GRPM Dataset

This repository hosts datasets generated using the GRPM system, a modular resource specifically designed to integrate and analyze genetic polymorphism data related to specific biomedical subjects in literature.

GitHub: GRPM_system

medrxiv DOI: 10.1101/2023.08.04.23293659 

Contents:

1. `grpm_dataset.zip`: This archive includes the GRPM Dataset, which represents a consolidated resource of genetic polymorphism information relevant to various biomedical traits. The dataset is constructed by harmonizing data from LitVar and PubMed and is further enhanced through the inclusion of Medical Subject Headings (MeSH) terms. The GRPM Dataset serves as a critical resource for researchers by providing a foundational dataset to examine the genetic factors influencing these traits.

2. `grpm_surveys.zip`: The GRPM Surveys archive contains the results of targeted queries submitted to the GRPM Dataset using predefined MeSH terms. These queries cover ten topics relevant to nutrigenetics and nutrition-related traits.  

3. `nutrigentic_dataset.zip`: This dataset is a collection of genetic polymorphisms associated with nutrigenetics. It has been enriched with data from Genome-Wide Association Studies (GWAS) to offer a comprehensive overview of genetic variations pertinent to personalized nutrition. This dataset is invaluable for researchers and nutritionists aiming to investigate the genetic basis of nutrition interventions.

The repository is supplemented with crucial files necessary for executing the software and reproducing the entire data integration and query workflow effectively:

4. `human_genes.csv` : Ensembl Human Genes dataset
5. `gwas_data.zip` : GWAS Catalog data and semantic allignmet with MeSH
6. `ref-mesh.zip` : MeSH terms associated with nutrition-related traits.
7. `nbib_data.zip`: Accessory data related to all the publications collected during the Medline data retrieval process.