A repository as an entry point for the DAta Tag Suite
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README.md

README.md

README

This repository provides and entry point for the DAta Tag Suite (DATS) repositories.

  • schema: This repository contains the JSON-schemas that constitute the DATS model.
  • context: This repository contains the JSON-LD context files that can be used in combination with the JSON-schemas to produce a JSON-LD representation of dataset descriptions. We provide three sets of context files, based on the following vocabularies: schema.org, OBO Foundry ontologies, DCAT vocabulary.
  • examples: This repository contains example instance data files (JSON or JSON-LD files) representing different datasets using the DATS model.
  • WG3-MetadataSpecifications: This repository is a fork of the original reposity where DATS development started, as part of the bioCADDIE project
  • dats-tools: This repository contains python code to validate DATS metadata.
  • ETL-Public: This repository is a fork of the initial repository by the NIH Data Commons Team Phosphorous ETL pipeline to convert GTEx data into DATS. This pipeline moved to the crosscut-metadata repository mentioned below.
  • crosscut-metadata: This repository is a fork of the NIH Data Commons crosscut-metadata repository, containing the ETL pipelines to convert AGR, GTEx, and TOPMed data into DATS.

DATS Publications

  • Xiaoling Chen, Anupama E Gururaj, Burak Ozyurt, Ruiling Liu, Ergin Soysal, Trevor Cohen, Firat Tiryaki, Yueling Li, Nansu Zong, Min Jiang, Deevakar Rogith, Mandana Salimi, Hyeon-eui Kim, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Claudiu Farcas, Todd Johnson, Ron Margolis, George Alter, Susanna-Assunta Sansone, Ian M Fore, Lucila Ohno-Machado, Jeffrey S Grethe, Hua Xu; DataMed – an open source discovery index for finding biomedical datasets, Journal of the American Medical Informatics Association, Volume 25, Issue 3, 1 March 2018, Pages 300–308, https://doi.org/10.1093/jamia/ocx121
  • Alejandra N Gonzalez-Beltran, John Campbell, Patrick Dunn, Diana Guijarro, Sanda Ionescu, Hyeoneui Kim, Jared Lyle, Jeffrey Wiser, Susanna-Assunta Sansone, Philippe Rocca-Serra; Data discovery with DATS: exemplar adoptions and lessons learned, Journal of the American Medical Informatics Association, Volume 25, Issue 1, 1 January 2018, Pages 13–16, https://doi.org/10.1093/jamia/ocx119
  • Lucila Ohno-Machado, Susanna-Assunta Sansone, George Alter, Ian Fore, Jeffrey Grethe, Hua Xu, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Anupama E Gururaj, Elizabeth Bell, Ergin Soysal, Nansu Zong & Hyeon-eui Kim; Finding useful data across multiple biomedical data repositories using DataMed; Nature Genetics 49, 816–819 (2017) https://doi.org/10.1038/ng.3864
  • Susanna-Assunta Sansone#, Alejandra Gonzalez-Beltran#, Philippe Rocca-Serra#, George Alter, Jeffrey S. Grethe, Hua Xu, Ian M. Fore, Jared Lyle, Anupama E. Gururaj, Xiaoling Chen, Hyeon-eui Kim, Nansu Zong, Yueling Li, Ruiling Liu, I. Burak Ozyurt & Lucila Ohno-Machado; DATS, the data tag suite to enable discoverability of datasets; Scientific Data volume 4, Article number: 170059 (2017) DOI: 10.1038/sdata.2017.59 #=equal contribution; Pre-print: bioRxiv DOI: 10.1101/103143 .