The Personal Genome Project-UK, an open access resource of human multi-omics data | Scientific Data

“Integrative analysis of multi-omics data is a powerful approach for gaining functional insights into biological and medical processes. Conducting these multifaceted analyses on human samples is often complicated by the fact that the raw sequencing output is rarely available under open access. The Personal Genome Project UK (PGP-UK) is one of few resources that recruits its participants under open consent and makes the resulting multi-omics data freely and openly available. As part of this resource, we describe the PGP-UK multi-omics reference panel consisting of ten genomic, methylomic and transcriptomic data. Specifically, we outline the data processing, quality control and validation procedures which were implemented to ensure data integrity and exclude sample mix-ups. In addition, we provide a REST API to facilitate the download of the entire PGP-UK dataset. The data are also available from two cloud-based environments, providing platforms for free integrated analysis. In conclusion, the genotype-validated PGP-UK multi-omics human reference panel described here provides a valuable new open access resource for integrated analyses in support of personal and medical genomics….”

Ten Prerequisites to Securely Fund Open Infrastructure

“The scholarly communication community needs to call for an open, sustainable infrastructure that is community-owned — one that speaks to our open and academic values. It must be open; not closed off by vendors creating a situation where the academy becomes dependent on a suite of products that are likewise dependent on essential infrastructure, often built by the academy in the first place. For this to truly work and to offer a viable and sustainable solution, we need to develop an interconnected rich and diverse ecosystem of open infrastructure where many flowers bloom upon which a plethora of for- and not-for-profit services can be built.

Imagine a future ten years from now where Open is the default, enabled by an open scholarly infrastructure that follows principles of Open as published by Cameron Neylon et al in 2015 or by COAR and SPARC in 2019. A world where the community is involved in the good governance of infrastructure, where services and infrastructure follow open standards such as open APIs and open source; where content, metadata and usage stats are made openly available, and where we have transparent pricing and contracts. Open Infrastructure is motivated by a drive for research excellence and open values rather than profit-making. This happens when communities of stakeholders fund and sustain this infrastructure, including the academy as a whole and its libraries, government, funders, learned societies, publishers, service providers and individuals. When institutions provide operational funding, this support extends beyond financing innovation, acknowledging successful projects that have continued to provide value to their communities over the years and rewarding them with funding for operational costs. Valued, tried and tested infrastructures that need a financial boost to bring them onto a more healthy footing have also been enabled through initiatives like SCOSS. This involves a new strategic vision of what needs to be funded and how it will be enabled by initiatives like Invest in Open Infrastructure, with new kinds of business models for the mid- to longer term. This will form the basis for a new, transparent, trustworthy and equitable scholarly communication society….”

New Dryad is Here | Dryad news and views

“Dryad’s newest features are centered around making data publishing as easy as possible for researchers:

In addition to supporting datasets as part of a journal submission, Dryad now also supports datasets being submitted independently
Data can be uploaded from cloud storage or lab servers 
Datasets can be as large as 300GB
Datasets can easily be updated or versioned at any time in our process
Standardized data usage and citation statistics are updated and displayed for each published dataset 
Data can be submitted and downloaded through our new REST APIs…”

InstantILL is being rolled out at IUPUI. Here’s how it works.

“In March, we announced InstantILL, a new, powerfully simple library tool that delivers articles?—?no subscription needed. Since then, over 250 libraries, of all sizes have joined the waiting list to save money, improve services, and advance Open. Today, we’re debuting the first iteration with our partner, IUPUI University Library.

We’re excited to show you how it works, but, if you haven’t read our announcement, we suggest you take a few minutes to do that first and join the waiting list if you’d like to stay up to date and explore bringing InstantILL to your campus.

InstantILL is a next-generation interlibrary loan form that integrates with and complements systems that you already use to improve services, save money, and accelerate Open Access. InstantILL embeds into your website and turns your interlibrary loan form into one simple place where patrons can get legal access to any article through the library. InstantILL checks Open Access availability and uses your existing systems to check your subscriptions and submit ILL requests for an article….

If there is an Open Access copy, which can be 23% of the time, and the library doesn’t subscribe to the work, we’ll use the Open Access Button API to give immediate access alongside clear instructions on how it can and can’t be used, and the option to submit an ILL….”

