HISCOM 2007 AGM Darwin
The 2007 HISCOM Annual General Meeting was held in Darwin from Monday 17 – Wednesday 19 September, 2007. This document represents the minutes of the meeting.
- 1 Report to CHAH
- 2 Attendance
- 3 Election of Officers
- 4 Timing of HISCOM meetings
- 5 Previous minutes (2006)
- 5.1 2006 Action 2
- 5.2 2006 Action 3
- 5.3 2006 Action 4
- 5.4 2006 Action 5
- 5.5 2006 Action 6
- 5.6 2006 Action 7
- 5.7 2006 Action 8
- 5.8 2006 Action 9
- 5.9 2006 Action 10
- 5.10 2006 Action 11
- 5.11 2006 Action 12
- 5.12 2006 Action 13
- 5.13 2006 Action 14
- 5.14 2006 Action 15
- 5.15 Action 1
- 5.16 2006 Action 16
- 5.17 2006 Action 17
- 5.18 2006 Action 18
- 5.19 2006 Action 19
- 5.20 2006 Action 20
- 5.21 2006 Action 21
- 5.22 2006 Action 22
- 5.23 2006 Action 23
- 5.24 2006 Action 24
- 5.25 2006 Action 25
- 5.26 2006 Action 26
- 5.27 2006 Action 27
- 5.28 2006 Action 28
- 6 Institutional reports
- 7 HISCOM software and web documentation licensing models
- 8 SourceForge site and code uploads
- 9 The HISCOM web site
- 10 The CHAH web site
- 11 Data validation
- 12 HISPID5
- 13 AVH2
- 13.1 AVH Project Report
- 13.2 Cultivated specimens
- 13.3 Filter records based on validation level
- 13.4 Support for output/download of maps in Shape file format
- 13.5 Hit counts
- 13.6 Status of milestones
- 13.7 Action 24
- 13.8 Action 25
- 13.9 Action 26
- 13.10 Interface design
- 13.11 Action 27
- 13.12 Action 28
- 13.13 Interface testing
- 14 AVH data requests and error reporting
- 15 APC and APNI/APC web service requirements (from HISCOM point of view)
- 16 Electronic Flora projects
- 17 Overview of ALA
- 18 Overview of (CERF) National Taxonomy Research Hub (NTR)
- 19 ASB "L.A.S. Johnson Review" paper on AVH
- 20 HISCOM involvement in 2008 ASBS Conference
- 21 Phrase names
- 22 Acronyms
Report to CHAH
See file HISCOM 2007 AGM Darwin (460 kB PDF) for the report as presented to CHAH on Friday 21 September.
I deleted the carry-over actions from 2006 - they were only headings by this stage anyway - which also deleted Action 1 of 2007. We ended up with two "Agreements" rather than one. The first agreement was previously an recommendation, I think - but not really necessary to discuss with CHAH. Anyway, it now reads, in part: "Agreement 1. Changes to HISPID should be released periodically as new versions, rather than continuously."
As you will see, actions, agreements and recommendations are slightly reformatted, to make them more visible in the printed report, and in addition I included an index to them on page 3 of the report.
You will have to wait for CHAH draft minutes to see what comments, if any, were recorded against our recommendations. In general, however, they were accepted.
CHAH in particular voted to unlink HISCOM from its meeting timetable - expressing a desire to link TDWG and HISCOM meeting if possible, but then allow a few weeks (or so) before HISCOM reports back to CHAH. I think I'm right in saying the concensus was to have a phone hookup devoted to HISCOM meeting outcomes, rather than the hurried editing of HISCOM minutes for next day's CHAH.
- Bill Barker (State Herbarium of South Australia, Department of Environment and Heritage, South Australia)
- Peter Bostock (Queensland Herbarium, Environmental Protection Agency, Queensland)
- Ian Cowie (Northern Territory Herbarium, Department of Natural Resources, the Environment and Arts, Northern Territory)
- 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 Water Resources, Canberra)
- Laurence Paine (Information Management, Department of Tourism, Arts and the Environment, Tasmania)
- Athina Pascoe-Bell (Northern Territory Herbarium, Department of Natural Resources, the Environment and Arts, Northern Territory)
- Ben Richardson (Western Australian Herbarium, Department of Environment and Conservation, Western Australia)
- Alison Vaughan (National Herbarium of Victoria, Royal Botanic Gardens Melbourne, Victoria)
- Karen Wilson (National Herbarium of New South Wales, Royal Botanic Gardens, New South Wales)
Election of Officers
Peter Bostock nominated and was elected Convenor, in the absence of Greg Whitbread. Alison Vaughan nominated and was elected Minute-taker for the meeting.
