HISCOM 2005 AGM Alice Springs

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The 2005 HISCOM Annual General Meeting was held in Alice Springs from Tuesday 18 – Wednesday 19 October, 2005. This document represents the minutes of the meeting.

Attendance and Apologies

  • Bill Barker (Plant Biodiversity Centre [State Herbarium of South Australia], Department of Environment and Heritage, South Australia)
  • Peter Bostock (Queensland Herbarium, Environment Protection Agency, Queensland)
  • Gary Chapple (National Herbarium of New South Wales, Royal Botanic Gardens, New South Wales)
  • Ian Cowie (Northern Territory Herbarium, Department of Natural Resources, the Environment and Arts, Northern Territory)
  • Peter Neish (National Herbarium of Victoria, Royal Botanic Gardens, Victoria)
  • Ben Richardson (Chair; Western Australian Herbarium, Department of Conservation and Land Management, Western Australia)
  • Greg Whitbread (Australian National Herbarium, Centre for Plant Biodiversity Research, Australian Capital Territory)
  • Aaron Wilton (Allan Herbarium, Landcare Research, New Zealand)
  • Robin Lawrence (Australian Biological Resources Study, Department of the Environment and Heritage, Canberra) Wednesday only
  • Steve Shattuck (Australian Biological Resources Study, Department of the Environment and Heritage, Canberra) Wednesday only

Election of Minute-taker for October meeting

Ian Cowie nominated and was elected Minute-taker for the meeting.

Minutes of Previous Meeting

Minutes of the previous meeting were accepted.

HISCOM Minute-taker (Teleconferences)

Ben Richardson pointed out that it is difficult to chair meetings including teleconferences and to take minutes at the same time. Various options including using Departmental secretaries were discussed. It was decided that using HISCOM members to take minutes of teleconferences was the best option. Nominees from HISCOM were called for.

Action 1

Minute-takers for future teleconferences were appointed. [Peter Bostock, Peter Neish, Ben Richardson]

Relationship between CHAH and HISCOM

There is a need for a clearer reporting mechanism between CHAH and HISCOM. With potential for HISCOM Rep – CHAH Rep, HISCOM Chair – CHAH Chair information flow, it is easy for one group to assume information flow is occurring via the other but for information transfer to falls through the gaps.

Recommendation 1

That there needs to be clearer communication between CHAH and HISCOM.

  • Communication between CHAH and HISCOM should occur via the Chairs.
  • CHAH and HISCOM need to be more formal in their interactions in other ways:
    • Timing HISCOM teleconferences to suit CHAH would be made easier if the HISCOM Chair was sent a copy of the CHAH minutes directly.
    • CHAH should initiate formal information/advice requests at any CHAH meeting and a document should be sent to the HISCOM chair. This might include:
      • Status of a project
      • Background documentation
    • HISCOM Chair should canvas opinion from the members and draw up a response document by the requested date. This document should be sent direct to the CHAH Chair
    • HISCOM continues to write a summary report at annual meetings and the HISCOM Chair presents this to CHAH.


Nominations were called for the next Chair of HISCOM. Greg Whitbread was elected unopposed as next HISCOM chair.

Teleconferences and date of next meeting

The utility of teleconferences was discussed and dates for future meetings were selected. The value of teleconferences was re affirmed. As a general rule it was agreed to hold teleconferences 2 weeks before CHAH teleconferences to enable the timely reporting of issues, recommendations and actions to CHAH.

Action 2

Next teleconference scheduled for Wed 14 Dec. 2005 @ 10am Perth time (1pm eastern daylight saving time; 11:30 am CST). [All HISCOM]

AVH software licensing

Incorporation of CHAH means that AVH software can be legally licensed. It was proposed that AVH software be made open source, with acknowledgement to AVH by third party users. Open sourcing would offer the advantages to AVH of allowing further development of the functionality of the software and maintenance of the code by a community of software developers. HISCOM considers that it is better to have the software maintained and used. The correct license type needs to be selected to promote the use and development of the software to maximise benefit to AVH without excessive restrictions on third party developers that inhibit development.

Action 3

Seek out relevant open source license options for publication of AVH software and put these forward for legal consideration. [All HISCOM]

Recommendation 2

That CHAH adopt the open source licensing option that allow for commercial re-use of the code on the provision that a required attribution is adopted and that any developments of the code by them are returned to CHAH.

