Open Repositories 2018

Repositories increasingly depend on external cloud storage or other complex distributed systems in order to satisfy ever-growing needs for storing larger data volumes. The cloud system helps repository manages store terabytes and petabytes of data, and often simplifies the file management in the underlying repository software. We trust these systems to store our files, yet, often we lack understanding of the operation and internals of these systems and how they can fail. This talk will present two file loss incidents on Zenodo, uncovering some ways these distributed systems can fail. One incident was caused by a coincidence of two software bugs in independent systems (the hit), and a second incident was caused by a human operational mistake in the cloud storage system (the near miss)

DOI Versioning Done Right

<p>Spring 2017 Zenodo launched a new DOI versioning scheme. Unlike DOI versioning schemes in other generic repositories, no semantic versioning information is included in the identifier string. Instead, DOIs for versions of the same resource are semantically linked in the DataCite metadata registered along with the DOI. Furthermore, an additional DOI representing all versions is also registered to provide an aggregated view for discovery systems. The poster presents use cases, user interface design considerations and implementation details of the new DOI versioning scheme on Zenodo.</p

Biodiversity Literature Repository (BLR), a repository for FAIR data and publications

Scholarly publications in taxonomy are used as the sole carrier of the communication channel to publicize the description of new species, more generally any kind of taxon, their augmentations in form of re-descriptions to small notes such as additional observation records, or deprecations when the name of a taxon is changing. This is communicated in a highly standardized way. For nomenclatural issues, the Codes (e.g. International Code of Zoological Nomenclature) require certain elements, and for comparative reasons, highly formalized language, document structure, illustrations and citation systems are used. This estimated corpus of 500M printed pages includes all we know about the biodiversity in the sciences as well as what has been processed in terms of specimens in the natural history collections. This includes tens of millions of scientific illustrations, taxonomic treatments, i.e. parts of articles that are clearly delimited and headed by a label including a taxonomic name, materials citation, citations of articles and treatments, specimens by their specimen codes, collections by their collection codes, and collectors by their name. Implicitly, the entire catalogue of life is waiting to be liberated. Only recently, with the advent of text and data mining and of publishing, a change is taking place to make all this data after publishing immediately widely accessible and digitally accessible knowledge in terms of findability, accessibility, interoperability and reuse (FAIR). The Biodiversity Literature Repository (BLR) is a community in Zenodo, the open science repository at CERN and part of the European project OpenAIRE. Its goal is to provide a long-term, stable, open access repository for the long tail, preferably FAIR research data. Together with Plazi (http://plazi.org)and Pensoft, BLR has been created to allow deposition of taxonomic articles enhanced with links to data extracted from therein and deposited in BLR, such as illustrations or taxonomic treatments. The metadata for these deposits is enriched with extensive links to cited sources, or the source article. For each of the deposits, a DataCite DOI is minted, unless one exists already. The deposits can be found using either the search functionality of Zenodo, or the BLR website, which makes use of the millions of facts extracted from the publications via the Plazi workflow. A prime user of the BLR data is GBIF which is using the taxonomic treatments and the figures in their respective view of the taxonomic articles. The input of new taxa allows updating the GBIF taxonomic backbone almost instantaneously and keeping it up-to-date  with publishing of new taxa or synonymies. Currently, 35,600 articles, and 190,000 images are available, with an expected 300,000 taxonomic treatments by Fall 2019 and almost 30% of the annually new described species are accessible online, both in human and machine readable format. With the support of the Arcadia Fund, the goal is to provide access to over 50% of the annually described new species, from the necessary number of taxonomic journals, over 600,000 taxonomic treatments and 350,000 illustrations by 2021, hopefully with an increasing community adding to this new resource as author, publisher, or data liberator

OpenAIRE Research Graph Dump

Manghi P, Atzori C, Bardi A, et al. OpenAIRE Research Graph Dump. Bielefeld University; 2019.The OpenAIRE Research Graph is exported as several dumps, so you can download the parts you are interested in. publication.gz: metadata records about research literature (includes types of publications listed here) dataset.gz:: metadata records about research data (includes the subtypes listed here) software.gz:: metadata records about research software (includes the subtypes listed here) orp.gz: metadata records about research products that cannot be classified as research literature, data or software (includes types of products listed here) organization.gz: metadata records about organizations involved in the research life-cycle, such as universities, research organizations, funders. datasource.gz: metadata records about providers whose content is available in the OpenAIRE Research Graph. They includes institutional and thematic repositories, journals, aggregators, funders&#39; databases. project.gz: metadata records about projects funded by a given funder. &lt;funder&gt;_result.gz: metadata records about research results (publications, datasets, software, and other research products) funded by a given funder. Version 1.0.0-bet

Guidelines for the use of flow cytometry and cell sorting in immunological studies

International audienceThe classical model of hematopoiesis established in the mouse postulates that lymphoid cells originate from a founder population of common lymphoid progenitors. Here, using a modeling approach in humanized mice, we showed that human lymphoid development stemmed from distinct populations of CD127(-) and CD127(+) early lymphoid progenitors (ELPs). Combining molecular analyses with in vitro and in vivo functional assays, we demonstrated that CD127(-) and CD127(+) ELPs emerged independently from lympho-mono-dendritic progenitors, responded differently to Notch1 signals, underwent divergent modes of lineage restriction, and displayed both common and specific differentiation potentials. Whereas CD127(-) ELPs comprised precursors of T cells, marginal zone B cells, and natural killer (NK) and innate lymphoid cells (ILCs), CD127(+) ELPs supported production of all NK cell, ILC, and B cell populations but lacked T potential. On the basis of these results, we propose a "two-family" model of human lymphoid development that differs from the prevailing model of hematopoiesis