HISCOM 2006 AGM Hobart
The 2006 HISCOM Annual General Meeting was held in Hobart from Monday 9 – Wednesday 11 October, 2006. This document represents the minutes of the meeting.
- 1 Attendance and Apologies
- 2 Election of Officers
- 3 Previous Minutes
- 4 Plant Systematics Research in Australasia (PSRA)
- 5 Australian Tropical Herbarium
- 6 Australian Plant Census (APC)
- 7 Commonwealth Environment Research Fund (CERF)
- 8 Australia’s Virtual Herbarium (Session 1)
- 9 AVH and Early Warning System (EWS Session)
- 10 TDWG Standards Development Process
- 11 Australia’s Virtual Herbarium (Session 2)
- 12 Data Validation
- 13 ABRS Report
- 14 Imaging (Te Papa Report)
- 15 Australia’s Virtual Herbarium (Session 3)
- 16 CHAH Web Presence
- 17 Acronyms
- 18 Conclusion
- 19 Notes
Attendance and Apologies
- Bill Barker (State Herbarium of South Australia, Department of Environment and Heritage, South Australia)
- Peter Bostock (Queensland Herbarium, Environmental Protection Agency, Queensland)
- Lyn Cave (Herbarium, Tasmanian Museum and Art Gallery, Tasmania)
- Gary Chapple (National Herbarium of New South Wales, Royal Botanic Gardens, New South Wales)
- Paul Coddington (The South Australian Partnership for Advanced Computing, The University of Adelaide, South Australia)
- Ian Cowie (Northern Territory Herbarium, Department of Natural Resources, the Environment and Arts, Northern Territory)
- Philip Edgar (Museum of New Zealand Te Papa Tongarewa, Wellington, New Zealand)
- Raelee Kerrigan (Northern Territory Herbarium, Department of Natural Resources, the Environment and Arts, Northern Territory)
- Robyn Lawrence (Australian Biological Resources Study, Department of the Environment and Heritage, Canberra)
- Peter Neish (National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Victoria)
- Laurence Paine (Information Technology, Department of Tourism, Arts and the Environment, Tasmania)
- Ben Richardson (Western Australian Herbarium, Department of Environment and Conservation, Western Australia)
- Kevin Thiele (Western Australian Herbarium, Department of Environment and Conservation, Western Australia)
- Alison Vaughan (National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Victoria)
- Greg Whitbread (Chair; Australian National Herbarium, Centre for Plant Biodiversity Research, Australian Capital Territory)
Election of Officers
Greg Whitbread accepted a nomination to fill the role of Convenor a second year running. Nominating the next chair a year ahead was discussed with the result that Peter Bostock was elected Convenor for the following year. It was agreed that Peter would work with Greg this year to try and bring some additional stability to the role, especially during the changeover period. Ben Richardson nominated and was elected Minute-taker for the meeting.
Relationship between HISCOM and CHAH meetings
Will try and keep the quarterly meetings going in a fairly rigid structure.
2005 Action 3
Submit a request for advice to ASK-OSS (http://www.ask-oss.mq.edu.au/) at Macquarie University — a group who already understands the licenses. [Laurence Paine, in progress]
|Right to perform||Yes||Yes||Yes||Yes|
|Right to display||Yes||Yes||Yes||Yes|
|Right to copy||Yes||Yes||Yes||Clarification needed|
|Right to modify||Yes||Yes||Yes||Clarification needed|
|Right to distribute||Yes||Yes||Yes, under license||Yes|
GBIF uses the Mozilla Public License, which effectively references GPL and LGPL.
We’d be happy to see:
- Developing a “plug-in” would not need to be open source;
- Creating a new version of the AVH software would need to be done in open source.
Postponed until we talk to Paul Coddington
2005 Action 4
- Dynamic Web Hosting;
- Chah.org.au was registered; hiscom.chah.org.au available for HISCOM use;
- Linux-based machine, tomcat, apache, mysql, perl, php, python;
- Mailing lists etc.;
- In progress.
2005 Action 5
2005 Action 6
John Hosking gave us his list, but it was large (over 5,000 names), which was too large to use as a “pick list” in software.
