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  • 1
    Online Resource
    Online Resource
    Biocode : The New Age of Genomics. (2015)
    Oxford :Oxford University Press, Incorporated,
    Details
    Keywords: Ecosystem. ; Electronic books.
    Description / Table of Contents: In Biocode, Dawn Field and Neil Davies capture the scale and excitement of the rapidly growing field of genomics. From automatic DNA sequencing of newborns to synthetic life, and the sequencing of whole ecosystems, genomics is set to revolutionize our understanding of life on Earth and affect us all.
    Type of Medium: Online Resource
    Pages: 1 online resource (209 pages)
    Edition: 1st ed.
    ISBN: 9780191511561
    URL: https://ebookcentral.proquest.com/lib/geomar/detail.action?docID=1930354
    DDC: 572.8/6
    Language: English
    Note: Cover -- Biocode: The New Age of Genomics -- Copyright -- Dedication -- Preface -- Contents -- List of Illustrations -- 1: DNA -- Immortal coil -- A world in your wardrobe -- The molecular narcissist -- `Who´s Your Daddy?´ -- The case of the unusual cat -- Stranger visions -- Advertising your genes -- 2: Personal Genomics -- Science rock star genomes -- `Six billion base pairs for six billion people´ -- A scant 30,000 genomes -- Genomics 101 -- Genomics Goliath -- Blindsided -- 3: Homo Evolutis -- BabySeq -- Devil´s Ark -- De-extinction -- Synthia -- Embryo genomics -- Genomematch.com -- Humanity rebooted -- 4: Zoo in My Sequencer -- Elvis lives -- Genomic GOLD -- Does size matter? -- Don´t call it junk -- The first tweenome -- Denisovan girl -- Single-celled sisters -- Microbial Earth -- Losing the Acropolis -- 5: No Organism Is an Island -- The biodiversity within -- Ratios matter -- Eating for trillions -- Microbes on the brink -- Genomic donations -- 2 per cent of pandas -- The last prairie -- 6: Terra-Genoming -- The lingering kiss -- Reunion -- Unicorns -- Invaders -- Genes on the move -- A dead sea comes to life -- Shock and awe -- 7: We Are All Ecosystems Now -- Quantified Self -- Roller derby -- A buoy in the ocean -- Cottonwood, cod, and corals -- The Moorea Biocode -- GEMs -- 8: Biocoding the Earth -- The Biocode -- Our place in nature -- Sunjammer -- You too can biocode -- The Planetary Genome Project -- Endnotes -- References -- Further Reading -- Index.
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  • 2
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    Building a strategy towards an Omic Biodiversity Observation Network (Omic BON) (2019)
    In:  EPIC3OceanObs'19 conference, Honolulu, Hawaii, USA, 2019-09-16-2019-09-20
    Details
    Publication Date: 2019-12-13
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
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  • 3
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    Genomic Observatories Network: socio-technical perspectives on the path to long-term multi-omic observation (2018)
    American Geophysical Union
    In:  EPIC3American Geophysical Union Fall Meeting, Washington D.C., USA, 2018-12-10-2018-12-14American Geophysical Union
    Details
    Publication Date: 2020-02-12
    Description: Four years after the Genomic Observatories Network was formally established as a collaboration between the Group on Earth Observations Biodiversity Observation Network and the Genomic Standards Consortium, we review the development of the network. Considering institutional infrastructure, we note the growing role of omic observation in active and increasingly interlinked marine networks, with examples such as EMBRC/ASSEMBLE, International Long Term Ecological Research Network, AtlantOS, National Association of Marine Labs, Smithsonian MarineGEO, and Partnership on Observation of the Global Oceans. We also note some key human elements essential to meeting the networks' goals, address how the community is evolving, and why performing seemingly simple tasks within a broadly distributed community presents significant challenges even among those who have agreed to use standards. From the perspectives above, we review lessons learned from use cases that leverage Genomic Observatories Network, such as the Autonomous Reef Monitoring Structures (ARMS), Ocean Sampling Day (OSD) and myOSD, which included experiences with citizen science. Looking forward, we survey 1) promising new technologies for in situ biological observation (e.g., cheap 3D printed omics samplers), 2) progress towards adoption of omics methods in marine policy and conservation programs, and 3) opportunities that a Genomic Observatory brings, alone or embedded in a network, to address novel scientific questions and support Essential Biodiversity Variables, Essential Ocean Variables, and indices such as the Ocean Health Index. Given the data intensive nature of omics investigation, we note emerging cyberinfrastructure solutions, such as the Genomic Observatories Metadatabase (GeOMe), an open-access repository for geographic and ecological metadata associated with biosamples, and predictive modeling efforts, such as those of the Island Digital Ecosystem Avatar (IDEA) Consortium. Finally, we explore the potential of Genomic Observatories as components of high-resolution calibration sites. Such observatories would provide super-contextualized "data trusts" for machine learning and artificial intelligence applications that draw on multi-omic observation.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , notRev
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  • 4
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    AtlantOS Deliverable 6.2: Roadmap for emerging networks (2018)
    AtlantOS
    In:  EPIC3AtlantOS
    Details
    Publication Date: 2020-02-12
    Description: Whilst the AtlantOS project is directed towards bringing together the existing, but currently disparate observing programmes in the Atlantic Ocean, there are still some gaps in terms of requirements for addressing the collection and curation of data around the Essential Ocean Variables. This deliverable will identify gaps and emerging observing networks. Here we use the term emerging network to classify science areas that are starting to gain importance with respect to EOV’s and their measurement and curation, or are existing small scale programmes or communities that might become more important in the future if we can find means of enhancing the collaboration among investigators/groups, increasing resources to the area or using new technological developments. In the AtlantOS project we have identified a number of areas in which there are gaps in our knowledge and where opportunities exist to enhance current small-scale networks. The scope of this document is to assess these networks, based on where we are now and where the networks could be in three and ten years’ time, respectively. An assessment of the state of the existing networks is useful to identify the level of international organisation and potential for further development in the future. We identify opportunities where synergies are possible with more established global projects, and where small levels of investment in resource and time for governance and coordination can productively and realistically develop the networks. We also identify if there are ways to develop coordinated approaches to metrology technology development. For this analysis, the networks have been allocated to one of the three groups outlined below.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Miscellaneous , notRev