Automating repository workflows with Orpheus, an Open Source database of journals and publishers

Abstract:  Repository management relies on knowledge of numerous attributes of academic journals, such as revenue model (subscription, hybrid or fully Open Access), self-archiving policies, licences, contacts for queries and article processing charges (APCs). While datasets collating some of this information are helpful to repository administrators, most cover only one or few of those attributes (e.g., APC price lists from publishers), do not provide APIs or their API responses are not machine readable (self-archiving policies from RoMEO), or are not updated very often (licences and APCs from DOAJ). As a result, most repositories still rely on administrative staff looking up and entering required attributes manually. To solve this problem and increase automation of tasks performed by the Cambridge repository team, I developed Orpheus, a database of academic journals/publishers written in Django. Orpheus was recently integrated with our DSpace repository Apollo and auxiliary systems via its RESTful API, enabling embargo periods to be automatically applied to deposited articles and streamlining the process of advising researchers on payments, licences and compliance to funders’ Open Access policies. Orpheus is Open Source (https://github.com/osc-cam/orpheus) and may be easily expanded or tailored to meet the particular needs of other repositories and Scholarly Communication services.

Invest in Open Infrastructure: An Interview with Dan Whaley – The Scholarly Kitchen

“Dan Whaley from the Invest in Open initiative answers questions about what IOI is doing, and sets a broad context for the global effort….

Open infrastructure is the solution to all this.  For me, open infrastructure is simply shorthand for technology in which the incentives to collaborate and work together are built in by design. That includes elements like open source software, open APIs, open data and open standards, but more fundamentally it’s a mindset in which your reward — either personal or organizational — comes from working together as a community for the benefit of all.  

As someone who is product focused, a question I always try to ask is what is the best user experience, regardless of who owns which piece? Does what we’re implementing actually make it easier for people to accomplish their goals? Closed systems often make decisions simply for the sake of preventing or restricting access that create terrible experiences and result in lower utility. Open systems do this too sometimes, but at least the inherent motivations are more likely to be aligned….”

Analyze the impact of the rising Open Access movement on your organization – Dimensions

Open Access is an integral part of the journey to a more collaborative research environment and continues to grow in importance across a variety of communities, including publishers, funders, librarians and of course the academic research community. Open Access in combination with Open Data has quickly become a key issue impacting both the quantity and the quality of scholarly communications.

In this recently published Digital Science Research report, Dimensions data were used to explore the implications that restricted access may impose and analyze current Open Access trends. Some of the reports key findings include that the volume of Open Access articles has clearly been rising in recent years and that countries that have invested in Open Access have typically increased their level of international collaboration.

All this and more can be discovered through Dimensions’ rich data and analytical capabilities as we recently developed and released a number of updates and new features which will help you to gain richer and more precise insights about Open Access for your organization.

Dimensions provides multiple filters to easily display results which are Open Access. Our filters are built around the four most commonly used basic classifications:

  • Bronze – available on websites hosted by their publisher, either immediately or following an embargo, but are not formally licensed for reuse.
  • Green – freely available somewhere other than the publisher’s website, e.g. in a subject or university repository, or the author’s personal website. Applies to self-archiving generally of the pre or post-print or potentially after an embargo period
  • Gold – refers to articles in fully accessible open access journals that are available immediately upon publication without a license
  • Hybrid – refers to subscription journals with open access to individual articles usually when a fee is paid to the publisher or journal by the author, the author’s organization, or the research funder….

Say you wanted to know how many gold Open Access papers by the University of Oxford, funded by the Wellcome Trust, were published in Springer Nature journals between 2013 – 2018? We made discovering that easy as you can see in the screenshot below….”

Analyze the impact of the rising Open Access movement on your organization – Dimensions

Open Access is an integral part of the journey to a more collaborative research environment and continues to grow in importance across a variety of communities, including publishers, funders, librarians and of course the academic research community. Open Access in combination with Open Data has quickly become a key issue impacting both the quantity and the quality of scholarly communications.

In this recently published Digital Science Research report, Dimensions data were used to explore the implications that restricted access may impose and analyze current Open Access trends. Some of the reports key findings include that the volume of Open Access articles has clearly been rising in recent years and that countries that have invested in Open Access have typically increased their level of international collaboration.

All this and more can be discovered through Dimensions’ rich data and analytical capabilities as we recently developed and released a number of updates and new features which will help you to gain richer and more precise insights about Open Access for your organization.

Dimensions provides multiple filters to easily display results which are Open Access. Our filters are built around the four most commonly used basic classifications:

  • Bronze – available on websites hosted by their publisher, either immediately or following an embargo, but are not formally licensed for reuse.
  • Green – freely available somewhere other than the publisher’s website, e.g. in a subject or university repository, or the author’s personal website. Applies to self-archiving generally of the pre or post-print or potentially after an embargo period
  • Gold – refers to articles in fully accessible open access journals that are available immediately upon publication without a license
  • Hybrid – refers to subscription journals with open access to individual articles usually when a fee is paid to the publisher or journal by the author, the author’s organization, or the research funder….

Say you wanted to know how many gold Open Access papers by the University of Oxford, funded by the Wellcome Trust, were published in Springer Nature journals between 2013 – 2018? We made discovering that easy as you can see in the screenshot below….”