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Aims
NA D will engage and aid the active participation by all European
Countries in the delivery of information systems about their taxonomic
collections. This system will bring the information held by SYNTHESYS
partners to all the user sectors that depend on organism-related
information for their research and/or decision making purposes.
NA D will build on and actively incorporate results of initiatives such as BioCASE and ENHSIN, which have laid the base for a European collection information service, and aims to take the research work from these initiatives as the core of a practical, sustainable, Europe-wide information network for users of taxonomic information. There will also be interaction with global biodiversity informatics infrastructure, represented by GBIF, and related European projects, such as ENBI.
Objectives
• Extend the amount and increase the technical quality and availability of networked data resources
• Pool, extend, and synchronise semantic definitions, standard data, and data standards
• Develop User interfaces
Progress and Deliverables
SYNTHESYS Help Desk:
The SYNTHESYS Helpdesk
provides support for collection holders intending to use the BioCASE
provider software for connecting their collections to the BioCASE/GBIF
network infrastructure. This includes help in understanding the
principles of the architecture, planning the actions and preparing
the collection databases for publication, installing and configuring
the provider software, troubleshooting, mapping the collection database
to the ABCD schema as well as bridging the gap between the collection
holder and the GBIF secretariat in Copenhagen. Assistance is provided
mainly by eMail contacts or telephone, but personal support at the
provider's institution is possible in difficult cases.
Contact: Jörg Holetschek
phone: +49 (0)30/838-50150
eMail: j.holetschek {at} bgbm.org
SYNTHESYS BioCASE Portal
SYNTHESYS is pleased to announce the launch of the BioCASE Portal
(Biological Collection Access Service Europe): search.biocase.org.
The BioCASE portal uses basic web services constructed by GBIF in
addition to some specialized ones. It is complementary to the GBIF
portal in that it provides more detailed information about specimen
and observation data in the GBIF network, especially when these
are based on the rich ABCD standard.
The European Distributed Institute of Taxonomy (EDIT) will support
further development with the aim to integrate the BioCASE portal
into the EDIT Internet Platform for Cybertaxonomy. This is to provide
an interface for taxonomic researchers, who need to access more
detailed data than do many other users of the GBIF portal.
This BioCASE portal demonstrates the modular and distributed nature
of the GBIF infrastructure, which allows regional networks such
as BioCASE to both contribute to and build upon the global efforts
in biodiversity informatics led by GBIF (www.gbif.org)
Objective 1: Extend the amount and increase the technical quality
and availability of networked data resources
Year One
A user requirements analysis was carried out by questionnaire
to the user community. A concept for rights management and access
control was dared to the user requirements analysis. A substantial
report was produced based on the results of the survey and including
the rights management and access control concept. This work was
presented at a number of meetings and a summary will be included
in the BioCASE publication. The helpdesk was set up to support new
and existing data providers.
Analysis
of the User Requirements
Analysis
of Duplicate detection Software
Year Two
A provider configuration upgrade tool
was developed and work started on the implementation of an annotation
feedback system for specimen data and on the BioCASE provider software
upgrade for the new TAPIR protocol.
The prototype of the authentication and rights management services
was developed and a feature list regarding the requirements of the
final version has been agreed. Based on these requirements, the
final version of authentication and rights management services was
implemented. An annotation feedback software enabling users to annotate
ABCD records was started: an authentication module as well as a
module for editing and validating xml records containing collection
information has been finalised.
The collection data User interface has been maintained throughout
the reporting period. SQL queries to the central registry database
have been optimized so that the performance of the system improved
significantly
Provider
Configuration upgrdade Tool ABCD 1.2 - 1.5
Report
on Operational Component of Authentication Services
Objective 2: Pool, extend, and synchronise semantic data definitions,
standard data, and data standards
Year 1
An XML schema is close to completion for handling biographical
data based on units of data extracted from biographical dictionaries
etc. As part of ongoing research into sources of biographical information
on people involved with the natural world a number of published
and unpublished sources were located at the NHM, London
Report
on the development of BiogML, an XML schema for biographical information
Year 2
The work on biographical data to create a data standard for holding
biographical data about workers in the biodiversity / conservation
subject area, leading to an authoritative Union List of Naturalists’
Names, directory of expertise or possible third-party name service
was continued and Version 1.0 of BiogML delivered. A revised timetable
swaps the timings for the remaining part of the Biography task with
the Collection task (Natural Collections Descriptions – NCD).
A preliminary version of this new standard was put to review at
the TDWG meeting in St. Petersburg, Russia in September 2005. The
activities concerning the development of comprehensive information
models for neglected collection information domains (anthropology
and earth sciences) were started, and workshops with experts were
held in both fields to mobilise data and work on standard development.
Reports on the outcome of the workshops were written. For earth
sciences collections an extension schema called EFG (extension for
earth sciences) ready for reference implementation has been created.
Report
on Geosciences Workshop
Standard
extension for Earth Sciences Collections
Standard extension
for Anthropological Collections
Objective 3: User interfaces
Year 2
Based on the user feedback of the BioCASE User Interface (UI)
an analysis of the different types of UI improvements and technical
solutions to obtain a new modular and adaptable UI was carried out,
the result of which is described in a modularization study. For
user testing and user interface feedback, a WIKI site was established.
This site also includes a password-protected area that allows for
publication of interview transcripts and initial survey analysis
results to be viewed. Existing end user requirements were studied
and underrepresented potential end user groups identified. Interviews
with 36 potential end users covering a range of disciplines were
carried out to give a picture of the tasks to be performed and the
data required for these tasks. A report detailing the results of
the survey was submitted. A novel cache prototype based on the current
GBIF caching system has been implemented and a report explaining
cache prototype issues has been submitted. A review of existing
GIS standards and software was completed and the Open Source software
Deegree was chosen for the task. The same software is to be used
as for the GIS task with which close collaboration has been established.
UI
Analysis and Modularisation Study V2
Detailed
UI Architecture Study V2
UI
Requirements Analysis
The
SYNTHESYS Cache Prototype
Report
of Exisiting GIS Standards and Software
Core
GIS Services
Milestone
Report
Meetings
NA
D First Standardisation workshop. BGBM, Berlin. 18&19 th November
2004
UI
task force meeting. MNHN, Paris. 14&15 th January 2005
Workshop
on standardusisation of Anthropological Collection Data. HNHM, Budapest.
12&13 August 2005
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