCy & scispacy wrappers

muddy_db - mud volcano database