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Building Expertise on FAIR Through Evolving Bring Your Own Data(BYOD) Workshops: Describing the Data, Software, and Management-focused Approaches and Their Evolution

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Data Intelligence 2024年第2期6卷 429-456页

作者： César H.Bernabé lieze Thielemans Rajaram Kaliyaperumal Claudio Carta Shuxin Zhang Celia W.G.van Gelder Nirupama Benis luiz Olavo Bonino da Silva Santos Ronald Cornet Bruna dos Santos Vieira Nawel lalout Ines Henriques Alberto Camara Ballesteros Kees Burger Martijn G.Kersloot Friederike Ehrhart Esther van Enckevort Chris T.Evelo Alasdair J.G.Gray Marc Hanauer Kristina Hettne Joep de ligt Arnaldo Pereira Nuria Queralt-Rosinach Erik Schultes Domenica Taruscio Andra Waagmeester Mark D.wilkinson egon l.wi.li.hagen Mascha Jansen Barend Mons Marco Roos Annika Jacobsen Biosemantics Group Department of Human GeneticsLeiden University Medical CentreLeidenThe Netherlands NIHR Academic Fellow in General Practice University College London and The Royal Free NHS Foundation Trust National Centre for Rare Diseases Istituto Superiore di SanitaRomeItaly Department of Medical Informatics Amsterdam UMC location University of AmsterdamMeibergdreef 9AmsterdamThe Netherlands Amsterdam Public Health Methodology&Digital HealthAmsterdamThe Netherlands Health-Rl UtrechtThe Netherlands Semantics Services and Cybersecurity groupUniversity of TwenteEnschedeThe Netherlands Department of Medical Imaging Radboud Institute for Health SciencesRadboud University Medical CenterNijmegenThe Netherlands Department of Medical BioSciences Radboud University Medical CenterNijmegenThe Netherlands The Duchenne Parent Project VeneendaalThe Netherlands Departamento de Biotecnologia-Biologia Vegetal Escuela Tecnica Superior de Ingenieria AgronomicaAlimentaria y de BiosistemasCentro de Biotecnologia y Genomica de PlantasUniversidad Politecnica de Madrid(UPM)-Instituto Nacional de Investigacion y Tecnologia Agraria y Alimentaria-CSIC(INIA-CSIC).Campus MontegancedoPozuelo de Alarcon(Madrid)Spain Castor AmsterdamThe Netherlands Department of Bioinformatics-BiGCaT Maastricht UniversityMaastrichtThe Netherlands University Medical Center Groningen University of GroningenGroningenThe Netherlands Maastricht Centre for Systems Biology(MaCSBio) Maastricht UniversityMaastrichtThe Netherlands Department of Computer Science Heriot-Watt UniversityEdinburghUK INSERM US14-OrphanetPlateforme Maladies RaresParisFrance Centre for Digital Scholarship Leiden University LibrariesThe Netherlands Center for Molecular Medicine Cancer Genomics NetherlandsDepartment of GeneticsUniversity Medical Center UtrechtUniversity UtrechtThe Netherlands University of Aveiro DETI/IEETAAveiroPortugal GO FAIR Foundation LeidenThe Netherlands The leiden Academic Center for Drug Research LeidenThe Netherlands Micel

Since 2014,"Bring Your Own Data"workshops(BYODs)have been organised to inform people about the process and benefits of making resources Findable,Accessible,Interoperable,and Reusable(FAIR,and the FAIRification process).The BYOD workshops'content and format differ depending on their goal,context,and the background and needs of ***-focused BYODs educate domain experts on how to make their data FAIR to find new answers to research ***-focused BYODs promote the benefits of making data FAIR and instruct project managers and policy-makers on the characteristics of FAIRification ***-focused BYODs gather software developers and experts on FAIR to implement or improve software resources that are used to support ***,these BYODs intend to foster collaboration between different types of stakeholders involved in data management,curation,and reuse(*** experts,trainers,developers,data owners,data analysts,FAIR experts).The BYODs also serve as an opportunity to learn what kind of support for FAIRification is needed from different communities and to develop teaching materials based on practical examples and *** this paper,we detail the three different structures of the BYODs and describe examples of early BYODs related to plant breeding data,and rare disease registries and biobanks,which have shaped the structure of the *** discuss the latest insights into making BYODs more productive by leveraging our almost ten years of training experience in these workshops,including successes and encountered ***,we examine how the participants'feedback has motivated the research on FAIR,including the development of workflows and software.

