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FAIRsharing Application: Schema

Milo Thurston, Allyson Lister, Ramon Granell, Dominique Batista, Peter McQuilton, Philippe Rocca-Serra, Susanna-Assunta Sansone
2022 Zenodo  
This document describes the form in which data are stored in the FAIRsharing application. It will give insight into the data which can be obtained via FAIRsharing's REST API. Howver, the document explains the internal data model rather than how to make requests for data and in what format the answers will be returned; this will be documented separately.
doi:10.5281/zenodo.6875036 fatcat:ipi7occ3sbgjtdjxjkvlpctd64

Inside FlyBase: Biocuration as a career

Susan St. Pierre, Peter McQuilton
2009 Fly  
As research in the biological sciences continues to advance at a rapid pace, it is increasingly important that the data be captured, standardized, organized and made accessible to the scientific community. This is the job of a biocurator. Here we describe the process of biocuration from our perspective as FlyBase curators.
doi:10.4161/fly.3.1.7769 pmid:19182544 pmcid:PMC2837272 fatcat:qxixus4knvf6xeazth2zm2kyba

Biocuration - mapping resources and needs

Alexandra Holinski, Melissa L. Burke, Sarah L. Morgan, Peter McQuilton, Patricia M. Palagi
2020 F1000Research  
Biocuration involves a variety of teams and individuals across the globe. However, they may not self-identify as biocurators, as they may be unaware of biocuration as a career path or because biocuration is only part of their role. The lack of a clear, up-to-date profile of biocuration creates challenges for organisations like ELIXIR, the ISB and GOBLET to systematically support biocurators and for biocurators themselves to develop their own careers. Therefore, the ELIXIR Training Platform
more » ... hed an Implementation Study in order to i) identify communities of biocurators, ii) map the type of curation work being done, iii) assess biocuration training, and iv) draw a picture of biocuration career development. Methods: To achieve the goals of the study, we carried out a global survey on the nature of biocuration work, the tools and resources that are used, training that has been received and additional training needs. To examine these topics in more detail we ran workshop-based discussions at ISB Biocuration Conference 2019 and the ELIXIR All Hands Meeting 2019. We also had guided conversations with selected people from the EMBL-European Bioinformatics Institute. Results: The study illustrates that biocurators have diverse job titles, are highly skilled, perform a variety of activities and use a wide range of tools and resources. The study emphasises the need for training in programming and coding skills, but also highlights the difficulties curators face in terms of career development and community building. Conclusion: Biocurators themselves, as well as organisations like ELIXIR, GOBLET and ISB must work together towards structural change to overcome these difficulties. In this article we discuss recommendations to ensure that biocuration as a role is visible and valued, thereby helping biocurators to proceed with their career.
doi:10.12688/f1000research.25413.1 pmid:33145007 pmcid:PMC7590901 fatcat:yqs3tufjnndktpnfvl6jzriwoq

Biocuration - mapping resources and needs

Alexandra Holinski, Melissa L. Burke, Sarah L. Morgan, Peter McQuilton, Patricia M. Palagi
2020 F1000Research  
Biocuration involves a variety of teams and individuals across the globe. However, they may not self-identify as biocurators, as they may be unaware of biocuration as a career path or because biocuration is only part of their role. The lack of a clear, up-to-date profile of biocuration creates challenges for organisations like ELIXIR, the ISB and GOBLET to systematically support biocurators and for biocurators themselves to develop their own careers. Therefore, the ELIXIR Training Platform
more » ... hed an Implementation Study in order to i) identify communities of biocurators, ii) map the type of curation work being done, iii) assess biocuration training, and iv) draw a picture of biocuration career development. Methods: To achieve the goals of the study, we carried out a global survey on the nature of biocuration work, the tools and resources that are used, training that has been received and additional training needs. To examine these topics in more detail we ran workshop-based discussions at ISB Biocuration Conference 2019 and the ELIXIR All Hands Meeting 2019. We also had guided conversations with selected people from the EMBL-European Bioinformatics Institute. Results: The study illustrates that biocurators have diverse job titles, are highly skilled, perform a variety of activities and use a wide range of tools and resources. The study emphasises the need for training in programming and coding skills, but also highlights the difficulties curators face in terms of career development and community building. Conclusion: Biocurators themselves, as well as organisations like ELIXIR, GOBLET and ISB must work together towards structural change to overcome these difficulties. In this article we discuss recommendations to ensure that biocuration as a role is visible and valued, thereby helping biocurators to proceed with their career.
doi:10.12688/f1000research.25413.2 fatcat:vfjhwc7u6jejffqug4lfhf6ko4

