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Fungal taxonomy and ecology have been revolutionized by the application of molecular methods and both have increasing connections to genomics and functional biology. However, data streams from traditional specimen- and culture-based systematics are not yet fully integrated with those from metagenomic and metatranscriptomic studies, which limits understanding of the taxonomic diversity and metabolic properties of fungal communities. This article reviews current resources, needs, and opportunities for sequence-based classification and identification (SBCI) in fungi as well as related efforts in prokaryotes. To realize the full potential of fungal SBCI it will be necessary to make advances in multiple areas. Improvements in sequencing methods, including long-read and single-cell technologies, will empower fungal molecular ecologists to look beyond ITS and current shotgun metagenomics approaches. Data quality and accessibility will be enhanced by attention to data and metadata standards and rigorous enforcement of policies for deposition of data and workflows. Taxonomic communities will need to develop best practices for molecular characterization in their focal clades, while also contributing to globally useful datasets including ITS. Changes to nomenclatural rules are needed to enable valid publication of sequence-based taxon descriptions. Finally, cultural shifts are necessary to promote adoption of SBCI and to accord professional credit to individuals who contribute to community resources. [ABSTRACT FROM AUTHOR]

Primary biodiversity data are often organised in federated databases in the framework of big international projects and initiatives. Other data are normally organised into isolated resources: ecological, morphological and morpho-anatomic databases, checklists, archives of digital identification tools, etc. These data, which do not refer specifically to one specimen or observation, but to a taxon, can be addressed to as “taxon-related data”. In the framework of the Italian Biodiversity Network, taxon-related data have been aggregated by using a federated approach, with the creation of a network of data providers, which required the development of a communication protocol, the species-related data (SRD) protocol and of a simple data format (the SRD format). The SRD federated database aggregates currently ca. 70,000 taxon pages for several groups of organisms: vascular plants, lichens, mosses, algae, freshwater fishes and butterflies. All these resources can be queried by using one simple interface in the web portal of the Italian Biodiversity Network (http://www.naturaitalia.it/nnb/). [ABSTRACT FROM AUTHOR]

The online platform "Wikiplantbase #Toscana" provides a framework where the full set of georeferenced floristic records of Tuscany (central Italy) can be entered, stored, updated and freely accessed through the Internet. As of 5 January 2015, the database stores 67,360 floristic records, referable to 3578 accepted specific and subspecific taxa. Most records are based on published data (80.6% of the total), then by published herbarium specimens (15.1%) and on unpublished field data (3.8%); unpublished herbarium records account only for 0.5% of the stored data. At present, the most represented species is the fern Pteridium aquilinum (L.) Kuhn subsp. aquilinum (Dennstaedtiaceae) with 234 records for 219 localities, but 625 species are still represented only by one record for a single locality. Data acquisition is far from complete, but in slightly more than one year a massive amount of data was accumulated, and can be maintained up-to-date with relatively little effort. This could power several researches such as, for example, (1) taxonomic researches especially on species and genera in Tuscany and Italy; (2) studies on the distribution of diversity across administrative or ecological boundaries; (3) evaluation of conservation status of endangered taxa; and (4) static and dynamic range modelling and evolution niche studies. [ABSTRACT FROM AUTHOR]

In recent years, research in botany was increasingly related with the use of large data-sets and data banks, in order to address emerging issues such as the severe risk of species, habitats and biodiversity loss. In this frame, theanArchivetaxonomic Checklist, an online synonymized list of botanical species names, developed to support the botanical data banking and vegetation analysis, is presented and discussed here. The benefits deriving from such a supervised and referenced tool are emphasized. They include the possibility to keep track of old and new species names, pointing out the latest reviewed accepted scientific name and its synonyms, and harmonizing different taxonomic points of view. Furthermore, the list is open access and expert qualified customers can collaborate to its improvement. The basic unit of the taxonomic Checklist is an object including thetaxonname at specific or, when present, infraspecific level; the taxonomic frame stops at the level of family and ranks higher than genus are not treated hierarchically. Some technical features, the main taxonomic references and the current state of the art are reported. [ABSTRACT FROM PUBLISHER]

