Buttigieg Pier Luigi

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Buttigieg
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Pier Luigi
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  • Article
    Editorial: Oceanobs19: An ocean of opportunity
    (Frontiers Media, 2019-09-06) Speich, Sabrina ; Lee, Tong ; Muller-Karger, Frank E. ; Lorenzoni, Laura ; Pascual, Ananda ; Jin, Di ; Delory, Eric ; Reverdin, Gilles ; Siddorn, John ; Lewis, Marlon R. ; Marba, Nuria ; Buttigieg, Pier Luigi ; Chiba, Sanae ; Manley, Justin ; Kabo-Bah, Amos Tiereyangn ; Desai, Kruti ; Ackerman, Abby
    The OceanObs conferences are held once every 10 years for the scientific, technical, and operational communities involved in the planning, implementation, and use of ocean observing systems. They serve to communicate progress, promote plans, and to define advances in ocean observing in response to societies' needs. Each conference provides a forum for the community to review the state of the ocean observing science and operations, and to define goals and plans to achieve over the next decade.
  • Presentation
    Aligned semantics to advance data interoperability across the ocean value chain - from raw data to societal goals [poster]
    (Woods Hole Oceanographic Institution, 2019-09-16) Shepherd, Adam ; Caltagirone, Scott ; Kokkinaki, Alexandra ; Leadbetter, Adam ; Moncoiffe, Gwenaelle ; Simpson, Pauline ; Thomas, Robert ; Buttigieg, Pier Luigi
    The FAIR principles (Findability, Accessibility, Interoperability, Re-usability) have pervaded discussions on data across disciplines and sectors.While data Findability and Accessibility has greatly improved, considerable difficulties in scalable interoperation remain. Without significant progress, the rapidly growing stores of ocean data risk being siloed for many years to come. A key aspect of Interoperability is "semantic": using knowledge representation (KR) to translate human understanding into machine-readable form. Quality KR allows machines to "understand" what any information artifact is about and relate it to similar artifacts, enabling discovery and enhancing reuse. KR products are usually expressed as vocabularies, glossaries, thesauri, or ontologies (collectively, terminologies), each with its own costs and benefits. Ironically, most marine terminologies are, themselves, not truly interoperable. This is an unfortunate but inevitable outcome of localised and transient funding, and the lack of sustained global infrastructures.Nonetheless, voluntary consortia are addressing this issue with urgency to realise the promise of KR in ocean observation. Here, we present 1) the alignment of well-adopted marine terminologies, 2) a collective strategy for sustained interoperability, and 3) a use case featuring the IOC-UNESCO Ocean Best Practice System. Initialised by the Biological and Chemical Oceanography Data Management Office, we are interlinking terminologies from the Natural Environment Research Council's Vocabulary Server, the Open Biological and Biomedical Ontologies Foundry, and the Earth Science Information Partners. To serve the UNESCO Decade of Ocean Science for Sustainable Development, this effort includes ontologies which represent both the Essential Ocean Variables and the UN Sustainable Development Goals. Finally, we provide perspectives on what measures are needed to meet the interoperability challenge at scale over the next decade.
  • Preprint
    Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications
    ( 2011-01-04) Yilmaz, Pelin ; Kottmann, Renzo ; Field, Dawn ; Knight, Rob ; Cole, James R. ; Amaral-Zettler, Linda A. ; Gilbert, Jack A. ; Karsch-Mizrachi, Ilene ; Johnston, Anjanette ; Cochrane, Guy R. ; Vaughan, Robert ; Hunter, Christopher ; Park, Joonhong ; Morrison, Norman ; Rocca-Serra, Philippe ; Sterk, Peter ; Arumugam, Manimozhiyan ; Bailey, Mark ; Baumgartner, Laura ; Birren, Bruce W. ; Blaser, Martin J. ; Bonazzi, Vivien ; Booth, Tim ; Bork, Peer ; Bushman, Frederic D. ; Buttigieg, Pier Luigi ; Chain, Patrick S. G. ; Charlson, Emily ; Costello, Elizabeth K. ; Huot-Creasy, Heather ; Dawyndt, Peter ; DeSantis, Todd ; Fierer, Noah ; Fuhrman, Jed A. ; Gallery, Rachel E. ; Gevers, Dirk ; Gibbs, Richard A. ; San Gil, Inigo ; Gonzalez, Antonio ; Gordon, Jeffrey I. ; Guralnick, Robert P. ; Hankeln, Wolfgang ; Highlander, Sarah ; Hugenholtz, Philip ; Jansson, Janet K. ; Kau, Andrew L. ; Kelley, Scott T. ; Kennedy, Jerry ; Knights, Dan ; Koren, Omry ; Kuczynski, Justin ; Kyrpides, Nikos C. ; Larsen, Robert ; Lauber, Christian L. ; Legg, Teresa ; Ley, Ruth E. ; Lozupone, Catherine A. ; Ludwig, Wolfgang ; Lyons, Donna ; Maguire, Eamonn ; Methe, Barbara A. ; Meyer, Folker ; Muegge, Brian ; Nakielny, Sara ; Nelson, Karen E. ; Nemergut, Diana ; Neufeld, Josh D. ; Newbold, Lindsay K. ; Oliver, Anna E. ; Pace, Norman R. ; Palanisamy, Giriprakash ; Peplies, Jorg ; Petrosino, Joseph ; Proctor, Lita ; Pruesse, Elmar ; Quast, Christian ; Raes, Jeroen ; Ratnasingham, Sujeevan ; Ravel, Jacques ; Relman, David A. ; Assunta-Sansone, Susanna ; Schloss, Patrick D. ; Schriml, Lynn M. ; Sinha, Rohini ; Smith, Michelle I. ; Sodergren, Erica ; Spor, Ayme ; Stombaugh, Jesse ; Tiedje, James M. ; Ward, Doyle V. ; Weinstock, George M. ; Wendel, Doug ; White, Owen ; Whiteley, Andrew ; Wilke, Andreas ; Wortman, Jennifer R. ; Yatsunenko, Tanya ; Glockner, Frank Oliver
    Here we present a standard developed by the Genomic Standards Consortium (GSC) to describe marker gene sequences—the minimum information about a marker gene sequence (MIMARKS). We also introduce a system for describing the environment from which a biological sample originates. The “environmental packages” apply to any sequence whose origin is known and can therefore be used in combination with MIMARKS or other GSC checklists. Finally, to establish a unified standard for describing sequence data and to provide a single point of entry for the scientific community to access and learn about GSC checklists, we establish the minimum information about any (x) sequence (MIxS). Adoption of MIxS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
  • Article
    Recurrent patterns of microdiversity in a temperate coastal marine environment
    (Nature Publishing Group, 2017-10-24) Chafee, Meghan E. ; Fernàndez-Guerra, Antonio ; Buttigieg, Pier Luigi ; Gerdts, Gunnar ; Eren, A. Murat ; Teeling, Hanno ; Amann, Rudolf I.
