TDWG
2000
DIGITIZING BIOLOGICAL COLLECTIONS
(16th Annual
Meeting of the International Working Group for Taxonomic Databases)
The 16th annual meeting of TDWG was jointly organized by the Senckenberg Museum, Frankfurt (Michael Türkay) and the Botanical Garden and Botanical Museum Berlin-Dahlem (Walter G. Berendsohn). It was attended by 94 participants from 15 countries. Abstracts for most of the presentations, including posters and computer demonstrations, can be seen at
http://www.bgbm.fu-berlin.de/tdwg/2000/Presentations.htm .
The meeting got off to an impressive start on Friday 10th November, with an evening reception held in the Senckenberg Museum – Michael Türkay introduced the two local wines in the shadow of the dinosaur skeletons!
The main meeting began the following morning, with an introduction by the Director, Fritz Steininger. He welcomed everyone to Frankfurt and the Senckenberg Museum, and gave a brief introduction to the institute. He was impressed by the international gathering, with four continents represented, and felt that this mirrored the interest in the topic of the meeting, “Digitizing Biological Collections”.
Walter Berendsohn chaired the meeting, as co-organiser and “stand-in” for chairperson Peter Stevens who could not attend. Walter continued the welcome, saying that it was unusual for a TDWG meeting to have four keynote speeches, but he felt that this showed the diverse range of the collections we had to deal with. He hoped that the keynote speeches would illustrate some of the problems that had been encountered, and which could be learnt from. Walter hoped that subgroup meetings, the traditional way of working in TDWG, would be productive and he looked forward to the reports ahead.
The first keynote speaker was Linda Hill, from the Alexandria Digital Library Project, University of California, Santa Barbara, USA. This project was one of the six original digital library projects funded by the NSF, and she described how it allowed a distributed collection to be searched in a generic way. There is a digital gazetteer (a geospatial dictionary of geographical names) with over 4 million entries, and comprising of 3 main core elements – the name, the footprint (location) and type (from a controlled vocabulary of categories for places/features). Full details can be obtained from the web site http://www.alexandria.ucsb.edu/ . This gazetteer was created by combining two US federal gazetteers, but this involved a lot of effort since they were quite different. Linda emphasised how important standards were to the flow of information, and that XML and Z39.50 were important to the project. Linda’s full presentation can be seen at
http://www.alexandria.ucsb.edu/~lhill/Powerpoint_presentations/Frankfurt_Presentation_all.ppt
in Powerpoint format, or
http://www.alexandria.ucsb.edu/~lhill/Powerpoint_presentations/Frankfurt_Presentation_all.htm
in html.
Charles Copp from Environmental Information Management (EIM), was the second keynote speaker, talking about the “UK Biodiversity Network Data Model and its implementation in Recorder 2000”. He described how he had been given the task of rewriting the Recorder software, but found that it was a much bigger job than expected – a logical model for recording data also had to be developed, and he hoped it could become a standard data model to encourage people to work together. In the design, a modular approach was used, as many people will be involved in maintenance, and standard dictionaries were used to standardise input, and to encourage intelligent retrieval. There is distributed data entry (the owner of the data can always be traced), and full validation of data when it is imported, with XML being used for data transfer. Further details can be obtained from Charles’s paper at http://www.tdwg.org/tdwg2000/NBN_Data_Model.pdf and also from the National Biodiversity Network’s website http://www.nbn.org.uk .
The third keynote speaker was Stan Blum, from the California Academy of Sciences, San Francisco, USA. In association with Anton Güntsch from Botanischer Garten und Botanisches Museum (BGBM) Berlin-Dahlem, Stan had been working on “The biological collection profile: a basis for integrating collection information systems”. He reported that there were emerging data retrieval systems for collections which imposed a “federation” schema on heterogenous databases, so that a user could formulate one query and a client translated this for the various databases and integrated their responses into a single answer for the user. He listed various examples of these – The Species Analyst, REMIB and ENHSIN. But these three systems are currently independent and do not talk to each other so Stan proposed that TDWG should endeavour to encourage the development of a standard profile to help with the interoperability. He suggested that a subgroup be set up to serve as a forum in which developers, providers and users could communicate, and reconcile differences, and asked for opinions from the meeting. Gary Waggoner commented that there were many funding agencies interested in more global views so this interoperability was important. It was agreed that a subgroup discussion should take place during the meeting, and Walter suggested that the place for this was the Accessions subgroup. Stan’s presentation can be viewed at [ link coming soon ] and a summary of the subgroup’s discussion can be found at http://www.bgbm.fu-berlin.de/TDWG/acc/2000Meeting.htm .