关键词： FAIR FAIRification FAIR expertise Bring Your Own Data Workshop BYOD

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Taking FAIR on the ChIN:The Chemistry Implementation Network

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Data Intelligence 2020年第1期2卷 131-138,310页

作者： Simon J.Coles Jeremy G.Frey egon l.wi.li.hagen Stuart J.Chalk School of Chemistry Faculty of Engineering and Physical SciencesUniversity of SouthamptonSouthampton SO171BJUK Department of Bioinformatics Maastricht UniversityMaastrichtLimburg 6200 MDThe Netherlands Department of Chemistry University of North FloridaJacksonvilleFL 32224-7699USA

The Chemistry Implementation Network(ChIN)is focused on supporting the FAIR Data needs of the research community regarding chemical related *** Implementation Network is a consortium drawn from a community,in this case the chemistry discipline,committed to defining and constructing standards,materials and software in the spirit of the FAIR data principles and under the structure of the GO FAIR ***,as a core science the ChIN has to reach beyond the chemistry community and support the use of chemical information in other *** will be facilitated through connections in the GO FAIR ecosystem of Implementation *** of the FAIR chemical concepts that need to be supported include molecular and materials structures,chemical reactions,nomenclature and other chemical terminology and *** ChIN aims to drive forward the application of the FAIR Data Principles relating to the full range of chemistry concepts that are key to the transparent and efficient communication of chemical *** the goal of FAIR chemistry data will require a culture change across the *** this is best addressed once a critical mass of tools and approaches has been developed.

关键词： Chemistry Chemical information Chemistry data Chemical data standards Infrastructure Nomenclature Molecular structure Materials structure Chemical reactions Education Community engagement Endorsement and governance

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Phylogeny and species delimitation of Flammulina: Taxonomic status of winter Mushroom in East Asia and new species uncovered from Europe by an integrated approach

Phylogeny and species delimitation of Flammulina: Taxonomic ...

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中国菌物学会第七届全国会员代表大会暨2017年学术年会

作者： Pan Meng Wang Xiao Bin liu Yu Cheng Dai egon Horak Kari Steffen Zhu l.Yang Key laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences University of Chinese Academy of Sciences Institute of Microbiology Beijing Forestry University

The winter Mushroom or Enokitake is economically important and widely cultivated in commercial large-scale in East Asia. However, the phylogeny and species delimitation of the winter mushroom genus Flammulina have not been fully elucidated previously. In this study, 81 collections of Flammulina from East Asia, Europe and North America were studied, and their phylogeny and species delimitation were inferred from partial sequences of the internal transcribed spacer regions（ITS）,translation elongation factor 1-α（tef1-α）, the second largest subunit of RNA polymerase II（rpb2） and partial sequence（labled as HD1-A） of homeodomain1（HD1） of mating gene in sublocus ***, genetic structure analyses based on genomic SSR markers and haplotype network analyses based on HD1-A were also employed in delimitation of the closely related taxa. 12 phylogenetic species were recognized, which was largely in consistence with previous ***, our integrated studies indicated that Enokitake is not identical with the true European winter Mushroom F. velutipes, and, thus, should be treated as a separated species, namely F. filiformis. All cultivated strains of "F. velutipes" in East Asia, including the strains labeled as F. velutipes from Korea and Japan with genome sequence, are in fact F. filiformis. In addition, a new species, F. finlandica, was unanticipatively discovered in Northern Europe. Eventually, morphological descriptions, color photos of fresh basidiomata, line-drawings of microscopic features of the two species were presented.

