Biotea: semantics for Pubmed Central

Authors : Alexander Garcia​, Federico Lopez, Leyla Garcia, Olga Giraldo, Victor Bucheli, Michel Dumontier

A significant portion of biomedical literature is represented in a manner that makes it difficult for consumers to find or aggregate content through a computational query. One approach to facilitate reuse of the scientific literature is to structure this information as linked data using standardized web technologies.

In this paper we present the second version of Biotea, a semantic, linked data version of the open-access subset of PubMed Central that has been enhanced with specialized annotation pipelines that uses existing infrastructure from the National Center for Biomedical Ontology.

We expose our models, services, software and datasets. Our infrastructure enables manual and semi-automatic annotation, resulting data are represented as RDF-based linked data and can be readily queried using the SPARQL query language.

We illustrate the utility of our system with several use cases. Our datasets, methods and techniques are available at http://biotea.github.io.

URL : Biotea: semantics for Pubmed Central

DOI : https://doi.org/10.7717/peerj.4201

Completeness and overlap in open access systems: Search engines, aggregate institutional repositories and physics-related open sources

Authors : Ming-yueh Tsay, Tai-luan Wu, Ling-li Tseng

This study examines the completeness and overlap of coverage in physics of six open access scholarly communication systems, including two search engines (Google Scholar and Microsoft Academic), two aggregate institutional repositories (OAIster and OpenDOAR), and two physics-related open sources (arXiv.org and Astrophysics Data System).

The 2001–2013 Nobel Laureates in Physics served as the sample. Bibliographic records of their publications were retrieved and downloaded from each system, and a computer program was developed to perform the analytical tasks of sorting, comparison, elimination, aggregation and statistical calculations.

Quantitative analyses and cross-referencing were performed to determine the completeness and overlap of the system coverage of the six open access systems.

The results may enable scholars to select an appropriate open access system as an efficient scholarly communication channel, and academic institutions may build institutional repositories or independently create citation index systems in the future. Suggestions on indicators and tools for academic assessment are presented based on the comprehensiveness assessment of each system.

URL : Completeness and overlap in open access systems: Search engines, aggregate institutional repositories and physics-related open sources

DOI : https://doi.org/10.1371/journal.pone.0189751

Research Transparency: A Preliminary Study of Disciplinary Conceptualisation, Drivers, Tools and Support Services

Authors : Liz Lyon, Wei Jeng, Eleanor Mattern

This paper describes a preliminary study of research transparency, which draws on the findings from four focus group sessions with faculty in chemistry, law, urban and social studies, and civil and environmental engineering.

The multi-faceted nature of transparency is highlighted by the broad ways in which the faculty conceptualised the concept (data sharing, ethics, replicability) and the vocabulary they used with common core terms identified (data, methods, full disclosure).

The associated concepts of reproducibility and trust are noted. The research lifecycle stages are used as a foundation to identify the action verbs and software tools associated with transparency.

A range of transparency drivers and motivations are listed. The role of libraries and data scientists is discussed in the context of the provision of transparency services for researchers.

URL : Research Transparency: A Preliminary Study of Disciplinary Conceptualisation, Drivers, Tools and Support Services

DOI : https://doi.org/10.2218/ijdc.v12i1.530

Research Data Management Instruction for Digital Humanities

Author : Willow Dressel

eScience related library services at Princeton University started in response to the National Science Foundation’s (NSF) data management plan requirements, and grew to encompass a range of services including data management plan consultation, assistance with depositing into a disciplinary or institutional repository, and research data management instruction.

These services were initially directed at science and engineering disciplines on campus, but the eScience Librarian soon realized the relevance of research data management instruction for humanities disciplines with digital approaches.

Applicability to the digital humanities was initially recognized by discovery of related efforts from the history department’s Information Technology (IT) manager in the form of a graduate-student workshop on file and digital-asset management concepts.

Seeing the common ground these activities shared with research data management, a collaboration was formed between the history department’s IT Manager and the eScience Librarian to provide a research data management overview to the entire campus community.

The eScience Librarian was then invited to participate in the history department’s graduate student file and digital asset management workshop to provide an overview of other research data management concepts. Based on the success of the collaboration with the history department IT, the eScience Librarian offered to develop a workshop for the newly formed Center for Digital Humanities at Princeton.

