HISCOM 2005 Teleconference 2

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2005 HISCOM Teleconference 2 was held by telephone on Thursday 15 September, 2005. This document represents the minutes of the meeting.

Attendance and Apologies

  • Bill Barker (Department of Environment and Heritage, South Australia)
  • Peter Bostock (Environmental Protection Agency, Queensland)
  • Alex Chapman (Department of Conservation and Land Management, Western Australia)
  • Gary Chapple (Royal Botanic Gardens, New South Wales)
  • Paul Coddington (School of Computer Science, University of Adelaide; Deputy Director, South Australian Partnership for Advanced Computing)
  • Ashleigh Coombs (Department of Environment and Heritage, South Australia)
  • Ian Cowie (Department of Infrastructure, Planning and Environment, Northern Territory)
  • Jim Croft (Centre of Plant Biodiversity Research, Australian Capital Territory)
  • Steve Jenkins (Department of Environment and Heritage, South Australia)
  • Peter Neish (Royal Botanic Gardens, Melbourne, Victoria)
  • Ben Richardson (Chair; Minute taker; Department of Conservation and Land Management, Western Australia)
  • Helen Thompson (ABRS, Department of the Environment and Heritage, Australian Capital Territory)
  • Greg Whitbread (Centre of Plant Biodiversity Research, Australian Capital Territory)
  • Karen Wilson (Royal Botanic Gardens, New South Wales)

Australia’s Virtual Herbarium progress report

  • Prototype EWS and AVH almost complete
  • Available shortly on the SAPAC site for testing
  • Indexing is working
  • Needs a decent set of weed species
  • AVH MoU fields a good starting point for herbarium BioCASe data providers, additional fields could include:
    • Altitude
    • Depth
    • Naturalised status
    • ?Cultivated status?
  • Development team view current implementation of map display using Mapserver better than those that using an applet-based page
    • Avoids cross-platform, cross-browser problems
    • Avoids long download time required before page starts to work

T2 Action 1

Send Paul Coddington the AVH MoU document and help with mapping. [Bill Barker]

T2 Action 2

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. [Greg Whitbread]

BioCASe 2 progress report

Table 1. Institution progress on implementation of a BioCASe 2 web service
Institution Progress Service Platform
AD In development for a fortnight; should be ready to go after that Oracle
BRI Contingent on access to a contract database programmer in another department; unable to give a time frame MySQL
CANB Testing now in development; ready to go in a week or two Oracle
DNA As for BRI, outside contractors needed Oracle
HO Database platform probably cannot be directly accessed from BioCASe; likely requirement to mirror in another database platform; time frame unknown FileMaker
MEL Draft service is working using a static copy of one third of the specimen database; a full implementation likely in November MySQL
PERTH Mirroring from Texpress and mapping a problem; draft service approaching testing; approximately 10 days required to complete this; production installation on top of this MySQL
NSW DiGIR service running now; Ken Hill comes in once a week; looking at BioCASe options PostgreSQL

Other potential data providers

(Proposal to ask CHAH in Alice Springs to have NZ, fungal collections, UNE come on board if able to implement BioCASe providers.)

We would welcome other providers to be part of the AVH, perhaps with minor change to project name.

Direct contact for BioCASe implementors

All initial contact for technical staff tasked with implementing a BioCASe provider should go through Bill Barker to ensure the lines of communication are well understood.

Assisting herbaria to implement BioCASe providers

It was noted that only one herbarium had managed to implement a production BioCASE provider, and that there were time and/or resourcing issues preventing others from completing the task.

