“The Biodiversity Literature Repository (BLR) has been growing from a community on Zenodo to be a service dedicated to liberate and make open access, FAIR (findable, accessible, interoperable and reusable) data hidden in the hundreds of millions of pages of scholarly publications.
It is built on top of Zenodo, a digital repository hosted at CERN, which provides a sustainable and robust infrastructure for long tail research data, which can consist of small datasets that otherwise would be lost.
Originally a collaboration between Zenodo, Plazi and Pensoft, BLR began as a repository for taxonomic publications which lacked Digital Object Identifiers (DOI) and thus were effectively orphaned from the network of online citations. As it grew its scope expanded to morphed into a highly interlinked repository that focuses on include illustrations and taxonomic treatments contained in publications with all these content types interlinked among themselves and enhanced with and rich metadata.
The source data for BLR are scholarly publications that are most often in PDF or html format but sometimes in XML formats whose structured data facilitates the automated data extraction.
The largest data users are the Global Biodiversity Information Facility (GBIF) and the United States’ National Center for Biotechnology Information (NCBI).
Support of BLR comes from the Arcadia Fund and the three partner institutions Zenodo, Plazi and Pensoft.”
“The Dryad and Zenodo teams are proud to announce the launch of our first formal integration. As we’ve noted over the last years, we believe that the best way to support the broad scientific community in publishing their outputs is to leverage each other’s strengths and build together. Our plan has always been to find ways to seamlessly connect software publishing and data curation in ways that are both easy enough that the features will be used but also beneficial to the researchers re-using and building on scientific discoveries. This month, we’ve released our first set of features to support exactly that….”
“4TU.ResearchData is an international repository for research data in science, engineering and design. After over 10 years of using Fedora, an open source repository system, to run 4TU.ResearchData, we have made a decision to migrate a significant part of our technical infrastructure to a commercial solution offered by figshare. Why did we decide to do it? Why now, at a time of increasing concerns about relying on proprietary solutions, particularly associated with large publishing houses, to run scholarly communication infrastructures? (see for example, In pursuit of open science, open access is not enough and the SPARC Landscape Analysis)
We anticipate that members of our community, as well as colleagues that use or manage scholarly communications infrastructures might be wondering the same. We are therefore explaining our thinking in this blogpost, hoping it will facilitate more discussion about such developments in the scholarly communications infrastructure….”
“Today, Zenodo announced their intentions to remove the altmetrics.com badges from their landing pages–and we couldn’t be more energized by their commitment to open infrastructure, supporting their mission to make scientific information open and free.
“We strongly believe that metadata about records including citation data & other data used for computing metrics should be freely available without barriers” – Zenodo Leadership….
In light of emerging needs for metrics and our work at Make Data Count (MDC) to build open infrastructure for data metrics, we believe that it is necessary for corporations or entities that provide analytics and researcher tools to share the raw data sources behind their work. In short, if we trust these metrics enough to display on our websites or add to our CVs, then we should also demand that they be available for us to audit….
These principles are core to our mission to build the infrastructure for open data metrics. As emphasis shifts in scholarly communication toward “other research outputs” beyond the journal article, we believe it is important to build intentionally open infrastructure, not repeating mistakes made in the metrics systems developed for articles. We know that it is possible for the community to come together and develop the future of open metrics, in a non-prescriptive manner, and importantly built on completely open and reproducible infrastructure.”
“With increasing mandates and initiatives around open data and software, researchers commonly have to make a choice about where to deposit their non-article outputs. Unfortunately, systems that are built to accommodate these objects work separately and can make the process more difficult. As a result, data, code, figures, and other outputs go to a variety of disconnected places, or improper homes (i.e. code with the wrong license or data not curated). To tackle this issue, and make open research best practices more seamless for researchers, we are thrilled to announce a partnership between Dryad and Zenodo….
To jumpstart this collaboration, we are proud to have been awarded an Alfred P. Sloan Foundation grant that will enable us to co-develop new solutions focused on supporting researcher and publisher workflows as well as best practices in data and software curation. By focusing on integrations between our systems, leveraging data and software expertise, we can both extend the reach of our services and open up more opportunities for broader research communities. We are looking forward to re-imagining the submission process for researchers and how we can better support our journal publishing and institutional communities along the way….”
The NASA ADS now extracts and indexes cited software repositories published with the DataCite registry, making them discoverable through its platform and resulting in new metrics for software use and reuse in astronomical research….
“The Biodiversity Literature Repository at Zenodo is holding now over 160,000 figures originally included in scientific publications and is daily updated. Each image is open access. It has a link to the original source – also included in the image metadata – and to related items, such as the taxonomic treatment that cites the image. Originally, Zenodo has been created as a repository for the deposition of single documents, research data, files, but with an option to automate the upload (and download) automatically using its API….”
I fully advocate leaving Academia.edu, but what purpose does it serve to simply delete your account? You are removing publications that are, in the very least, freely and openly available at the moment. Essentially, the best decision is to migrate documents to Zenodo.org, and allow at least one week for Google to fully index migrated content before deleting the Academia.edu account. My MA thesis entitled ‘Recent Advances in Roman Numismatics,’ about the application of Linked Open Data methodologies toward Roman numismatics with Nomisma.org and Online Coins of the Roman Empire, had been available in both the ANS Digital Library and Academia.edu as of January 28, 2016. Due to our superior use of microdata and full-text indexing, the ANS Digital Library version surpassed Academia days after it was published. I uploaded my thesis to Zenodo.org January 29, 2016, and it was already on the first page of Google three days later.
Many of us have uploaded a substantial number of documents to Academia.edu, and it might be tedious to re-upload these documents into a new system, especially with regard to re-entering publication metadata. I have sought to rectify this by facilitating a more efficient migration system. I have developed a framework that is capable of parsing metadata from an Academia.edu profile (although not all publications are listed when the profile page loads), accepting re-uploaded documents (since these cannot be extracted from Academia.edu directly), and uploading these contents into Zenodo.org. This framework itself is open source and available on Github. I will save the technical discussion for different venue.”
“Among those researchers that do archive and share data, GitHub is indeed the most often used, but just as many people indicate using ‘others’ (i.e. tools not mentioned as one of the preselected options). Figshare comes in third, followed by Bitbucket, Dryad, Dataverse, Zenodo and Pangaea (Figure 3)….Another surprising finding is the overall low use of Zenodo – a CERN-hosted repository that is the recommended archiving and sharing solution for data from EU-projects and -institutions. The fact that Zenodo is a data-sharing platform that is available to anyone (thus not just for EU project data) might not be widely known yet….”
“Dissemin is a web platform gathering metadata from many sources and analyzing the full text availability of publications of researchers. It has been designed to foster the use of repositories (rather than preprints posted on personal homepages)….Dissemin helps researchers ensure that their publications are freely available to their readers. Our free service spots paywalled papers and lets you upload them in one click to Zenodo, an innovative repository backed by the EU….Uploading your papers on your own webpage is not enough. Such copies are less stable and harder to find than documents uploaded to well-indexed repositories. Dissemin searches for copies of your papers in a large collection of open repositories and tells you which ones cannot be accessed….”