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BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences

Peter McQuilton, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Milo Thurston, Allyson Lister, Eamonn Maguire, Susanna-Assunta Sansone
2016 Database: The Journal of Biological Databases and Curation  
These resources cover standards (terminologies, formats and models, and reporting guidelines), databases, and data policies in the life sciences, broadly encompassing the biological, environmental and  ...  Launched in 2011 and built by the same core team as the successful MIBBI portal, BioSharing harnesses community curation to collate and cross-reference resources across the life sciences from around the  ...  Acknowledgements We are grateful to the University of Oxford e-Research Centre, IMI eTRIKS and the BBSRC COPO project, ELIXIR UK node and the NIH BD2K bioCADDIE and CEDAR projects for co-funding this work  ... 
doi:10.1093/database/baw075 pmid:27189610 pmcid:PMC4869797 fatcat:nhw3xv3pp5cw3eoola6owfkeeq

DaTo: an atlas of biological databases and tools

Qilin Li, Yincong Zhou, Yingmin Jiao, Zhao Zhang, Lin Bai, Li Tong, Xiong Yang, Björn Sommer, Ralf Hofestädt, Ming Chen
2016 Journal of Integrative Bioinformatics  
It extracts raw information from all PubMed articles which contain exact URLs in their abstract section, followed by a manual curation of the abstract and the URL accessibility.  ...  Using DaTo, the geographical locations, the health statuses, as well as the journal associations were evaluated with respect to the historical development of bioinformatics tools and databases over the  ...  ., BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.  ... 
doi:10.1515/jib-2016-297 fatcat:72j7or3fhfgllifn2dpptw5w2e

Meeting Institutional Goals by Working Beyond Institutional Walls

John Chodacki, Daniella Lowenberg
2021 Against the Grain  
BioSharing: Curated and crowd-sourced metadata standards, databases and data policies in the life sciences.  ...  But with Dryad we can satisfy the campuses that would like all curation to be handled externally, and we also can engage with the data curation programs at campuses that would like to get involved in the  ... 
doi:10.7771/2380-176x.8422 fatcat:kcel3wsnz5dtlptprcd6ntaap4

Report of the 13th Genomic Standards Consortium Meeting, Shenzhen, China, March 4–7, 2012

Jack A. Gilbert, Yiming Bao, Hui Wang, Susanna-Assunta Sansone, Scott C. Edmunds, Norman Morrison, Folker Meyer, Lynn M. Schriml, Neil Davies, Peter Sterk, Jared Wilkening, George M. Garrity (+5 others)
2012 Standards in Genomic Sciences  
Interactions to Communities to Models, highlighted the role of data standards associated with genomic, metagenomic, and amplicon sequence data and the contextual information associated with the sample.  ...  In addition, the meeting hosted a Genomic Observatories Network session, a Genomic Standards Consortium biodiversity working group session, and a Microbiology of the Built Environment session sponsored  ...  Acknowledgments This work was supported in part by the US Department of Energy under Contract DE-AC02-06CH11357 and in part by the US National Science Foundation through the research coordination network  ... 
doi:10.4056/sigs.2876184 pmid:22768370 pmcid:PMC3387801 fatcat:ysflrsim55dmpmrvbch4kxxl5u

Supporting evidence-based analysis for modified risk tobacco products through a toxicology data-sharing infrastructure

Stéphanie Boué, Thomas Exner, Samik Ghosh, Vincenzo Belcastro, Joh Dokler, David Page, Akash Boda, Filipe Bonjour, Barry Hardy, Patrick Vanscheeuwijck, Julia Hoeng, Manuel Peitsch
2017 F1000Research  
Curated data and methods descriptions have been prepared in ISA-Tab format and stored in a database accessible via a search portal on the INTERVALS website.  ...  As datasets are often generated by diverse methods and standards, they need to be traceable, curated, and the methods used well described so that knowledge can be gained using data science principles and  ...  Page 10: "Therefore, herein, we propose a new ISA-Tab scheme that follows the data-production workflow and combines data production and documentation into a single step by the researcher, who is the expert  ... 
doi:10.12688/f1000research.10493.1 pmid:29123642 pmcid:PMC5657032 fatcat:w2snic5s35am3gbnbjexhcgti4

Supporting evidence-based analysis for modified risk tobacco products through a toxicology data-sharing infrastructure

Stéphanie Boué, Thomas Exner, Samik Ghosh, Vincenzo Belcastro, Joh Dokler, David Page, Akash Boda, Filipe Bonjour, Barry Hardy, Patrick Vanscheeuwijck, Julia Hoeng, Manuel Peitsch
2017 F1000Research  
Curated data and methods descriptions have been prepared in ISA-Tab format and stored in a database accessible via a search portal on the INTERVALS website.  ...  As datasets are often generated by diverse methods and standards, they need to be traceable, curated, and the methods used well described so that knowledge can be gained using data science principles and  ...  Page 10: "Therefore, herein, we propose a new ISA-Tab scheme that follows the data-production workflow and combines data production and documentation into a single step by the researcher, who is the expert  ... 
doi:10.12688/f1000research.10493.2 pmid:29123642 pmcid:PMC5657032 fatcat:rdsfka2ytvfvtaskur7wkj7eui

