BioCASE PortalSpecimens and observations on Europe
EDIT Specimen Explorer
German botanical specimens and oberservation
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The Biological Collection Access Service for Europe, BioCASE, is a transnational network of biological collections of all kinds. BioCASE enables widespread unified access to distributed and heterogeneous European collection and observational databases using open-source, system-independent software and open data standards and protocols.
In the latest version 3.4 of the BioCASe Provider Software, the XML archiving features have been re-implemented completely and aligned with GBIF’s new dataset-aware Registry. Now each dataset published by a BioCASe web service will end up in a separate XML archive, storing all information published by the web service. GBIF will use the newly introduced BioCASe dataset inventory to discover these archives and use them for faster indexing. If desired, individual archives or the complete list of XML archives can be transformed into DarwinCore archives.
In addition, the archiving process has been streamlined and should be significantly faster on most installations; instead of using the CGI interface, the BioCASe libraries are now called directly. Dispensable formatting has been removed, reducing the size of XML documents stored in the archives by about one third. The archiving interface underwent a a comprehensive redesign.
The new release contains several fixes and other small changes; the complete list can be found in the version history.
A version of the BioCASe Provider Software with smaller bug fixes and changes has been released. Now it is possible to transfer the mappings from one schema to another schema with the namespace. This allows, for example, upgrading from ABCD 2.06 to one of the extensions ABCD-EFG or ABCD-DNA or vice versa. More upgrade paths have been added.
For a complete list of changes and fixes, see the version history.
A new version of the BioCASe Provider Software has been released. It now supports the archiving processes to be triggered through a deep link, without using the configuration tool interface. This allows archiving to be scheduled; for example, a DarwinCore Archive could be created monthly for being harvested by GBIF or any other biodiversity network. Both XML and DarwinCore Archives can be created through the deep link.
Several other changes have been implemented; for example, the ordering of Scan request results has been changed in order to increase compatibility with widely used indexing approaches. For a complete list of changes, see the version history.
Version 3.2 of the BioCASe Provider Software has been released. It allows easy creating of DarwinCore Archives from an ABCD web service with just one click in the user interface. For special interest networks relying on the full richness of ABCD concepts, ABCD archives or other XML archives can be created in a similar fashion. Both archive types can be used to speed up and ease harvesting and indexing processes.For a complete list of changes, see the version history.
A new version of the BioCASe Provider Software has been released. The focus for improvements has been on the new XML archiving feature: The web interface has been overhauled and reacts faster now. If it is kept open during the archiving process, less load is put on the server for showing the progress log. Several smaller bugs have been fixed.For a complete list of changes, see the version history.
Shortly before Easter, a new version of the BioCASe Provider Software has been released. It comprises mainly bug fixes. Compatibility with Internet Information Server has been improved; if SQL Server is used, the configuration tool now provides drop-down lists for table and column names.
A complete list of bug fixes can be found in the version history.
A new major version of the BioCASe Provider Software has been released. As an important new feature, version 3 can now create XML archives that store all information published by a BioCASe web service in a single file. If required, these archives can be transformed into DarwinCore Archives in a subsequent step.
In addition, a number of smaller changes and optimizations have been implemented. Metadata retrieval is now also supported for Oracle databases, which allows an easier configuration of the according web services. For a complete list of changes, see the version history.
A new version of the Provider Software has been released. Now most configuration pages feature a “Help” link that points directly to the respective tutorial of the new PyWrapper documentation wiki. Moreover, it contains a number of smaller bug fixes, please see the version history for a complete list.
It features several step-by-step tutorials on installation, configuration, debugging, on preparing a database for publication with BioCASe, a beginner’s guide, a short documentation of ABCD, and a list of frequently asked questions. Many pages in the upcoming version of the Provider Software will include a “Help” link that points directly to the respective page in the online documentation.
Version 2.6 of the Provider Software has been released. It features major changes in the user interface for the configuration tool that should ease the setup of the BPS considerably. Table setup has been completely overhauled; table and column names will now be retrieved from the database and shown in drop-down-boxes for commonly used DBMS. The mapping editor also uses drop-down-boxes now.
If MySQL or Postgres are used, the Provider Software now takes advantage of the OFFSET SQL clauses for serving Search requests, which increases performance for harvesting applications. Last but not least, a number of bugs have been fixed. See the Version History for a complete list of changes.
The OpenUP! project launched in March will use BioCASe Technology to connect millions of multimedia objects stored in natural history collections to the European network Europeana, thereby making them accessible to the public in a high quality.
In order to build the required expertise in the associated project partners, a two day hands-on workshop was held on May 30th and 31st at the Botanic Museum in Berlin to teach the installation and configuration of the BioCASe Provider Software. 17 Participants from 9 countries will now use their knowledge to set up BioCASe installations in their own institutions.
