MACE – An Open Access Data Repository of Mass Spectra for Chemical Ecology | SpringerLink

Abstract:  MACE is an open access collection of electron impact (EI) mass spectra for coupled gas chromatography-mass spectrometry (GC/MS) that serves as an add-on database, comprising curated spectra not present in widely available commercial mass spectral libraries, such as the NIST or WILEY databases. The spectra are stored as text files that allow easy integration into individual GC/MS systems. The article describes the concept of MACE, the data structure, how to contribute, and its usage. MACE is designed as a community effort and will require contributions from the community to be successful.

Depositing Data: A Usability Study of the Texas Data Repository

Abstract:  Objective: The purpose of this study is to examine the usability of the Texas Data Repository (TDR) for the data depositors who are unfamiliar with its interface and use the results to improve user experience.

Methods: This mixed-method research study collected qualitative and quantitative data through a pre-survey, a task-oriented usability test with a think-aloud protocol, and an exit questionnaire. Analysis of the quantitative (i.e., descriptive statistics) and qualitative data (e.g., content analysis of the thinking-aloud protocols) were employed to examine the TDR’s usability for first-time data depositors at Texas A&M University.

Results: While the study revealed that the users were generally satisfied with their experience, the data suggest that a majority of the participants had difficulty understanding the difference between a dataverse collection and dataset, and often found adding or editing metadata overwhelming. The platform’s tiered model for metadata description is core to its function, but many participants did not have an accurate mental model of the platform, which left them scrolling up and down the page or jumping back and forth between different tabs and pages to perform a single task. Based on the results, the authors made some recommendations.

Conclusions: While this paper relies heavily on the context of the Harvard Dataverse repository platform, the authors posit that any self-deposit model, regardless of platform, could benefit from these recommendations. We noticed that completing various metadata fields in the TDR required participants to pivot their mindset from a data creator to that of a data curator. Moreover, the methods used to investigate the usability of the repository can be used to develop additional studies in a variety of repository and service model contexts. 

COAR Welcomes Significant Funding for the Notify Project

We are delighted to announce that COAR has been awarded a US$4 million grant from Arcadia, a charitable fund of Lisbet Rausing and Peter Baldwin. The 4 year grant will go towards the COAR Notify Project, which is developing and implementing a standard protocol for connecting the content in the distributed repository network with peer reviews and assessments in external services, using linked data notifications.

Why did clinical trial registries fail to prevent Covid research chaos?

“There is a long-standing global ethical obligation to register all trials before they start, shored up by regulatory requirements in some jurisdictions. Data from 18 registries worldwide feed into the WHO-managed International Clinical Trials Registry Platform (ICTRP), providing a continuously updated overview of who is researching what, when, where and how – at least in theory.

 

 

If the registry infrastructure had worked and been used as intended, much of the COVID-19 research chaos would have been avoided.

 

 

For example, researchers considering launching a hydroxychloroquine trial could have searched ICTRP and discovered that the drug was already being investigated by numerous other trials. Those researchers could accordingly have focused on investigating other treatment options instead, or aligned their outcome measures with existing trials. …

The global registry infrastructure has long been inadequately supported by legislators and regulators, and is woefully underfunded.

 

 

 

This persistent neglect of the world’s only comprehensive directory of medical research led to costly research waste on an incredible scale during the pandemic.

 

 

The WHO recommends that member states should by law require every interventional trial to be registered and reported. In addition, WHO recommends that all trial results should be made public specifically on a registry within 12 months, and that registry data should be kept up to date.

 

 

 

By enforcing these three simple rules, regulators would ensure that there is a comprehensive, up-to-date global database of all trials and their results.

 

In reality, existing laws in the EU and the US only cover a small minority of trials and are not being effectively enforced, while many other jurisdictions have no relevant laws at all. …”

 

 

Arcadia Fund supports Plazi in its endeavor to rediscover known biodiversity | 16/05/2022

“The Swiss-based Plazi NGO has received a grant of EUR 1.5 million from Arcadia Fund– a charitable fund of Lisbet Rausing and Peter Baldwin – to further develop its Biodiversity Literature Repository(BLR) established in collaboration with Zenodo, the open science repository hosted and managed by the European Organization for Nuclear Research (CERN), and the open-access scholarly publisher and technology provider Pensoft. The Arcadia-supported project helps rediscover known biodiversity by liberating taxonomic treatments, material citations and images trapped in scholarly biodiversity publications, and making them FAIR and open. The project engages the community in the huge and decisive challenge to understand and preserve the biodiversity of our planet. Our knowledge about biodiversity is largely imprisoned in a corpus of more than 500 million pages of scientific research publications that is growing daily. Many of these publications are only available in print, and others are PDFs behind a paywall. These data are not FAIR; they are not findable, accessible, interoperable, or reusable. They cannot be linked to new digital resources such as gene sequences, citizen science observations, taxonomic names, or specimens of digitized natural history collections. Extracting and using text and data from such PDFs comes at very high cost, if possible at all. Through itsTreatmentBank production service, Plazi is a leader in providing access to biodiversity data liberated from publications. Thanks to the Arcadia Fund support and in collaboration with Pensoft, Zenodo and the Swiss Institute for Bioinformatics Literature Services (SIBiLS), Plazi provides access to over 750,000 taxonomic treatments, 450,000 figures and over 1.1 million material citations from over 53,000 publications in the BLR….”

Recommendations for repositories and scientific gateways from a neuroscience perspective | Scientific Data

“Digital services such as repositories and science gateways have become key resources for the neuroscience community, but users often have a hard time orienting themselves in the service landscape to find the best fit for their particular needs. INCF has developed a set of recommendations and associated criteria for choosing or setting up and running a repository or scientific gateway, intended for the neuroscience community, with a FAIR neuroscience perspective….”

