HISCOM AGM 2013 Sydney minutes

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28-30 October

National Herbarium of New South Wales, Royal Botanic Gardens, Sydney

For a summary of Action items, see Action Items 2013.



Wayne Cherry (NSW), Ian Cowie (DNA), Eleanor Crichton (AD), Jim Croft (CANB), Anne Fuchs (CANB), Robyn Lawrence (ABRS), Dave Martin (ALA, Tuesday), Ben Richardson (PERTH), Alison Vaughan (MEL), Michelle Waycott (AD), Aaron Wilton (CHR) (Chair)


FCIG Representative, Peter Bostock (BRI), Philip Edgar (WELT), Niels Klazenga (MEL), Greg Whitbread (CANB)

No response


1. HISCOM housekeeping

1.1 Minutes of previous meeting

Michelle moved to approve the minutes of the 2012 meeting. The motion was seconded by Wayne and approved by all.

1.2 Actions from previous meetings

Actions from 2012 AGM

Action Description Assigned to Status
1 Attempt to recover the minutes of the 2010 meeting. Niels Klazenga, Greg Whitbread Attempted but not possible
2 Get the reverse proxy to work at MEL, or put the HISCOM Wiki back in the Aussie Hosting domain.

It was agreed that there is no real benefit in putting the HISCOM Wiki back in the Aussie Hosting domain. Niels got the reverse proxy working, but the http://hiscom.chah.org.au URL was broken so it couldn’t be implemented. We could shift the DNS record from the old site to the RBG site, but it was agreed that the HISCOM Wiki doesn’t need its own domain.

Niels Klazenga, Greg Whitbread, Ben Richardson Not required
3 Provide a short workshop on using MediaWiki on Tuesday afternoon, if time permits. Niels Klazenga Completed
4 Re-organise the Wiki and add user administration tools for the current version (consult with MAHC to see if there are shared categories for Wiki structure). Niels Klazenga Completed, but HISCOM members should continue to improve Wiki structure if needed.
5 Delete spam users from the Wiki and ensure past and present HISCOM members have appropriate editing privileges. Niels Klazenga Completed
6 Finalise the role descriptions and circulate to CHAH and HISCOM for further consideration. Aaron Wilton Completed
7 Remove John Tann and avh@googlecode.com from HISCOM-L, and update Rex Croft’s e-mail address. Check with Jeremy Bruhl whether Jon Burne should still be on the list. Jim Croft, Ben Richardson Completed

Herbaria to review the fields they are providing and deliver additional fields if possible. All



Herbaria to list which HISPID concepts they use in their collections database. TBA (someone needs to make a place for this to be recorded) Carried over


Provide those herbaria who have debugging turned on with a list of the errors that their BioCASe providers are reporting. Niels Klazenga

Completed. See e-mail from Niels dated 19/03/2013 and http://bit.ly/17T9UVq


Write a news item about collections management and data delivery in a university herbarium (e.g. UNE) and communicate to the university herbaria. Alison Vaughan, Niels Klazenga, Michelle Waycott Carried over


Address image storage and metadata with the same rigour that we address specimen storage and metadata. All



Transfer suggestions for new functionality and bug fixes (with suggested priority ranking) into Google Code and circulate summary to HISCOM and CHAH

We need to decide on the best way to record this feedback. We can use the Mantis bug tracker in place at MEL, but we can’t export from it, which could be a problem.

Alison Vaughan

Carried over


Circulate a summary of other feedback to  HISCOM and CHAH.

Alison Vaughan


See if we can change the contact e-mail for AVH to avh@chah.org.au. Greg Whitbread



Each herbarium to check the contacts on their Collectory page and send updates to Miles Nicholls. All



User Liaison person to learn how the sensitive data gatekeeping works. Alison Vaughan, Dave Martin Completed

18 Check how far the ALA has progressed with replacing Resources of Australasian Herbaria with the Collectory pages. Helen Thompson Refer to CHAH
19 Add a list of data providers to the AVH data page, and link them to the Collectory. Niels Klazenga, Alison Vaughan Completed
20 Suggest that FCIG adopt the same strategy of linking to the Collectory from OZCAM. Aaron Wilton Not appropriate
21 Keep HISCOM members in the loop with the progress of the WFO TWG, so that HISCOM can comment and provide feedback where appropriate. Greg Whitbread Carried over
22 Circulate copies of the queries used in the MEL FQCM and GPI error checkers. Alison Vaughan Completed
23 Create a HISPID review team. Aaron Wilton Completed
24 Update HISPID to accommodate atomised hybrid names fields. HISPID review team Needs further discussion
25 Expand the HISPID vocabulary for phenology to better provide for non-flowering plants. Michelle Waycott, HISPID review team as above
26 Add ExpeditionID to HISPID. HISPID review team as above
27 Update HISPID to provide separate fields for geocode method and georeferenced by concepts. HISPID review team as above
28 Revise the posnat vocabulary. Michelle Waycott, HISPID review team as above
29 Clarify the definition of the existing substrate field, and add a new concept to cover microhabitat. HISPID review team as above
30 Add a deaccession flag field to HISPID. Peter Bostock, HISPID review team as above
31 Implement deaccession flag field in each herbarium’s collection database. All as above
32 Add a deaccession reason field to HISPID, and come up with a vocabulary. Peter Bostock, HISPID review team as above
33 Implement deaccession reason field in each herbarium’s collection database. All as above
34 Communicate proposed changes to standards to FCIG. Aaron Wilton as above
35 Communicate changes made to HISPID to the ABCD authors. HISPID review team as above

