Repositories list

• topic_modeling_imputation

  Public
  This repository contains the code associated with the project "Improving Disease Document Labeling in CaseOLAP LIFT via Topic Modeling" Joanne Qiu Alexander Pelletier Ping Lab UCLA Cardiovascular Data Science Summer Internship Program September 15, 2023

  Jupyter Notebook

  •1•0•0•0•Updated Nov 20, 2023Nov 20, 2023

• CardioKG

  Public
  Ping Lab Intern Project, Summar, 2022: Link prediction through Graph Neural Network (GNN) model over the Knowledgegraph in the interface of Cardiovascular Disease (CVD) and Drugs.

  diseasescardiovascularknowledgegraph+ 2oxidative-stressgnn

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Sep 15, 2023Sep 15, 2023

• Multi-Omics-Proteomics-Integration

  Public
  This repository contains the code and input data for the multi-omics proteomics integration project.

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Mar 26, 2023Mar 26, 2023

• caseolap-pipeline

  Public
  Samir (akre96): Implementation of the caseOLAP pipeline for mapping relationships between oxidative stress and drugs.

  pythonelasticsearchmongodb+ 2neo4jd3js

  Jupyter Notebook

  •0•0•0•7•Updated Feb 11, 2023Feb 11, 2023

• Cardio-MeSH2Pgraph

  Public
  Ping Lab Intern Project, Summar, 2022: Mapping MeSH (ICD codes) to molecular mechanism through protein-protein co-occurance graph -toward high precission medicine

  knowledge-graphmeshcardiovascular-diseases

  MIT License

  •0•0•0•0•Updated Jul 29, 2022Jul 29, 2022

• Cardio-NER-BioBERT

  Public
  Ping Lab Intern Project, Summar, 2022: Building Named Entity Recognition model with fine tuning BioBERT - a data engineering approach

  nerknowledgegraphbiobert

  Jupyter Notebook

  •

  MIT License

  •0•1•1•0•Updated Jul 29, 2022Jul 29, 2022

• pig-proteomics-database

  Public
  Building a bioinformatics tool for generating a more reliable protein sequence database for Sus scrofa cardiac proteomics studies

  Jupyter Notebook

  •1•0•0•0•Updated Jul 28, 2022Jul 28, 2022

• engineering-protein-graph-data

  Public
  By Irsyad: The project documentation and codes in the study of ion-channel in OS-CVD categories implementing graph data API. Summer 2021.

  Jupyter Notebook

  •1•1•0•0•Updated Nov 18, 2021Nov 18, 2021

• Oxidative-Stress-Knowledge-Graph

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Oct 1, 2021Oct 1, 2021

• caseolap-protein-to-CVD-categories

  Public
  Match UnitRef Protein IDs to CVD disease categories with their corresponding CaseOLAP scores

  Jupyter Notebook

  •1•0•0•0•Updated Sep 8, 2021Sep 8, 2021

• engineering_chemical_graph_data

  Public
  BY Joseph: The project documentation and codes in study of ion-channels over CVD and OS categories.

  Jupyter Notebook

  •0•0•0•0•Updated Aug 21, 2021Aug 21, 2021

• os_cvd_project

  Public
  By Aaruchi: A documentation for Oxidative Stress and CVD

  0•0•0•0•Updated Aug 20, 2021Aug 20, 2021

• Drugbank-to-Node-List-CSV

  Public
  creates a csv file with all of the cardiovascular drugs and all of their respective categories

  Jupyter Notebook

  •1•0•0•0•Updated Aug 20, 2021Aug 20, 2021

• Uniprot_to_DrugBank_CVD_CSV

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Aug 18, 2021Aug 18, 2021

• cvd-pathway-map-KG

  Public
  Jupyter Notebook

  •1•0•0•0•Updated Aug 1, 2021Aug 1, 2021

• Textmining_caseOLAP

  Public
  Jupyter Notebook

  •1•0•0•0•Updated May 13, 2021May 13, 2021

• Textmining

  Public
  Jupyter Notebook

  •2•0•0•0•Updated May 12, 2021May 12, 2021

• heart_caseolap_EDA

  Public
  Exploratory data analysis of CaseOLAP scores of cardiac proteins.

  1•0•0•0•Updated May 11, 2021May 11, 2021

• project-docs-by-nick

  Public
  Exploration of covidgraph for the association of Covid-19 with Cardiovascular Diseases and Age Group by Nic Chung (Fall 2020)

  Jupyter Notebook

  •0•0•0•0•Updated Jan 30, 2021Jan 30, 2021

• project-docs

  Public
  By Anirudh: A study of Network and Graph in DRKG for the association of Cardiovascular Disease with Drugs and Pathways by Anirudh Eranki (Fall 2020)

  Jupyter Notebook

  •0•1•0•0•Updated Jan 30, 2021Jan 30, 2021

• PubTator-API-Wrapper

  Public
  Functions to retrieve and process annotations with PubTator API

  Python

  •1•0•0•0•Updated Dec 14, 2020Dec 14, 2020

• Spark-tutorials

  Public
  Kevin Chen: Spark tutorials by Kevin 🚀

  Jupyter Notebook

  •0•0•0•0•Updated Dec 14, 2020Dec 14, 2020

• PTC_Data_Extraction

  Public
  Extract disease data from PubTator Central for a given query (in this case, 'heart failure'). Link each disease with PMID and MESH ID for use in later projects.

  Python

  •1•0•0•0•Updated Nov 13, 2020Nov 13, 2020

• mesh2molecules

  Public
  🚀 Exploration of Molecular Mechanism following MeSH Descriptors by JASON (Wangjie Zheng), (Summer and Fall 2020) 🎓

  Jupyter Notebook

  •1•5•0•0•Updated Nov 12, 2020Nov 12, 2020

• NLP-Congenital_Heart_Defects

  Public
  A Natural Language Processing project for automatically identifying which type of congenital heart defect is being described in a clinical case report. Created by Jun Bae in Summer 2020 while working with the Ping Lab (UCLA).

  Python

  •1•0•0•0•Updated Nov 11, 2020Nov 11, 2020

• covidGraph-cvdEntities

  Public
  🚀 COVID19 Knowledgegraph Exploration with CV Entities (e.g., ICD, MeSH, Pathways, Proteins, Genes) by Maya Gupta (Summer and Fall 2020) 🎓

  Jupyter Notebook

  •0•1•0•0•Updated Oct 27, 2020Oct 27, 2020

• WQE_proteomics_WGCNA

  Public
  Code and results for WQE, using WGCNA analyzing proteomics data

  R

  •1•0•0•0•Updated Oct 26, 2020Oct 26, 2020

• RaghavaDocs

  Public
  Documentation by Raghava

  MIT License

  •1•0•0•0•Updated Oct 6, 2020Oct 6, 2020

• drug-target-graph

  Public
  Documentation and starter code for drug-target-graph implementing CompoundDB4j.

  Jupyter Notebook

  •0•1•0•0•Updated Aug 11, 2020Aug 11, 2020

• covidGraph-cvd-age

  Public
  Introduction to the project "Exploration of Covid Graph with CVD association" and important references (Summer and Fall of 2020)

  0•1•0•0•Updated Jul 10, 2020Jul 10, 2020