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Biodiversity

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  • Scratchpads are an online virtual research environment for biodiversity scientists, allowing anyone to share their data and create their own research networks. Sites are hosted at the Natural History Museum London, and offered freely to any scientist that completes an online registration form. Sites can focus on specific taxonomic groups, or the biodiversity of a biogeographic region, or indeed any aspect of natural history. Scratchpads are also suitable for societies or for managing and presenting projects. Key features of Scratchpads include: tools to manage biological classifications, bibliography management, media (images, video and audio), rich taxon pages (with structured descriptions, specimen records, and distribution data), and character matrices. Scratchpads support various ways of communicating with site members and visitors such as blogs, forums, newsletters and a commenting system. Translations of the Scratchpads software are available via our localization server and site content can be created in multiple languages. Developed by: The Scratchpads Virtual Research Environment is developed and supported by the Natural History Museum, London. It has received funding from several European Union and UK funded projects including the EU-FP6 EDIT and FP7 ViBRANT projects (http://vbrant.eu/) as well as the NERC-funded eMonocot Project (http://about.e-monocot.org/). Used in tools: As of August 2015 there are almost 700 active research communities using Scratchpads. Examples of major projects using multiple Scratchpad sites include: eMonocot: A project to aggregate information on the taxonomy and distribution of monocot plants. Each major monocot family using a separate community Scratchpad and these data are centrally aggregated through the e-monocot portal. http://about.e-monocot.org/ Encyclopedia of Life (EOL): Scratchpads replace the EOL LifeDesk system which was one of the systems previously used to supply community contributions to Encyclopedia of Life. An example of an EOL contributing site is Antkey, a community resource for the identification of invasive, introduced and commonly intercepted ant species from across the globe. http://eol.org/ AVIS-IBIS: The Avian Information System (AVIS) is an extensive database information system about all birds of the Indian subcontinent in the series of web-based portals under IBIS to contribute plethora of information available on birds to science and conservation. http://avis.indianbiodiversity.org/ Flora of Thailand: The e-Flora of Thailand aims to provide a web-based flora as a decentralized platform where authors manage, share, and publish taxonomic data online. It will eventually bring together taxonomic data of all of Thailand’s 303 plant families, with keys, descriptions, uses, illustrations, maps, and high-quality photographs of the estimated total number of 10,624 species. http://floraofthailand.myspecies.info/ Technology or platform: Scratchpads are built on top of the Open Source CMS, Drupal. Drupal has been extended with over 150 custom modules developed by the Scratchpads development team, and over 100 contributed modules developed by the Drupal community. The majority (>700 of ~750) of the Scratchpads are hosted at the Natural History Museum, London (NHM). The current setup, which has been honed and improved since its initiation in 2007, uses a single load balancing server running Varnish, two application servers running Apache/PHP, two data servers running Percona (MySQL) and Memcache, and one search server running Apache Solr. This setup can be easily extended to increase capacity for more users or more Scratchpads. Sites are managed using Aegir, a Drupal specific tool for creating and managing Drupal websites.

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    The dataset comprises: species records from benthic surveys commissioned by SNH or projects where SNH were a partner and the outputs are under the custodianship of SNH. Additionally species records determined from SNH analysis of third party commissioned benthic survey video footage are included. The dataset contains surveys which contributed to the Marine Nature Conservation Review (MNCR) programme, EU-funded BioMar Life project, SNH Site Condition Monitoring including broad scale surveys in support of the Natura process, surveys to establish the impact of specific activities on marine habitats and species and surveys to support the Scottish Marine Protected Areas project.

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    This dataset contains data on marine species recorded in Ireland during field suveys by EcoServe, Ecological Consultancy Services Ltd.

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    During the last 40 years of survey in the Lebanese seawaters and the Levantine Basin, we identified and described about 400 species, belonging to 85 genera, including 230 dinoflagellates and 156 diatoms, 10 Silicoflagellates and 4 Ebriidae, many of them are introduced or migrated from Red Sea and Indian Ocean into the Mediterranean, through the Suez Canal pathway.

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    Different dataset added toghether to make a common database for the workshop in Oslo and for the upcoming worskhop on Crete.

  • Free and Open Access to Biodiversity Data GBIF is an international open data infrastructure, funded by governments. It allows anyone, anywhere to access data about all types of life on Earth, shared across national boundaries via the internet. By encouraging and helping institutions to publish data according to common standards, GBIF enables research not possible before, and informs better decisions to conserve and sustainably use the biological resources of the planet. GBIF operates through a network of nodes, coordinating the biodiversity information facilities of Participant countries and organization, collaborating with each other and the Secretariat to share skills, experiences and technical capacity. Developed by: GBIF arose from a recommendation in 1999 by the Biodiversity Informatics Subgroup of the Megascience Forum, set up by the Organization for Economic Cooperation and Development (OECD). That recommendation was endorsed by OECD science ministers and in 2001, GBIF was officially established through Memorandum of Understanding between participating governments.

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    During the expeditions of the e-learning projects Expeditie Zeeleeuw and Planet Ocean, high school students come on board the research vessel and are introduced to the marine life of the Belgian part of the North Sea (BCP). Four days long, the water column and bottom of the BCP are sampled, respectively with beam trawl or otter trawl and a Van Veen grab. All samples are processed on board.

  • The Swedish Biodiversity Data Infrastructure is an open-source software e-infrastructure financed by the Swedish Research Council and developed in close collaboration with the Living Atlases community and the Global Biodiversity Information Facility. The infrastructure will make biodiversity data available, provide powerful analysis and visualization tools, and thereby offer new opportunities for innovative and interdisciplinary research on biodiversity and ecosystems. The core mission of SBDI is to support Open Science and the FAIR (Findable, Accessible, Interoperable, Reusable) principles in biodiversity and ecosystems research. The SBDI consortium includes 11 universities and government agencies in Sweden.

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    The aim of this data collection was to improve the knowledge on the occurrence of Echinoderms in the Adriatic Sea.

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    This dataset contains macrobenthos data from the French Sector of the North Sea from 2000. Dataset in the framework of the North Sea Benthos Project, which integrated recent (1999–2002) macrobenthic infaunal and environmental data from various national sources.