Document specimen concepts at different herbaria and how UnitIDs are assigned. Niels Klazenga, Michelle Waycott

(All to contribute)

To be completed, see:


37 Develop a working paper on numbering units and the assignment of GUIDs. TBC (include ALA person) Carried over

Actions from meeting with ALA

Action Description Assigned to Status
1 Include information about how AVH works and how it relates to the BioCache and other hubs in the AVH Help page. Niels Klazenga and Alison Vaughan Completed
2 Write a proposal to CHAH about how to use query assertions to make a functioning weed tracker. TBA Superseded
3 Add support to the customising downloads issue in the Google code issue tracker Alison Vaughan Completed
4 Document AVH data aggregation and delivery. Niels Klazenga Completed (add links)

Actions from teleconference

Action Description Assigned to Status
T1 All to review Service Level Agreement for ALA and provide comments to Aaron ALL Completed
T2 Add item on data standardisation to AGM agenda Aaron Completed
T3 Add item on extra-state records to AGM agenda Aaron Completed
T4 All to review and provide feedback on the MOU to Aaron ALL Completed
T5 Add drafting of technical schedule for MOU to AGM agenda Aaron Completed
T6 Provide documentation on the services, architecture etc for NSL Greg Documented on biodiversity.org.au
T7 Gather information on institutional processes for managing names, as well as issues and opportunities of adopting NSL All In progress

Actions arising from previous meetings

Action 1: Document the specimen data concepts and definitions used in collections databases (and how they are mapped to exchange standards). This will help us compare database structure between herbaria, provide valuable system documentation and help identify projects for HISCOM. (All)
Action 2: Write a news item about collections management and data delivery in a university herbarium (e.g. UNE) and communicate to the university herbaria. (Alison, Michelle, Niels )
Action 3: Investigate options for issue management software for recording AVH feedback, bugs and suggestions. (Alison, Ben)
Action 4: Add NE to list of contributing herbaria on Data page. (Alison)
Action 5: Look at API and standards for GRBio and see if it can also be used to deliver institutional metadata to ALA http://grbio.org/ (Ben et al.)
Action 6: Post regular updates to the HISCOM list on the WFO (Greg)

1.3 Timing and structure of meetings

It was agreed that it would be more productive to move the HISCOM meeting forward two months to allow time for actions to be completed before reporting to CHAH. This would also tie in better with the TDWG standards review, which it is important for HISCOM to contribute to. It would also eliminate the clash between HISCOM and TDWG.  It would reduce the time commitment of members attending multiple meetings in the same week (esp. CHAH members attending HISCOM etc.), and allow people to attend multiple members.

Recommendation: That the HISCOM meeting is scheduled approximately two months ahead of CHAH and TDWG, rather than in October-November


To be added to the list

  • Cathy Downs
  • Anne Fuchs: anne(dot)fuchs(at)environment(dot)gov(dot)au

To be removed from the list

  • Gary Chapple
  • Brett Summerell (TBC)
  • Jerry Cooper (TBC)
  • Matthew Miles
  • Nicholas Lander


  • Peter Bostock’s e-mail addres
  • Sally Stewart
Action 7: Check Peter Bostock’s e-mail address, and whether Sally Stewart wants to remain on the HISCOM list (Alison) - this is sorted, Alison!(Peter)
Action 8: Check if Jerry and Brett want to remain on the list (Aaron)
Action 9: Make the above changes to the HISCOM list (Ben)

1.5 Reports


Beth has resigned as the GBIF node manager and there is currently no replacement. She has recommended to John Le Salle that an ALA person takes up the role, as that would remove the financial obstacle.

Recommendation: That CHAH takes an interest in the role and consider whether it should be a member of the herbarium community, instead of an ALA staff member


Paul Flemons is resigning as regional representative for TDWG. Nominations for Aaron and Greg are being taken to the TDWG meeting in Florence this week. Aaron talked to CHAH about funding regional representative to attend TDWG.


The ALA Technical Architecture Group had an inaugural meeting last week looking at their Terms of Reference and the need for environmental/policy representation in the group. Dave gave update on ALA architecture, which he’ll provide to the meeting tomorrow. Dave will also summarise the main areas of work for ALA in the coming year. There is an opportunity for HISCOM to provide input into what the virtual taxonomic infrastructure (VTI) should comprise.