Biodiversity is one of the most important concepts in contemporary biology, with a broad range of applications. In November 1995, South Africa ratified the Convention on Biological Diversity (CBD). Signatories are obligated to develop a strategic plan for the conservation and sustainable use of biodiversity. To meet the requirements of the CBD, the South African National Survey of Arachnida (SANSA) was initiated in 1997. This national project has several aims: to document and describe the arachnid fauna of South Africa; to consolidate all the available data on South African arachnids into one relational database and to make this biodiversity information available to science; and to address issues concerning their conservation and sustainable use. Extensive sampling took place and the SANSA database contains a wealth of biodiversity data that are used to provide answers to ecological questions. Presently 71 spider families, 471 genera and 2170 species are known from South Africa, representing approximately 4.8% of the world fauna. This paper presents the current state of spider biodiversity information and how it is managed. It demonstrates the importance of running a national inventory; emphasises the significance of using a good database application; and the importance of capacity development to improve the quality and integration of biodiversity information. Further, it shows the role SANSA has played in unifying and strengthening arachnid research, with the major thrust to discover the spider diversity in South Africa. We discuss the present status of knowledge, constraints to improving this, and the future directions for research. SANSA has provided the foundations for a more integrative approach to spider diversity research. Future research should build on this legacy by linking taxonomic diversity with that of functional diversity, predicting the response of this diversity to global change drivers. Functional approaches will link these studies to ecosystem processes. Global collaborative studies at several sites following standardised sampling protocols and focused research questions would add value to the SANSA collection and the importance of spiders for the health of ecosystems. [ABSTRACT FROM PUBLISHER]

The checklist of hornworts, liverworts and mosses of Italy is available online as a federated database, which can be queried by combining taxonomic and distributional information. Several digital identification keys have been included in the system, which will be part of the forthcoming Italian Biodiversity Network. [ABSTRACT FROM AUTHOR]

Checklists are fundamental for accessing information about organisms known to occur in a given area. It is possible to convert textual, paper-printed checklists into structured digital formats. This process can eventually lead to the development of digital information systems, for which the output can be far more complex than a list of taxa. Digital information systems can be continuously updated by a constant flow of information, and their content can be exported in many other different formats, hence not only mobilising, but also making biodiversity data reusable on different platforms. The conversion of the Checklist of Italian Lichens into an information system is discussed, in order to provide some general guidelines of such a process. [ABSTRACT FROM PUBLISHER]

Two years after its official start, the national vegetation database VegItaly, a collaborative project supported by the Italian scientific community and developed by a large group of scientists, is presented. This article offers a concise overview of the content of the database, currently consisting of 31,100 vegetation plot, including published and unpublished data. Some basic statistics are analysed; for example, data distribution in space and time, represented vegetation types expressed as physiognomic categories. Although rather young and still in progress, VegItaly already contains data from all the Italian regions and stands as an optimal candidate for the development of an Italian national vegetation database. Its main goals,theoretical basis, technical features, functionalities and recent progresses are outlined, showing glimpses of future prospects. [ABSTRACT FROM PUBLISHER]

This article describes the experience of project Dryades, coordinated by the University of Trieste, in developing interactive identification keys in the form of applications for mobile devices (iPhone/iPad/iPodtouch). All of our keys were previously generated from a database of morpho-anatomical characters using software FRIDA. The applications for mobile devices, which were tested Europe-wide during the project KeyToNature, have proved to be useful in education, in the promotion of nature-aware tourism and in projects of citizen science. The first-generation apps were stand-alone packages which consisted into a sequence of stand-alone HTML pages, while those of the second generation do incorporate the digital key as a true database into the mobile device. All of the hitherto published applications are basically in the form of illustrated dichotomous keys. Future developments will also include a multi-entry query interface, and will be extended to devices which use the Android system. [ABSTRACT FROM PUBLISHER]

Several national and global initiatives aim to increase access to biodiversity information worldwide. The Italian National Biodiversity Network, started in the framework of the project “Sistema Ambiente 2010”, will organise and manage biodiversity data hosted by museums, universities and research centres in Italy, in order to make them widely available on the Web. [ABSTRACT FROM PUBLISHER]

Since its formal institution in May 2012, the Italian Biodiversity Network is aggregating data from several research centres, for a total ofca. 1.5 million records. Botanical data madeca.50% of the total, and range from primary biodiversity data to ecological, morpho-anatomical and taxonomical information. However, this is only a small portion of the total amount of botanical data which could be aggregated and exposed to the scientific community, professionals and citizens. In this paper we present the current status of data aggregation of the Network and its impact on digitalisation of biodiversity data, research, conservation and environmental management and education in Italy. [ABSTRACT FROM PUBLISHER]

Plant Biosystems dedicated a special issue to present and discuss new trends in biodiversity and informatics. The definition and theoretical framework of this challenging and stimulating research field are delineated together with several examples that illustrate data collection, organisation, dissemination, analysis and application. [ABSTRACT FROM PUBLISHER]