Timing of HISCOM meetings
We need to ensure we are in step with both CHAH and TDWG. As a result of HISCOM's use of TDWG standards, it is critical that we avoid meeting clashes with TDWG. It is also critical that, as a subcommittee of CHAH, we continue to supply CHAH with timely technology advice.
That HISCOM meetings are timed to succeed TDWG meetings, and precede CHAH meetings.
Previous minutes (2006)
2006 Action 2
Action closed. To be incorporated into APC discussions.
2006 Action 3
Action closed. To be discussed with web services.
2006 Action 4
Partially completed. MEL, AD & CANB are providers.
2006 Action 5
2006 Action 6
Completed except for BRI.
2006 Action 7
Completed except for BRI.
2006 Action 8
2006 Action 9
Ongoing as part of HISPID5.
2006 Action 10
Completed? (Greg to check)
2006 Action 11
2006 Action 12
2006 Action 13
Resolved. Dealt with by HISPID5.
2006 Action 14
Resolved. Dealt with by HISPID5.
2006 Action 15
Resolved. Dealt with by HISPID5.
Ensure that 2006 Actions 12-15 and Agreement 1 have been incorporated in to the HISPID5 documentation. [HISPID working party]
2006 Action 16
Resolved. Superseded by TDWG funded project to recast HISPID on ABCD - discussed under Item 8.
2006 Action 17
Resolved. Superseded by TDWG funded project to recast HISPID as ABCD - discussed under Item 8.
2006 Action 18
Ongoing. To be discussed under Item 7.2.
2006 Action 19
Ongoing. To be discussed under Item 7.
2006 Action 20
Outstanding. To be discussed under Item 9.
2006 Action 21
2006 Action 22
2006 Action 23
2006 Action 24
2006 Action 25
Ongoing. Will be addressed under Item 9.
2006 Action 26
2006 Action 27
2006 Action 28
ABRS / CANB
- AFD (Australian Faunal Directory) - being rewritten from a perl application into one using java spring technologies. Once AFD is up, ABRS will work with Jim and Greg to get APNI and APC to consider adopting the same technologies. The hope is to then make all these systems feed into ALA using web services.
- Flora of Australia - have been working with other institutions interested in setting up Flora schemas.
- Species Profiles / Fact Sheets - need to establish standards with other interested parties. (see discussion under Item ??12)
- Working with the Australian Museum to look at YouTube projects relating to taxonomy and the number of species in Australia.
- LSIDs - Greg has started to implement LSIDs as unique Ids on his collection data and taxon concepts, but hasn't added a resolver. Greg has also started setting up TAPIR and has a working BioCASE data provider.
- Moving Census part of system from Texpress to Oracle, which has taken over two years. This feeds into the electronic Flora, which is a basic text and image program with data linkage.
- All fields have been delivered to SAPAC
- Have had recent meetings relating to data validation
- BioCASE installed; awaiting rollout of AVH 2.0
- Andy Lowe has been heavily involved in ecological equivalent of ALA; was TERN, now AEON (Australian Ecological Observation Network); no global (or Australia-wide) standards for delivering ecological data; through Joanne Daly, getting juxtaposition of ALA and AEON so that ALA feeds into AEON. Four times funding of ALA. Paul Coddington has been involved in IT side with regard to federating data.
- BRI has been fairly stationary over the past year, and the focus has been on data entry and maintenance.
- It is doubtful that BRI will be able to get BioCASE installed on the current system. BRI will make every effort to send data to SAPAC.
- Have changed to Oracle 10g throughout the Department, which insulates BRI from much of the cost.
- Flora work: QFlora progress: Eucalyptus, Cyperaceae, Acacia and rainforest taxa will be going on the web at some point.
- Currently sitting on 200+ Gb worth of images. Looking at storing them on CBIT. $4,500 would obtain 200 Gb worth of storage space per year, with the ability to interpret metadata, give clients password-controlled access and to provide customised views of subsets of images.
- BioCASE provider has been installed by Athina.
- Have mapped MoU fields, but need to know what to do from here, in terms of AVH 2.0. (Bill advised that it's up to individual herbaria whether they want to maintain their own portal. If they don't want to build their own site, they can use a mirror site with individual herbarium logo. See HISCOM list discussions for more information.)