关键词： Agaricales Physalacriaceae Flammulina DNA Barcoding Edible mushroom Genetic structure Mating type gene

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Water Quality and the Impact by Contaminants of Emerging Concern: The Case of Verde River in Campos Gerais

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Journal of Water Resource and Protection 2022年第11期14卷 740-757页

作者： Renato Itamar Duarte da Fonseca Juliana Aparecida da Silva Karine Andréa Costa Gabrielle Delfrate egon Chiquito de Castro Rosilene Prestes Sheisa Fin Dantas Sierpinski Adriano Gonçalves Viana Elizabeth Weinhardt O. Scheffer State University of Ponta Grossa Ponta Grossa Brazil Federal University of Technology Ponta Grossa Brazil

In this article, we report the results of the work carried out on the Verde River, a predominantly urban river located in the city of Ponta Grossa, Paraná, Brazil. Developed in three stages, it aimed to evaluate the water quality through physical-chemical parameters, the presence of caffeine as a chemical tracer, and the compound Triclosan (TCS), considered a pollutant of emerging concern. An attempt was made to identify possible polluting sources along the river. Samples were collected at 4 points from the spring region, with sampling upstream and downstream of a Sewage Treatment Plant (STP). The physical-chemical parameters were determined in situ, through portable analysers, as well as in the laboratory, in this case, through analyses using molecular absorption spectroscopy. For the determination of TCS and Caffeine, high-performance liquid chromatography (HPlC) was used, preceded by a pre-concentration step in the solid phase (SPE), and the techniques were implemented after validation. The physicochemical evaluations of the surface samples showed a decline in water quality after the STP. Mean total phosphorus concentrations of 1.0 mg·l-1 (±0.4), as well as dissolved oxygen (DO) levels below 5.0 mg·l-1 were verified downstream of the STP. Caffeine concentrations for Verde River were between 49.0 to 299.0 μg·l-1, verified upstream and downstream of the STP. The results demonstrated the relationship between the presence of caffeine and impaction, either by the input of raw sewage or by treated effluent. TCS was detected by chromatographic analysis, downstream of the STP, with an average concentration of 27.6 (±1.7) μg·l-1, noting that its presence was associated with the reactor maintenance procedure, with the STP in the process called bypass. Obtaining quality data from Verde River is important for the protection of the environment and affects the health of the population.

关键词： Surface Water Micropollutants Triclosan

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FAIR Principles:Interpretations and Implementation Considerations

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Data Intelligence 2020年第1期2卷 10-29,293-302,322页