2005 Action 7
2005 Action 8
2005 Action 9
2005 Action 10
2005 Action 11
2005 Action 12
2005 Action 13
Both need to be developed further before this is possible. Additionally, Greg Whitbread noted that a full concept needs to be used in DET slips (i.e. “in the sense of”) before the mapping of names in AVH is possible.
2005 Action 14
Completed. Resulted in another agenda item for this meeting.
2005 Action 15
No action taken. Will discuss.
2005 Action 16
The minutes were otherwise accepted.
Plant Systematics Research in Australasia (PSRA)
This is a database of current plant systematics research in Australia (http://www.anbg.gov.au/chah/psra/), created from a book by Chris Puttock but is out-of-date.
- Links to authors of plant names would be useful;
- Links to author’s current official institutional web profile would be useful;
- Suggest that IT staff, artists, field workers etc. could be included.
The redevelopment of PSRA is warranted.
Australian Tropical Herbarium
What advice could HISCOM provide as to how best to database?
- Have records in FoxPro;
- Setting up the Australian Tropical Herbarium;
- Amalgamating collections from James Cook University (JCU), Atherton Herbarium (QRS), and Mareeba (MBA).
An interim option is for CANB to provide a hosting service for the data.
Australian Plant Census (APC)
Available in basic electronic form online (http://www.anbg.gov.au/chah/apc/) and 60% of the taxa have been checked. The draft APC was ratified by CHAH and loaded into the APNI database. A global plant census may need to be done the same way, group by group, but also by region to ensure full coverage.
- The names in most specimen databases are not identified/determined to a concept;
- Concepts are required in order to properly link between names. For example, Viola hederacea Labill. (Labillardière’s concept) and Viola hederacea Labill. (Thiele & Prober’s concept) will be used by different institutions, but without the full concept there is no way to disambiguate the names.
That we integrate the census mapping process into the APC working group process to decrease the amount of double handling.
A draft protocol for Recommendation 3 to be made available by the next teleconference. [Greg Whitbread et al.]
That each Working Group conspectus as ratified by CHAH be recognised in APNI to make it equivalent to other publications. This means that each APC concept gets an APNI entry in its own right so that the decisions of the APC Working Group are recognised properly.
CANB to report the practicality of the above change to APNI at the next teleconference. [Greg Whitbread]
Commonwealth Environment Research Fund (CERF)
(Kevin Thiele, Greg Whitbread.)
Federal Government announced a large round of funding recently (last year?) – for $5-8 million per grant. Most of the money was for ecology work, including reserve selection. Judy West and others put in a proposal for taxonomic work. Plan is to do some taxonomy in a smarter way with electronic systems (doing taxonomy online/electronically, essentially).
Implications for HISCOM
Australia’s Virtual Herbarium (Session 1)
(Bill Barker, Ben Richardson, Kevin Thiele.)
|Institution||BioCASE Installed||Software platform||Data (subset)||Data (full set)||Dynamic?||Completion (full time weeks)|
|Perth||In development only||Solaris||Yes||In progress (ca 80 fields)||Yes (in development)||4|
How to simplify the process of implementing a BioCASE web service?
Building a web appliance that has all the documentation to ensure it meets all security considerations would cost as much as $250,000. Unlikely to find a simpler way if an external contractor or HISCOM (perceived as an external source) supplied the IT solution. Systems administration needs to be convinced of the reliability of any installation as a secure, effective and robust product.
With the availability of the new CHAH web server, it is now possible that one portal could be used, rather than institutions developing one each.
- Timing of data updates would be an issue;
- Heartbeat queries to allow any one portal to list others that are “alive”, and thus make it easier for the user to move to another site if the one they are using is not working.
The advantage of multiple portals was the ability to use another portal in the event that one was unavailable. It is likely that portals will be provided by herbaria on the basis of their ability to install and maintain it separate from the BioCASE web service.
AVH and Early Warning System (EWS Session)
(Paul Coddington, Bill Barker.)
Paul Coddington joined the meeting on the morning of Tuesday 10 October to present the current development status of the AVH and EWS projects.
