New model for datasets citation and extraction reproducibility in VAMDC

In this paper we present a new paradigm for the identification of datasets extracted from the Virtual Atomic and Molecular Data Centre (VAMDC) e-science infrastructure. Such identification includes information on the origin and version of the datasets, references associated to individual data in the datasets, as well as timestamps linked to the extraction procedure. This paradigm is described through the modifications of the language used to exchange data within the VAMDC and through the services that will implement those modifications. This new paradigm should enforce traceability of datasets, favour reproducibility of datasets extraction, and facilitate the systematic citation of the authors having originally measured and/or calculated the extracted atomic and molecular data.Comment: 48 page

BEAMDB and MOLD—Databases at the Serbian Virtual Observatory for Collisional and Radiative Processes

In this contribution we present a progress report on two atomic and molecular databases, BEAMDB and MolD, which are web services at the Serbian virtual observatory (SerVO) and nodes within the Virtual Atomic and Molecular Data Center (VAMDC). The Belgrade Electron/Atom (Molecule) DataBase (BEAMDB) provides collisional data for electron interactions with atoms and molecules. The Photodissociation (MolD) database contains photo-dissociation cross sections for individual rovibrational states of diatomic molecular ions and rate coefficients for the chemi-ionisation/recombination processes. We also present a progress report on the major upgrade of these databases and plans for the future. As an example of how the data from the BEAMDB may be used, a review of electron scattering from methane is described

Referencing Sources of Molecular Spectroscopic Data in the Era of Data Science: Application to the HITRAN and AMBDAS Databases

The application described has been designed to create bibliographic entries in large databases with diverse sources automatically, which reduces both the frequency of mistakes and the workload for the administrators. This new system uniquely identifies each reference from its digital object identifier (DOI) and retrieves the corresponding bibliographic information from any of several online services, including the SAO/NASA Astrophysics Data Systems (ADS) and CrossRef APIs. Once parsed into a relational database, the software is able to produce bibliographies in any of several formats, including HTML and BibTeX, for use on websites or printed articles. The application is provided free-of-charge for general use by any scientific database. The power of this application is demonstrated when used to populate reference data for the HITRAN and AMBDAS databases as test cases. HITRAN contains data that is provided by researchers and collaborators throughout the spectroscopic community. These contributors are accredited for their contributions through the bibliography produced alongside the data returned by an online search in HITRAN. Prior to the work presented here, HITRAN and AMBDAS created these bibliographies manually, which is a tedious, time-consuming and error-prone process. The complete code for the new referencing system can be found at \url{https://github.com/hitranonline/refs}.Comment: 11 pages, 5 figures, already published online at https://doi.org/10.3390/atoms802001

Theory and Practice of Data Citation

Citations are the cornerstone of knowledge propagation and the primary means of assessing the quality of research, as well as directing investments in science. Science is increasingly becoming "data-intensive", where large volumes of data are collected and analyzed to discover complex patterns through simulations and experiments, and most scientific reference works have been replaced by online curated datasets. Yet, given a dataset, there is no quantitative, consistent and established way of knowing how it has been used over time, who contributed to its curation, what results have been yielded or what value it has. The development of a theory and practice of data citation is fundamental for considering data as first-class research objects with the same relevance and centrality of traditional scientific products. Many works in recent years have discussed data citation from different viewpoints: illustrating why data citation is needed, defining the principles and outlining recommendations for data citation systems, and providing computational methods for addressing specific issues of data citation. The current panorama is many-faceted and an overall view that brings together diverse aspects of this topic is still missing. Therefore, this paper aims to describe the lay of the land for data citation, both from the theoretical (the why and what) and the practical (the how) angle.Comment: 24 pages, 2 tables, pre-print accepted in Journal of the Association for Information Science and Technology (JASIST), 201

Implementing in the VAMDC the New Paradigms for Data Citation from the Research Data Alliance

VAMDC bridged the gap between atomic and molecular (A&M) producers and users by providing an interoperable e-infrastructure connecting A&M databases, as well as tools to extract and manipulate those data. The current paper highlights how the new paradigms for data citation produced by the Research Data Alliance in order to address the citation issues in the data-driven science landscape, have successfully been implemented on the VAMDC e-infrastructure

A Decade with VAMDC: Results and Ambitions

This paper presents an overview of the current status of the Virtual Atomic and Molecular Data Centre (VAMDC) e-infrastructure, including the current status of the VAMDC-connected (or to be connected) databases, updates on the latest technological development within the infrastructure and a presentation of some application tools that make use of the VAMDC e-infrastructure. We analyse the past 10 years of VAMDC development and operation, and assess their impact both on the field of atomic and molecular (A&M) physics itself and on heterogeneous data management in international cooperation. The highly sophisticated VAMDC infrastructure and the related databases developed over this long term make them a perfect resource of sustainable data for future applications in many fields of research. However, we also discuss the current limitations that prevent VAMDC from becoming the main publishing platform and the main source of A&M data for user communities, and present possible solutions under investigation by the consortium. Several user application examples are presented, illustrating the benefits of VAMDC in current research applications, which often need the A&M data from more than one database. Finally, we present our vision for the future of VAMDC