EOSC-Life FAIR Requirements Document

Isabelle Perseil, Susanna-Assunta Sansone, Peter McQuilton, Michel Dumontier, Marco Roos, Luiz Bonino, Rudolf Wittner, Petr Holub, Jörg Geiger
2020 Zenodo  
This deliverable is the blueprint of the requirements needed to make European life science research data and infrastructures Findable, Accessible, Interoperable and Reusable according to the FAIR Principles. This first deliverable (i) focuses on database resources such as data repositories and knowledge bases, as well as (meta)data standards and data policies. In particular, how the FAIRsharing service helps and (ii) lays the groundwork for making datasets FAIR. The FAIRification efforts will
more » ... based on the diversity of the proposed datasets of the project, in order to set up a FAIRification methodology suitable for any type of data in life sciences. This work will be tackled by subsequent deliverables via guidance from the FAIRassist tool.
doi:10.5281/zenodo.3693882 fatcat:3jlskapcijbfvmpb3i3vyeqc2m

FlyBase 102—advanced approaches to interrogating FlyBase

Susan E. St. Pierre, Laura Ponting, Raymund Stefancsik, Peter McQuilton
2013 Nucleic Acids Research  
FlyBase (http://flybase.org) is the leading website and database of Drosophila genes and genomes. Whether you are using the fruit fly Drosophila melanogaster as an experimental system or wish to understand Drosophila biological knowledge in relation to human disease or to other model systems, FlyBase can help you successfully find the information you are looking for. Here, we demonstrate some of our more advanced searching systems and highlight some of our new tools for searching the wealth of
more » ... ata on FlyBase. The first section explores gene function in FlyBase, using our TermLink tool to search with Controlled Vocabulary terms and our new RNA-Seq Search tool to search gene expression. The second section of this article describes a few ways to search genomic data in FlyBase, using our BLAST server and the new implementation of GBrowse 2, as well as our new FeatureMapper tool. Finally, we move on to discuss our most powerful search tool, QueryBuilder, before describing pre-computed cuts of the data and how to query the database programmatically.
doi:10.1093/nar/gkt1092 pmid:24234449 pmcid:PMC3964969 fatcat:mwzvr4w5ajhn7phzqly6iwjari

Natural Language Processing in aid of FlyBase curators

Nikiforos Karamanis, Ruth Seal, Ian Lewin, Peter McQuilton, Andreas Vlachos, Caroline Gasperin, Rachel Drysdale, Ted Briscoe
2008 BMC Bioinformatics  
Despite increasing interest in applying Natural Language Processing (NLP) to biomedical text, whether this technology can facilitate tasks such as database curation remains unclear. Results: PaperBrowser is the first NLP-powered interface that was developed under a usercentered approach to improve the way in which FlyBase curators navigate an article. In this paper, we first discuss how observing curators at work informed the design and evaluation of PaperBrowser. Then, we present how we
more » ... e PaperBrowser's navigational functionalities in a user-based study using a text highlighting task and evaluation criteria of Human-Computer Interaction. Our results show that PaperBrowser reduces the amount of interactions between two highlighting events and therefore improves navigational efficiency by about 58% compared to the navigational mechanism that was previously available to the curators. Moreover, PaperBrowser is shown to provide curators with enhanced navigational utility by over 74% irrespective of the different ways in which they highlight text in the article. Conclusion: We show that state-of-the-art performance in certain NLP tasks such as Named Entity Recognition and Anaphora Resolution can be combined with the navigational functionalities of PaperBrowser to support curation quite successfully.
doi:10.1186/1471-2105-9-193 pmid:18410678 pmcid:PMC2375127 fatcat:mkbkdp2ld5ge7ia4s4274odta4

BioSharing: Harnessing Metadata Standards For The Data Commons [article]