House keeping: List servers and domains

There are long term, unresolvable problems with the functionality and maintenance of the CHAH and HISCOM list servers as a result of running these behind corporate firewalls, in particular with emails and maintenance of the HISCOM web site and access to the MEL CVS. Also, the present CHAH/HISCOM list servers, domains, archives and CVS cache are fragmented and spread across three states. Purchase of space and domains on the server(s) of a commercial Application Service Provider (ASP) would overcome firewall problems, allow consolidation of web sites and allow them to be more easily maintained and accessed.

Recommendation 3

That CHAH approve the purchase of disk space/access on a commercial ASP’s server to run the CHAH and HISCOM list servers, web sites, CVS cache, and Mantis bug tracker. The cost is estimated at c. $30 per month.

Action 4

Use of a commercial ASP site for hosting of CHAH/HISCOM list servers, web sites and the CVS cache needs to be firmly costed. Once approved by CHAH, an ASP site is to be developed for these applications. [Peter Neish, Gary Chapple, Greg Whitbread]

Australian Plant Census

The utility of the APC as a master list for AVH was discussed. Deficiencies in using APC as a master list for AVH include the need to be able to pull in the various state censuses, lack of state threatened / non threatened and naturalised flags against names and documentation of species concepts.

Recommendation 4

That CHAH note that extra functionality will need to be added to the Australian Plant Census before it can be used as a master list for AVH and that this is likely to require some resources. Issues are being investigated by HISCOM and a full report to CHAH will be made in due course.

Action 5

Investigate the extra functionality that will need to be added to the Australian Plant Census before it can be used as a master list for AVH. [All HISCOM]

Review of previous actions

2002/17 NSW, AD and CANB representatives to provide their State census to Greg Whitbread. Some state censuses were still outstanding; carry forward.
2003/18 Compile a list of attributes used to indicate relationships between names eg. Types of synonymy – send to Greg Whitbread. No longer entirely relevant; in train
2004/01 That CANB expedite the provision of online access for modifying APNI and the developments approved in the recommendations [(a) That CHAH endorse APNI as the appropriate central repository for the Consensus Census; (b) To streamline name/concept management, that CHAH support the development of an online interface to the Consensus Census; (c) That CHAH support the Consensus Census being upgraded so that multiple taxonomies may be compiled and managed online.] APNI is being developed as the consensus census. The online tool is technically feasible but problems remain with protocols, politics and training.
2004/11 All HISCOM members to show their CHAH head and interested staff the draft version of APNI’s XML output to web pages. The context is that we are trying to sell APNI as a tool for building state censuses. The xml output is experimental; SA is experimenting with use as a state census and other institutions will look to their experience.

AVH Milestones

'Milestones'1,2,3,4,5,7. Ticked off.

Milestone 6. AVH and EWS specimen indexing

EWS needs to query on date last modified, but not all databases store this information.

Milestone 8. Mapping solutions

It was agreed that Mapserver is still the best option and that AVH stick with the latest version.

Milestone 9. Implementation of BioCASE providers

Only MEL and CANB currently have BioCASE providers installed and more are urgently needed for testing of the new AVH. MEL is still based on static data. This is hampering work by SAPAC on the AVH because they need more than one institution to be serving data so they can test their software. Expected completion data for the data query portal is 23 Sept 2005 and for mapping is 30 Sept 2005. At least one additional dynamic BioCASE provider is needed and this will probably be AD.

It was noted that genus and family level IDs need to be available to the EWS as these may include new weed records.

Action 6

AVH EWS needs master weed list from John Hosking. [Bill Barker]

Recommendation 5

CHAH members continue to be vigilant concerning the need for fully operational BioCASE providers delivering a full set of agreed fields as a matter of high priority.

HISCOM notes that once BioCASE providers are running it will be possible to utilise a variety of other ABCD and BioCASE-compatible software such as data cleaning modules and Google Earth.

Milestone 11. Additional mapping functionality

Bounding box and date range functionality being added. Cultivated specimens need to be filtered out with default to exclude. Naturalised specimen – flag as future update, but not all herbaria database this information. AVH Icon is being added on map. Infraspecies built in as lowest rank but hybrids not supported. (Full data set query capability was mentioned, but no further discussion ensued.)

Milestone 12. Documentation and installation guide for EWS

The initial draft is available and HISCOM needs to look at this.

Action 7

HISCOM to review draft documentation and installation guide for EWS. [All HISCOM]

Milestones 13-17.

The expected completion of these milestones is delayed for three weeks. However, this is not seen as critical given the delay in rollout of BioCASE providers at herbaria.