- DNA has to migrate from Oracle 8 to 10g, due to a Departmental initiative.
- Considering moving taxon database from Platypus to BioLink, which is primarily a taxon database that includes conservation status. It was recommended that DNA go with the Oracle program being developed by ABRS (tentatively called Australian Flora and Fauna Directory (AFFD)- due out ca. December 2007).
- Athina will be replacing Raelee as DNA's representative on HISCOM.
DNA to contact Paul Coddington to advise that their BioCASE provider has been installed. [Athina Pascoe-Bell]
- Hobart has been in maintenance mode whilst a decision is made with respect to the preferred option for replacing the existing FileMaker Pro collection management environment.
- Static data dumps have been provided to SAPAC to be uploaded into the cache for AVH2, and it is intended to provide updates on a quarterly basis to SAPAC or whoever takes over the central portal in the future.
- It is not anticipated that a BioCASE or TAPIR provider will be implemented until the new collection management system is determined, however, the skills and capacity to deliver a temporary solution based on a snapshot of existing data are available if it becomes critical.
- Laurence attended the Council of Heads of Australian Faunal Collections meeting in August 2007. CHAFC is initiating its own HISCOM-type committee, which will be meeting for the first time in October, after the CHAFC meeting.
Inform CHAH that CHAFC have started it's own HISCOM-type committee. [Peter Bostock]
- Texpress is not meeting our current needs, let alone our future needs, so MEL has been investigating other database options:
- The BRAHMS database (Herbarium of Oxford) is a specialised herbarium database and was found to be rich in features, but lacking in usability, robustness and extensibility.
- Specify (University of Kansas) appears to be designed primarily for Museum data, but was found to be usable and robust. The Specify software is being completely rewritten and will be released as open source. This looks to be the most promising database option.
- A lot of maintenance work has been going on at Sydney, due to the departmental decision that everybody needed to operate on the same desktop platform. This has had a great impact on other work.
- Have had to employ a contractor to get BioCASE installed.
- Looking at employing another hybrid "IT/Botany" person to work with Gary.
- Had an information workshop last August to see what institutions are doing in terms of databasing, which led to the conclusion to stay with the current database platform (EMu) at this stage.
- NSW has money this year to replace their Unix database server and to get a new development server. It is expected that the web server will be replaced next year.
- The next step for implementing BioCASE is for Gary to create a POSTGres database to feed data to AVH2.
- Just released a new version of FloraBase that includes interactive keys. It includes families and genera from WA, with a genus-level key and a family-level key, using +/- 900 characters. 48 keys have been prepared so far from the families and genera dataset.
- Have revamped taxon profiles so they link back to Nuytsia articles in pdf format (where they exist) and taxonomic literature links to the most useful references for a particular taxon.
- In future versions of FloraBase, users will be able to query on local government regions etc.
- PERTH is replacing their web server.
- Ben, Alex and Kevin have been involved in the LSID workshop. Ben was involved in the HISPID/ABCD workshop. Kevin attended the ALA workshop.
- Preparing a case for a Perth TDWG meeting.
HISCOM software and web documentation licensing models
Revised action from last year regarding which licensing model should be used for publication of AVH source code. Laurence consulted with ASK-OSS and provided a recommendation to CHAH to accept the Mozilla Public License (MPL) v1.1. Laurence thanked Ben and Peter N for their assistance.
HISCOM endorses the recommendation put forward to CHAH to adopt the MPL v1.1 for publication of AVH source code, which will assist Paul Coddington in completing the AVH requirements.
It was also recognised that electronic documentation that is being produced by the HISCOM group through the wiki is currently promoted as being created and distributed under an Free Documentation License (FDL) (see the footer of any of the wiki pages) and that no copyright statement is provided. This may not be acceptable as it may undermine CHAH's ownership of its intellectual property. This issue potentially applies to other CHAH documentation on the web.
The FDL is not the only available license (the Creative Commons license is quite popular).
To submit the FDL and Creative Commons licenses to the Chair of CHAH for review, and as necessary, update the CHAH and HISCOM web sites to either (a) one of the existing free licenses or (b) to an alternative license which is developed on behalf of CHAH. [Laurence Paine]
SourceForge site and code uploads
It was agreed to continue using the Biodiversity Information Group (BIG) SourceForge project. BIG is to be made available to other Australian biodiversity data stakeholders.
