Ontology-Based Queries over Cancer Data

The ever-increasing amount of data in biomedical research, and in cancer research in particular, needs to be managed to support efficient data access, exchange and integration. Existing software infrastructures, such as caGrid, support access to distributed information annotated with a domain ontology. However, caGrid's current querying functionality depends on the structure of individual data resources without exploiting the semantic annotations. In this paper, we present the design and development of an ontology-based querying functionality that consists of: the generation of OWL2 ontologies from the underlying data resources’ metadata and a query rewriting and translation process based on reasoning, which converts a query at the domain ontology level into queries at the software infrastructure level. We present a detailed analysis of our approach as well as an extensive performance evaluation. While the implementation and evaluation was performed for the caGrid infrastructure, the approach could be applicable to other model and metadata-driven environments for data sharing

SAVE-SD 2017: Third Workshop on Semantics, Analytics and Visualisation: Enhancing Scholarly Data

The third edition of the Workshop on Semantics, Analytics and Visualisation: Enhancing Scholarly Data (SAVE-SD 2017) is taking place in Perth, Australia on the 3rd of April 2017, co-located with the 26th International World Wide Web Conference. The main goal of the workshop is to provide a venue for researchers, publishers and other companies to engage in discussions about semantics, analytics and visualisations on scholarly data

Editorial: Special Issue on Scholarly Data Analysis (Semantics, Analytics, Visualisation)

The increasing interest in analysing, describing, and improving the research process requires the development of new forms of scholarly data publication and analysis that integrates lessons and approaches from the field of Semantic Technologies, Science of Science, Digital Libraries, and Artificial Intelligence. This editorial summarises the content of the Special Issue on Scholarly Data Analysis (Semantics, Analytics, Visualisation), which aims to showcase some of the most interesting research efforts in the field. This issue includes an extended version of the best papers of the last two editions of the “Semantics, Analytics, Visualisation: Enhancing Scholarly Dissemination” (SAVE-SD 2017 and 2018) workshop at The Web Conference

It ROCS! The RASH Online Conversion Service

In this poster paper we introduce the RASH Online Conversion Service, i.e., a Web application that allows the conversion of ODT documents into RASH, a HTML-based markup language for writing scholarly articles, and from RASH into LaTeX according to Springer LNCS and ACM ICPS

A Framework for Active DMPs in Photon and Neutron Science Large-Scale Facilities

In this paper, a framework and a system architecture are presented to support researchers in DMP creation and execution, with a focus on the generation of FAIR data. Using the research data lifecycle within Photon and Neutron analytical facilities as a detailed exemplar of this approach in practice, it shows how combining the creation of the DMP with the project management framework PMBOK makes it easier to integrate DMP creation within the researchers’ workflow and reuse pre-existing information within the research infrastructure and related project roles. The paper identifies requirements and introduces a lifecycle for pre-existing information that helps in automatic population of the DMP. This paper also discusses a data model for the reuse of pre-existing information. It shows possible approaches to support scientists through the (semi-)automation of the creation, execution, and use of a DMP and knowledge transfer. The approach is based on work within the PaNData ODI, ExPaNDS, and PaNOSC projects

Semantic concept schema of the linear mixed model of experimental observations

In the information age, smart data modelling and data management can be carried out to address the wealth of data produced in scientific experiments. In this paper, we propose a semantic model for the statistical analysis of datasets by linear mixed models. We tie together disparate statistical concepts in an interdisciplinary context through the application of ontologies, in particular the Statistics Ontology (STATO), to produce FAIR data summaries. We hope to improve the general understanding of statistical modelling and thus contribute to a better description of the statistical conclusions from data analysis, allowing their efficient exploration and automated processing.</p

Software Citation Implementation Challenges

The main output of the FORCE11 Software Citation working group (https://www.force11.org/group/software-citation-working-group) was a paper on software citation principles (https://doi.org/10.7717/peerj-cs.86) published in September 2016. This paper laid out a set of six high-level principles for software citation (importance, credit and attribution, unique identification, persistence, accessibility, and specificity) and discussed how they could be used to implement software citation in the scholarly community. In a series of talks and other activities, we have promoted software citation using these increasingly accepted principles. At the time the initial paper was published, we also provided guidance and examples on how to make software citable, though we now realize there are unresolved problems with that guidance. The purpose of this document is to provide an explanation of current issues impacting scholarly attribution of research software, organize updated implementation guidance, and identify where best practices and solutions are still needed

Community standards for open cell migration data

Cell migration research has become a high-content field. However, the quantitative information encapsulated in these complex and high-dimensional datasets is not fully exploited owing to the diversity of experimental protocols and non-standardized output formats. In addition, typically the datasets are not open for reuse. Making the data open and Findable, Accessible, Interoperable, and Reusable (FAIR) will enable meta-analysis, data integration, and data mining. Standardized data formats and controlled vocabularies are essential for building a suitable infrastructure for that purpose but are not available in the cell migration domain. We here present standardization efforts by the Cell Migration Standardisation Organisation (CMSO), an open community-driven organization to facilitate the development of standards for cell migration data. This work will foster the development of improved algorithms and tools and enable secondary analysis of public datasets, ultimately unlocking new knowledge of the complex biological process of cell migration