Abstract: Genomic data repositories like The Cancer Genome Atlas (TCGA), Encyclopedia of DNA Elements (ENCODE), Bioconductor’s AnnotationHub and ExperimentHub etc., provide public access to large amounts of genomic data as flat files. Researchers often download a subset of data files from these repositories to perform exploratory data analysis. We developed Epiviz File Server, a Python library that implements an in-situ data query system for local or remotely hosted indexed genomic files, not only for visualization but also data transformation. The File Server library decouples data retrieval and transformation from specific visualization and analysis tools and provides an abstract interface to define computations independent of the location, format or structure of the file. We demonstrate the File Server in two use cases: 1) integration with Galaxy workflows and 2) using Epiviz to create a custom genome browser from the Epigenome Roadmap dataset.
Category Archives: oa.repositories.data
A Highly Phenotyped Open Access Repository of Alpha-1 Antitrypsin Deficiency Pluripotent Stem Cells
Abstract: Individuals with the genetic disorder alpha-1 antitrypsin deficiency (AATD) are at risk of developing lung and liver disease. Patient induced pluripotent stem cells (iPSCs) have been found to model features of AATD pathogenesis but only a handful of AATD patient iPSC lines have been published. To capture the significant phenotypic diversity of the patient population, we describe here the establishment and characterization of a curated repository of AATD iPSCs with associated disease-relevant clinical data. To highlight the utility of the repository, we selected a subset of iPSC lines for functional characterization. Selected lines were differentiated to generate both hepatic and lung cell lineages and analyzed by RNA sequencing. In addition, two iPSC lines were targeted using CRISPR/Cas9 editing to accomplish scarless repair. Repository iPSCs are available to investigators for studies of disease pathogenesis and therapeutic discovery.
TRUST Principles Mini Symposium – July 7, 2020 | RDA
“The TRUST Principles for digital repositories, recently published in Nature Research’s Scientific Data, present a new set of guiding principles to demonstrate digital repository trustworthiness, centered around Transparency, Responsibility, User focus, Sustainability, and Technology. As the article states, “Repositories must earn the trust of the communities they intend to serve and demonstrate that they are reliable and capable of appropriately managing the data they hold,” and the TRUST principles provide a framework to facilitate discussion and implementation of best practices in digital preservation.
Research Data Canada (RDC), Research Data Alliance (RDA), World Data Systems (WDS), and the TRUST Principles authors are pleased to present a virtual Mini Symposium that will provide an introduction to the principles for a global audience, along with an overview of key concepts and implementations from a variety of stakeholder perspectives. See the schedule below for a full list of topics and presenters.”
TRUST Principles Mini Symposium – July 7, 2020 | RDA
“The TRUST Principles for digital repositories, recently published in Nature Research’s Scientific Data, present a new set of guiding principles to demonstrate digital repository trustworthiness, centered around Transparency, Responsibility, User focus, Sustainability, and Technology. As the article states, “Repositories must earn the trust of the communities they intend to serve and demonstrate that they are reliable and capable of appropriately managing the data they hold,” and the TRUST principles provide a framework to facilitate discussion and implementation of best practices in digital preservation.
Research Data Canada (RDC), Research Data Alliance (RDA), World Data Systems (WDS), and the TRUST Principles authors are pleased to present a virtual Mini Symposium that will provide an introduction to the principles for a global audience, along with an overview of key concepts and implementations from a variety of stakeholder perspectives. See the schedule below for a full list of topics and presenters.”
The TRUST Principles for digital repositories | Scientific Data
“As information and communication technology has become pervasive in our society, we are increasingly dependent on both digital data and repositories that provide access to and enable the use of such resources. Repositories must earn the trust of the communities they intend to serve and demonstrate that they are reliable and capable of appropriately managing the data they hold.
Following a year-long public discussion and building on existing community consensus1, several stakeholders, representing various segments of the digital repository community, have collaboratively developed and endorsed a set of guiding principles to demonstrate digital repository trustworthiness. Transparency, Responsibility, User focus, Sustainability and Technology: the TRUST Principles provide a common framework to facilitate discussion and implementation of best practice in digital preservation by all stakeholders….”