Installation of BioCASE providers

The BioCASE documentation is good but there are still glitches in the installation process. Corporate structure in some organisations could be a problem in getting the installation process going at some herbaria.

Action 8

In relation to IT contractors installing BioCASE, it was noted that:

  • They need to be given access to the HISCOM mailing list;
  • It be impressed upon them that they should utilise expertise amongst HISCOM members regarding technical problems and solutions. [HISCOM members utilising outside contractors]

Review of previous AVH Actions

2002/03 If required, NSW to host the CHR and PDD data as interim measure to enable participation in the AVH. Still open but NZ will probably try to do themselves.
2002/04 Send the model of the WeedAlert system to HISCOM-L. Further help to be requested from Gary by individual herbaria. Done
2002/12 Canberra, Darwin (and perhaps Sydney) to develop an example of a simple area search before the launch of the AVH. No longer relevant
2002/13 Develop a distributed query to fact sheets in AVH. Promote discussion on HISCOM list on various query issues. Carry forward to future of AVH discussions
2002/14a Change current restricted AVH site password and populate each local node with this new password. Done?
2002/14b Review the security policy to determine if passwords should be instituted on the basis of individual nodes or institutions. To be considered in current AVH project.
2002/15 All AVH sites to ensure they project locality to the public domain in the form of Nearest Named Place. In train; if nodes can’t provide then display “not available”
2002/16 To gain access to full specimen data, build a URL link from the Query display back to the original specimen in the case of restricted access. Part of new AVH
2003/09 Place common set of layers on to MEL cvs server: Coastline, Rivers, Major towns, IBRA regions, Satellite regions, Topography, Temperature, Rainfall, Roads, Lat long grid. New Action, see below
2003/10 Post BRI Mapper to Sourceforge or MEL cvs web site. Peter Bostock; will try again
2005T1/04 Discuss the difference between AVH MoU agreement and GBIF agreement on data provision with CHAH member, as a resolution on this is needed at the next CHAH teleconference. New Action, see below
2005T1/05 Place [BRI's Full Label Text parser] code in MEL CVS and discuss findings on the HISCOM Mailing List. New Action, see below.
2005T1/06 Send the “best effort” results in a data file to BRI via PB, including the records that were unable to be separated. Use any format that includes Acquision Number and the data field. Done, see above
2005T1/09 BioCASe Provider software must be up and running at each institution by the delivery date of the AVH Stage 3. As many as possible should be running by next teleconference so that these can be used as test sites. In progress
2005T1/10 Post [AVH] report and specification documents to HISCOM web site. Not appropriate, distribute to HISCOM members via list server [Bill Barker]
2005T2/01 Send Paul Coddington the AVH MoU document and help with mapping. Done in part; ongoing
2005T2/02 After CANB gets their BioCASe provider online, send mapping between ABCD and AVH MoU fields (perhaps as HISPID fields) to the HISCOM-L mailing list. ongoing

AVH Map layers

An easy to install, standard set of map layers needs to be made available on the CVS server. Old ones may need updating and they also need to be made available to Paul Coddington to install on the new AVH. Originally these layers were requested in name of CHAH and the data agreement was signed by CHAH. The status of this agreement needs investigating.

Action 9

Place common set of layers on to the CVS server: Coastline, Rivers, Major towns, IBRA regions, Satellite regions, Topography, Temperature, Rainfall, Roads, Lat long grid. [Peter Neish]

Differences between AVH MOU agreement and GBIF agreement

GBIF want us to give data freely; it is incumbent on CHAH members that they only give out the data that they want to and individual states need to specify levels of access and quality of data provided.

CHAH needs to be aware that there are inconsistencies between level and quality of data that is provided to GBIF through individual institutions and data which is/would be provided to GBIF through AVH.

Action 10

Recommendation to CHAH to be fleshed out. [Bill Barker, Peter Bostock, Ben Richardson; completed]

Review of AVH Strategic Plan

The vision of AVH was endorsed, but money is needed to make it happen.

How we go forward with AVH

There are ongoing areas where improvements can be made for example with maintenance and data cleaning, delivery and improving of home systems, atomisation of data fields. It was noted that AVH has resulted in increased data requests to herbaria. The issue of standardisation of geocodes was raised. It was noted that there is potential to seek funding for South Pacific data acquisition.

