Omics Data Sharing Resources

A collection of links to resources, tools, papers, etc. that address best practices for sharing high-throughput biomedical omics data sets, and generally fostering reproducible, accessible biomedical research, FAIR data and open science.

The FGED Society began compiling this collection and it has continued to grow in the Society's "afterlife." If you know of other relevant resources which should be included here, let us know, thanks!

Last updated: 10 May 2022

Resources

Alphabetical list of organizations, standards, tools, and other resources related to omics data sharing and reproducible research.

• Biocommons - Collection of open source bioinformatics tools

• Bioconductor - Software & reproducible analysis for the R language

• Bioinformatics.org's wiki

• Council for Big Data, Ethics, and Society

• FAIR Data Initiative - "Findable, Accessible, Interoperable, Reusable"

• FAIR Sharing - Registry of standards, databases, and FAIR data sharing policies

• FGED Projects - FGED Society's efforts to define what should be shared

• FHIR - HL7's Fast Healthcare Interoperability Resources Specification (HL7 product brief)

• FORCE11 - Research communications

• GA4GH - Global Alliance for Genomics & Health

• Galaxy - Online, open-source platform for genomics data analysis & research

• GMOD - Generic Model Organism Database - open source software tools for managing, visualising, storing, disseminating genetic & genomic data.

• ISA Commons and ISA Tools - Investigation-Study-Assay framework to describe experimental metadata

• i2b2 transSMART - A modular open source software platform for feasibility queries, exploration and analysis of clinical, translational and genomics data.

• MIBBI - Minimum Information for Biological and Biomedical Investigations - a minimum information standards portal

• NIH BD2K - Big Data to Knowledge program (Phil Bourne perspectives from 2015 & 2016)

• NIH Data Commons

• OBO Foundry - Open Biological and Biomedical Ontologies

• Open Bioinformatics Foundation - BioJava, BioPerl, BioPython, BioRuby, BioSQL etc.

• OpenWetWare - Sharing wisdom among researchers working in biology & biological engineering

• Wellcome Trust Sanger Institute: Open Access Science

Publications

Listed in reverse chronological order. Most are open access, unless noted otherwise.

• What senior academics can do to support reproducible and open research: a short, three-step guide (Kowalcyzk et al. 2022)

• GA4GH: International policies and standards for data sharing across genomic research and healthcare (Rehm et al., 2021)

• Why it takes a village to manage and share data (Borgman & Bourne, 2021)

• Please give me a copy of my child’s raw genomic data (Chad & Szego, 2021)

• Blockchain for genomics and healthcare: a literature review, current status, classification and open issues (Dedeturk, 2021)

• A global omics data sharing and analytics marketplace: Case study of a rapid data COVID-19 pandemic response platform (Farah et al., 2020)

• Multi-omics data sharing (Nature collection, 2019)

• Federated discovery and sharing of genomic data using Beacons (Fiume et al., 2019)

• Blockchain-based platforms for genomic data sharing: a de-centralized approach in response to the governance problems? (Shabani, 2019)

• Quantifying the impact of public omics data (Perez-Riverol et al., 2019)

• Ten quick tips for sharing open genomic data (Brown et al., 2018)

• Raw Genomic Data: Storage, Access, and Sharing (Shabani et al., 2018 -- PAYWALL)

• 10 Simple Rules for Sharing Human Genomic Data (Corpas et al., 2017)

• Data Sharing: Convert Challenges into Opportunities (Figueiredo, 2017)

• The FAIR Guiding Principles for scientific data management and stewardship (Wilkinson et al., 2016)

• DNAdigest and Repositive: Connecting the World of Genomic Data (Kovalevskaya et al., 2016)

• Perspectives on Big Data, Ethics, and Society (Metcalf et al., 2016)

• A federated ecosystem for sharing genomic, clinical data (GA4GH, 2016 -- PAYWALL)

• Perspective: Sustaining the big-data ecosystem (Bourne et al., 2015)

• Research data sharing: Developing a stakeholder-driven model for journal policies (Sturges et al., 2015 -- PAYWALL)

• Biomedical Data Sharing and Reuse: Attitudes and Practices of Clinical and Scientific Research Staff (Federer et al., 2015)

• Beyond research: a primer for considerations on using viral metagenomics in the field and clinic (Hall et al., 2015)

• The need to redefine genomic data sharing: A focus on data accessibility (van Shaik et al., 2014)

• Perspective: Learning to share (Quackenbush, 2014)

• Best Practices for Data Sharing in Phylogenetic Research (Cranston et al., 2014)

• Data sharing policy design for consortia: challenges for sustainability (Kaye et al., 2014)

• Ten Simple Rules for Reproducible Computational Research (Sandve et al., 2013)

• The conundrum of sharing research data (Borgman, 2012 -- PAYWALL)

• Data Standards for Omics Data: The Basis of Data Sharing and Reuse (Chervitz et al., 2011)

• 'Omics Data Sharing (Field et al., 2009)

• Data reporting standards: making the things we use better (Quackenbush, 2009)

Talks, Presentations

• Challenges and opportunities in using "Big Data" to drive precision medicine (Quackenbush, 2015 talk)

• Secure Data Sharing and Related Matters – An NIH View (Bourne, 2015, slide deck)

• Presentations from the 2013 FGED conference in Seattle, WA.

Worst practices

• Research Parasites

Challenges

• Software archivability: How I learned to stop worrying and love the coming archivability crisis in scientific software (C. Titus Brown, 11 Jan 2017)