Clean up, re-brand and promote the BIG SourceForge site. [Ben Richardson]
Promote the availability of the BIG site to the CHAFC IT community. [Laurence Paine]
The HISCOM web site
Overview of the HISCOM wiki
Ben ran through the background and functioning of the HISCOM wiki, and encouraged everyone to use it to contribute to the ongoing discussion and documentation of HISCOM issues.
Overview of the new HISCOM site
Ben also encouraged everyone to create an account and contribute to the HISCOM site. This requires Ben, Greg or Peter N to approve the new account. Users can edit any documents on the site (not just those that they have authored). HISCOM members are encouraged to add informative documents outlining new developments at different herbaria, and add links under the Member Sites page.
More work needs to be put in to link the Joomla! front-end to the wiki, to enable more effective searching.
HISCOM thanked Peter N and Ben for their hard work in developing these sites.
That CHAH members familiarise themselves with the HISCOM page and wiki, and keep up-to-date with HISCOM activities.
The CHAH web site
The CHAH web site was reviewed during the meeting, and the following changes were suggested:
- On the banner line on the CHAH home page:
- The objectives of CHAH should be outlined on the front page
- Remove the ABN line in the Introduction and add to bottom of the page
- In the Membership section:
- Change 'Plant Biodiversity Centre' to 'State Herbarium of South Australia'
- Change membership to separate Core Membership and General Membership and include a statement about observers
- Ensure the links in the banner line match the links in the Membership section
- Delete New Zealand from the Observers list
- Subcommittes and working groups
- Correct 'technologie'
- Add ALA
- Delete dates from ABLO section
- CHAH Participants:
- Change 'Dave Cantrill' to 'David Cantrill'
- Correct Ilse Breitweisser spelling
- Add Ewan Cameron's name to AK
- Update ABRS, PERTH, HO, AD logos
- General url cleanup required
That CHAH act on the suggested changes to their website, and that those changes are also made to other pages (e.g. AVH) if they are relevant.
General data validation
General discussion reinforced the importance of developing a strategy for the ongoing maintenance of data. The proposal of introducing an annotation system for flagging suspect records on AVH and updates to data between herbaria (see Item 12 in 2006 minutes) is endorsed as a viable opportunity.
That CHAH sanction the development of an automated annotation system for AVH as an important project, and support HISCOM in the application for funding to hold a workshop to develop a strategy for the implementation of this solution.
Resurrect Action 20 from 2006 minutes, i.e. SAPAC to quote on the annotation proposal with the view to HISCOM approaching TDWG for funding. [Greg Whitbread & Paul Coddington]
Synchronising conservation status between States and Commonwealth
General discussion took place regarding the issues of maintaining the status of rare and threatened species information, and ensuring that species records are not inadvertently made available in the public domain.
Ultimately, we need to map the Commonwealth statuses against APC. At the State/Territory level, some states do not have links between the state censuses and state conservation statuses. A step forward is to hold a single workshop between the relevant custodians.
That CHAH recognise that we have a problem with our capacity to communicate up-to-date rare and threatened species information, and that it supports the development of a filter to apply to AVH and ALA (etc.) to control the dissemination of sensitive information to data users.
CHAH and HISCOM to facilitate a workshop at an appropriate time. [CHAH & HISCOM Chairs]
GIS and spatial standards
MEL's Outlier Validation Protocol was tabled by Alison for inclusion, and was added to the web site.
Continue to source funding for the development of spatial data validation tools (e.g. outlier detection tools) for AVH. [Greg Whitbread & Paul Coddington]
That CHAH supports HISCOM's application for funding to develop spatial data validation tools for AVH.
The aim of this session was to introduce HISPID5 to HISCOM members, review the current work and assess if it meets our needs.
Peter Neish, Ben, Bill, Rex Croft and Greg met in Adelaide at a TDWG-funded meeting to see if there was a way to build HISPID5 from ABCD. In some instances, there were fields missing from ABCD that Australian herbaria use in HISPID. The HISPID5 working party proposed the use of an xml extension mechanism to build HISPID5 atop ABCD. See the executive summary.
The attendees reviewed the proposed exclusion of the following fields from HISPID5:
- numrecords: Agreed to exclude.
- non-standard: Agreed to exclude.
- fileaction: Agreed to exclude.
- dataurl: Agreed to exclude.
- filedescriptor: Agreed to exclude.
The following name fields are dealt with by the new field 'NameFormula' in ABCD. This will allow for infinite extension of hybrid formula i.e. a x b x c
- Second Hybrid Genus Name (genhy2): Agreed to exclude.