A subset of the MoU subset would constitute: geocode, names, dates, and accession number. This could be used as the basis for getting the four other sites (BRI, DNA, HO, NSW) online sooner, along with hosting direct on the SAPAC server.
Get sign-off on two providers delivering the full dataset dynamically to the SAPAC test site and complete Quality Assurance Testing to complete CHAH’s contract with SAPAC. [AD, CANB, MEL, ?PERTH, Paul Coddington]
AVH and EWS Presentation
- Prototype of AVH Stage 3 now running at SAPAC
- Conforms to standards
- Improved interface, functionality, robustness
- Support TAPIR
- Migrate to using standard GBIF components and code?
- Web service interfaces?
- Data cleaning services (preliminary work done)
- Atlas of Living Australia
Quality Assurance Testing
It is critical to the eventual quality of the AVH and EWS that HISCOM members get involved in testing the sites at their test locations:
The most basic requirement for the Weed EWS is recordID, botanical name fields, date of edit, date collected, and geocode. A file containing these fields for each specimen might be a quick way to populate the EWS, temporarily (particularly for those herbaria without a BioCASE web service). Alternatively, this file could be done each night as a cron job that is emailed to SAPAC.
Could existing AVH provider scripts be updated to include the necessary extra fields?
This would only include “in the wild” collections, not cultivated records.
Fast track EWS and AVH with an interim caching solution.
Paul Coddington to check and report back to HISCOM the format for text files to be imported into EWS or AVH. [Paul Coddington]
Herbaria will follow this Recommendation and deliver at least the CHAH MoU subset of fields to the AVH Cache. [BRI, DNA, HO, NSW, PERTH]
Herbaria not delivering data to check and report back to HISCOM whether it is possible to provide their whole specimen database in HISPID or CSV format and a timeframe for this. This will provide an interim Australia-wide view. [BRI, DNA, HO, NSW, PERTH]
Flagging cultivated records in AVH
This is considered to be something to look at in a future update to the site.
TDWG Standards Development Process
(Lee Belbin, TDWG Infrastructure Project Manager.)
- Redevelop TDWG’s infrastructure
- US$1.5M over 2.5 years
- Two rounds of ca US$250,000 grants
- 3 F/T, 2 P/T staff — Roger Hyam (architect), Ricardo Peirera (software), Donald Hobern, Stan Blum
- Improve processes (Lee, Stan, Roger)
- Online environment (Ricardo)
- Documentation (Roger)
- GUIDs (Donald and Ricardo)
- Rod Page has examples (http://ispecies.blogspot.com/)
- TDWG ongoing support (Lee)
- What can TDWG do for you?
- Unique forum
- Cost benefits
- Enable synergies
- Minimise reinvention
- Raises profile
- Feedback & direction
- Max one page
- What are you addressing?
- Where is it going to happen?
- How much do you want?
- What are you going to produce?
(Proposals for TDWG support were discussed later.)
Lee indicated that Australia was uniquely placed to be a case study for developing TDWG policies. HISCOM and Paul Coddington were seen as potential resources.
- HISCOM management and operational framework
- AVH Documentation
- LSID implementation policy, plan and costing
- TAPIR plan, costing and implementation
- Funding of the AVH development (e.g. validation annotations by registered users)
That CHAH support HISCOM’s approach to TDWG (via CHAH) for funding for HISCOM activities.
HISCOM develop a draft proposal for TDWG funding along the lines suggested by Lee Belbin. [All HISCOM]
Australia’s Virtual Herbarium (Session 2)
Press ABCD to clear up confusion between the ABCD schema dateTime and dateTimeISO types. [All HISCOM]
CANB to fix rank issue. [Greg Whitbread]
AD to fix document structure issue. [Bill Barker]
Agent Text and Sequence ID do not need to be changed. [Resolved]
HigherTaxonRank must comply with the ABCD constraints. [All HISCOM]
States must be provided in full, mixed case. [All HISCOM]
Country Name must be provided in mixed case, e.g. (“Australia”, not “AUSTRALIA”). [All HISCOM]
Agreement 1: For the mandatory fields, if the field contains one of the values from HISPID that represent “unknown”, it should be left in the field, and considered real data (e.g. State: “Unknown”, Country: “Unknown”, Collector’s Name: “Anonymous”), others as specified in HISPID. Any non-mandatory field that contains unknown data should not be sent. Collection Date should contain “s.dat.” when it is “unknown”, and Collector’s Identifier (cid) should to contain “s.n.” when the collecting number is unknown.