Supporting knowledge creation and sharing by building a standardised interconnected repository of biodiversity data | Zenodo

“This EOSC in practice story was developed within the Cos4cloud project and targets a very wide user base as it is addressed to any researchers, teachers, students, companies, institutions and, more generally, anyone interested in knowing, studying or analysing biodiversity information.

The story presents Cos4Bio, a co-designed, interoperable and open-source service that integrates biodiversity observations from multiple citizen observatories in one place, allowing experts to save time in the species identification process and get access to an enormous number of biodiversity observations. This resource is available on the EOSC Portal Catalogue and Marketplace …”

Supporting knowledge creation and sharing by building a standardised interconnected repository of biodiversity data | EOSC Portal

“This EOSC in practice story targets a very wide user base as it is addressed to any researchers, teachers, students, companies, institutions and, more generally, anyone interested in knowing, studying or analysing biodiversity information. It was developed within the Cos4cloud project….

Cos4Bio is a co-designed, interoperable and open-source service that integrates biodiversity observations from multiple citizen observatories in one place, allowing experts to save time in the species identification process and get access to an enormous number of biodiversity observations….”

SciELO Preprints server completes two years of operation, contributing to the advancement of Open Science | SciELO in Perspective

The positioning of the SciELO Program as an open science program, provided for the creation of a preprints’ server, announced in 2017. In September 2018, during the SciELO 20 Years Week, the partnership between SciELO and the Public Knowledge Project (PKP) was launched with the objective of developing an open source preprints server based on the already consolidated Open Journal Systems (OJS).

Professor Ramin Zabih named arXiv faculty director | arXiv.org blog

“arXiv, the world’s leading open access research sharing platform, is pleased to welcome Professor Ramin Zabih as faculty director.

Zabih is a computer science professor at Cornell Tech and president and founder of the Computer Vision Foundation (CVF). His research focuses on computer vision and its applications, especially in medical imaging. He trained at the Massachusetts Institute of Technology and Stanford University, and he has authored or coauthored more than 265 papers that have been cited more than 32,000 times….”

Recommendations for Discipline-Specific FAIRness Evaluation Derived from Applying an Ensemble of Evaluation Tools

Abstract:  From a research data repositories’ perspective, offering research data management services in line with the FAIR principles is becoming increasingly important. However, there exists no globally established and trusted approach to evaluate FAIRness to date. Here, we apply five different available FAIRness evaluation approaches to selected data archived in the World Data Center for Climate (WDCC). Two approaches are purely automatic, two approaches are purely manual and one approach applies a hybrid method (manual and automatic combined).

The results of our evaluation show an overall mean FAIR score of WDCC-archived (meta)data of 0.67 of 1, with a range of 0.5 to 0.88. Manual approaches show higher scores than automated ones and the hybrid approach shows the highest score. Computed statistics indicate that the test approaches show an overall good agreement at the data collection level.

We find that while neither one of the five valuation approaches is fully fit-for-purpose to evaluate (discipline-specific) FAIRness, all have their individual strengths. Specifically, manual approaches capture contextual aspects of FAIRness relevant for reuse, whereas automated approaches focus on the strictly standardised aspects of machine actionability. Correspondingly, the hybrid method combines the advantages and eliminates the deficiencies of manual and automatic evaluation approaches.

Based on our results, we recommend future FAIRness evaluation tools to be based on a mature hybrid approach. Especially the design and adoption of the discipline-specific aspects of FAIRness will have to be conducted in concerted community efforts.

Scholarly Communication Assessment Forum | April 2022 | Sacramento State University, US

Summary: “In 2019, Sacramento State University and San Jose State University were awarded an IMLS National Forum grant to assess scholarly communication programs at M1 Carnegie classified public institutions. With new technologies and paradigms for creating and sharing work, scholars across all fields have seen changes in research output, dissemination and preservation of the scholarly record, emergent publishing models, and the measurement of scholarly impact. Libraries have broadly defined their efforts to address these concerns as “scholarly communication” services. During the past two decades, academic libraries have begun to further invest in scholarly communication through the allocation of staffing and resources and even establishing institutional repositories. However, quantifying the actual outcome or impact of these scholarly communication activities remains elusive, beyond output measures such as simple counts of consultations, workshop attendance, or by repository downloads or growth. This grant, the “Scholarly Communication Assessment Forum,” or “SCAF”, investigated best practices and made recommendations for better tracking academic libraries’ engagement in supporting the research lifecycle.”

The University of Alabama at Birmingham Portal | Institutional Repository Outreach Librarian- UAB Libraries

“The University of Alabama at Birmingham (UAB) Libraries seek an innovative and creative Institutional Repository Outreach Librarian to grow and maintain the libraries’ new Digital Commons repository, an open access digital repository platform for publishing and preserving the scholarly research and creative achievements of the UAB community. The primary responsibilities for the position include developing and managing the UAB Digital Commons institutional repository in collaboration with faculty and staff from Technology and Technical Services, liaising with reference librarians and UAB faculty and staff regarding content deposit, and performing outreach to expand institutional repository services and awareness. The successful candidate will lead the UAB Libraries in promoting UAB Digital Commons throughout the campus.

This position falls within the UAB Libraries’ Office of Scholarly Communication (OSC) and will report to the Associate Dean for Research and Scholarly Communication. This person will work collaboratively with other library departments to promote the use and awareness of the institutional repository. This is a 12-month non-tenure track faculty position at the initial rank of Assistant or Associate Professor….”