Susanna-Assunta Sansone, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Peter McQuilton, Massimiliano Izzo, Allyson Lister, Milo Thurston
2017 bioRxiv   pre-print
The use of community-driven metadata standards, such as minimal information guidelines, terminologies, formats/models, is essential to ensure that data and other digital research outputs are Findable, Accessible, Interoperable, and Reusable, according to the FAIR principles. As with other types of digital assets, metadata standards also need be FAIR. Their discoverability and accessibility is ensured by BioSharing, the most comprehensive resource of metadata standards, interlinked to data
more » ... tories and policies, available in the life, environmental and biomedical sciences. With its growing content, endorsements, and collaborative network, BioSharing is part of a larger ecosystem of interoperable resources. Here we describe some of the activities under the USA National Institutes of Health (NIH)'s Big Data to Knowledge (BD2K) Initiative, illustrating how we track the evolution and use of metadata standards and work to connect them to indexes and annotation tools.
doi:10.1101/144147 fatcat:jhnsh6gknra5rmo7zcr6cgedta

Hagan, J., McQuilton, J., and Carter, H. (1997). Dispossessed, Diggers and Democrats: Australia 1788 1880s. Wollongong: Department of History and Politics and Centre for Educational Development and Interactive Resources, University of Wollongong

Peter Reynolds, Mark Brogan
1998 Australian Journal of Teacher Education  
., McQuilton, J., and Carter, H. (1997) . information systems, the medium is increasingly the message, and developers must make full use of the tools available to them or the message will be lost.  ... 
doi:10.14221/ajte.1998v23n2.6 fatcat:d32qwy4blrgvzawosonxrme3we

The Drosophila phenotype ontology

David Osumi-Sutherland, Steven J Marygold, Gillian H Millburn, Peter A McQuilton, Laura Ponting, Raymund Stefancsik, Kathleen Falls, Nicholas H Brown, Georgios V Gkoutos
2013 Journal of Biomedical Semantics  
Phenotype ontologies are queryable classifications of phenotypes. They provide a widely-used means for annotating phenotypes in a form that is human-readable, programatically accessible and that can be used to group annotations in biologically meaningful ways. Accurate manual annotation requires clear textual definitions for terms. Accurate grouping and fruitful programatic usage require high-quality formal definitions that can be used to automate classification. The Drosophila phenotype
more » ... y (DPO) has been used to annotate over 159,000 phenotypes in FlyBase to date, but until recently lacked textual or formal definitions. We have composed textual definitions for all DPO terms and formal definitions for 77% of them. Formal definitions reference terms from a range of widely-used ontologies including the Phenotype and Trait Ontology (PATO), the Gene Ontology (GO) and the Cell Ontology (CL). We also describe a generally applicable system, devised for the DPO, for recording and reasoning about the timing of death in populations. As a result of the new formalisations, 85% of classifications in the DPO are now inferred rather than asserted, with much of this classification leveraging the structure of the GO. This work has significantly improved the accuracy and completeness of classification and made further development of the DPO more sustainable. The DPO provides a set of well-defined terms for annotating Drosophila phenotypes and for grouping and querying the resulting annotation sets in biologically meaningful ways. Such queries have already resulted in successful function predictions from phenotype annotation. Moreover, such formalisations make extended queries possible, including cross-species queries via the external ontologies used in formal definitions. The DPO is openly available under an open source license in both OBO and OWL formats. There is good potential for it to be used more broadly by the Drosophila community, which may ultimately result in its extension to cover a broader range of phenotypes.
doi:10.1186/2041-1480-4-30 pmid:24138933 pmcid:PMC3816596 fatcat:tu5xlh2svfh7voqrmxuk7cs3km

Evaluating FAIR-Compliance Through an Objective, Automated, Community-Governed Framework [article]

Mark D Wilkinson, Michel Dumontier, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Mario Prieto, Julian Gautier, Peter McQuilton, Derek Murphy, Merce Crosas, Erik Schultes
2018 bioRxiv   pre-print
With the increased adoption of the FAIR Principles, a wide range of stakeholders, from scientists to publishers, funding agencies and policy makers, are seeking ways to transparently evaluate resource FAIRness. We describe the FAIR Evaluator, a software infrastructure to register and execute tests of compliance with the recently published FAIR Metrics. The Evaluator enables digital resources to be assessed objectively and transparently. We illustrate its application to three widely used
more » ... st repositories - Dataverse, Dryad, and Zenodo - and report their feedback. Evaluations allow communities to select relevant Metric subsets to deliver FAIRness measurements in diverse and specialized applications. Evaluations are executed in a semi-automated manner through Web Forms filled-in by a user, or through a JSON-based API. A comparison of manual vs automated evaluation reveals that automated evaluations are generally stricter, resulting in lower, though more accurate, FAIRness scores. Finally, we highlight the need for enhanced infrastructure such as standards registries, like FAIRsharing, as well as additional community involvement in domain-specific data infrastructure creation.
doi:10.1101/418376 fatcat:km4gamvoizaldl6dcp3lxpar7y