The final keynote speaker was
Simon Owens from Royal Botanic Gardens, Kew, UK. In association with Alison
Prior, his paper was entitled “Beset with pitfalls – specimens and databases,
intellectual property and copyright”. Simon explained that during his five
years as Keeper of the Herbarium at Kew, he had been exposed to a lot of
intellectual property rights issues etc. He explained that Kew now employ two
lawyers to deal with these matters – one handles issues relating to the
Biodiversity Convention, and the other deals with policy and implementation. Ownership
of all aspects of herbarium specimens has to be considered – DNA, seeds,
drawings, paintings, images, as well as the ownership of the specimen itself.
European institutions hold enormous global collections, and access is generally
free from money-exchange to scientists, but they may incur travel costs,
stationery etc to see or borrow the specimens. Governments are now very keen on
electronic distribution, as it should reduce costs. However, Simon reported
that there are many issues to consider, which became apparent during discussion
about the European Natural History Specimen Information Network (ENHSIN):
exchange of information from collections; reducing direct financial support
from governments; intellectual property rights (IPR); Convention of Biological
Diversity, particularly those issues on access and benefit sharing. The need to
get alternative sources of funding has led to many institutions considering
charging for access to the information – but do they have the right?
Intellectual Property Rights are totally separate from the rights to the
physical property in the work itself. Databases can have copyright protection,
and database protection, which may belong to two different people. If employers
don’t specify who owns copyright it can end up with the employee even if the
employer provided the resources to carry out the work. Within ENHSIN, no museum
or garden yet has a firm policy on IPR. Of those that have published their own
website, only one has a copyright statement and that is only on the home page.
So copyright may be forfeited in every case. All are considering some form of
charging, but for what to whom is not clear. The REMIB system from CONABIO is
aiming to improve their free distribution of data, but they will be respecting
database protection, and will be acknowledging the source of all information –
this is very important according to Simon. CONABIO and the owner of the data
can restrict access to sensitive data such as the location of rare species.
Another important point is that REMIB does not accept responsibility for
accuracy of the data. This system represents the general trend for free
distribution, but with some restrictions on sensitive information. Simon’s full
presentation can be seen at
http://www.tdwg.org/tdwg2000/ipr.htm.
Officer Reports:
The afternoon session on Saturday 11th November began with the TDWG business session. Georgina MacKenzie presented the secretary’s report summarising the activities of TDWG during the year since the last meeting. This activity was mainly about making contacts with CODATA and GBIF (see http://www.tdwg.org/tdwg2000/2000secrep.htm), and the report was accepted by the meeting.
In the absence of the treasurer John Wiersema, Walter Berendsohn read the report that John had submitted. It showed a drop in the reserves, but the balance did not include many subscriptions etc. taken just before and during the meeting. John was retiring from the position so the meeting accepted the report and agreed that thanks should be conveyed to John for his efforts during his term as treasurer. See http://www.tdwg.org/tdwg2000/2000treas.htm for details.
Subgroup Reports:
Walter reported that the Executive committee had decided to disband subgroups that showed no activity or did not provide a report. This involved the zoology sub group, and the names subgroup (to extend the standard to zoology). But it should be noted that during the remainder of the meeting, there was activity in these areas, leading to these subgroups being resurrected!
Dick Brummitt had submitted a report, even although he had tried to retire as convenor in 1999! In his absence at the meeting, Paco Pando presented the report. Paco had been acting as editor to get the second edition of the geography standard published – Dick reported that he hoped this would be achieved before the end of the year. See http://www.tdwg.org/tdwg2000/Geog2000report.htm for further details. It was hoped that during the meeting, another convenor could be appointed.
In the absence of the convenor Frances Cook, Mark Jackson from Kew reported that Frances was on a career break at the moment, so a new convenor was required. Walter asked the subgroup members to find a replacement.
Stan Blum summarised that this subgroup aimed to deal with changes in the organisation of TDWG. He had presented a paper at the last TDWG meeting (see http://www.tdwg.org/process/tdwg99_blum.html), and there had been some discussion in the Executive Committee meeting about modifying the constitution and byelaws, to remove the need for a postal vote for example. An email list had been established for the group (see http://usobi.org/archives/tdwg.html), and Stan said he would be sending out an email to start the discussion.
Botanico-periodicum-huntianum (BPH)
Dave Boufford reported that a new edition was being produced by the Hunt Institute for Biological Documentation.
