The OpenAIRE Research Community Dashboard: On blending scientific workflows and scientific publishing

First Online 30 August 2019Despite the hype, the effective implementation of Open Science is hindered by several cultural and technical barriers. Researchers embraced digital science, use “digital laboratories” (e.g. research infrastructures, thematic services) to conduct their research and publish research data, but practices and tools are still far from achieving the expectations of transparency and reproducibility of Open Science. The places where science is performed and the places where science is published are still regarded as different realms. Publishing is still a post-experimental, tedious, manual process, too often limited to articles, in some contexts semantically linked to datasets, rarely to software, generally disregarding digital representations of experiments. In this work we present the OpenAIRE Research Community Dashboard (RCD), designed to overcome some of these barriers for a given research community, minimizing the technical efforts and without renouncing any of the community services or practices. The RCD flanks digital laboratories of research communities with scholarly communication tools for discovering and publishing interlinked scientific products such as literature, datasets, and software. The benefits of the RCD are show-cased by means of two real-case scenarios: the European Marine Science community and the European Plate Observing System (EPOS) research infrastructure.This work is partly funded by the OpenAIRE-Advance H2020 project (grant number: 777541; call: H2020-EINFRA-2017) and the OpenAIREConnect H2020 project (grant number: 731011; call: H2020-EINFRA-2016-1). Moreover, we would like to thank our colleagues Michele Manunta, Francesco Casu, and Claudio De Luca (Institute for the Electromagnetic Sensing of the Environment, CNR, Italy) for their work on the EPOS infrastructure RCD; and Stephane Pesant (University of Bremen, Germany) his work on the European Marine Science RCD

MicroRNAs are stored in human MII oocyte and their expression profile changes in reproductive aging

Maternal RNAs are synthesized by the oocyte during its growth; some of them are utilized for oocyte-specific processes and metabolism, others are stored and used during early development before embryonic genome activation. The appropriate expression of complex sets of genes is needed for oocyte maturation and early embryo development. In spite of the basic role of noncoding RNAs in the regulation of gene expression, few studies have analyzed their role in human oocytes. In this study, we identified the microRNAs (miRNAs) expressed in human metaphase II stage oocytes, and found that some of them are able to control pluripotency, chromatin remodeling, and early embryo development. We demonstrated that 12 miRNAs are differentially expressed in women of advanced reproductive age and, by bioinformatics analysis, we identified their mRNA targets, expressed in human oocytes and involved in the regulation of pathways altered in reproductive aging. Finally, we found the upregulation of miR-29a-3p, miR-203a-3p, and miR-494-3p, evolutionarily conserved miRNAs, also in aged mouse oocytes, and demonstrated that their overexpression is antithetically correlated with the downregulation of DNA methyltransferase 3A (Dnmt3a), DNA methyltransferase 3B (Dnmt3b), phosphatase and tensin homolog (Pten), and mitochondrial transcription factor A (Tfam). We propose that oocyte miRNAs perform an important regulatory function in human female germ cells, and their altered regulation could explain the changes occurring in oocyte aging

Results from the OpenAIRE Call for Innovation: Enrich local data via the OpenAIRE Graph

In the context of the OpenAIRE Open Innovation programme, 4Science proposed the project named “Enrich local data via the OpenAIRE Graph” to develop two data products for the repository community, and more specifically for the DSpace and DSpace-CRIS platforms. The solutions were built on top of the OpenAIRE Research Graph and the OpenAIRE Broker Service to enrich the data locally available and identify new data of interest reducing the friction of deposit. The Open Innovation programme selects innovative projects in the field of Open Science to develop products and services linked to scholarly works, repositories, data management, OpenAIRE infrastructure and OpenAIRE services. The 4Science proposal was awarded in 2020 and went through an accurate process of design, validation, prototyping and finalization of the solution, in continuous dialogue with the OpenAIRE team and gathering feedback from the repository community as well. In Feb 2021 the project was completed after a pilot phase with the University of Trieste, and the implemented solution was released as free open source. This presentation aims to show the developed solution and discuss how collaboration between large initiatives such OpenAIRE and repository platforms can enrich both

High-Performance Annotation Tagging over Solr Full-text Indexes

In this work, we focus on the problem of “annotation tagging” over Information Spaces of objects stored in a full-text index. In such a scenario, tags are assigned to objects by “data curator” users with the purpose of classification, while generic end-users will perceive tags as searchable and browsable object properties. To carry out their activities, data curators need “annotation tagging tools” which allow them to “bulk” tag or untag large sets of objects in temporary work sessions, where they can “virtually” and in “real-time” experiment the effect of their actions before making the changes visible to end-users. The implementation of these tools over full-text indexes is a challenge, since bulk object updates in this context are far from being real-time and in critical cases may slow down index performance. We devised TagTick, a tool which offers to data curators a fully functional annotation tagging environment over the full-text index Apache Solr, regarded as a “de-facto standard” in this area. TagTick consists of a TagTick Virtualizer module, which extends the APIs of Solr to support real-time, virtual, bulk-tagging operations, and a TagTick User Interface module, which offers end-user functionalities for annotation tagging. The tool scales optimally with the number and size of bulk tag operations, without compromising index performance