HISPID Extension to ABCD
The fields that are unavailable in ABCD are documented on the MEL CVS site. There was an initial idea to extend ABCD to include a number of extra HISPID-specific fields. This extension is to ensure the transfer of a complete specimen record is possible without loss of meaning, as opposed to the export of data in some agreed format for AVH.
Method of Extension
- The UnitExtension element of ABCD can be used to extend it temporarily;
- MeasurementOrFact can be used for some small number of additional fields.
Document the outcome of implementing a number of HISPID fields as MeasurementOrFacts in ABCD and standardise the parameter name. [Peter Neish]
HISCOM to review and implement in our BioCASE mapping. [All HISCOM]
We could develop a suite of validation tests that could be published and used to provide some guarantee, e.g. a level of compliance, to which a set of data passed.
As the AVH has the ability to perform data validation, and it will also be a store for Australian records, having a way to annotate the fact that a record in the AVH Cache has been marked as containing an error of some kind might be useful.
In order to properly enable data validation, and the return of that information back to institutions, Life Science Identifiers (LSIDs) are a critical part of the technical implementation. Use of LSIDs are potentially useful, for example in identifying/tracking duplicate records and maintaining access to data as it was at a moment in time, amongst other uses.
That HISCOM produce a Working Paper on spatial data validation preliminary to development of a more complete data validation policy. [Alison Vaughan]
That CHAH agree to extend the Data Use Agreement to include requests for a report on data fitness at the individual record level. The Agreement needs to require users of the data to report back invalid records.
[CHAH noted subsequently that, under a previous agreement, it is currently feeding AVH data requests through NSW (Brett Summerell, Chair of CHAH; Gary Chapple) and using NSW’s Data Use Agreement until the new AVH data delivery method is in place.]
At the Cache level we alter the specification so that annotations can be attached to specimens for the following reasons:
- For those with research-level access to AVH to flag an error in a specimen, or otherwise annotate a specimen record;
- For other herbaria to flag that they have changed the data for a duplicate of a specimen held elsewhere;
- The annotation would include: the date of annotation, a note, who made the annotation, and the specimen the annotation refers to. [All HISCOM].
SAPAC to quote on the annotation proposal with the view to HISCOM approaching TDWG for funding. [Paul Coddington]
That CHAH supports an Extraordinary HISCOM meeting on LSIDs, subject to a successful CHAH request for TDWG funding.
That HISCOM research information on LSIDs and inform ourselves of the GBIF and TDWG requirement for LSIDs for discussion at the next HISCOM Teleconference, or in preparation for an Extraordinary HISCOM meeting on LSIDs subject to TDWG funding. [All HISCOM]
Australian Faunal Directory
AFD replaces the Platypus fauna checklist software. This system is now an online web application at beta stage written in Java rather than a desktop Access application written in VB.
Australian Marine Algal Names Index
- Available to public in late September 2006;
- Includes name and cross reference information for 2478 Australian macroalgal names as well as protists and diatoms, many from Roberta Cowan;
- The recent edition of Biologue includes an article on the new AMANI development.
ABRS Flora Online
- On hold for the last year while Helen Thompson has been acting ABRS Director, but the new Director, Cameron Slatyer, has started;
- Incorporates information from Australian Plant Census.
Australian Biodiversity Information Facility (ABIF)
Not yet fully specified, but are currently trialling various technologies.
- Due for launch in February 2007;
- Taxonomic Names Service — http://tns.abif.org/NameService/gui/search.html;
- Specimen Cache of 3 million records;
- BioCASE AVH records to come, depending upon discussion of technical implementation with Paul Coddington;
- Data sharing using SOAP and binary SOAP for images;
- Ajax page refreshing;
- Google Maps map tiling to represent many specimens.
