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    37 repositories

    • 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 Pel…
      Jupyter Notebook
      •1•0•0•0•Updated Nov 20, 2023Nov 20, 2023

    • CardioKG

      Public
      Ping Lab Intern Project, Summar, 2022: :octocat: Link prediction through Graph Neural Network (GNN) model over the Knowledgegraph in the interface of Cardiovas…
      diseasescardiovascularknowledgegraph
      diseasescardiovascularknowledgegraphoxidative-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
      pythonelasticsearchmongodbneo4jd3js
      Jupyter Notebook
      •0•0•0•7•Updated Feb 11, 2023Feb 11, 2023

    • Cardio-MeSH2Pgraph

      Public
      Ping Lab Intern Project, Summar, 2022: :octocat: Mapping MeSH (ICD codes) to molecular mechanism through protein-protein co-occurance graph -toward high preciss…
      knowledge-graphmeshcardiovascular-diseases
      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: :octocat: Building Named Entity Recognition model with fine tuning BioBERT - a data engineering approach
      nerknowledgegraphbiobert
      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: :octocat: 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: :octocat: 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: :octocat: 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: :octocat: 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 :rocket:
      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
      :rocket: Exploration of Molecular Mechanism following MeSH Descriptors by JASON (Wangjie Zheng), (Summer and Fall 2020) :mortar_board:
      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 …
      Python
      •1•0•0•0•Updated Nov 11, 2020Nov 11, 2020

    • covidGraph-cvdEntities

      Public
      :rocket: COVID19 Knowledgegraph Exploration with CV Entities (e.g., ICD, MeSH, Pathways, Proteins, Genes) by Maya Gupta (Summer and Fall 2020) :mortar_board:
      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
      :octocat: Documentation by Raghava
      MIT License
      •1•0•0•0•Updated Oct 6, 2020Oct 6, 2020

    • drug-target-graph

      Public
      :octocat: 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
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