open data

Walking the talk – reflections on working ‘openly’

As part of Open Access Week 2016, the University of Cambridge Office of Scholarly Communication published a series of blog posts on open access and open research. In this post, Dr Lauren Cadwallader discusses her experience of researching openly. Earlier this year I was awarded the first Altmetric.com Annual Research grant to carry out a proof-of-concept study looking at using altmetrics as a way of identifying journal articles that eventually get included into a policy document. As part of the grant condition I am required to share this work openly. “No problem!” I thought, “My job is all about being open. I know exactly what to do.” However, it’s been several years since I last carried out an academic research project and my previous work was carried out with no idea of the concept of open research (although I’m now sharing lots of it here!). Throughout my project I kept a diary documenting my reflections on being open (and researching in general) – mainly the mistakes I made along the way and the lessons I learnt. This blog post summarises those lessons. To begin at the beginning I carried out a PhD at Cambridge not really aware of scholarly best practice. […]

When Counting is Hard: the Making Data Count project

This is a guest post by Jennifer Lin, project manager for the Making Data Count project. Originally published here. Counting is hard. But when it comes to research data, not in the way we thought it was (example 1, example 2, example 3. The Making Data Count (MDC) project aims to go further – measurement. But to do so, we must start with basic counting: 1, 2, 3… uno, dos, tres… MDC is an NSF-funded project to design and develop metrics that track and measure data use, “data-level metrics” (DLM). DLM are a multi-dimensional suite of indicators, measuring the broad range of activities surrounding the reach and use of data as a research output. Our team, made up of staff from the University of California Curation Center at California Digital Library, PLOS, and DataONE, investigated the validity and feasibility of using metrics by collecting and investigating the use of harvested data to power discovery and reporting of datasets that are part of scholarly outputs. To do this, we extended Lagotto, an open source application, to track datasets and collect a host of online activity surrounding datasets from usage to references, social shares, discussions, and citations. During this pilot phase we […]

How doing Open Science has helped advance my career

Last week we sent details of how to win $1,000 in The Winnower open science writing competition. This week we bring you a blog post from Bastian Greshake, one of the participants in the competition. Bastian’s story shows how supporting open genetic data access had a lasting impact on his academic career, contributed to lots of new skills, led to winning awards and helped him find jobs and collaborators. Bastian Greshake, co-founder of OpenSNP. What Have I Done?! There are many firm believers in the different kinds of openness: open access, open source, open data, open science, open you-name-it. And at least to me, some of the most interesting things happen at the intersection of those different opens. Which probably is where openSNP – the project I co-founded in 2011 – can be located. It’s an open source project which tries to crowdsource collecting open genetic data. This is done by enabling people to donate their personal genetic information into the public domain, alongside phenotypic annotations. And for good measure we also factor in open access, by text mining the Public Library of Science and other open databases for primary literature. What started as a somewhat freakish idea in 2011 has by mid–2015 […]

ecology concept

Ecological Perspective on Data Sharing

We have invited Charlie Outhwaite (@charlielouo) to write a guest blog post on the topic of openness and data sharing from an ecological point of view. The post give us the great opportunity to draw a parallel on how the same type of data sharing problems we are experiencing in the field of genomics are observed across different scientific disciplines. The field of ecology is a vast and varied one. As a result, the types and quantities of data produced differ hugely.  Whether a study is small in scale, such as a field or lab based project, or a large, country or global scale, big data study: the amount of data that could be made available is enormous.  Yet the field of ecology has been considered as behind in terms of its openness when compared to other areas of biology such as genomics. With such vast amounts and types of data available, sharing that data openly has the potential to boost research opportunities and open up collaboration within and between fields. As is the case within many scientific disciplines, a major barrier for data sharing in ecology is the fear of being scooped. For this reason, many researchers would be unlikely […]

Centre for Open Science

The Reproducibility Project: Cancer Biology

The Reproducibility Project: Cancer Biology has continued to make steady progress over the last few months.Since December, they have published four new Registered Reports with eLife, and one more has been accepted and on the way.Now that these protocols and analyses plans have been reviewed, the replication experiments themselves can begin. All of the protocols, analyses, and data are freely available on the Open Science Framework (OSF). In total, eleven replications have begun or are poised to begin in the coming weeks.You can keep track of theReproducibility Project progress for all these Registered Reports and all of the rest of the 50 studies included in the project on the Open Science Framework.Take a look at their most recent Science Exchange blog post and read the completed description of their progress so far.

DNAdigest interviews Free the Data – Part 1

DNAdigest is happy to welcome all of you, our blog readers, into the 2015 new year! We are fresh, with recharged batteries and ready to publish new interesting posts for you. In the first week of this, hopefully, very prolific year, we would like to introduce you to Sharon Terry (@sharonfterry). She kindly agreed on an interview for our series and will be telling us everything about Free the Data project (@FreeBRCA). This is only the first part of Sharon’s interview… Yes! There is more! Read the second part of the interview with FreeTheData here. Enjoy the read and in order to be the first one to know when we publish more interviews, sign up for our newsletter. 🙂 Sharon F. Terry is President and CEO of Genetic Alliance 1. Free The Data is a creation of Genetic Alliance, and still it has its own mission and goals. Could you please tell us more about this project of yours? Free the Data has two goals: first, to increase awareness about the benefits of open access to genetic data, both within the genetics community and at large, and second, to build the commons for the BRCA1/2 genes by empowering individual men and women […]

data and bio-specimens

Sharing Bio-specimens and Data

Nowadays, the increasing value of data and bio-specimen collections does not correspond with an equal increase in data/sample-sharing and data/sample access. As we all know sharing data and bio-specimens is essential for the discovery, the knowledge creation and translation of various biomedical research findings into improved diagnostics, biomarkers, treatment development, patient care, health service planning and general population health. There is a constantly increasing international agreement on the urgency to provide access to research datasets, to advance their use and fully apply their long term value. All of this has been clearly noted in many documents such as the OECD Principles and Guidelines for Access to Research Data from Public Funding, the Toronto Statement, and more recently the Global Alliance for Genomics and Health’s White Paper. Even though sharing of data and samples is confirmed to be favourable for most health-related research, it is of highest importance for rare-disease research because of the high deficiency of research participants, samples, data, resources and researchers for any given RD. Thinking in the most perfect way, data and bio-specimens should be made broadly available, but often failed because of institutions and individuals fearing, they will not receive recognition for their investment in building […]

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