Discussion surrounded the presentation of the ABIF and the need for understanding and communication, in any presentation of the site and its functionality of its context in relation to GBIF, national portals for GBIF, the AVH and OZCAM. It was pointed out that this was the subject of considerable discussion in Alice Springs a year before of HISCOM, CHAH and a joint CHAH, CHAFC and ABRS meeting.
There is a need to rationalise and coordinate effort to maximise resources and returns for effort meeting the needs of all parties.
That ABRS and CHAH should work together to integrate AFD and APC as far as possible.
Imaging (Te Papa Report)
- Have pushed KE to implement the import of EXIF metadata available in digital photos;
- Have media in analog format (e.g. slides, negatives) as well as digital images and can relate the records if the accessions are related;
- Can share various metadata standards they use for HISCOM’s interest.
The Collections Management Conference in Adelaide was noted, along with the potential for major funding opportunities.
Distribute the data dictionary for managing digital collections by next Teleconference. [Phil Edgar]
That an interested person monitor the global imaging standards and keep HISCOM up-to-date. [Phil Edgar]
Australia’s Virtual Herbarium (Session 3)
(Greg Whitbread, Paul Coddington, Ben Richardson.)
Ben to provide PERTH’s initial BioCASE data use agreement metadata statements for comment to HISCOM with the aim of building similar statements for the AVH ABCD output by next Teleconference. [Ben Richardson]
For implementation purposes, it is important that CHAH develop a policy for who can get access to the AVH Cache and what they can do with the data. (In reference to the full dataset, not the freely available MoU subset.)
Form a short-term subcommittee to look at the AVH and EWS interface design and report at the next HISCOM Teleconference. [Ben Richardson, Kevin Thiele, Peter Neish, Bill Barker]
Download Shape files and provide configuration options to SAPAC for freely available layers. [Peter Neish]
CHAH Web Presence
(Ben Richardson, Peter Neish, Greg Whitbread.)
During the year, chah.org.au and hiscom.chah.org.au sites were created and the mailing lists used for communication and discussion migrated.
Create archive of the entire directory pointed to by the URL http://plantnet.rbgsyd.nsw.gov.au/HISCOM/ and send the resulting archive via FTP to the new HISCOM site using the agreed credentials. [Gary Chapple, Ben Richardson, Peter Neish, Greg Whitbread]
Migrate other content available from various institutional sites into new HISCOM site. [Peter Neish, Ben Richardson]
- ABCD — Access to Biological Collections Data (TDWG Specimen data standard)
- ABRS — Australian Biological Resources Study
- AFD — Australian Faunal Directory
- ALA — Atlas of Living Australia (NCRIS)
- AMANI — Australian Marine Algal Name Index
- APC — Australian Plant Census
- ATH — Australian Tropical Herbarium
- CERF — Commonwealth Environment Research Fund
- EWS — Early Warning System (AVH)
- GBIF — Global Biodiversity Information Facility (http://www.gbif.org/)
- GUID — Globally Unique Identifier
- HISPID — Herbarium Information Standards and Protocols for the Interchange of Data
- LSID — Life Science Identifier
- NCRIS — National Collaborative Research Infrastructure Strategy
- PSRA — Plant Systematics Research in Australia
- SAPAC — South Australian Partnership for Advanced Computing
- TAG — TDWG Technical Architecture Group
- TAPIR — TDWG Access Protocol for Information Retrieval
- TDWG — Taxonomic Databases Working Group (http://www.tdwg.org/)
- TIP — TDWG Infrastructure Project
The Tasmanian Herbarium (Gintaras Kantvilas, Lyn Cave and Kim Hill) and Laurence Paine were thanked for making the meeting an effective and efficient one.
- BioCASE software installed on the production web server
- CHAH MoU-agreed subset of specimen database fields being served through BioCASE software
- Complete specimen records (as many fields as possible) set being served through BioCASE software
- BioCASE server is querying a database whose records are being maintained
- The most likely avenue to completion for this web service is extra funding, perhaps through NCRIS