作者： Annika Jacobsen Ricardo de Miranda Azevedo Nick Juty Dominique Batista Simon Coles Ronald Cornet Melanie Courtot Merce Crosas Michel Dumontier Chris T.Evelo Carole Goble Giancarlo Guizzardi Karsten Kryger Hansen Ali Hasnain Kristina Hettne Jaap Heringa Rob W.W.Hooft Melanie Imming Keith G.Jeffery Rajaram Kaliyaperumal Martijn GKersloot Christine R.Kirkpatrick Tobias Kuhn Ignasi labastida Barbara Magagna PeterMcQuilton Natalie Meyers Annalisa Montesanti Mirjam van Reisen Philippe Rocca-Serra Robert Pergl Susanna-Assunta Sansone luiz Olavo Bonino da Silva Santos Juliane Schneider George Strawn Mark Thompson Andra Waagmeester Tobias Weigel Mark D.wilkinson egon l.wi.li.hagen Peter wittenburg Marco Roos Barend Mons Erik Schultes leiden University Medical Center Leiden2333 ZAThe Netherlands Institute of Data Science Maastricht UniversityUniversiteitssingel 60Maastricht 6229 ERThe Netherlands Department of Computer Science The University of ManchesterOxford RoadManchester M139PLUK Oxford e-Research Centre Department of Engineering SciencesUniversity of OxfordOxford OX13PJUK School of Chemistry Faculty of Engineering and Physical SciencesUniversity of SouthamptonSO171BJUK Amsterdam UMC University of AmsterdamAmsterdam 1000 GGThe Netherlands European Bioinformatics Institute(EMBl-EBI) HinxtonCambridgeCB101SDUK Harvard University CambridgeMassachusetts 02138USA Department of Bioinformatics–BiGCaT NUTRIMMaastricht UniversityMaastricht 6229 ERThe Netherlands Conceptual and Cognitive Modeling Research Group(CORE) Free University of Bozen-BolzanoBolzano 39100Italy Aalborg University Aalborg DK-9220Denmark Insight Centre for Data Analytics National University of Ireland GalwayH91 TK33Ireland Centre for Digital Scholarship Leiden University LibrariesLeiden2333 ZAThe Netherlands Department of Computer Science Vrije Universiteit AmsterdamDe Boelelaan 11051081 HV AmsterdamThe Netherlands Dutch Techcentre for life Sciences(DTl) UtrechtThe Netherlands SURF Utrecht 3511 EPThe Netherlands Keith G Jeffery Consultants FaringdonUK Castor EDC Paasheuvelweg 25Wing 5D1105 BPAmsterdamThe Netherlands San Diego Supercomputer Center University of California San DiegoLa JollaCalifornia 92093USA learning and Research Resources Centre(CRAI) Universitat de Barcelona08007 BarcelonaSpain Environment Agency Austria A-1090 ViennaAustria University of Notre Dame 75004 ParisFrance Health Research Board(HRB) Dublin 2DO2 H638Ireland liacs Institute of Advanced Computer Science Leiden University2311 GJ LeidenThe Netherlands Czech Technical University in Prague Faculty of Information Technology(FIT CTU)16000 Prague 6Czech Republic GO FAIR International Support&Coordination Office(GFISCO) LeidenThe Netherlands Harvard Catalys

The FAIR principles have been widely cited,endorsed and adopted by a broad range of stakeholders since their publication in *** intention,the 15 FAIR guiding principles do not dictate specific technological implementations,but provide guidance for improving Findability,Accessibility,Interoperability and Reusability of digital *** has likely contributed to the broad adoption of the FAIR principles,because individual stakeholder communities can implement their own FAIR ***,it has also resulted in inconsistent interpretations that carry the risk of leading to incompatible ***,while the FAIR principles are formulated on a high level and may be interpreted and implemented in different ways,for true interoperability we need to support convergence in implementation choices that are widely accessible and(re)-*** introduce the concept of FAIR implementation considerations to assist accelerated global participation and convergence towards accessible,robust,widespread and consistent FAIR *** self-identified stakeholder community may either choose to reuse solutions from existing implementations,or when they spot a gap,accept the challenge to create the needed solution,which,ideally,can be used again by other communities in the ***,we provide interpretations and implementation considerations(choices and challenges)for each FAIR principle.

关键词： FAIR guiding principles FAIR implementation FAIR convergence FAIR communities choices and challenges

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Notes,outline and divergence times of Basidiomycota

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Fungal Diversity 2019年第6期99卷 105-367页