The Virtual Atomic and Molecular Data Centre (VAMDC) Consortium

The Virtual Atomic and Molecular Data Centre (VAMDC) Consortium is a worldwide consortium which federates atomic and molecular databases through an e-science infrastructure and an organisation to support this activity. About 90% of the inter-connected databases handle data that are used for the interpretation of astronomical spectra and for modelling in many fields of astrophysics. Recently the VAMDC Consortium has connected databases from the radiation damage and the plasma communities, as well as promoting the publication of data from Indian institutes. This paper describes how the VAMDC Consortium is organised for the optimal distribution of atomic and molecular data for scientific research. It is noted that the VAMDC Consortium strongly advocates that authors of research papers using data cite the original experimental and theoretical papers as well as the relevant databases

A decade with vamdc: Results and ambitions

This paper presents an overview of the current status of the Virtual Atomic and Molecular Data Centre (VAMDC) e-infrastructure, including the current status of the VAMDC-connected (or to be connected) databases, updates on the latest technological development within the infrastructure and a presentation of some application tools that make use of the VAMDC e-infrastructure. We analyse the past 10 years of VAMDC development and operation, and assess their impact both on the field of atomic and molecular (A&amp;M) physics itself and on heterogeneous data management in international cooperation. The highly sophisticated VAMDC infrastructure and the related databases developed over this long term make them a perfect resource of sustainable data for future applications in many fields of research. However, we also discuss the current limitations that prevent VAMDC from becoming the main publishing platform and the main source of A&amp;M data for user communities, and present possible solutions under investigation by the consortium. Several user application examples are presented, illustrating the benefits of VAMDC in current research applications, which often need the A&amp;M data from more than one database. Finally, we present our vision for the future of VAMDC.</jats:p

NIFS Atomic and Molecular Numerical Database for Collision Processes

The National Institute for Fusion Science (NIFS) has compiled and developed atomic and molecular numerical databases for various collision processes and makes it accessible from the internet to the public. The database contains numerical data of cross sections and rate coefficients for electron collision or ion collisions with atoms and molecules, attached with bibliographic information on their data sources. The database system provides query forms to search data, and numerical data are retrievable. The graphical output is helpful to understand energy dependence of cross sections and temperature dependence of rate coefficients obtained by various studies. All data are compiled mainly from published literature, and data sources can be tracked by the bibliographic information. We also have data of sputtering yields and back-scattering coefficients for solid surfaces collided by ions in the database. All data in the database are applicable to understand atomic and molecular processes in various plasmas, such as fusion plasma, astrophysical plasma and applied plasma, as well as for understanding plasma–surface interaction in plasmas

Scientific data citation : scoping review

Objetivo: Para acompanhar a evolução dos estudos relacionados a dados científicos, investigou-se o significado das citações a eles, buscando responder: 1) Quais as motivações dos pesquisadores para citar dados científicos?; 2) Quais as práticas de citação de dados apresentadas nas áreas cobertas pelo presente estudo?; 3) Quais as análises métricas para citação de dados? Método: Caracteriza-se como pesquisa do tipo qualitativa e descritiva, sendo uma revisão de literatura do tipo Scoping Review, com busca às bases de dados Emerald, LISA, LISTA, Scopus e Web of Science. Resultados: Como motivação, identificaram-se estudos sobre a correlação do incremento de citações às publicações tradicionais ao citarem os dados que as embasavam, muitos confirmaram a correlação, outros não, surgindo também a hipótese de causa comum: qualidade da pesquisa associada a mais recursos. Quanto às práticas, a comunidade está ciente que as citações atuais a dados não estão padronizadas, surgindo a tendência para a adoção de um padrão de citação que atenda às demandas de diferentes tipos de dados. Esta falta de padrão dificulta a análise métrica de citação a dados científicos, que ainda precisa ser explorada em pesquisas, tendo em vista que há uma repetição em utilizar as mesmas técnicas da citação tradicional para essa nova fonte de informação. Conclusões: Promover o avanço da ciência é a principal vantagem em disponibilizar dados, mas existem dificuldades técnicas e de atribuição de crédito que precisam ser enfrentadas em conjunto pelos pesquisadores, instituições, agências de fomento, repositórios de dados e equipes editoriais de publicações.Objective: This paper investigates the meaning assigned to data citation in order to follow the evolution of studies related to data citation, it tries to answer: 1) What are the motivations of researchers to cite scientific data?; 2) What are the data citation practices presented by the areas covered by this study?; 3) What are the metric analysis for data citation? Methods: It is a qualitative and descriptive research, being a scoping review of literature, by searching the Emerald, LISA, LIST, Scopus and Web of Science databases. Results : The studies investigated the correlation of citations increment to traditional publications by citing the data that supported them, many studies confirmed the correlation, others did not, and a common cause hypothesis arose: research quality associated with more resources. As for practices, the community is aware that current citations to data are not standardized, and there is a tendency to adopt a citation standard that meets the demands of different types of data. This lack of standard hinders the metric analysis of citation to scientific data that still needs to be explored in research, given that there is a repetition in using the same techniques of traditional citation for this new source of information. Conclusions : Promoting the progress of science is the main advantage in making data available, but there are credit and technical difficulties that need to be tackled together by researchers, institutions, funding agencies, data repositories, and publishing editorial teams