Enabling Open Science: Wikidata For Research

Daniel Mietchen, Gregor Hagedorn, Egon Willighagen, Mariano Rico, Asuncion Gomez-Perez, Eduard Aibar, Karima Rafes, Cécile Germain, Alastair Dunning, Lydia Pintscher, Daniel Kinzler, Anonymous
2015 Zenodo  
, and the development of policies for information quality and interchange.  ...  Wiki4R will create an innovative virtual research environment (VRE) for Open Science at scale, engaging both professional researchers and citizen data scientists in new and potentially transformative forms  ...  This overview will include general repositories like re3data 134 as well as data sources in the respective fields (both domain-general like BioSharing 135 and more specific ones) and from citizen science  ... 
doi:10.5281/zenodo.13906 fatcat:rtk247ghhfcvdcluant523fnoi

Connecting high-throughput biodiversity inventories - opportunities for a site-based genomic framework for global integration and synthesis

Paula Arribas, Carmelo Andújar, Martin I Bidartondo, Kristine Bohmann, Éric Coissac, Simon Creer, Jeremy R deWaard, Vasco Elbrecht, Gentile Francesco Ficetola, Marta Goberna, Susan Kennedy, Henrik Krehenwinkel (+13 others)
2021 Molecular Ecology  
The universality, reliability, and efficiency of HTS data can potentially facilitate the seamless linking of data among species assemblages from different sites, at different hierarchical levels of diversity  ...  inventory data generated independently at local, regional and global scales.  ...  It provides protocols and standards, and supports prepublication data sharing and crowd-sourcing data analysis to enable universal patterns of microbial diversity to be explored (Shoemaker et al., 2017  ... 
doi:10.1111/mec.15797 pmid:33432777 fatcat:icfy53upl5hh5fhgoi7hm7x5by

Conceptual design blueprint for the DiSSCo digitization infrastructure - DELIVERABLE D8.1

Alex Hardisty, Hannu Saarenmaa, Ana Casino, Mathias Dillen, Karsten Gödderz, Quentin Groom, Helen Hardy, Dimitris Koureas, Abraham Nieva de la Hidalga, Deborah Paul, Veljo Runnel, Xavier Vermeersch (+2 others)
2020 Research Ideas and Outcomes  
mass digitisation and digitisation-on-demand, and for the subsequent management (i.e., curation, publication, processing) and use of the resulting data.  ...  Proceed with the explicit aim of avoiding divergences of approach in global natural science collections data management and research.  ...  in and contributing to the ICEDIG project.  ... 
doi:10.3897/rio.6.e54280 fatcat:ia4ihoylfvcmvphm6mhd46fyne

ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR

L. Larcombe, R. Hendricusdottir, T.K. Attwood, F. Bacall, N. Beard, L.J. Bellis, W.B. Dunn, J.M. Hancock, A. Nenadic, C. Orengo, B. Overduin, S-A Sansone (+6 others)
2017 F1000Research  
McQuilton P, Gonzalez-Beltran A, Rocca-Serra P, et al.: BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences.  ...  ELIXIR-UK is the UK node of ELIXIR, the European infrastructure for life science data.  ...  Training resources within TeSS are linked to content from other ELIXIR registries, such as tools in the bio.tools registry 8 , and databases, standards and policies from Biosharing 9 .  ... 
doi:10.12688/f1000research.11837.1 pmid:28781748 pmcid:PMC5521157 fatcat:ilajvsaxsvcgtaqrkhjvslxsim

eKNOW Special Area Chairs Technological foresight and socio-economic evolution modelling eKNOW 2016 Committee eKNOW Advisory Committee eKNOW Special Area Chairs Technological foresight and socio-economic evolution modelling

Conceição Granja, Dirk Malzahn, Dirk Malzahn, Roy Oberhauser, Conceição Granja, Andrzej Skulimowski, Dirk Malzahn, Roy Oberhauser, Conceição Granja, Andrzej Skulimowski, Panos Alexopoulos, Jesus Manuel (+68 others)
2016 unpublished
Information technologies allow optimization in searching and interpreting data, yet special constraints imposed by the digital society require on-demand, ethics, and legal aspects, as well as user privacy  ...  Progress in cognitive science, knowledge acquisition, representation, and processing helped to deal with imprecise, uncertain or incomplete information.  ...  ACKNOWLEDGMENT The research reported upon in this paper, would not have been possible without the support of the Dutch Immigration and Naturalization Service.  ... 
fatcat:i7a74lm6uzfh5espfdh2ekzrai

The evaluation of ontologies: quality, reuse and social factors

Marzieh Talebpour
2020
Finding a "good" or the "right" ontology is a growing challenge in the ontology domain, where one of the main aims is to share and reuse existing semantics and knowledge.  ...  This thesis aimed to investigate the notion of quality and reusability in the ontology domain and to explore and identify the set of metrics that can affect the process of ontology evaluation and selection  ...  FairSharing 51 , previously known as BioSharing, has been identified as a community driven portal for different types of registries in the life sciences, namely, standards, databases and data policies.  ... 
doi:10.26174/thesis.lboro.12287273 fatcat:ci7wazue5bdpnk7r4p6mn4rb3y