- Second Hybrid Species Epithet (sphy2): Agreed to exclude.
- Second Hybrid Infraspecific Rank Flag (isprkhy2): Agreed to exclude.
- Second Hybrid Infraspecific Epithet (isphy2): Agreed to exclude.
- Second Hybrid of the Second Infraspecific Rank Flag (isp2rkhy2): Agreed to exclude.
- Second Infraspecific Rank Flag (isp2rk): Agreed to exclude.
- Second Infraspecific Epithet (isp2): Agreed to exclude.
- Second Hybrid of the Second Infraspecific Epithet (isp2hy2): Agreed to exclude.
- Second Infraspecific Author (isp2au): Agreed to exclude.
- Second Most Recent Type Qualifier (tql2): Agreed to exclude.
- Second Most Recent Type Status (tsta2): Agreed to exclude.
- Second Most Recent Basionym (basnam2): Agreed to exclude.
- Third Most Recent Type Qualifier (tql3): Agreed to exclude.
- Third Most Recent Type Status (tsta3): Agreed to exclude.
- Third Most Recent Basionym (basnam3): Agreed to exclude.
- Name Comments 2 (namcom2): Agreed to exclude.
- 'Per' Collector (cper): Temp solution to put this as the last AgentText in the repeatable Agents/GatheringAgent (that with the largest @sequence attribute and append "(per)"). This interim solution, which is necessary because there is no equivalent in ABCD, has been accepted.
- Conservation Status - Threat (consta): It was agreed that this was a taxon attribute rather than a specimen attribute, and should be excluded.
- Number of Replicates (numrep): The requirement to keep the field is dependent on the definition ascribed to it, which in turn is dependent on the definition of the desrep field. The current definition of numrep is ambiguous: it is unclear whether it represents the count of desrep (i.e. the number of distributed replicates), or whether it represents the total number of replicates of a collection, including undistributed replicates.
It was agreed to amend the definition of numrep to the total number of replicates held by source institutions plus those that have been distributed (and recorded in desrep). There was some discussion about whether non-sheet material (e.g. spirit and/or carpological material), should be counted in numrep. Given that spirit material, carpological collections and wood material are considered 'special collections' in HISPID, it was agreed numrep should only include sheet material, unless there is no sheet material. We therefore suggest resurrecting numrep in HISPID5, with a new field name to eliminate confusion over the previous definitions. It was suggested that the new field be called 'TotalReplicates' or something similar.
- Record Creation Date (credat): There is no place to record creation date in ABCD, that can be validated. It was agreed that this information is not useful for exchange.
- Record Creation Operator (crenam): It was agreed that this information is not useful for exchange.
- Record Creation Institution (creins): Agreed to exclude.
- Record Update Operator (modnam): It was agreed that this information is not useful for exchange.
- Record Update Institution (modins): Agreed to exclude.
It was suggested that comments be added to the excluded fields list to indicate which fields are useful for database administration (e.g. crenam, modnam), and should be included in database design.
Move those excluded fields that should be included in HISPID5 as database administration fields (as opposed to data exchange fields) into an Appendix, to aid in database design. [HISPID working party]
It was noted that the plant occurrence fields are inadequate for recording the naturalised status of a specimen (and all its variations). In some instances, we need the ability to record specimen-level naturalised status in AVH2, for data validation and display purposes. It would also be advantageous to use a controlled vocabulary.
Herbaria to provide their lists of naturalised plant statuses, for consideration of new fields to be added to HISPID. [Alison Vaughan]
Each herbarium to submit proposed new fields to be included in the next version of HISPID5 (particularly in relation to the databasing of cryptogams), within three months. [All]
Changes to HISPID should be released periodically as new versions, rather than continuously. HISPID working party to coordinate changes, and advise HISCOM of new versions. Suggested changes can be added to the wiki under HISPID5.
- Are the controlled vocabularies okay?
The HISCOM list discussions relating to controlled vocabularies were reviewed.
Review the proposed values for the phenology field in HISPID5 and circulate to HISCOM. [Bill Barker & Jim Croft]
- Do we continue to restrict the formatting of the DuplicatesDistributedTo field to comma separated values?
No - we need a set of separate, repeatable, sub-elements to record multiple institution entries (in Index Herbariorum format where available, and allow for other free text values used at each institution).