作者： Mao-Qiang He Rui-lin Zhao Kevin D.Hyde Dominik Begerow Martin Kemler Andrey Yurkov Eric H.C.McKenzie Olivier Raspe Makoto Kakishima Santiago Sanchez-Ramırez Else C.Vellinga Roy Halling Viktor Papp Ivan V.Zmitrovich Bart Buyck Damien Ertz Nalin N.wijayawardene Bao-Kai Cui Nathan Schoutteten Xin-Zhan liu Tai-Hui li Yi-Jian Yao Xin-Yu Zhu An-Qi liu Guo-Jie li Ming-Zhe Zhang Zhi-lin ling Bin Cao Vladimir Antonin Teun Boekhout Bianca Denise Barbosa da Silva Eske De Crop Cony Decock Balint Dima Arun Kumar Dutta Jack W.Fell Jozsef Geml Masoomeh Ghobad-Nejhad Admir J.Giachini Tatiana B.Gibertoni Sergio P.Gorjon Danny Haelewaters Shuang-Hui He Brendan P.Hodkinson egon Horak Tamotsu Hoshino Alfredo Justo Young Woon lim Nelson Menolli Jr Armin Mesic Jean-Marc Moncalvo Gregory M.Mueller la szlo G.Nagy RHenrik Nilsson Machiel Noordeloos Jorinde Nuytinck Takamichi Orihara Cheewangkoon Ratchadawan Mario Rajchenberg Alexandre G.S.Silva-Filho Marcelo Aloisio Sulzbacher Zdenko Tkalcec Ricardo Valenzuela Annemieke Verbeken Alfredo Vizzini Felipe Wartchow Tie-Zheng Wei Michael WeiB Chang-lin Zhao Paul M.Kirk State Key laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101People’s Republic of China Department of Entomology and Plant Pathology Faculty of AgricultureChiang Mai UniversityChiang Mai 50200Thailand Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand College of life Sciences University of Chinese Academy of SciencesHuairou DistrictBeijing 100408People’s Republic of China Ruhr-Universitat Bochum AG GeobotanikND03UniversitatsstraBe 15044801 BochumGermany leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures InhoffenstraBe 7B38124 BrunswickGermany Manaaki Whenua-landcare Research Private Bag 92170AucklandNew Zealand Research Department Meise Botanic GardenNieuwelaan 381860 MeiseBelgium Service General de l'Enseignement superieur et de la Recherche scientifique Federation Wallonie-BruxellesLavallee 11080 BrusselsBelgium University of Tsukuba TsukubaIbaraki 305-8572Japan Department of Ecology and Evolutionary Biology University of Toronto25 Willcocks St.TorontoON M5S 3B2Canada Berkeley USA Institute of Systematic Botany The New York Botanical GardenBronxNY 10458-5126USA Department of Botany Szent Istvan University1518 BudapestHungary Komarov Botanical Institute Russian Academy of SciencesProfessor Popov st.2Saint PetersburgRussia 197376 Institut pour Systematique Ecologie Biodiversite(ISYEB UMR 7205) Sorbonne universiteMuseum National d’Histoire Naturelle CP 39CNRSDepartement Origines et Evolution12 Rue Buffon75005 ParisFrance Institute of Microbiology Beijing Forestry UniversityBeijing 100083People’s Republic of China Department of Biology Research Group MycologyGhent UniversityK.L.Ledeganckstraat 359000 GhentBelgium State Key laboratory of Applied Microbiology Southern China Guangdong Provincial Key Laboratory of Microbial Culture Collection and ApplicationGuangdong Institute of MicrobiologyGuangzhou 510070People’s Republic of China Department of Botany Moravian Mu

The Basidiomycota constitutes a major phylum of the kingdom Fungi and is second in species numbers to the *** present work provides an overview of all validly published,currently used basidiomycete genera to date in a single *** outline of all genera of Basidiomycota is provided,which includes 1928 currently used genera names,with 1263 synonyms,which are distributed in 241 families,68 orders,18 classes and four *** provide brief notes for each accepted genus including information on classification,number of accepted species,type species,life mode,habitat,distribution,and sequence ***,three phylogenetic analyses with combined lSU,SSU,5.8s,rpb1,rpb2,and ef1 datasets for the subphyla Agaricomycotina,Pucciniomycotina and Ustilaginomycotina are conducted,*** time estimates are provided to the family level with 632 species from 62 orders,168 families and 605 *** study indicates that the divergence times of the subphyla in Basidiomycota are 406-430 Mya,classes are 211-383 Mya,and orders are 99-323 Mya,which are largely consistent with previous *** this study,all phylogenetically supported families were dated,with the families of Agaricomycotina diverging from 27-178 Mya,Pucciniomycotina from 85-222 Mya,and Ustilaginomycotina from 79-177 *** times as additional criterion in ranking provide additional evidence to resolve taxonomic problems in the Basidiomycota taxonomic system,and also provide a better understanding of their phylogeny and evolution.