Structure of Descriptive Data (SDD)
Gregor Hagedorn reported that since the last meeting an email discussion list had been set up, and was very active (see http://usobi.org/archives/tdwg-sdd.html). So far, it had been a fruitful discussion - although not in complete agreement, some progress had been made. It was agreed that a universal lexicon was not possible, and the aim of the group was to have a standard on how to describe data sets. There was general agreement that the new structure description should be in XML, but conflict between those who are developing applications in XML. The group have found it difficult sometimes to identify which level of problem is being discussed. Gregor finished by saying that the planned new structure description is a recommendation, not a standard.
Walter Berendsohn said he thought the aim of the subgroup for this meeting was to define the group’s direct aim! He had kept the web site updated
(see http://bgbm3.bgbm.fu-berlin.de/TDWG/acc/) but asked for contributions to continue. He reported that the discussions on what to do with collection data had mainly been project based, and to make it more universal a common profile was required, as described by Stan. He had been seeking funding to set up a work group to discuss this, and felt that would encourage a real step forward.
Walter asked if the attendees felt any new subgroups should be set up to discuss particular topics. Reed Beaman from Royal Botanic Gardens, Sydney, Australia asked if a group could be formed to discuss geographic data transfer standards. He felt the existing geography group should continue, to maintain the existing geography standard. But there were other areas that needed discussion. Several other attendees agreed, and agreed to meet later to discuss this further.
After the business session was concluded, the meeting split up into groups preparing for subgroup meetings.
After coffee, there was a special session on digital imaging of specimens. Several speakers illustrated how their organisations had approached this topic, and links to their presentations are available below:
Jorg Habersetzer: Digital Imaging at the Senckenberg Museum
http://www.bgbm.fu-berlin.de/tdwg/2000/Abstracts/Habersetzer.htm
Robert Huxley: Planning and resourcing a digital imaging project at the Natural History Museum, London
http://www.tdwg.org/Huxley.htm
Gerald Guala: Lessons from the Virtual Herbarium
http://www.bgbm.fu-berlin.de/tdwg/2000/Abstracts/Guala.htm
http://www.virtualherbarium.org/lvh.htm
Gregor Hagedorn, Dagmar Triebel & Markus Weiss: LabelScan: A tool to optimise the establishment of big collection information systems using selective label data transcription
http://www.bgbm.fu-berlin.de/tdwg/2000/Abstracts/hagedornEtAl.htm
http://www.tdwg.org/tdwg2000/Hagedorn_TDWG2000.htm
Dominik Röpert, Heidemarie Nowak-Krawietz & Walter G. Berendsohn: Digital imaging of specimens at the Botanical Museum Berlin-Dahlem
http://www.bgbm.fu-berlin.de/tdwg/2000/Abstracts/RoepertEtAl.htm
There were also poster sessions and computer demonstrations during this late afternoon session, and throughout Sunday, 12th November.
Sunday, 12th November
In parallel with meetings of subgroups such as zoology and SDD, there was a special session on “Unit-level Information Systems”:
Rudolf May: Floristic mapping data in German plant information systems.
http://www.bgbm.fu-berlin.de/tdwg/2000/Abstracts/May.htm
Sabine Roscher: Federal Information System on Genetic Resources (BIG).
http://www.bgbm.fu-berlin.de/tdwg/2000/Abstracts/RoscherBIG.htm
Liliana Lara: Informatic tools for the management of biodiversity information.
http://www.bgbm.fu-berlin.de/tdwg/2000/Abstracts/Lara.htm
Jacques Le Renard: TAXIS, a taxonomic information system for managing large biological collections.
http://www.bgbm.fu-berlin.de/tdwg/2000/Abstracts/LeRenard.htm
Francisco Pando de la Hoz: Bibmaster - a database application for nomenclature, literature and specimen management.
http://www.bgbm.fu-berlin.de/tdwg/2000/Abstracts/Pando.htm
This was followed by the subgroup meeting of the Accessions group, and another special session on “Taxonomic databasing in China”:
Suhua Shi & Mingguang Li: Recent development of biological databases in China.
http://www.bgbm.fu-berlin.de/tdwg/2000/Abstracts/SuhuaShiEtMingguangLi.htm
Hong Song: 'Flora On-line' and the Flora of China databases.
http://www.bgbm.fu-berlin.de/tdwg/2000/Abstracts/Hong.htm
Mingguang Li & Suhua Shi: Practical standardisation method of herbarium databases.
