Welcome to SMARTER-backend’s documentation!
This documentation describes how to install and interact with the SMARTER database backend. If you need to access SMARTER data using a web browser, please see SMARTER database about page. If you need to access SMARTER data programmatically, please see Accessing SMARTER-backend.
Hint
We have a R package that can be used to interact with SMARTER-backend API, see SMARTER R package for more information.
About SMARTER-backend
Briefly, the SMARTER database created and maintained with the SMARTER-database project is made accessible to the community using this API. This API is the same used by the SMARTER-frontend in order to access and browse SMARTER data using a web browser.
SMARTER-backend is a flask-API application developed on top of a MongoDB instance. The application works inside Docker containers managed with docker-compose. Users who need to subset or retrieve genotypes from the entire genotypes dataset need to retrieve first variants and samples according their needs, in order to filter out the data they need using a PLINK command line.
Documentation is organized as following: in Introduction we describe what SMARTER-backend is and we provide general information. In Backend installation we describe how to install a local instance of SMARTER-backend. Then in Accessing SMARTER-backend we describe how to programmatically access to data.
Citation
If you use SMARTER data or any part of SMARTER software, please cite:
Cozzi P, Manunza A, Ramirez-Diaz J, Tsartsianidou V, Gkagkavouzis K, Peraza P, Johansson A, Arranz J, Freire F, Kusza S, Biscarini F, Peters L, Tosser-Klopp G, Ciappesoni G, Triantafyllidis A, Rupp R, Servin B, Stella A (2024). SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds. GigaByte. DOI: 10.46471/gigabyte.139
BibTeX entry:
@Article{cozzi2024smarter,
title = {SMARTER-database: a tool to integrate SNP array datasets for sheep and goat breeds},
author = {Paolo Cozzi and Arianna Manunza and Johanna Ramirez-Diaz and Valentina Tsartsianidou and Konstantinos Gkagkavouzis and Pablo Peraza and Anna Maria Johansson and Juan José Arranz and Fernando Freire and Szilvia Kusza and Filippo Biscarini and Lucy Peters and Gwenola Tosser-Klopp and Gabriel Ciappesoni and Alexandros Triantafyllidis and Rachel Rupp and Bertrand Servin and Alessandra Stella},
journal = {GigaByte},
year = {2024},
url = {https://github.com/cnr-ibba/SMARTER-database},
doi = {10.46471/gigabyte.139},
}