Literature DB >> 28585923

DATS, the data tag suite to enable discoverability of datasets.

Susanna-Assunta Sansone1, Alejandra Gonzalez-Beltran1, Philippe Rocca-Serra1, George Alter2, Jeffrey S Grethe3, Hua Xu4, Ian M Fore5, Jared Lyle2, Anupama E Gururaj4, Xiaoling Chen4, Hyeon-Eui Kim3, Nansu Zong3, Yueling Li3, Ruiling Liu4, I Burak Ozyurt3, Lucila Ohno-Machado3.   

Abstract

Today's science increasingly requires effective ways to find and access existing datasets that are distributed across a range of repositories. For researchers in the life sciences, discoverability of datasets may soon become as essential as identifying the latest publications via PubMed. Through an international collaborative effort funded by the National Institutes of Health (NIH)'s Big Data to Knowledge (BD2K) initiative, we have designed and implemented the DAta Tag Suite (DATS) model to support the DataMed data discovery index. DataMed's goal is to be for data what PubMed has been for the scientific literature. Akin to the Journal Article Tag Suite (JATS) used in PubMed, the DATS model enables submission of metadata on datasets to DataMed. DATS has a core set of elements, which are generic and applicable to any type of dataset, and an extended set that can accommodate more specialized data types. DATS is a platform-independent model also available as an annotated serialization in schema.org, which in turn is widely used by major search engines like Google, Microsoft, Yahoo and Yandex.

Entities:  

Year:  2017        PMID: 28585923      PMCID: PMC5460592          DOI: 10.1038/sdata.2017.59

Source DB:  PubMed          Journal:  Sci Data        ISSN: 2052-4463            Impact factor:   6.444


  7 in total

1.  The NIH Big Data to Knowledge (BD2K) initiative.

Authors:  Philip E Bourne; Vivien Bonazzi; Michelle Dunn; Eric D Green; Mark Guyer; George Komatsoulis; Jennie Larkin; Beth Russell
Journal:  J Am Med Inform Assoc       Date:  2015-11       Impact factor: 4.497

2.  Perspective: Sustaining the big-data ecosystem.

Authors:  Philip E Bourne; Jon R Lorsch; Eric D Green
Journal:  Nature       Date:  2015-11-05       Impact factor: 49.962

3.  Discovering and linking public omics data sets using the Omics Discovery Index.

Authors:  Yasset Perez-Riverol; Mingze Bai; Felipe da Veiga Leprevost; Silvano Squizzato; Young Mi Park; Kenneth Haug; Adam J Carroll; Dylan Spalding; Justin Paschall; Mingxun Wang; Noemi Del-Toro; Tobias Ternent; Peng Zhang; Nicola Buso; Nuno Bandeira; Eric W Deutsch; David S Campbell; Ronald C Beavis; Reza M Salek; Ugis Sarkans; Robert Petryszak; Maria Keays; Eoin Fahy; Manish Sud; Shankar Subramaniam; Ariana Barbera; Rafael C Jiménez; Alexey I Nesvizhskii; Susanna-Assunta Sansone; Christoph Steinbeck; Rodrigo Lopez; Juan A Vizcaíno; Peipei Ping; Henning Hermjakob
Journal:  Nat Biotechnol       Date:  2017-05-09       Impact factor: 54.908

4.  Finding useful data across multiple biomedical data repositories using DataMed.

Authors:  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
Journal:  Nat Genet       Date:  2017-05-26       Impact factor: 38.330

5.  The center for expanded data annotation and retrieval.

Authors:  Mark A Musen; Carol A Bean; Kei-Hoi Cheung; Michel Dumontier; Kim A Durante; Olivier Gevaert; Alejandra Gonzalez-Beltran; Purvesh Khatri; Steven H Kleinstein; Martin J O'Connor; Yannick Pouliot; Philippe Rocca-Serra; Susanna-Assunta Sansone; Jeffrey A Wiser
Journal:  J Am Med Inform Assoc       Date:  2015-06-25       Impact factor: 4.497

