RESOURCESRESOURCES

Data Management Tools

It is increasingly important for researchers to develop effective strategies for the management of the data they produce. Therefore the resources on this page aim to guide researchers as to how they might deal with issues surrounding the effective sharing and management of their data.

BioSharing

https://biosharing.org/

BioSharing is a curated, informative and educational resource on inter-related data standards, databases, and policies in the life, environmental and biomedical sciences. They catalogue many of the available standards, databases and data policies so that you don’t have to!

Publication on Database.

Collaborative-Open-Plant-Omics (COPO)

http://copo-project.org/

The BBSRC-funded Collaborative-Open-Plant-Omics (COPO) project aims to develop a portal for plant scientists to describe, store and retrieve data more easily, using community standards and public repositories that enable the open sharing of results. In addition COPO plans to set up a system of DOIs so that users can get credit for their work. Finally they aim to help with automating metadata submission.

Dryad

http://datadryad.org/

The Dryad Digital Repository is a curated resource that makes the data underlying scientific publications discoverable, freely reusable, and citable. Dryad provides a general-purpose home for a wide diversity of datatypes.

Dryad aims to make data archiving as simple and as rewarding as possible through a suite of services not necessarily provided by publishers or institutional websites. Many journals are directly linked to Dryad so data can be deposited with them at the time of manuscript submission.

ELIXIR

https://www.elixir-europe.org/

ELIXIR unites Europe’s leading life science organisations in managing and safeguarding the increasing volume of data being generated by publicly funded research. It coordinates, integrates and sustains bioinformatics resources across its member states and enables users in academia and industry to access vital services for their research.

FAIR guiding principles of Data Management and Stewardship

http://fair-dom.org/

Findability, Accessibility, Interoperability, and Reusability

The intent for FAIR is for these principles to act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals.

Link to Paper.

ISA-Commons

http://www.isacommons.org/

ISA Commons is a growing community that uses the ISA metadata tracking framework to facilitate standards-compliant collection, curation, management and reuse of datasets in an increasingly diverse set of life science domains.

The URL includes a comprehensive list of journals and other users.

ISA-Tools

http://isa-tools.org/

The open source ISA Framework and Tools help to manage an increasingly diverse set of experiments that employing one or a combination of technologies. This is very important to help the rich description of metadata.

David Johnson from Oxford e-Research Centre outlined the use of Biosharing and ISA-Tools at a recent GARNet-Egenis meeting.

MIAPPE: Minimum Information about Plant Phenotyping Experiment

http://cropnet.pl/phenotypes/

Plant Phenotyping data is extremely complicated especially when you consider field experiments that are subject to enormous variation in environmental conditions and growing practices. Therefore the MIAPPE principles aim to provide guidance about the metadata that might be included when data is submitted.

Publication in Plant Methods on this topic.

OpenBIS

https://wiki-bsse.ethz.ch/display/bis/Home

OpenBIS is an Open Source Biology Information System and its purpose is the management, annotation and sharing of data that have been measured in biological experiments. The OpenBIS software framework can be easily extended and has been customized for the following technologies:

>High Content Screening

>Proteomics

>Metabolomics

>Deep Sequencing

OpenBIS can be downloaded here.

SEEK for Science

http://www.seek4science.org/

The SEEK platform is a web-based resource for sharing heterogeneous scientific research datasets, models or simulations, processes and research outcomes. It preserves associations between them, along with information about the people and organisations involved.

Sequence Read Archive

https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?

The Sequence Read Archive (SRA) stores raw sequence data from "next-generation" sequencing technologies including Illumina, 454, IonTorrent, Complete Genomics, PacBio and OxfordNanopore. It is the NIH’s primary archive of high-throughput sequencing data and is part of the international partnership of archives (INSDC) at the NCBI, EBI and the DNA Database of Japan. Data submitted to any of the three organizations are shared among them.

This is the submission page.