Italy is planning to set up its own BioCASe-based biodiversity network. Funded by the Ministry of Environment, in the first phase of the project several data providers will publish at least 1 million records. The BioCASe Provider Software will be used to feed specimen information from the data providers to a central node, which will then propagate the data to the BioCASe network and GBIF.
In order to build local BioCASe expertise, a hands-on workshop was held on March 2nd and 3rd in Rome. An overview on the architecure of biodiversity networks, the basic principles and the standards used was given. On the second day the participants installed their own BioCASe instance on local computers and configured the publication of a small collection database. Once working, they were used to set up a small, local biodiversity network with a prototypic data portal allowing a distributed query.
Moreover, a BioCASe feed will provide the AVH data to the Atlas of Living Australia, whose data portal will become operational this fall.
For this reason, LifeWatch is conducting an online survey. Questions deal mainly with the LifeWatch "Services" and all the features LifeWatch could offer. Filling out the questionnaire will take about 20 minutes. At the end respondents will be able to indicate if they wish to be kept informed about the results and to subscribe to the LifeWatch Newsletter.
This software makes it possible to easily install and configure your own web portal to access biodiversity data.
The software offers a range of options for configuring the web portal. Configurable features include the specimen and observation database (implemented in either MySQL or MS-SQL and based on the GBIF-Index); the display of metadata (e.g. data about providers, institutions and collections); and query expansion process using taxonomic databases implementing the TOQE protocol.
The user interface design can also be modified without changing a single line of program code.
For more information on how to obtain and install the software please send a message to email@example.com.
This transition, in conjunction with minor changes in the underlying data model, will markedly improve the performance of these portals. The data is still drawn from the mySQL-based GBIF index.
Research into biodiversity relies on the use of specimens. These specimens are held in reference collections around the world. BCI is a central index to these collections and was instigated in October 2007 by Roger Hyam as a response to the work on Globally Unique Identifiers and Natural Collections Descriptions that was going on within Biodiversity Information Standards (TDWG).
The Biodiversity Service & Application Tracker is a collection of links to software, tools and resources useful to taxonomists. All applications and services are categorised into an expandable and otentially hierarchical system covering major biodiversity topics. The site was developed and initially populated with the help of the EDIT WP5. EDIT also certifies software to be compatible with EDIT's Platform for Cybertaxonomy, a variety of tools known to work together to assist taxonomic work.
In the long term after the project has finished (~2010) we ope the site will be maintained by the user community.
Anonymous users can search for tools and suggest new software to be reviewed. They also have the option to file bug tickets and suggest new features for the system. If they register and create an account, they can write comments to any review or even write reviews themselves that then have to be eleased for publication by the EDIT site administrator.
Each review page is dedicated to a single version of an application or service. It provides details such as system requirements, interfaces and standards, information on licensing and cost and most important a review from editors as well as a comments section at the bottom that is open for everyone.
The data chaches behinde the two portals are linked to the global GBIF data index through the "slice generator". But instead of exposing all records through one interface as GBIF does, the portals focus on European and German botanical objects respectively. The portals are continuously available during the synchronisation phase, but you may experience some slightly slower responses as usual.
The European Strategic Forum for Research Infrastructures (ESFRI) published today its selection of the most promising next generation large-scale Research Infrastructures. In the area of biodiversity research the LIFE WATCH (http://www.lifewatch.eu) plan was selected. The plan aims at constructing an e-Science and Technology Infrastructure for biodiversity data and observatories.
This initiative developed by 8 major EU scientific networks is the first step towards the realisation of the infrastructure. It builds upon preceding developments such as the Global Biodiversity Information Facility (GBIF), and brings together facilities for data generation and interoperability in support of networks of biodiversity observatories (biological collections and field sites), together with digital laboratories offering analytical and modeling tools.
The Life Watch infrastructure will boost many developments. The wealth of large data sets from different levels of biodiversity opens up new and exciting research opportunities. This large-scale approach supports the understanding and managing of the impacts of climate change on the distribution, adaptation and functions of biodiversity. The infrastructure will promote and facilitate value-added networking both with respect to data and tools, and will enable a more focused attention of the scientific communities on common problems.
The project XML Security Services for BioCASe presents the first public release of the project’s software distribution. In addition, based on the developed software components, an example scenario is online now demonstrating the integral functionality of the security services.
The project is funded by the EU project SYNTHESYS and the BMBF project GBIF-D and take place in cooperation with the Botanical Museum and Botanical Garden Berlin (BGBM) and Networked Information Systems (NBI).
Our task concerns the integration of security services providing role based access control and rights management enforcement as well as the addition of confidentiality, integrity and authenticity of data (sources) in the preexisting XML protocol environment (BioCASE). For that, some specialised XACML components and policies have been developed and implemented in conjunction with the XML-Signature standard.
The software was implemented in Java and published under the Mozilla Public License (V1.1).
For older news items please see the news archive.