http://www.bgbm.fu-berlin.de/tdwg/2000/Abstracts/MingguangLiEtSuhuaShi.htm
The final session of the 2000 TDWG Meeting was another business session. The session to elect the Executive Committee was led by Scott Peterson. He explained that the previous committee had made some suggestions and asked Gary Waggoner to field these suggestions to the meeting for comments, other suggestions etc. Gary had unfortunately had to leave the meeting early so had passed on the task of presenting these suggestions to the meeting for a vote. The proposed Executive for 2001 was:
Chairperson: Jim Croft, Australian National Herbarium, AUSTRALIA
Treasurer: Walter Berendsohn, Botanischer Garten und Botanisches Museum, Berlin-Dahlem, GERMANY
Secretary/
Web Master: Georgina MacKenzie, BIOSIS UK, UK
Members: Stan Blum, California Academy of Sciences, USA
Gerald “Stinger” Guala, Fairchild Tropical Gardens, USA
Michael Türkay, Forschungsinstitut Senckenberg, GERMANY
Regional Secretaries: Asia: Li Mingguang, Sun Yatseng University, CHINA
Latin America: Liliana Lara Morales, CONABIO, MEXICO
North America:Dave Boufford, Harvard University, USA
Oceania: Barry Conn, Royal Botanic Garden, Sydney, AUSTRALIA
This proposed committee was accepted by the meeting. Walter thanked Scott and Gary for their efforts in obtaining the volunteers! He also thanked Michael Türkay and the Senckenberg museum for all their efforts in organising the meeting, and said that the committee was suggesting that an institutional membership be given to the Senckenberg as thanks. This was agreed.
Zoology
Michael Türkay reported that the initial meeting identified some problems and ways of getting ideas together. There were 4 core areas: marine zones for geography codes; status – occurrence and abundance (amend POSS standard?); a controlled vocabulary for life stages etc; and knowledge of the differences between the ICZN code and the botanical code.
Spatial Data Standards
Reed Beaman reported that “Stinger” Guala would create a web site to report their activities. They agreed that there was a need to examine the existing geography standards, look at OpenGIS, and the ADL gazetteer. Latitude, longitude and elevation would probably form the core of any “standard”, but the details were still to be worked out. They also agreed that metadata was very important, with the need to develop a transfer format in XML. See his report at http://www.tdwg.org/tdwg2000/SpatialData.htm for further details.
Frank Bisby apologised for the inactivity, but said that there was a growing need to highlight the differences between the nomenclatural codes, and to look for ways of dealing with viruses and cultivated plants (trade names etc). He hoped there would be a meeting in the following year, and he would report on this at the next TDWG meeting. Walter commented that the work on the BioCode should be taken into consideration.
Walter reported that some interest had been shown by Helmut Knüpffer and Jörg Ochsmann:
“In connection with our task to index free-text entries of “Mansfield’s Word Encyclopedia of Agricultural and Horticultural Crops” with regard to economic uses, we will contact Kew staff in order to utilise the “Uses” standard. We will discuss issues of economic uses during this process. Possibly this will result in proposals to update the Economic Botany Standard. This might be considered as a revival of this TDWG subgroup.”
Gregor reported that this group had a very lively discussion. They decided they would develop a web site to help with resource discovery, and hoped to organise a workshop on this topic, since they needed more time to discuss the various issues in a more concentrated fashion. See his report at http://www.tdwg.org/tdwg2000/SDDreport.htm for further details.
The meeting accepted the proposal that Neil Brummitt and Rafael Govaerts should be co-convenors of the geography sub-group. There was an informal gathering of a few interested members at the meeting, with the main topic of conversation being the differences between the geography and geospatial subgroups, and the need to communicate with them.
The final topic for the business meeting was the date and time of the next meeting. It was hoped that this would be held in Sydney, Australia from November 10 – 11, 2001, but this was yet to be confirmed. Hopefully, there would be several other meetings around that time, such as Species 2000, IOPI and others.
Walter asked if there were any suggestions for a special topic, as he had found it very useful when organising this meeting. He suggested three topics:
Geo-referencing of collection data
Modern Fauna and Flora – web-based taxonomic descriptions, role models etc.
Checklists – how to organise on world wide web, coordinate, bring together.
Stan Blum commented that if all the planned/requested workshops take place, then they should be reported on at the main meeting, so the agenda might be full!
Frank Bisby commented that further contact with CODATA and GBIF may help with funding for meetings – Walter reminded everyone that the 2000 meeting had been co-sponsored by CODATA.
The meeting was then formally closed by Walter, with thanks again to everyone involved in the organisation of the meeting.
GMM 12/12/00