Digital multi-text editions from scratch to electronic performance. Transcription and collation routines transformed in a flexible database system

The poster demonstrates the preparatory steps of a digital multi-text edition that are abstracted from the experiences made in the Parzival Project, based at the University of Bern, the Berlin-Brandenburg Academy of Sciences and the University of Erlangen. This edition of Wolfram von Eschenbach’s German Grail novel, written shortly after 1200 and transmitted during several centuries in ca. hundred witnesses, has now been completed by more than a half of the textual corpus.

Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints

Background Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures). Results Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances. Conclusions 3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch webcite and should provide useful assistance to drug discovery projects.

Spatial database of canopy plant densities created from satellite images over Galapagos in 2011, with intent to manage invasive species

Mapping is an important tool for the management of plant invasions. If landscapes are mapped in an appropriate way, results can help managers decide when and where to prioritize their efforts. We mapped vegetation with the aim of providing key information for managers on the extent, density and rates of spread of multiple invasive species across the landscape. Our case study focused on an area of Galapagos National Park that is faced with the challenge of managing multiple plant invasions. We used satellite imagery to produce a spatially-explicit database of plant species densities in the canopy, finding that 92% of the humid highlands had some degree of invasion and 41% of the canopy was comprised of invasive plants. We also calculated the rate of spread of eight invasive species using known introduction dates, finding that species with the most limited dispersal ability had the slowest spread rates while those able to disperse long distances had a range of spread rates. Our results on spread rate fall at the lower end of the range of published spread rates of invasive plants. This is probably because most studies are based on the entire geographic extent, whereas our estimates took plant density into account. A spatial database of plant species densities, such as the one developed in our case study, can be used by managers to decide where to apply management actions and thereby help curtail the spread of current plant invasions. For example, it can be used to identify sites containing several invasive plant species, to find the density of a particular species across the landscape or to locate where native species make up the majority of the canopy. Similar databases could be developed elsewhere to help inform the management of multiple plant invasions over the landscape.

Global Lithological Map Database v1.0 (gridded to 0.5° spatial resolution)

Lithology describes the geochemical, mineralogical, and physical properties of rocks. It plays a key role in many processes at the Earth surface, especially the fluxes of matter to soils, ecosystems, rivers, and oceans. Understanding these processes at the global scale requires a high resolution description of lithology. A new high resolution global lithological map (GLiM) was assembled from existing regional geological maps translated into lithological information with the help of regional literature. The GLiM represents the rock types of the Earth surface using 1,235,400 polygons. The lithological classification consists of three levels. The first level contains 16 lithological classes comparable to previously applied definitions in global lithological maps. The additional two levels contain 12 and 14 subclasses, respectively, which describe more specific rock attributes. According to the GLiM, the Earth is covered by 64 % sediments (a third of which is carbonates), 13 % metamorphics, 7 % plutonics, and 6 % volcanics, and 10% are covered by water or ice. The high resolution of the GLiM allows observation of regional lithological distributions which often vary from the global average. The GLiM enables regional analysis of Earth surface processes at global scales.

Time series of zooplankton abundance at station L4 in the English Channel from 1988 to 2011

Ongoing zooplankton research at the Plymouth Marine Laboratory has established a time series of zooplankton species since 1988 at L4, a coastal station off Plymouth. Samples were collected by vertical net hauls (WP2 net, mesh 200 µm; UNESCO 1968) from the sea floor (approximately 50 m) to the surface and stored in 4% formalin. Much of the zooplankton analysis has been to the level of "major taxonomic groups" only, and a number of different analysts have participated over the years. The level of expertise has generally been consistent, but the user should be aware that levels of taxonomic discrimination may vary during the course of the dataset. The dominant calanoid copepods are generally well discriminated to species throughout. Calanus has not been routinely examined for species determination, the assumption being that the local population is entirely composed of Calanus helgolandicus. In certain years there has been a particular interest in Temora stylifera, Centropages cherchiae and other species reflected in the dataset. The lack of records in other previous years does not necessarily reflect species absence. We view it as essential for all users of L4 plankton data to establish and maintain contact with the nominated current data originators as well as fully consulting the metadata. While not impinging on free data access, this ensures that this large, species-rich but slightly complex species database is being used in the correct way, and any potential issues with the data are clarified. Furthermore, a proper dialogue with these local experts on the time series will enable where appropriate the most recent sampling timepoints to be used. The data can be downloaded from BODC or from doi:10.1594/PANGAEA.778092 as files for each year by searching for "L4 zooplankton". The most comprehensive dataset is the version downloadable directly from this page. The entire set of zooplankton samples is stored at the Plymouth Marine Laboratory in buffered formalin, and may be available for further taxonomic analysis on request.

Integrated topographic database for King George Island, South Shetland Islands, with links to shapefiles

SCAR KGIS (SCAR King George Island GIS Project) was an integrated topographic database for King George Island, South Shetland Islands, including the SCAR Feature Catalogue to semantically integrate the data sets. The project, operated by the University of Freiburg, was available at http://portal.uni-freiburg.de/AntSDI as "The Antarctic Spatial Data Infrastructure (AntSDI)". Operation ended in 2007. The remaining data files were archived in shape format (zipped) in projections as recommended by SCAR. The source data was provided by a variety of institutions which were not referenced in the original product.

The CoastColour Round Robin datasets: a database to evaluate the performance of algorithms for the retrieval of water quality parameters in coastal waters

The CoastColour project Round Robin (CCRR) project (http://www.coastcolour.org) funded by the European Space Agency (ESA) was designed to bring together a variety of reference datasets and to use these to test algorithms and assess their accuracy for retrieving water quality parameters. This information was then developed to help end-users of remote sensing products to select the most accurate algorithms for their coastal region. To facilitate this, an inter-comparison of the performance of algorithms for the retrieval of in-water properties over coastal waters was carried out. The comparison used three types of datasets on which ocean colour algorithms were tested. The description and comparison of the three datasets are the focus of this paper, and include the Medium Resolution Imaging Spectrometer (MERIS) Level 2 match-ups, in situ reflectance measurements and data generated by a radiative transfer model (HydroLight). The datasets mainly consisted of 6,484 marine reflectance associated with various geometrical (sensor viewing and solar angles) and sky conditions and water constituents: Total Suspended Matter (TSM) and Chlorophyll-a (CHL) concentrations, and the absorption of Coloured Dissolved Organic Matter (CDOM). Inherent optical properties were also provided in the simulated datasets (5,000 simulations) and from 3,054 match-up locations. The distributions of reflectance at selected MERIS bands and band ratios, CHL and TSM as a function of reflectance, from the three datasets are compared. Match-up and in situ sites where deviations occur are identified. The distribution of the three reflectance datasets are also compared to the simulated and in situ reflectances used previously by the International Ocean Colour Coordinating Group (IOCCG, 2006) for algorithm testing, showing a clear extension of the CCRR data which covers more turbid waters.