To develop the workshop, background research on digital humanities curation was performed revealing similarities and differences between digital humanities curation and research data management in the sciences. These similarities and differences, workshop results, and areas of further study are discussed.

URL : Research Data Management Instruction for Digital Humanities

DOI : https://doi.org/10.7191/jeslib.2017.1115

Exploration of an Interdisciplinary Scientific Landscape

Author : Juste Raimbault

Patterns of interdisciplinarity in science can be quantified through diverse complementary dimensions. This paper studies as a case study the scientific environment of a generalist journal in Geography, Cybergeo, in order to introduce a novel methodology combining citation network analysis and semantic analysis.

We collect a large corpus of around 200,000 articles with their abstracts and the corresponding citation network that provides a first citation classification. Relevant keywords are extracted for each article through text-mining, allowing us to construct a semantic classification.

We study the qualitative patterns of relations between endogenous disciplines within each classification, and finally show the complementarity of classifications and of their associated interdisciplinarity measures. The tools we develop accordingly are open and reusable for similar large scale studies of scientific environments.

URL : https://arxiv.org/abs/1712.00805

Where Are We Now? Survey on Rates of Faculty Self-Deposit in Institutional Repositories

Author : Ruth Kitchin Tillman

INTRODUCTION

The literature of institutional repositories generally indicates that faculty do not self-deposit, but there is a gap in the research of reported self-deposit numbers that might indicate how widespread and common this is.

METHODS

This study was conducted using a survey instrument that requested information about whether a repository allowed self-deposit and what its rates of self-deposit were, if known.

The instrument contained additional questions intended to gather a broader context of repositories to be examined for any correlations with higher rates of self-deposit. It also included questions about the kinds of labor required to populate an IR as well as satisfaction with the rates of self-deposit.

RESULTS

Of 82 respondents, 80 were deemed to fall within the study’s parameters. Of these, 55 respondents’ institutions allowed self-deposit, and 10 reported rates of self-deposit of more than 20 items per month.

More than half the total respondents reported using at least three methods other than relying on self-deposit to add content to their repository. Respondents are generally unsatisfied with their deposit profiles, including one at a school reporting the highest rate of self-deposit.

DISCUSSION

From the responses, no profile could be formed of respondents reporting high rates of self-deposit that did not entirely overlap with many others reporting little or no self-deposit. However, the survey identifies factors without which high rates are unlikely.

CONCLUSION

The results of this survey may be most useful as a factor in administrative prioritizations and expectations regarding institutional repositories as sites of scholarly self-deposit.

URL : Where Are We Now? Survey on Rates of Faculty Self-Deposit in Institutional Repositories

DOI : http://doi.org/10.7710/2162-3309.2203

 

Données de la recherche en SHS. Pratiques, représentations et attentes des chercheurs : une enquête à l’Université Rennes 2

Auteurs/Authors : Alexandre Serres, Marie-Laure Malingre, Morgane Mignon, Cécile Pierre, Didier Collet

Quels sont les types de données de recherche collectées, traitées et produites dans une université de lettres et sciences humaines et sociales ? Quelles sont les pratiques des chercheurs en SHS en matière de stockage, d’archivage, de diffusion, de partage de leurs données de recherche ?

Quelles sont leurs représentations et leurs définitions des données de recherche, leur position par rapport au libre accès ? Quels sont leurs besoins prioritaires en matière de gestion ou de partage des données de recherche ?

Comment perçoivent-ils le bon niveau d’une politique des données ? C’est pour répondre à toutes ces questions qu’une double enquête, statistique et qualitative, a été menée à l’Université Rennes 2 au printemps 2017, enquête portée par l’URFIST (Unité Régionale de Formation à l’Information Scientifique et Technique) de Rennes, la Maison des Sciences de l’Homme en Bretagne et le Service Commun de Documentation Rennes 2, avec le soutien des instances de l’université.

Le rapport et ses annexes en présentent ici tous les résultats, avec un certain nombre de propositions pour une politique des données de recherche.

URL : Données de la recherche en SHS. Pratiques, représentations et attentes des chercheurs : une enquête à l’Université Rennes 2

Alternative location : https://hal.archives-ouvertes.fr/hal-01635186