HISPID working party to integrate comments into HISPID5, prior to the next HISCOM meeting. [HISPID working party]
AVH Project Report
See report from Paul Coddington re: Development of New AVH Stage 3 and EWS Stage 2. SAPAC has implemented almost all of the required specification for AVH2 (all stages), but the functionality remains to be tested. The missing components recorded in the report are discussed below.
Implementation of this field on the Collection page has been noted. Although this field has been implemented, not all herbaria are able to deliver this data.
As a starting point, we should focus on only providing wild-collected records (including naturalised records).
All herbaria to ensure that cultivated records are excluded from AVH data (as far as possible), but that naturalised records are included. [All]
Filter records based on validation level
This field has been implemented, and is currently using AD's proposed validation levels. HISCOM needs to establish a standard vocabulary for this field and map it to ABCD.
AD to post their proposed validation levels on the HISCOM wiki. [Bill Barker]
Develop a standard vocabulary for the validation level in HISPID5. [HISPID working party]
Support for output/download of maps in Shape file format
Discussed with Paul during meeting. He will investigate further.
Discuss the exact requirements for shape file export from AVH Stage 3 with Paul Coddington. [Peter Bostock & Laurence Paine]
HISCOM to develop a specification for reporting statistics relating to AVH website hits that will be useful for business reporting, including a breakdown of individual custodians.
Status of milestones
It was noted that a number of milestones have been completed. Those that weren't are listed below.
|Milestone 3||Refer to Recommendation 2 (MPL v.1.1 action). See Action 20.|
|Milestone 6||It is acknowledged that there is not a corresponding one to one mapping between HISPID3 and ABCD. HISPID5 is working towards providing that mapping. The current MoU fields are considered adequate for the existing implementation. Should further fields need to be mapped to accommodate new features, a new funding arrangement will be negotiated.|
|Milestone 14: EWS testing||In discussion with Paul during meeting, it was agreed to sort out the AVH functionality before testing the EWS, through a process that has already been established involving engagement with Weeds CRC clients. See Action 21.|
|Milestone 15: Completion of AVH Stage 3||See Milestone 6. Interface testing was undertaken during the meeting. See Action 21.|
|Milestone 16: Deployment of EWS on one site nominated by HISCOM||HISCOM agreed that SAPAC was the best place to deploy the EWS on behalf of the Weeds CRC. (The Weeds CRC does not currently have suitable infrastructure.) See Action 22.|
|Milestone 17: Deployment of AVH on two sites||See Action 23.|
Inform SAPAC when CHAH approves license model. [Peter Bostock]
Forward outcomes of interface testing to SAPAC. [Peter Bostock] (completed by Ben Richardson during the meeting).
Coordinate the deployment of the EWS in consultation with the Weeds CRC after testing. [Bill Barker & Paul Coddington]
To expedite the testing of the deployment process. [Greg Whitbread & Bill Barker]
For the chair of HISCOM to formally communicate our appreciation to Paul Coddington. [Peter Bostock]
Progress reports (this section should be checked by absentees where necessary):
- BRI: Unsure how to progress; Peter B will follow up with Paul Coddington re: data extract.
- MEL: All fields have been mapped, but unsure whether everything has been sent to SAPAC. MEL has TAPIR Link (php version) installed, but it's not configured properly yet.
- DNA: BioCASE installed and MoU fields are mapped (see institutional report).
- CANB: BioCASE and TAPIR have been installed, but waiting to test TAPIR.
- AD: Have mapped all fields, and have been delivering to SAPAC for the last two months. We're in the process of sending our data to SAPAC for the second time. We are waiting on CANB's test of TAPIR before testing it ourselves.
- NSW: BioCASE has been installed, but database has now to be set up to deliver the data from EMu.
- HO: There are no intentions for BioCASE to come out of the current sandpit environment. It is intended to wait for the new collections management system prior to the implementation of BioCASE/TAPIR. We will continue to provide updates of the MoU fields every three months to SAPAC.
- PERTH: A MoU set has been handed to SAPAC, so the SAPAC site is querying a static set of PERTH data now. BioCASE server working in development, but not in production. A new web server is required before any further progress can be made. It should be up and running early next year.