OpenAIRE: Advancing open science

OpenAIRE, the point of reference for Open Access in Europe, is now addressing the problem of enabling the Open Science paradigm. To this aim it will provide services to: (i) overcome the limits of today’s scientific communication landscape, by allowing research communities and the relative e-infrastructures to fully publish, interlink, package and reuse their research artefacts (e.g. literature, data, and software) and their funding grants within the European and global ecosystem as supported/promoted by OpenAIRE, (ii) enable end-users (e.g. researchers, funder officers) to search and consult a rich and up-to-date knowledge graph of research results and (iii) enable scientific and educational information repositories and publishers to subscribe and be notified of changes in the OpenAIRE knowledge graph. These combined actions will bring long-term and immediate benefits to research communities, research organisations, repository managers, and funders by affecting the way research results are disseminated and reused. On the one hand, publishing the interlinked and packaged research literature, data and software via OpenAIRE drives research communities to an Open Science transition in a consistent and interoperable fashion. On the other hand, the resulting infrastructure concretely enables the construction of Open Science oriented services, supporting practices such as machine-assisted research reproducibility and evaluation.This research was supported by EU funded project OpenAIRE-Connect (grant agreement: 731011; Call: H2020-EINFRA-2016-1). We thank our colleague Stefania Biagioni for her help during the writing of this paper

OpenAIRE Research Graph: Dumps for research communities and initiatives

Manghi P, Atzori C, Bardi A, et al. OpenAIRE Research Graph: Dumps for research communities and initiatives. Bielefeld University; 2022.This dataset contains dumps of the OpenAIRE Research Graph containing metadata records relevant for the research communities and initiatives collaborating with OpenAIRE and&nbsp;with a public Open Research Gateway on OpenAIRE CONNECT&nbsp;&nbsp;as of May 2022. Each dump is a tar file containing gzip files with one json per line. Each json is compliant to the schema available at&nbsp;https://doi.org/10.5281/zenodo.6372977</p

OpenAIRE Research Graph Dump

Manghi P, Atzori C, Bardi A, et al. OpenAIRE Research Graph Dump. Bielefeld University; 2022.The OpenAIRE Research Graph is exported as several dumps, so you can download the parts you are interested into. publication_[part].tar: metadata records about research literature (includes types of publications listed here) dataset.tar: metadata records about research data (includes the subtypes listed here)&nbsp; software.tar: metadata records about research software (includes the subtypes listed here) otherresearchproduct.tar: metadata records about research products that cannot be classified as research literature, data or software (includes types of products listed here) organization.tar: metadata records about organizations involved in the research life-cycle, such as universities, research organizations, funders., datasource.tar: 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.tar: metadata records about projects funded by a given funder. relation_[part].tar: metadata records about relations between entities in the graph. communities_infrastructures.tar: metadata records about research communities and research infrastructures Each file is a tar archive containing gz files, each with one json per line. Each json is compliant to the schema available at http://doi.org/10.5281/zenodo.5799514. Learn more about the OpenAIRE Research Graph at https://graph.openaire.eu. Discover the content of the graph on OpenAIRE EXPLORE&nbsp;and our API for developers.</p