6.  Toward interoperable bioscience data.

Authors:  Susanna-Assunta Sansone; Philippe Rocca-Serra; Dawn Field; Eamonn Maguire; Chris Taylor; Oliver Hofmann; Hong Fang; Steffen Neumann; Weida Tong; Linda Amaral-Zettler; Kimberly Begley; Tim Booth; Lydie Bougueleret; Gully Burns; Brad Chapman; Tim Clark; Lee-Ann Coleman; Jay Copeland; Sudeshna Das; Antoine de Daruvar; Paula de Matos; Ian Dix; Scott Edmunds; Chris T Evelo; Mark J Forster; Pascale Gaudet; Jack Gilbert; Carole Goble; Julian L Griffin; Daniel Jacob; Jos Kleinjans; Lee Harland; Kenneth Haug; Henning Hermjakob; Shannan J Ho Sui; Alain Laederach; Shaoguang Liang; Stephen Marshall; Annette McGrath; Emily Merrill; Dorothy Reilly; Magali Roux; Caroline E Shamu; Catherine A Shang; Christoph Steinbeck; Anne Trefethen; Bryn Williams-Jones; Katherine Wolstencroft; Ioannis Xenarios; Winston Hide
Journal:  Nat Genet       Date:  2012-01-27       Impact factor: 38.330

7.  BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.

Authors:  Peter McQuilton; Alejandra Gonzalez-Beltran; Philippe Rocca-Serra; Milo Thurston; Allyson Lister; Eamonn Maguire; Susanna-Assunta Sansone
Journal:  Database (Oxford)       Date:  2016-05-17       Impact factor: 3.451

  7 in total
  24 in total

Review 1.  Model organism data evolving in support of translational medicine.

Authors:  Douglas G Howe; Judith A Blake; Yvonne M Bradford; Carol J Bult; Brian R Calvi; Stacia R Engel; James A Kadin; Thomas C Kaufman; Ranjana Kishore; Stanley J F Laulederkind; Suzanna E Lewis; Sierra A T Moxon; Joel E Richardson; Cynthia Smith
Journal:  Lab Anim (NY)       Date:  2018-09-17       Impact factor: 12.625

2.  Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement.

Authors:  Ibrahim Burak Ozyurt; Jeffrey S Grethe
Journal:  Database (Oxford)       Date:  2018-01-01       Impact factor: 3.451

3.  Improving average ranking precision in user searches for biomedical research datasets.

Authors:  Douglas Teodoro; Luc Mottin; Julien Gobeill; Arnaud Gaudinat; Thérèse Vachon; Patrick Ruch
Journal:  Database (Oxford)       Date:  2017-01-01       Impact factor: 3.451

Review 4.  Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine.

Authors:  Peipei Ping; Henning Hermjakob; Jennifer S Polson; Panagiotis V Benos; Wei Wang
Journal:  Circ Res       Date:  2018-04-27       Impact factor: 17.367

5.  ImmuneData: an integrated data discovery system for immunology data repositories.

Authors:  Nan Deng; Canglin Wu; Ashraf Yaseen; Hulin Wu
Journal:  Database (Oxford)       Date:  2022-03-09       Impact factor: 4.462

6.  A content-based dataset recommendation system for researchers-a case study on Gene Expression Omnibus (GEO) repository.

Authors:  Braja Gopal Patra; Kirk Roberts; Hulin Wu
Journal:  Database (Oxford)       Date:  2020-01-01       Impact factor: 3.451

7.  Finding useful data across multiple biomedical data repositories using DataMed.

Authors:  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
Journal:  Nat Genet       Date:  2017-05-26       Impact factor: 38.330

8.  A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge.

Authors:  Trevor Cohen; Kirk Roberts; Anupama E Gururaj; Xiaoling Chen; Saeid Pournejati; George Alter; William R Hersh; Dina Demner-Fushman; Lucila Ohno-Machado; Hua Xu
Journal:  Database (Oxford)       Date:  2017-01-01       Impact factor: 3.451

9.  Baseline and extensions approach to information retrieval of complex medical data: Poznan's approach to the bioCADDIE 2016.

Authors:  Artur Cieslewicz; Jakub Dutkiewicz; Czeslaw Jedrzejek
Journal:  Database (Oxford)       Date:  2018-01-01       Impact factor: 3.451

10.  Recommendations for the FAIRification of genomic track metadata.

Authors:  Sveinung Gundersen; Sanjay Boddu; Salvador Capella-Gutierrez; Finn Drabløs; José M Fernández; Radmila Kompova; Kieron Taylor; Dmytro Titov; Daniel Zerbino; Eivind Hovig
Journal:  F1000Res       Date:  2021-04-01
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