Expedite the testing of TAPIR by CANB and AD, so we know whether we should be installing BioCASE or TAPIR at other sites. [Greg Whitbread & Bill Barker]
|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 (once software installed on new web server)|
|Darwin||Yes||Check with Athina||No||Yes, but not to SAPAC||No||NCRIS|
|Hobart||Development only||Windows||No||No||No||Dependent on implementation of new CMS.|
MEL to check calculation of latitude in data provided for AVH 2.0 test site. [Peter Neish]
SAPAC are responsible for making the AVH site functional, but HISCOM is responsible for the user interface. CANB have offered to provide resources to finetune the user interface. CANB will need to liaise with SAPAC where access to the java code is required to make changes to the user interface. Should AVH 2.0 be released without changes to the user interface?
Work has been done to describe the expected layout and features of the AVH user interface in the AVH and EWS Interface Design report.
Request that SAPAC release the AVH code onto SourceForge so that HISCOM can use the code to refine the user interface. [Ben Richardson]
The following things need fixing on the map output page:
- List of species needs to be tidied up
- Four black dots around the white square is no good as a symbol (it was later realised that this was a white cross on a black background)
- Legend needs full taxon name
- Need full distribution map in box instead of World map
- Download button on specimen results table
- Add drop-down list for infraspecific rank
- Query on an variety produced results that were only identified to species level
- Date last edited should be in Australian format, not US
- Configuration file format for dates
- All queries should be case insensitive
- Clear form button required on query page
- Query point should be the default
- Consistent symbols to be used for each herbarium
- Include herbarium code as well as institutional name
- Bug in query; a query on Cyathea cooperi brought up empty results in WA (no data provided when these points are queried). When the map was redrawn it drew it without any layers, rechecking the layers fixed the problem (i.e. no C. australis in WA this time).
- There is some sort of caching issue
- Change UnitID to Accession ID
- Locality field column should not be centred
- small map always to show distribution rather than general locality within world context
User interface to be fine-tuned. [CANB]
The functionality of the extended query pages was tested during the meeting, and errors were sent to Paul Coddington.
AVH data requests and error reporting
It was acknowledged by all that bulk data requests are taking a lot of time to service.
Expedite AVH2 so that clients can access data themselves. Some types of requests cannot be serviced by the software, and we need to get better at servicing these requests collaboratively.
It is recommended that CHAH consider charging a service fee for time-consuming data requests, where the data will be used for commercial purposes. However, when we receive requests from external clients, CHAH needs to consider the possibility that servicing certain requests may be in conflict with CHAH projects.
(Jim Croft joined the meeting by phone to discuss the remaining agenda items.)
APC and APNI/APC web service requirements (from HISCOM point of view)
HISCOM acknowledged that web services for APNI/APC are essential for the future. As subscribers to the service, the herbaria need to have some influence on the actual requirements and the services to be delivered.
The following requirements were raised:
- The ability to integrate an APNI web service with state/territory census databases
- The provision of a sandpit for researchers and others to utilise APNI in taxonomic and other projects, and, at the appropriate time, feed an alternative classification data set back to an appropriate APNI repository
HISCOM to communicate a consolidated view from Australian herbaria on our expectations of the APNI/APC web services. [Bill Barker]
Jim informed the meeting that work will be undertaken to map alternative taxonomies (i.e. State/Territory censuses). The technology of how it will work is yet to be clarified, but they will be ensuring that each census is mapped in APNI as an alternative taxonomy. It was raised that this may be an impossible task given the quality of synonymy provided in revisions, checklists etc. Mapping circumscriptions requires much more rigorous recording of synonymies and misapplications of names. Can this be achieved in a quick and dirty way that may not be perfect? Jim raised the problem of taxonomic concepts not being recorded on det. slips, which makes it impossible to interpret the concept associated with the name.
HISCOM to be informed of any developments arising from TDWG. [Greg Whitbread]
Jim reported that he and Brendan Lepschi are looking at a higher level classification for plants, algae and fungi.
That CANB consult the APC working group regarding the mapping of higher level taxonomies, as all institutions are considering this.
Electronic Flora projects
It was acknowledged that all State and Territory herbaria are considering issues related to the development of electronic floras. Standardising the development of electronic flora profiles has the advantage of presenting a consistent product to our audience, and reducing the duplication of effort in their development. The current TDWG meeting is likely to produce useful information on this front.
That CHAH support a workshop to develop guidelines for the implementation of taxon profile models in Australia, taking the existing work into consideration.
