Biological Collection Access Services

The European FP7-ESFRI project LifeWatch, e-science and technology infrastructure for biodiversity research and observatories is now one year into its preparatory phase, and in the next decade, LifeWatch will construct and bring into operation the facilities, hardware, software and governance structures for all aspects of biodiversity research. In order to make sure LifeWatch will live up the expectations, it is important to collect as many suggestions and contributions from future users of the new infrastructure.
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.

The new BioCASE-SYNTHESYS/EDIT portal software is now available.
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 support@biocase.org.

The SYNTHESYS data portals for European data and for German botanical data, as well as the EDIT Specimen and Observation Explorer for Taxonomists, now use Microsoft SQL Server for their database backends, which previously used mySQL.
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.

The Biodiversity Collections Index (BCI) is now online. It replaces the metadata network formerly part of BioCASE.
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 new provider software v2.5.0 has been released. It now works with Python 2.5, which eliminates the necessity to install additional python packages (apart from the module required for connecting to the DBMS you're using). Authentication and debugging support have completely been redesigned, several smaller bugs have been removed. Additional configuration templates have been added, which, for example, allow the setup of a BRAHMS 6 provider without any configuration work.

The EDIT Biodiversity Service & Application Tracker (BDTracker) is now available online http://www.bdtracker.net
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.

With the help of the Synthesys project a network for geological, minerological and paleaological data is being created. An initial GeoCASE Portal is available now based on the BioCASE Simple UI and currently 2 data sources. More data providers are in the process of joining the network which is based on BioCASE and the earth science extension EFG for ABCD.

The Synthesys and the German Botany Portal are synchronised with GBIF every night at 2am CET now.
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).

The new BioCASE portal v 2 has been released. This new user interface implementation is based on architecture study including BioCASE, DiGIR, and TAPIR protocol support, with cache query mechanisms. A bugtracker site driven by TRAC is available and will help us to manage bugs and issues in a comfortable way by its tickets mechanism.

GBIF announced that the latest ABCD 2.06 version, which had been ratified by TDWG, is now supported by the GBIF indexing and registration tools. For more information about ABCD 2 please see the ABCD documentation wiki or the ABCD CODATA site. If you still have a non registered ABCD provider out there, please include them in the GBIF registry which is easily done here: http://www.gbif.org/DataProviders/registerme

The new provider software v 2.4.0 has been released. The new version uses native python file logging for the web applications, the querytool has a simplified configuration and includes standard stylesheets for abcd1.2, abcd(efg)2.06 and darwincore. A major bug in CMF pickling was removed as well. See the version history for details.

We have created a new site for the development of the PyWrapper software: http://www.pywrapper.org. The site is driven by TRAC and will help us to manage bugs and issues in a comfortable way by its tickets mechanism. There is also a nice access to the subversion repository, a Roadmap to know where we are and some fresh documentation that we will hopefully update often using the integrated Wiki. We would like to invite everybody to participate!

The new provider software v 2.3.2 update has been released. The new version includes support for ABCDEFG; ABCD and the ExtensionForGeosciences. The EFG extension for ABCD is being developed by the Synthesys project and allows to share detailed mineralogical, palaeological and rock data. The QueryTool now is capable to query DiGIR providers for single record details.

In the framework of its SYNTHESYS related task (Providing itinerary related services, http://www.biocase.org/products/geo_services/itineraries/), the RMCA is hosting a workshop on GIS related projects around GBIF (www.GBIF.org) and TDWG (www.TDWG.org).

The workshop will be attended by several international partners of the SYNTHESYS project and by GIS experts of GBIF-Germany and Spain. The status of ongoing tasks will be presented and discussed.
A substantial part of the workshop will be devoted to evaluate several technical options and to brainstorming.
Practical Information
- Date : Wednesday 22 February  2006 - 10 to 17h
- Venue : Royal Museum for Central Africa - groundfloor of CAPA building  (Leuvensesteenweg 17, B - 3080 Tervuren).
- Provisional program  (pdf)
   If you or representatives of your Institution/department/group are interested in participating to this GIS workshop, please contact patricia.mergen@africamuseum.be (until Friday 17th).

The redesigned site informs about all BioCASE related activities. It is not restricted to the European BioCASE project or its successor Synthesys. If you or your project wants to be included in this site, please contact the BioCASE team. The old BioCASE website is still available for reference.

The Generation Challenge Program is now using BioCASE to deploy their web services infrastructure. So far 11 CGIAR centers have set up BioCASE services with support from the team at IPGRI.

This will make history. The BGBM with Anton and Walter in first line are interviewed by the Geant consortium. This is a must-see if you want to have some fun!

The new provider software v 2.3 has been released. The new version is compatible with Python 2.4. Graphviz's dot is being used to visualize the database structure in JPEGs. It ships with ABCD 2.06 instead of v2.0. The BioCASe team would like to thank all people who have been participating in the debugging and tuning of this new release. Enjoy!