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be298finalproject

Fall 2022 Bioengineering 298 Final Project: using protein networks to understand drug and disease mechanisms

calcium_proteins_os_cvd

Calcium-binding and -signaling proteins in oxidative stress and cardiovascular disease

caseolap

CaseOLAP: A cloud computing platform for phrase mining. This consists of downloading, parsing, and indexing of data, text-cube creation, entity count with search functionality, and caseOLAP score calculation.

caseolap_lift

Fall 2022 Project collaborating with Alexander Pelletier et al. to improve CaseOLAP's input data quantity, result quality, and usability.

classifying_pubmed_documents

dgs

gene_to_anatomy_text_mining

Uses PubTator3 to identify genes in PubMed articles. Uses PubMed API and MeSH annotations to identify articles studying anatomies. Uses co-occurrence of gene mentions and anatomy topics to calculate gene-anatomy associations. Allows users to choose anatomies (MeSH) and to choose genes (NCBI) or automatically curate genes via GO terms

grape

🍇 GRAPE is a Rust/Python Graph Representation Learning library for Predictions and Evaluations

know2bio

Know2BIO: A Comprehensive Dual-View Benchmark for Evolving Biomedical Knowledge Graphs

knowledge_graph_of_text_mined_pubmed

knowledge_graph_of_text_mined_pubmed

metapaths

Augmenting a network to find metapaths that capture a Drugs MoA

pandemic-forecast

pubmed_pmid_to_pmc

Take PubMed IDs and map them to PubMed Central IDs

superstr

A lightweight, alignment-free utility for detecting repeat-containing reads in short-read WGS, WES and RNA-seq data.

test

textmining_ndmds

Summer 2021: CaseOLAP-based protein and pathway analyses on neurodegenerative mitochondrial disease publications

ucla_assignments

Some homework assignments to be shared