Mapping to ABCD fields from AVH MoU and/or HISPID

  • Denormalised databases are harder to map in BioCASe software
  • Make sure solutions are communicated to other herbaria wherever possible
  • MEL solutions documented on MEL CVS server
  • Fields not represented in ABCD must be stored as MeasurementOrFact elements with an attribute, such as “Naturalised”. The problem is that we must agree on the attribute name to be sure we are all sending the same data!
  • State is another value not easily represented in ABCD

Business Arising from Previous Minutes

Table 2. Outstanding Actions
No. Item Who Progress Resolution
T1 Action 2 Review TRACT and report on suitability for collaborative management by HISCOM members. Greg Whitbread Greg found TRACT would not work. Offered to have another go and report findings at next meeting. Carried forward
T1 Action 3 HISCOM members to post information on the structure and field list of their institutional census database to the HISCOM mailing list for further discussion in this area. All No progress. Carried forward
T1 Action 4 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. All Some progress. Carried forward
T1 Action 5 Place code in MEL CVS and discuss findings on the HISCOM mailing list. Gary Chapple, Ben Richardson Gary has completed his effort, Ben not completed. Peter Bostock noted that the resulting fields would probably not be imported into the database. Carried forward
T1 Action 6 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 Acquisition Number and the data field. Ben Richardson, Gary Chapple It was decided that a discussion on how to best complete this task should be had at the next meeting in Alice Springs. Carried forward
T1 Action 9 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. All Subject of previous major item. Carried forward
T1 Action 10 Post report and specification documents to HISCOM web site. Bill Barker No progress. Carried forward
T1 Action 11 Send email to HISCOM Mailing List noting URL of the new BRI AVH provider so that other nodes can be configured to use it and direct feedback to the list. Peter Bostock Completed Closed
T1 Action 12 Test querying of reworked [Type Photo Index] interface and direct feedback to the mailing list. All It was suggested that a CHAH action covers this
T1 Action 13 Test loading and editing [Type Photo Index] interface and direct feedback to NSW and the list. Peter Bostock Completed Closed
T1 Action 14 HISCOM members to inform thos attending [TDWG] of their interest in particular topics. All No attendees this year from HISCOM members. Response suggested was to review the demos and content on the TDWG web site. Closed

GBIF & BioCASe — Are Australian herbaria planning to move to contributing directly to GBIF?

  • Generally agreed that herbaria are planning to publish their data directly in the GBIF network as a result of their work in implementing a BioCASe web service for AVH
  • It was noted that AVH membership at the GBIF level would be prudent for political reasons, but also that currently, institutions must register their web services individually because it is not possible to register a collection of services

What has been learnt from AVH validation procedures

It was generally agreed that getting data out of herbaria using BioCASe might be a very handy way to perform some validation of the data at a national scale, instead of piecemeal in each herbarium.

Are the implied plans to move beyond specimen data in AVH post funding?

  • Important to value add on AVH
  • Consensus Census moving things along
  • “Unfinished business”
  • A species bank style site might be doable with funding from GBIF

Google Earth and AVH

  • Google Earth is not permitted at BRI due to its use of network bandwidth
  • Has potential for use in natural resources, mapping of properties, council planning, protected species, tracking acid sulphate soils, point data for threatened species
  • Something to watch
  • Google Map may be better because it is a web site, and thus unlikely to be blocked by IT departments

Consensus Census

  • Australian Plant Census (APC) is the name of the dataset being constructed by CHAH’s Consensus Census Working Group
  • Will only include Australian records (e.g. will not include Papua New Guinean taxa)
  • Includes naturalised and native information, but not records of taxa that are only cultivated in Australia
  • APC is available via the CHAH web site

What is happening with the images resulting from the Australian Type Images initiative? Is the Kew work a de-facto standard?

  • There are approximately 1000 images in the collection, available via query from the ANHSIR web site
  • Goodeniaceae is an example of a group known to have images
  • Kew standard is not necessarily our standard
    • 2–10 MB JPEG images
    • Upside-down Epson scanners not working
  • IBC Vienna had a symposium on this

T2 Action 3

Email IBC Vienna Imaging Symposium to the HISCOM-L list. [Karen Wilson]

Should HISCOM put up its hand to take a leading role in organising the bioinformatics component of the next IBC in Melbourne?


Discussion points for Alice Springs

  • Check CHAH Agenda for likely topics
  • How we go forward with AVH; review the Strategic Plan
  • Consensus Census
  • Specimen Imaging
  • Intersection of AVH and Consensus Census (i.e. handling queries in AVH that refer to different names in different states)
  • What is happening with ABIF; how does it relate to AVH etc.

Getting a handle on the TDWG trends

Visit the TDWG site and view the demos and abstracts.