Importation of data from duplicate specimens

In some cases, label data from duplicate specimens sent to other herbaria is being manually re-entered at the receiving herbarium. This represents a significant duplication of effort and at a time of expected funding shortfall for AVH databasing represents a poor use of resources. Peter Neish has developed a query that transfers data directly from the online CANB specimen database to the MEL database. Once BioCASE is installed at all AVH nodes it will become much easier to implement similar solutions at other herbaria.

Recommendation 6

It was seen as both important and urgent that CHAH members find resources to enable importation of duplicate specimen data to individual herbarium databases through the AVH private node (where relevant). Such a facility would save the large amounts of time and effort currently expended on databasing duplicate specimens from other herbaria.

Text parsing

The text parsing module is on the MEL CVS server and consists of about 20 lines of code. This has been tested on BRI data with reasonable results. There is potential for this software to be developed further, in particular as a general solution applicable to a range of data parsing problems and Paul Coddington is believed to be interested. BioCASE data cleaning modules were mentioned in passing but their applicability to AVH was not discussed.

Action 11

Continue discussion and work on data parsing module with Paul Coddington’s team so that it may be possible to embed the feature in AVH and develop links with him to further develop the module. [Ben Richardson]

Data Validation Module

The need for validation of the full AVH dataset and for the ongoing validation of new specimen data was raised. There is still a need for this module, and it should be discussed.

Action 12

Discuss Data Validation module at next teleconference. [All HISCOM]

Intersection of AVH and APC

This issue was held over until the end and was not discussed as the meeting ran out of time.

Action 13

Discuss intersection of AVH and APC at next teleconference. [All HISCOM]

Mapping of HISPID fields to ABCD

HISPID 3 fields were mapped to the ABCD 2.06 schema, with about 20 still outstanding after time ran out. In most cases mapping was fairly straightforward while in a number of cases, the more specific HISPID standards were adopted.

Action 14

Complete mapping of HISPID fields to ABCD 2.06. [All HISCOM, almost completed]

Specimen Imaging

This issue was held over until the end and was not discussed as the meeting ran out of time.

Action 15

Discuss issue of specimen imaging at next teleconference. [All HISCOM]

Type Photo Database

The type specimen database at NSW has been deleted. It was noted that although it was incomplete, little used and that the photos were dispersed, the database was still a useful archive. It was noted that it was difficult to input data, and that type photos were being data based at home institutions.

Recommendation 7

That the NSW Type Photo database be resurrected as an online archive that may be of use.

ABIF Vision

Steve Shattuck gave a presentation on the development of ABIF. HISCOM was impressed at the innovative integration of a variety of existing data search, reporting and analysis tools from various web sites and the ability of ABIF to move data between theses various tools. It was noted that ABIF provides badging that acknowledges data providers on the front page but that this is not evident on subsequent pages. The source of search, reporting and analysis tools is explicitly acknowledged.

ABIF relationship to AVH/CHAH

It was seen as important that ABIF be developed cooperatively with recognition of the role and rights of AVH and other data providers. There could be a perception amongst some that ABIF is merely creaming off AVH data and claiming the credit. It was considered necessary that an MOU be drawn up which defines the relationship with ABIF and protects the interests of CHAH, its members and other data providers. It should be recognised that individual data providers must be functional for ABIF to be successful and that resources need to flow down to make this happen.

Recommendation 8

That CHAH draw up an MOU with ABIF that defines the relationship between the parties and protects the interests of CHAH, its members and other data providers in the future development of ABIF, specifically one that:

  • Recognises the separate roles of ABIF, OZCAM and AVH and other data providers but also recognise them as equal partners in the project.
  • Defines how AVH/CHAH/data providers are recognised on the ABIF web site and in data downloads (badging)
  • Provides for reporting of data usage back to AVH / CHAH members.
  • Protects the interests of CHAH and defines what happens if the goals of ABIF change.
  • Defines any financial/budgetary relationships.
  • Provides for the appointment of a project team composed of representatives from AVH, OZCAM, ABIF and other data providers to coordinate, ensure the integration of sites and to avoid duplication of effort.

It was recognised that CHAH may need to revisit the current AVH agreement to take account of the ABIF MOU.

Linking AVH and Flora of Australia

Robin Lawrence gave a presentation on the current state of Flora of Australia online. She noted that the Flora of Australia online URL could soon be added to the species link page on AVH, so that users could go from an AVH search to an online description of specific taxa. 20% of the published FOA material is currently available online and this will soon be 25%.

Action 16

The new AVH needs to have a standardised species links page equivalent to that on the MEL CVS site and that this also needs to incorporate a link to FOA online. [Peter Neish]