关键词： Classification Molecular clock Fungi Systematics Taxonomy

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从埃贡·邦迪的本体论研究看中国古代哲学的当代价值和影响力

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伦理学术 2018年第1期4卷 250-262页

作者： [斯洛伐克]卢博米尔·多瑙蒋益(译) 斯洛伐克普列索夫大学政治学系复旦大学哲学学院

捷克哲学家埃贡·邦迪认为,本体论的明晰是建立一个公正、和谐的社会的重要先决条件。他与合作者玛丽娜·阿诺古什卡从《道德经》等中国古代哲学中获取思想资源,构建了其非实体的、非二元的、动态的、整全的本体论模型。他们一方面希望... 详细信息

捷克哲学家埃贡·邦迪认为,本体论的明晰是建立一个公正、和谐的社会的重要先决条件。他与合作者玛丽娜·阿诺古什卡从《道德经》等中国古代哲学中获取思想资源,构建了其非实体的、非二元的、动态的、整全的本体论模型。他们一方面希望从这一整全的本体论发展出一套应对社会危机的批判理论,另一方面认为在中国传统思想的和谐理念中已经拥有这种本体论思维。本文作者认为,邦迪及阿诺古什卡的研究忽略了自我与存在、主体与具体的社会环境之间的关系分析,也没有去发展一种伦理学。因此,他们的研究,首先需要使整全性的本体论与尊重规范性的方法相联系。诸如安靖如、何乏笔、毕来德等学者就如何进一步发展邦迪及阿诺古什卡的研究,提供了具体的选择方案。

关键词：本体论中国哲学伦理学《道德经》新儒学

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The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry

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Horticulture Research 2021年第1期8卷 2785-2797页

作者： Nicholas P.Howard Cameron Peace Kevin A.T.Silverstein Ana Poets James J.luby Stijn Vanderzande Charles-Eric Durel Helene Muranty Caroline Denance Eric van de Weg Institut fur Biologie und Umweltwissenschaften Carl von Ossietzky UniversityOldenburgGermany Department of Horticultural Science University of MinnesotaSt.PaulMNUSA Department of Horticulture and landscape Architecture Washington State UniversityPullmanWashingtonWAUSA Minnesota Supercomputing Institute University of MinnesotaMinneapolisMNUSA Universited’Angers Institut AgroINRAEIRHSSFR 4207 QuaSaVBeaucouzeFrance Plant Breeding Wageningen University and ResearchWageningenThe Netherlands

Pedigree information is of fundamental importance in breeding programs and related genetics ***,many individuals have unknown *** methods to identify and confirm direct parent–offspring relationships are routine,those for other types of close relationships have yet to be effectively and widely implemented with plants,due to complications such as asexual propagation and extensive *** objective of this study was to develop and demonstrate methods that support complex pedigree reconstruction via the total length of identical by state haplotypes(referred to in this study as“summed potential lengths of shared haplotypes”,SPloSH).A custom Python script,HapShared,was developed to generate SPloSH data in apple and sweet *** was used to establish empirical distributions of SPloSH data for known relationships in these *** distributions were then used to estimate previously unknown *** studies in each crop demonstrated various pedigree reconstruction scenarios using SPloSH *** cherry,a full-sib relationship was deduced for‘Emperor Francis,and‘Schmidt’,a half-sib relationship for‘Van’and‘windsor’,and the paternal grandparents of‘Stella’were *** apple,29 cultivars were found to share an unknown parent,the pedigree of the unknown parent of‘Cox’s Pomona’was reconstructed,and‘Fameuse’was deduced to be a likely grandparent of‘McIntosh’.Key genetic resources that enabled this empirical study were large genome-wide SNP array datasets,integrated genetic maps,and previously identified pedigree *** with similar resources are also expected to benefit from using HapShared for empowering pedigree reconstruction.

关键词： Python breeding crops

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