Overview of ALA
Jim reported that the new Director of ALA is under recruitment. Kevin Thiele has been heading a scoping team who have been investigating a number of proposals to put to ALA in order to get the ball rolling before the new Director commences. Proposals under consideration include:
- A presentation tool to display and visualise data for promotion
- Providing resources to enable herbaria who are not yet delivering data in the new format (BioCASE) to be able to do so
HISCOM agreed that the second proposal above is of great importance to both the AVH and ALA, particularly when applied to the major state and territory herbaria.
That CHAH supports the development of a proposal to be put to the ALA management committee, particularly to deliver data from collections not yet contributing to AVH2.
Delivery of AVH data to ALA:
HISCOM and CHAH need to be mindful of delivering of data to systems at appropriate levels of access, in order to maintain some control over the dissemination of sensitive information.
It was suggested that the only information delivered to ALA is the publicly accessible level of data, and that clients requiring more detailed information should be directed to AVH. It was agreed that this is an issue that needs to be dealt with by CHAH.
It is important to remember that another specification built in to AVH2 is the ability for individual herbaria to withhold information e.g. works in progress or unvalidated data. We do not yet have the ability to support this function.
That CHAH be mindful that there are upcoming business decisions to be made regarding the delivery of data to ALA, e.g. in regard to sensitive data or unpublished work.
The question of the relevance of AVH given the development of ALA was raised. It was agreed that it is important that AVH co-exist with ALA in order for CHAH to retain custodianship of Australian flora data.
That the AVH continues to be the flagship for Australian plant taxonomic data, and that it coexists and complements ALA.
Overview of (CERF) National Taxonomy Research Hub (NTR)
Jim provided an update on CERF. He indicated that HISCOM will have some collaboration in the foreseeable future on e-floras, and other developments.
The meeting supported the concept of a sandpit linked to APNI and the APC for researchers developing alternative taxonomies and delivering results in a way that facilitates updating of APNI and the APC.
That CHAH promote the concept of creating a sandpit linked to APNI and the APC for researchers developing alternative taxonomies and delivering results in a way that facilitates updating of APNI and the APC.
ASB "L.A.S. Johnson Review" paper on AVH
Bill Barker has been invited to submit a paper on the AVH to the ASB Journal, and would like the paper to be a collaborative effort involving HISCOM and other parties.
Bill to keep HISCOM up-to-date on the progress of this, and request input from members where required. [Bill Barker]
HISCOM involvement in 2008 ASBS Conference
Adelaide is hosting the ASBS conference next year, which will include a theme of new tools and technologies including developments in biodiversity informatics. This will present a great opportunity for HISCOM members to be involved.
HISCOM to be kept up-to-date on opportunities to be involved. [Bill Barker]
The use of the term 'HISPID name' instead of 'phrase name' is misleading. 'Phrase names' is the preferred term to be used when referring to informally named taxa. The format of phrase names has been standardised by CHAH and should be publicised on various web sites (CHAH, APC, HISCOM etc.) and in HISPID5.
Bill Barker to contact Murray Fagg to arrange the linking to the article on phrase name formats in the ASBS newsletter from the CHAH and APC sites. [Bill Barker]
HISPID5 to reference the correct phrase name format. [HISPID working party]
The meeting was closed at 4pm on Wednesday. The NT Herbarium (especially Dale Dixon, Raelee Kerrigan, Athina Pascoe-Bell and Ian Cowie) were thanked for their generous hospitality. Rousing applause ensued.
- ABCD — Access to Biological Collections Data (TDWG Specimen data standard)
- ABIF – Australian Biodiversity Information Facility
- ABRS — Australian Biological Resources Study
- AEON – Australian Ecological Observation Network
- AFD — Australian Faunal Directory
- ALA — Atlas of Living Australia (NCRIS)
- APC — Australian Plant Census
- APNI – Australian Plant Names Index
- BIG – Biodiversity Information Group (SourceForge)
- CBIT – Centre for Biological Information Technology (www.cbit.uq.edu.au)
- CERF — Commonwealth Environment Research Fund
- CHAFC – Council of Heads of Australian Faunal Collections
- CHAH – Council of Heads of Australasian Herbaria
- EWS — Early Warning System (AVH)
- GBIF — Global Biodiversity Information Facility (http://www.gbif.org/)
- HISPID — Herbarium Information Standards and Protocols for the Interchange of Data
- LSID — Life Science Identifier
- NCRIS — National Collaborative Research Infrastructure Strategy
- SAPAC — South Australian Partnership for Advanced Computing
- TAPIR — TDWG Access Protocol for Information Retrieval
- TDWG — Taxonomic Databases Working Group (http://www.tdwg.org/)
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