Evaluating FAIR Maturity Through a Scalable, Automated, Community-Governed Framework [article]

Mark D Wilkinson, Michel Dumontier, Susanna-Assunta Sansone, Luiz Olavo Bonino da Silva Santos, Mario Prieto Godoy, Dominique Batista, Peter McQuilton, Tobias Kuhn, Philippe Rocca-Serra, Mercè Crosas, Erik Schultes
2019 bioRxiv   pre-print
Transparent evaluations of FAIRness are increasingly required by a wide range of stakeholders, from scientists to publishers, funding agencies and policy makers. We propose a scalable, automatable framework to evaluate digital resources that encompasses measurable indicators, open source tools, and participation guidelines, which come together to accommodate domain relevant community-defined FAIR assessments. The components of the framework are: (1) Maturity Indicators - community-authored
more » ... fications that delimit a specific automatically-measurable FAIR behavior; (2) Compliance Tests - small Web apps that test digital resources against individual Maturity Indicators; and (3) the Evaluator, a Web application that registers, assembles, and applies community-relevant sets of Compliance Tests against a digital resource, and provides a detailed report about what a machine "sees" when it visits that resource. We discuss the technical and social considerations of FAIR assessments, and how this translates to our community-driven infrastructure. We then illustrate how the output of the Evaluator tool can serve as a roadmap to assist data stewards to incrementally and realistically improve the FAIRness of their resources.
doi:10.1101/649202 fatcat:y25vyuyu5zfddc6v7zn5p4anuq

Repository features: response to the COAR, OpenAIRE, LIBSENSE [article]

Cannon Matthew, Chris Graf, Catriona MacCallum, Jonathan Threlfall, Imogen Cranston, Sarah Callaghan, Ilaria Carnevale, Varsha Khodiyar, Scott Edmunds, Thomas Lemberger, Wei Mun Chan, Kiera McNeice (+4 others)
2021 Zenodo  
McQuilton & Susanna-A Sansone FAIRsharing  ...  Elsevier Varsha Khodiyar Springer Nature Scott Edmunds GigaScience Press Thomas Lemberger EMBO Press Wei Mun Chan eLife Kiera McNeice CUP Iain Hrynaszkiewicz PLOS Adam Leary OUP Peter  ... 
doi:10.5281/zenodo.4458081 fatcat:riwejcu2a5hnvprvf3gx47cdky

FAIRsharing: working with and for the community to describe and link data standards, repositories and policies [article]

Susanna-Assunta Sansone, Peter McQuilton, Philippe Rocca-Serra, Alejandra Gonzalez-Beltran, Massimiliano Izzo, Allyson Lister, Milo Thurston
2018 bioRxiv   pre-print
Community-developed standards, such as those for the identification and reporting of data, underpin reproducible and reusable research. The number of community-driven efforts has been on the rise since the early 2000s, their uptake, however, is slow and uneven. Analyzing 70 journals and publishers data policies, we find that these recommend databases and repositories 37 times more often than standards. When a reporting standard is recommended by a publisher, it is more likely to be a minimal
more » ... orting guideline than a model, format or ontology even if the latter are the machine-readable standards that underpin the utility of databases and repositories. Here, we evaluate the standards landscape, focusing on those for reporting data and metadata, and their implementation by databases and repositories; we also propose key performance indicators, and highlight the importance of developing open linked data models that instantiate these community standards. Lastly, we launch a call to action highlighting the role producers and consumers of standards and repositories must play to maximize the visibility and adoption of these resources.
doi:10.1101/245183 fatcat:xehrcdz4z5aibevocklspqufwy

Drosophila Neurotrophins Reveal a Common Mechanism for Nervous System Formation

Bangfu Zhu, Jenny A Pennack, Peter McQuilton, Manuel G Forero, Kenji Mizuguchi, Ben Sutcliffe, Chun-Jing Gu, Janine C Fenton, Alicia Hidalgo, Michael Bate
2008 PLoS Biology  
doi:10.1371/journal.pbio.0060284 pmid:19018662 pmcid:PMC2586362 fatcat:c5h6zb43wjg4pm2e2lmjmmekay
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