ORCID Profile
0000-0001-5306-5690
Current Organisation
University of Oxford
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Publisher: Mary Ann Liebert Inc
Date: 06-2006
Abstract: Researchers working on environmentally relevant organisms, populations, and communities are increasingly turning to the application of OMICS technologies to answer fundamental questions about the natural world, how it changes over time, and how it is influenced by anthropogenic factors. In doing so, the need to capture meta-data that accurately describes the biological "source" material used in such experiments is growing in importance. Here, we provide an overview of the formation of the "Env" community of environmental OMICS researchers and its efforts at considering the meta-data capture needs of those working in environmental OMICS. Specifically, we discuss the development to date of the Env specification, an informal specification including descriptors related to geographic location, environment, organism relationship, and phenotype. We then describe its application to the description of environmental transcriptomic experiments and how we have used it to extend the Minimum Information About a Microarray Experiment (MIAME) data standard to create a domain-specific extension that we have termed MIAME/Env. Finally, we make an open call to the community for participation in the Env Community and its future activities.
Publisher: Springer Science and Business Media LLC
Date: 25-05-2006
Abstract: Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field. One of the major bottlenecks in developing bio-ontologies is the lack of a unified methodology. Different methodologies have been proposed for different scenarios, but there is no agreed-upon standard methodology for building ontologies. The involvement of geographically distributed domain experts, the need for domain experts to lead the design process, the application of the ontologies and the life cycles of bio-ontologies are amongst the features not considered by previously proposed methodologies. Here, we present a methodology for developing ontologies within the biological domain. We describe our scenario, competency questions, results and milestones for each methodological stage. We introduce the use of concept maps during knowledge acquisition phases as a feasible transition between domain expert and knowledge engineer. The contributions of this paper are the thorough description of the steps we suggest when building an ontology, ex le use of concept maps, consideration of applicability to the development of lower-level ontologies and application to decentralised environments. We have found that within our scenario conceptual maps played an important role in the development process.
Publisher: Oxford University Press (OUP)
Date: 18-11-2010
DOI: 10.1093/NAR/GKQ1173
Publisher: Springer Science and Business Media LLC
Date: 05-2008
DOI: 10.1038/NBT1360
Publisher: Springer Science and Business Media LLC
Date: 19-06-2020
Publisher: Oxford University Press (OUP)
Date: 04-01-2011
Publisher: Oxford University Press (OUP)
Date: 02-08-2010
DOI: 10.1093/BIOINFORMATICS/BTQ415
Abstract: Summary: The first open source software suite for experimentalists and curators that (i) assists in the annotation and local management of experimental metadata from high-throughput studies employing one or a combination of omics and other technologies (ii) empowers users to uptake community-defined checklists and ontologies and (iii) facilitates submission to international public repositories. Availability and Implementation: Software, documentation, case studies and implementations at www.isa-tools.org Contact: isatools@googlegroups.com
Publisher: Springer Science and Business Media LLC
Date: 07-2005
DOI: 10.1038/NBT0705-833
Publisher: Springer Science and Business Media LLC
Date: 27-01-2012
DOI: 10.1038/NG.1054
Publisher: Springer Science and Business Media LLC
Date: 24-08-2014
DOI: 10.1038/NBT.2957
Publisher: Oxford University Press (OUP)
Date: 24-11-2011
DOI: 10.1093/NAR/GKR1051
Publisher: Wiley
Date: 25-04-2020
DOI: 10.1111/NPH.16544
Publisher: Cold Spring Harbor Laboratory
Date: 03-06-2019
DOI: 10.1101/657676
Abstract: As more datasets, tools, workflows, APIs, and other digital resources are produced by the research community, it is becoming increasingly difficult to harmonize and organize these efforts for maximal synergistic integrated utilization. The Findable, Accessible, Interoperable, and Reusable (FAIR) guiding principles have prompted many stakeholders to consider strategies for tackling this challenge by making these digital resources follow common standards and best practices so that they can become more integrated and organized. Faced with the question of how to make digital resources more FAIR, it has become imperative to measure what it means to be FAIR. The ersity of resources, communities, and stakeholders have different goals and use cases and this makes assessment of FAIRness particularly challenging. To begin resolving this challenge, the FAIRshake toolkit was developed to enable the establishment of community-driven FAIR metrics and rubrics paired with manual, semi- and fully-automated FAIR assessment capabilities. The FAIRshake toolkit contains a database that lists registered digital resources, with their associated metrics, rubrics, and assessments. The FAIRshake toolkit also has a browser extension and a bookmarklet that enables viewing and submitting assessments from any website. The FAIR assessment results are visualized as an insignia that can be viewed on the FAIRshake website, or embedded within hosting websites. Using FAIRshake, a variety of bioinformatics tools, datasets listed on dbGaP, APIs registered in SmartAPI, workflows in Dockstore, and other biomedical digital resources were manually and automatically assessed for FAIRness. In each case, the assessments revealed room for improvement, which prompted enhancements that significantly upgraded FAIRness scores of several digital resources.
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
Location: United Kingdom of Great Britain and Northern Ireland
No related grants have been discovered for Susanna-Assunta Sansone.