    Format: application/pdf
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  • 5
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    Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies (2014)
    In:  EPIC3PLoS ONE, 9(3), pp. e89606, ISSN: 1932-6203
    Details
    Publication Date: 2017-01-30
    Description: The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev , info:eu-repo/semantics/article
    Format: application/pdf
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  • 6
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    Meeting report: advancing practical applications of biodiversity ontologies (2014)
    In:  EPIC3Standards in Genomic Sciences, 9(1), pp. 17, ISSN: 1944-3277
    Details
    Publication Date: 2017-01-30
    Description: We describe the outcomes of three recent workshops aimed at advancing development of the Biological Collections Ontology (BCO), the Population and Community Ontology (PCO), and tools to annotate data using those and other ontologies. The first workshop gathered use cases to help grow the PCO, agreed upon a format for modeling challenging concepts such as ecological niche, and developed ontology design patterns for defining collections of organisms and population-level phenotypes. The second focused on mapping datasets to ontology terms and converting them to Resource Description Framework (RDF), using the BCO. To follow-up, a BCO hackathon was held concurrently with the 16th Genomics Standards Consortium Meeting, during which we converted additional datasets to RDF, developed a Material Sample Core for the Global Biodiversity Information Framework, created a Web Ontology Language (OWL) file for importing Darwin Core classes and properties into BCO, and developed a workflow for converting biodiversity data among formats.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , peerRev , info:eu-repo/semantics/article
    Format: application/pdf
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  • 7
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    The founding charter of the Genomic Observatories Network (2014)
    GigaScience journal.com
    In:  EPIC3GigaScience, GigaScience journal.com, 3(2), pp. 1-5
    Details
    Publication Date: 2017-02-03
    Description: The co-authors of this paper hereby state their intention to work together to launch the Genomic Observatories Network (GOs Network) for which this document will serve as its Founding Charter. We define a Genomic Observatory as an ecosystem and/or site subject to long-term scientific research, including (but not limited to) the sustained study of genomic biodiversity from single-celled microbes to multicellular organisms.An international group of 64 scientists first published the call for a global network of Genomic Observatories in January 2012. The vision for such a network was expanded in a subsequent paper and developed over a series of meetings in Bremen (Germany), Shenzhen (China), Moorea (French Polynesia), Oxford (UK), Pacific Grove (California, USA), Washington DC (USA), and London (UK). While this community-building process continues, here we express our mutual intent to establish the GOs Network formally, and to describe our shared vision for its future. The views expressed here are ours alone as individual scientists, and do not necessarily represent those of the institutions with which we are affiliated.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 8
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    Report of the POGO Task Force on Ocean Biological Observations. (2021)
    Partnership for Observation of the Global Ocean (POGO) | Plymouth, UK
    Details
    Publication Date: 2021-05-19
    Description: This report consists of three sections and an appendix. Section I discusses the scientific and societal questions that require the development of large scale and/or long-term ocean biological observation capabilities and how POGO might assist the ocean observational community in developing this capability. Section II outlines the state of development of various ocean biological observation techniques and issues. Section III discusses some of the issues associated with the development of large scale and/or long term biological observations. Appendix I includes information and references used in our discussion and deliberation.
    Description: POGO Biological Observations Taskforce
    Description: Richard Lounsbery Foundation
    Description: Published
    Description: Non Refereed
    Repository Name: AquaDocs
    Type: Report
    Format: 17pp.
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  • 9
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    Toward a Global Public Repository of Community Protocols to Encourage Best Practices in Biomolecular Ocean Observing and Research (2021)
    In:  EPIC3Frontiers in Marine Science, 8(758694)
    Details
    Publication Date: 2021-10-28
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , isiRev
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  • 10
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    The ocean sampling day consortium (2015)
    BioMed Central
    Details
    Publication Date: 2022-10-18
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in GigaScience 4 (2015): 27, doi:10.1186/s13742-015-0066-5.
    Description: Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits.
    Description: This work was supported by the Micro B3 project, which is funded from the European Union’s Seventh Framework Programme (FP7; Joint Call OCEAN.2011‐2: Marine microbial diversity – new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589.
    Keywords: Ocean sampling day ; OSD ; Biodiversity ; Genomics ; Health index ; Bacteria ; Microorganism ; Metagenomics ; Marine ; Micro B3 ; Standards
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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