The TRUST Principles for digital repositories | Scientific Data
“As information and communication technology has become pervasive in our society, we are increasingly dependent on both digital data and repositories that provide access to and enable the use of such resources. Repositories must earn the trust of the communities they intend to serve and demonstrate that they are reliable and capable of appropriately managing the data they hold.
Following a year-long public discussion and building on existing community consensus1, several stakeholders, representing various segments of the digital repository community, have collaboratively developed and endorsed a set of guiding principles to demonstrate digital repository trustworthiness. Transparency, Responsibility, User focus, Sustainability and Technology: the TRUST Principles provide a common framework to facilitate discussion and implementation of best practice in digital preservation by all stakeholders….”
Addgene’s AAV Data Hub | Open Neuroscience
“AAV are versatile tools used by neuroscientists for expression and manipulation of neurons. Many scientists have benefited from the high-quality, ready-to-use AAV prep service from Addgene, a nonprofit plasmid repository. However, it can be challenging to determine which AAV tool and techniques are best to use for an experiment. Scientists also may have questions about how much virus to inject or which serotype or promoter should be used to target the desired neuron or brain region. To help scientists answer these questions, Addgene launched an open platform called the AAV Data Hub (https://datahub.addgene.org/aav/) which allows researchers to easily share practical experimental details with the scientific community (AAV used, in vivo model used, injection site, injection volumes, etc.). The goal of this platform is to help scientists find the best AAV tool for their experiments by reviewing combined data from a broad range of research labs. The AAV Data Hub launched in late 2019 and over 100 experiments have since been contributed to this project. The dataset includes details and images from experiments conducted in six different species and several different expression sites….”
Journal research data sharing policies
Abstract: The practices for if and how scholarly journals instruct research data for published research to be shared is an area where a lot of changes have been happening as science policy moves towards facilitating open science, and subject-specific repositories and practices are established. This study provides an analysis of the research data sharing policies of highly-cited journals in the fields of neuroscience, physics, and operations research as of May 2019. For these 120 journals, 40 journals per subject category, a unified policy coding framework was developed to capture the most central elements of each policy, i.e. what, when, and where research data is instructed to be shared. The results affirm that considerable differences between research fields remain when it comes to policy existence, strength, and specificity. The findings revealed that one of the most important factors influencing the dimensions of what, where and when of research data policies was whether the journal’s scope included specific data types related to life sciences which have established methods of sharing through community-endorsed public repositories. The findings surface the future research potential of approaching policy analysis on the publisher-level as well as on the journal-level. The collected data and coding framework is provided as open data to facilitate future research and journal policy monitoring.
Virtual workshop: How repositories can contribute their FAIR share
“Findable, accessible, interoperable and reusable (FAIR) data are an increasingly important aspect of open scholarship. Increasing the production and use of FAIR data requires a wide range of stakeholders across the research ecosystem to actively play their parts. FAIRsFAIR – Fostering Fair Data Practices in Europe – aims to supply practical solutions for applying the FAIR data principles throughout the research data life cycle, which can be included in the strategies that research organisations and implemented to enable a FAIR data culture.
This 90 minute virtual workshop will focus on the work FAIRsFAIR carries out in collaboration with repositories to enable them to play their role in helping to make and keep data FAIR over time. We will present an early draft of a transition support programme for repositories wishing to improve their capacity to support FAIR data production and use. Following an overview of the draft programme, attendees will participate in group discussions and activities to review and discuss the draft support programme, consider how it might be applied within their own repositories, and how they can support and promote relevant aspects of the programme within their institutions and the wider community….”
The TRUST Principles – An RDA Community Effort | RDA
“An RDA community effort has led to the development and publication, in Nature Research’s Scientific Data, of the article, “The TRUST Principles for digital repositories”. These principles offer guidance for maintaining the trustworthiness of digital repositories, especially those responsible for the stewardship of research data. Guidance for each of the TRUST Principles is reproduced below.”