PhD Project Plan published to invite community feedback early on

Development and implementation of novel methods for publication, visualisation and dissemination of the constantly growing biodiversity and genomic bioinformatic data are the main objective of the first PhD Project Plan available from the open-access Research Ideas and Outcomes journal, a journal created to publish the outputs of the whole research cycle. Founded on the principles of open science, the project addresses digitally born scholarly papers and digitised data, aiming to make them more accessible and citable, and the results more reproducible.

The gradual realisation of the project, inspired by the Open Biodiversity Knowledge Management System, begins with the publishing of data in semantically enriched publications, and is completed when this data is properly linked to the Web of data, also known as the Semantic Web, ensuring its re-usability and citability. PhD student Viktor Senderov and advisor Prof. Lyubomir Penev, both affiliated with Pensoft Publishers and the Bulgarian Academy of Sciences, believe that this is the way the entire scientific data life-cycle should opera.

A fundamental part of the project is the so-called Enhanced Publication (EP), which unlike a conventional academic paper enables the user to easily access the data contained within a publication, while providing various dynamic features. For instance, there are interlinked external resources or tools that gather information on certain objects or data elements in real time. Most importantly, an EP is an object-based artifact that is highly interactive and machine-readable.

The project’s idea is that all of the featured objects should be exportable and citable. The authors of the project plan give examples with the biodiversity-themed journals ZooKeysPhytoKeys, and the Biodiversity Data Journal, which have already adopted some of the features of an EP.

The plan also includes development of visualisations of genomic and other biodiversity-related data. This is planned to be executed within the BIG4 consortium, where Viktor Senderov is a trainee. Both data from BIG4’s expeditions and from museum collections are to be utilised for the purposes of the project.

“As part of the scientific and methodological results, we expect to develop new approaches, methods and formats for data publishing, and for publishing in biodiversity science,” explain the scientists. “We also expect to develop novel methods for exchange between publications and external data repositories, and to illustrate the aforementioned methods by means of examples using data gathered in the consortium.”

The Open Science Pyramid


Original source:

Senderov V, Penev L (2016) The Open Biodiversity Knowledge Management System in Scholarly Publishing. Research Ideas and Outcomes 2: e7757. doi: 10.3897/rio.2.e7757


Additional information:

The work has been supported by the ITN Horizon 2020 project BIG4 (Biosystematics, informatics and genomics of the big 4 insect groups: training tomorrow’s researchers and entrepreneurs), under Marie Sklodovska-Curie grant agreement No. 542241.

Austrian Science Fund grant proposal goes public with RIO Journal

Controlled manipulation of matter on the scale of atoms is the topic of a new cutting edge Austrian Science Fund (FWF) project “Heteroatom quantum corrals and nanoplasmonics in graphene” (HeQuCoG), led by Finnish-born physicist Toma Susi. The project is the first to openly publish its proposal via the innovative platform of the Research Ideas & Outcomes (RIO) Journal, designed to uncover the entire research cycle.

The mission of RIO is to catalyse change in research communication by publishing ideas, proposals and outcomes in order to increase transparency, trust and efficiency of the whole research ecosystem. The journal harnesses the full value of investment in the academic system by registering, reviewing, publishing and permanently archiving a wider variety of research outputs than those traditionally made public.

RIO offers one of the most transparent, open and public peer-review processes, including pre-submission and post-publication peer-review options. The journal is designed to encourage collaboration between scientists within and across disciplines by making the entire research cycle open, and by mapping the social impact for its publications.

Dr. Susi, based at the University of Vienna in Austria, shares why he chose to make his research accessible to peers and the wider public from the proposal stage. “I must be honest: it was an instinctively scary prospect to publish a grant proposal, even a funded one. However, once I carefully weighed the potential pros and cons and discussed the idea with my close peers, I concluded that those fears most likely were unfounded. Moreover, there really can be no doubt that science as a whole would benefit if this became common practice.”

The aim of the HeQuCoG project is to create atomically precise structures consisting of silicon and phosphorus atoms embedded in the lattice of graphene using a combination of ion implantation, first principles modeling and electron microscopy. The expected outcome is a systematic demonstration of atomic-level material design and the creation of freestanding “quantum corral” structures for the first time.

“We are happy to have such an exciting and ambitious project as one of the first to publish its proposal in RIO. This goes to show that the platform is an ideal hub for forward-thinking young researchers wishing to take science to a new level of collaboration and real-world impact” comments Prof. Lyubomir Penev, co-founder of RIO.



Original source:

Susi T (2015) Heteroatom quantum corrals and nanoplasmonics in graphene (HeQuCoG). Research Ideas and Outcomes 1: e7479. doi: 10.3897/rio.1.e7479


Additional information:

The Austrian Science Fund FWF is devoted to the support of the ongoing development of Austrian science and basic research at a high international level. In this way, the FWF makes a significant contribution to cultural development, to the advancement of a knowledge-based society, and to the creation of value and wealth in Austria and abroad.

The Research Ideas and Outcomes (RIO) Journal publishes all outputs of the research cycle, including: project proposals, data, methods, workflows, software, project reports and research articles together on a single collaborative platform offering one of the most transparent, open and public peer-review processes. Its scope encompasses all areas of academic research, including science, technology, the humanities and the social sciences.