OpenAIRE Graph Dataset

&lt;p&gt;The OpenAIRE Graph is exported as several dataseta, so you can download the parts you are interested into.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;publication_[part].tar&lt;/strong&gt;: metadata records about research literature (includes types of publications listed &lt;a href="http://api.openaire.eu/vocabularies/dnet:result_typologies/publication"&gt;here&lt;/a&gt;)&lt;br&gt; &lt;strong&gt;dataset_[part].tar&lt;/strong&gt;: metadata records about research data (includes the subtypes listed &lt;a href="http://api.openaire.eu/vocabularies/dnet:result_typologies/dataset"&gt;here&lt;/a&gt;)&nbsp;&lt;br&gt; &lt;strong&gt;software.tar&lt;/strong&gt;: metadata records about research software (includes the subtypes listed &lt;a href="http://api.openaire.eu/vocabularies/dnet:result_typologies/software"&gt;here&lt;/a&gt;)&lt;br&gt; &lt;strong&gt;otherresearchproduct_[part].tar&lt;/strong&gt;: metadata records about research products that cannot be classified as research literature, data or software (includes types of products listed &lt;a href="http://api.openaire.eu/vocabularies/dnet:result_typologies/other"&gt;here&lt;/a&gt;)&lt;br&gt; &lt;strong&gt;organization.tar&lt;/strong&gt;: metadata records about organizations involved in the research life-cycle, such as universities, research organizations, funders.&lt;br&gt; &lt;strong&gt;datasource.tar&lt;/strong&gt;: metadata records about data sources whose content is available in the OpenAIRE Graph. They include&nbsp;institutional and thematic repositories, journals, aggregators, funders&#39; databases.&lt;br&gt; &lt;strong&gt;project.tar&lt;/strong&gt;: metadata records about project grants.&lt;br&gt; &lt;strong&gt;relation_[part].tar&lt;/strong&gt;: metadata records about relations between entities in the graph.&lt;br&gt; &lt;strong&gt;communities_infrastructures.tar&lt;/strong&gt;: metadata records about research communities and research infrastructures&lt;/p&gt; &lt;p&gt;Each file is a tar archive containing gz files, each with one json per line. Each json is compliant to the schema available at &lt;a href="http://doi.org/10.5281/zenodo.8238874"&gt;http://doi.org/10.5281/zenodo.8238874&lt;/a&gt;. The documentation for the model is available at&nbsp;&lt;a href="https://graph.openaire.eu/docs/data-model/"&gt;https://graph.openaire.eu/docs/data-model/&lt;/a&gt;&lt;/p&gt; &lt;p&gt;Learn more about the OpenAIRE Graph at &lt;a href="https://graph.openaire.eu"&gt;https://graph.openaire.eu&lt;/a&gt;.&lt;/p&gt; &lt;p&gt;Discover the graph&#39;s content on &lt;a href="https://explore.openaire.eu"&gt;OpenAIRE EXPLORE&lt;/a&gt;&nbsp;and our &lt;a href="https://develop.openaire.eu"&gt;API for developers&lt;/a&gt;.&lt;/p&gt;&lt;p&gt;Note: This is a new update to fix some issues found in the relation file names. The content is the same as the deposition of August.&lt;/p&gt;&lt;p&gt;The schema of the result and relation is changed. Have a look at https://graph.openaire.eu/docs/. The three-char prefix has been removed from the OpenAIRE identifiers. A new version of this dataset is published every 6 months. The content available on the OpenAIRE EXPLORE and CONNECT portals might be more up-to-date with respect to the data you find here.&lt;/p&gt

OpenAIRE Graph Beginner's Kit

Baglioni M, Atzori C, Bardi A, et al. OpenAIRE Graph Beginner's Kit. OpenAIRE Nexus; 2022.The OpenAIRE Graph is an Open Access dataset containing metadata about research products (literature, datasets, software, etc.) linked to other entities of the research ecosystem like organisations, project grants, and data sources.&nbsp; The large size of the OpenAIRE Graph is a major impediment for beginners to familiarise with the underlying data model and explore its contents. Working with the Graph in its full size typically requires access to a huge distributed computing infrastructure which cannot be easily accessible to everyone.&nbsp;&nbsp; The OpenAIRE Beginner&rsquo;s Kit aims to address this issue. It consists of two components: A subset of the OpenAIRE Graph composed of the research products published between 2022-06-29 and 2022-12-29, all the entities connected to them and the respective relationships. The subset is composed of the following parts: publication.tar: metadata records about research literature (includes types of publications listed here) dataset.tar: metadata records about research data (includes the subtypes listed here) software.tar: metadata records about research software (includes the subtypes listed here) otherresearchproduct.tar: metadata records about research products that cannot be classified as research literature, data or software (includes types of products listed here) organization.tar: metadata records about organizations involved in the research life-cycle, such as universities, research organizations, funders. datasource.tar: metadata records about data sources&nbsp;whose content is available in the OpenAIRE Graph. They include&nbsp;institutional and thematic repositories, journals, aggregators, funders&#39; databases. project.tar: metadata records about project grants. relation.tar: metadata records about relations between entities in the graph. communities_infrastructures.tar: metadata records about research communities and research infrastructures Each file is a tar archive containing gz files, each with one json per line. Each json is compliant to the schema available at http://doi.org/10.5281/zenodo.7492151. A Zeppelin notebook that demonstrates how you can use PySpark to analyse the Graph and get answers to some interesting research questions:&nbsp;beginners_kit_zeppelin_notebook.json. Here&nbsp;a guide to Apache Zeppelin. </ul

OpenAIRE Research Graph: Dumps for research communities and initiatives

Manghi P, Atzori C, Bardi A, et al. OpenAIRE Research Graph: Dumps for research communities and initiatives. OpenAIRE; 2020.This dataset contains dumps of the OpenAIRE Research Graph containing metadata records relevant for the research communities and initiatives collaborating with OpenAIRE. Each dataset is a gzip containing a file with one JSON per line. Each JSON is compliant to the schema available at DOI: 10.5281/zenodo.397422