Metrology best practice manuals

The outputs of workshops: genomic observatories (Ribocon and AWI), nutrients and oxygen sensor observations (Ifremer), carbonate chemistry sensors measurements (IO PAN) and trace elements measurements (UOP) will be turned into best practice manuals for free on-line dissemination

Ultra-high-resolution paleoenvironmental records via direct laser-based analysis of lipid biomarkers in sediment core samples

Marine microorganisms adapt to their habitat by structural modification of their membrane lipids. This concept is the basis of numerous molecular proxies used for paleoenvironmental reconstruction. Archaeal tetraether lipids from ubiquitous marine planktonic archaea are particularly abundant, well preserved in the sedimentary record and used in several molecular proxies. We here introduce the direct, extraction-free analysis of these compounds in intact sediment core sections using laser desorption ionization (LDI) coupled to Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS). LDI FTICR-MS can detect the target lipids in single submillimeter-sized spots on sediment sections, equivalent to a sample mass in the nanogram range, and could thus pave the way for biomarker-based reconstruction of past environments and ecosystems at subannual to decadal resolution. We demonstrate that ratios of selected archaeal tetraethers acquired by LDI FTICR-MS are highly correlated with values obtained by conventional liquid chromatography/MS protocols. The ratio of the major archaeal lipids, caldarchaeol and crenarchaeol, analyzed in a 6.2-cm intact section of Mediterranean sapropel S1 at 250-µm resolution (∼4-y temporal resolution), provides an unprecedented view of the fine-scale patchiness of sedimentary biomarker distributions and the processes involved in proxy signal formation. Temporal variations of this lipid ratio indicate a strong influence of the ∼200-y de Vries solar cycle on reconstructed sea surface temperatures with possible amplitudes of several degrees, and suggest signal amplification by a complex interplay of ecological and environmental factors. Laser-based biomarker analysis of geological samples has the potential to revolutionize molecular stratigraphic studies of paleoenvironments

Metrology reference and standard materials

Reference material for trace elements linked to the International GEOTRACES programme (GEOMAR and UOP), create genomic standards and organize their community analysis (Ribocon), and standardize DNA extraction and sequencing (Ribocon and AWI)

Transforming the study of organisms: Phenomic data models and knowledge bases

The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their scientific impact because they are not accompanied by computable phenomic data. The majority of phenomic data are contained in countless small, heterogeneous phenotypic data sets that are very difficult or impossible to integrate at scale because of variable formats, lack of digitization, and linguistic problems. One powerful solution is to represent phenotypic data using data models with precise, computable semantics, but adoption of semantic standards for representing phenotypic data has been slow, especially in biodiversity and ecology. Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable. In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits. We discuss barriers to integration of phenotypic data and make recommendations for developing an operationally useful, semantically interoperable phenotypic data ecosystem

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation

Background The Environment Ontology (ENVO; http://www.environmentontology.org/), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description. We have thus expanded, enhanced, and generalised the ontology to support its increasingly diverse applications. Methods We have updated our development suite to promote expressivity, consistency, and speed: we now develop ENVO in the Web Ontology Language (OWL) and employ templating methods to accelerate class creation. We have also taken steps to better align ENVO with the Open Biological and Biomedical Ontologies (OBO) Foundry principles and interoperate with existing OBO ontologies. Further, we applied text-mining approaches to extract habitat information from the Encyclopedia of Life and automatically create experimental habitat classes within ENVO. Results Relative to its state in 2013, ENVO's content, scope, and implementation have been enhanced and much of its existing content revised for improved semantic representation. ENVO now offers representations of habitats, environmental processes, anthropogenic environments, and entities relevant to environmental health initiatives and the global Sustainable Development Agenda for 2030. Several branches of ENVO have been used to incubate and seed new ontologies in previously unrepresented domains such as food and agronomy. The current release version of the ontology, in OWL format, is available at http://purl.obolibrary.org/obo/envo.owl. Conclusions ENVO has been shaped into an ontology which bridges multiple domains including biomedicine, natural and anthropogenic ecology, ‘omics, and socioeconomic development. Through continued interactions with our users and partners, particularly those performing data archiving and sythesis, we anticipate that ENVO’s growth will accelerate in 2017. As always, we invite further contributions and collaboration to advance the semantic representation of the environment, ranging from geographic features and environmental materials, across habitats and ecosystems, to everyday objects in household settings

Epigrammi

Ġabra ta’ poeżiji u proża li tinkludi: Bandiera Maltija ta’ Karmenu Ellul Galea – Il-ħares tad-dar tagħna ta’ Tarcisio L. Xerri – Iżjed mill-għoli ta’ Dun Frans Camilleri – Il-kaċċatur ta’ P. P. Theuma – Siġra tal-ħawħ ta’ P. P. Theuma – Riflessjoni ta’ Ġużi Abela – Nawfraġju ta’ Ġużi Abela – Lill-Prof. Ġużè Galea fostna ta’ Ġużè Cardona – Poeta ta’ Wallace Ph. Gulia – Inti mifdija wkoll...! ta’ Pawlu Aquilina – Epigrammi ta’ Anton Buttigieg.peer-reviewe

A Response to Scientific and Societal Needs for Marine Biological Observations

Development of global ocean observing capacity for the biological EOVs is on the cusp of a step-change. Current capacity to automate data collection and processing and to integrate the resulting data streams with complementary data, openly available as FAIR data, is certain to dramatically increase the amount and quality of information and knowledge available to scientists and decision makers into the future. There is little doubt that scientists will continue to expand their understanding of what lives in the ocean, where it lives and how it is changing. However, whether this expanding information stream will inform policy and management or be incorporated into indicators for national reporting is more uncertain. Coordinated data collection including open sharing of data will help produce the consistent evidence-based messages that are valued by managers. The GOOS Biology and Ecosystems Panel is working with other global initiatives to assist this coordination by defining and implementing Essential Ocean Variables. The biological EOVs have been defined, are being updated following community feedback, and their implementation is underway. In 2019, the coverage and precision of a global ocean observing system capable of addressing key questions for the next decade will be quantified, and its potential to support the goals of the UN Decade of Ocean Science for Sustainable Development identified. Developing a global ocean observing system for biology and ecosystems requires parallel efforts in improving evidence-based monitoring of progress against international agreements and the open data, reporting and governance structures that would facilitate the uptake of improved information by decision makers

Mhux li kieku jaħasra!

Ġabra ta’ poeżiji u proża li tinkludi: Ħsieb ta’ Trevor Zahra – Rebħu t-tnejn ta’ Alfred Massa – Nikol Biancardi ta’ Manwel Nicholas Borg – Alcide de Gasperi ta’ Karmenu Ellul Galea – L-għanja tax-xogħol ta’ Wallace Ph. Gulia – “Jien Alla Sidek......” ta’ J. Camilleri – Meta morna z-zoo ta’ Pawlu Mifsud – Sbuħija ta’ Tarcisio L. Xerri – Twajjeb Ġesù, aħfirli ta’ P. Alb. Sammut – Il-poeżija tal-ħajja ta’ Pawlu Cachia – Karba ta’ suldat ta’ Louis Buttigieg – Mhux li kieku jaħasra! ta’ Spiro Buhagiar.peer-reviewe