    Temperate coastal marine environments are replete with complex biotic and abiotic interactions that are amplified during spring and summer phytoplankton blooms. During these events, heterotrophic bacterioplankton respond to successional releases of dissolved organic matter as algal cells are lysed. Annual seasonal shifts in the community composition of free-living bacterioplankton follow broadly predictable patterns, but whether similar communities respond each year to bloom disturbance events remains unknown owing to a lack of data sets, employing high-frequency sampling over multiple years. We capture the fine-scale microdiversity of these events with weekly sampling using a high-resolution method to discriminate 16S ribosomal RNA gene amplicons that are >99% identical. Furthermore, we used 2 complete years of data to facilitate identification of recurrent sub-networks of co-varying microbes. We demonstrate that despite inter-annual variation in phytoplankton blooms and despite the dynamism of a coastal–oceanic transition zone, patterns of microdiversity are recurrent during both bloom and non-bloom conditions. Sub-networks of co-occurring microbes identified reveal that correlation structures between community members appear quite stable in a seasonally driven response to oligotrophic and eutrophic conditions.
  • Article
    Evolving and sustaining ocean best practices and standards for the next decade
    (Frontiers Media, 2019-06-04) Pearlman, Jay ; Bushnell, Mark ; Coppola, Laurent ; Karstensen, Johannes ; Buttigieg, Pier Luigi ; Pearlman, Francoise ; Simpson, Pauline ; Barbier, Michele ; Muller-Karger, Frank E. ; Munoz-Mas, Cristian ; Pissierssens, Peter ; Chandler, Cynthia L. ; Hermes, Juliet ; Heslop, Emma ; Jenkyns, Reyna ; Achterberg, Eric P. ; Bensi, Manuel ; Bittig, Henry C. ; Blandin, Jerome ; Bosch, Julie ; Bourles, Bernard ; Bozzano, Roberto ; Buck, Justin J. H. ; Burger, Eugene ; Cano, Daniel ; Cardin, Vanessa ; Llorens, Miguel Charcos ; Cianca, Andrés ; Chen, Hua ; Cusack, Caroline ; Delory, Eric ; Garello, Rene ; Giovanetti, Gabriele ; Harscoat, Valerie ; Hartman, Susan ; Heitsenrether, Robert ; Jirka, Simon ; Lara-Lopez, Ana ; Lantér, Nadine ; Leadbetter, Adam ; Manzella, Giuseppe ; Maso, Joan ; McCurdy, Andrea ; Moussat, Eric ; Ntoumas, Manolis ; Pensieri, Sara ; Petihakis, George ; Pinardi, Nadia ; Pouliquen, Sylvie ; Przeslawski, Rachel ; Roden, Nicholas P. ; Silke, Joe ; Tamburri, Mario N. ; Tang, Hairong ; Tanhua, Toste ; Telszewski, Maciej ; Testor, Pierre ; Thomas, Julie ; Waldmann, Christoph ; Whoriskey, Frederick G.
    The oceans play a key role in global issues such as climate change, food security, and human health. Given their vast dimensions and internal complexity, efficient monitoring and predicting of the planet’s ocean must be a collaborative effort of both regional and global scale. A first and foremost requirement for such collaborative ocean observing is the need to follow well-defined and reproducible methods across activities: from strategies for structuring observing systems, sensor deployment and usage, and the generation of data and information products, to ethical and governance aspects when executing ocean observing. To meet the urgent, planet-wide challenges we face, methods across all aspects of ocean observing should be broadly adopted by the ocean community and, where appropriate, should evolve into “Ocean Best Practices.” While many groups have created best practices, they are scattered across the Web or buried in local repositories and many have yet to be digitized. To reduce this fragmentation, we introduce a new open access, permanent, digital repository of best practices documentation (oceanbestpractices.org) that is part of the Ocean Best Practices System (OBPS). The new OBPS provides an opportunity space for the centralized and coordinated improvement of ocean observing methods. The OBPS repository employs user-friendly software to significantly improve discovery and access to methods. The software includes advanced semantic technologies for search capabilities to enhance repository operations. In addition to the repository, the OBPS also includes a peer reviewed journal research topic, a forum for community discussion and a training activity for use of best practices. Together, these components serve to realize a core objective of the OBPS, which is to enable the ocean community to create superior methods for every activity in ocean observing from research to operations to applications that are agreed upon and broadly adopted across communities. Using selected ocean observing examples, we show how the OBPS supports this objective. This paper lays out a future vision of ocean best practices and how OBPS will contribute to improving ocean observing in the decade to come.