The communication role of the TAG members needs to be clarified in their Terms of Reference.

2. Biodiversity Data Recording System

  • ABRS has been given a National Environmental Research Program grant to develop the Biodiversity Data Recording System (BDRS), an online field data capture tool for BushBlitz
  • The BDRS will be trialled on mobile devices at the December 2013 BushBlitz in Namadgi NP
  • Robyn is interested in field data capture protocols for different herbaria, and what BDRS output formats herbaria want (csv, DwC, JSON etc); it was agreed that csv with clear field definitions is sufficient
  • Robyn is also interested in the ability of herbaria to incorporate a BushBlitz identifier into their collections database.
Action 10: Provide feedback to Robyn in consultation with MAHC members (All)
Action 11: Send MEL collecting template and guidelines to Robyn and Michelle (Alison)

3. MoU and Technical Schedule

  • The Technical Schedule should be limited to data delivered to a particular project (AVH, Seedbank), i.e. a separate schedule should be drafted for each class of project (specimen data, images, DNA data etc.), with the one overriding MoU that needs the legal sign-off. This approach would allow more flexibility for adding new content without re-litigating agreements.
    • Head agreement that allows schedules to be appended, and doesn’t implicitly limit scope of AVH/HISCOM activity
    • Shift focus to botanical information, rather than specimen information
  • The wording of the MoU/Technical Schedule could be more inclusive and talk about the different modules that make up AVH
  • The head agreement should define a default licence for all information types (e.g. CC BY), with the caveat that different licence options may be specified in one of the attached schedules (e.g. images).
  • There is a relatively urgent need for CHAH to decide on a default licence for release of images
  • A statement of commitment to data quality should be included in the MoU, as well as a commitment to engage with users and respond to feedback.
Recommendation: Adopt CC By as default licence for the sharing of specimen-related images
Action 12: Provide additional feedback to CHAH on the MoU (Aaron)
Action 13: If required by CHAH, finalise the minimum fields for delivery in the Technical Schedule.

The discussion about the MoU led to a wider discussion on duplicate management, data exchange and the need to understand how differing curatorial practices affect our ability to effectively share data.

  • We need to collect information on how each herbarium deals with duplicate specimens so we can figure out what information is available and (see document on duplicate and loan management capabilities); we also need to provide some guidelines to ALA about how they can best use the data we provide to detect duplicates
  • A lot of focus has been on pushing data out, but little consideration has been given to how we manage data internally.

4. Future planning brainstorming session

Aaron and Michelle led a planning and brainstorming session for HISCOM to identify needs of different herbaria, and to identify practical work tasks for HISCOM. It was agreed that we need to consider new opportunities for collaboration, new projects that we should get involved with, and to think about the best and most productive way for HISCOM to operate.

The main areas of work that were identified are outlined below (also see Appendix 2).

Transition planning/Resourcing/Skills/Sharing advice

  • invite more members on to the HISCOM list (MAHC) and use it as a forum for seeking assistance and sharing knowledge and advice
  • provide skills sharing and training support (cost issues)
  • organisational resilience/succession planning
  • separate the meetings out to allow cross participation
  • work more closely with FCIG?

Standards in the Australasian context

  • engage with MAHC, FCIG and ALA
  • field definitions
  • standards for ancillary collections
  • descriptive data content
  • vital attribute data
  • nomenclature
  • make decisions about GUIDs
  • species interactions


  • incorporate GPI images into AVH
  • extend HISPID to include metadata image standards (for all types of specimen-related images)

Thinking beyond specimen data

  • eFloras
  • nomenclatural update services
  • need an equitable and optimal funding structure: state and regional herbaria often don’t benefit from – and so can’t contribute to – some of the major initiatives that are being funded
  • assigning uncertainty to records (e.g. based on non-synonymous identifications on “duplicate” specimens)

Engage more closely with ALA

  • make better use of the existing ALA services
  • develop annotation services
  • develop de-duplication solutions
  • data processing tools


  • determine how duplicates are treated in each herbarium
  • improve curation of duplicate specimen data
  • workshop with MAHC and HISCOM
  • work with ALA to determine the best way to identify duplicates

Software development/dealing with obsolescence

  • sharing information about database development
  • skill-sharing
  • cloud-based software solutions
  • update CHAH on current state of herbarium information systems, and flag issues with obsolescence, succession planning etc.

Role of CHAH

  • PR exercise; need to promote the value of herbaria in a collaborative way
  • website really needs to focus on PR
Action 14: Summarise the workshop outcomes for circulation to HISCOM, MAHC and CHAH (Aaron and Michelle)
Action 15: Add MAHC members to the HISCOM list (Ben)
Action 16: Request an update on the website review and requirements from CHAH (Michelle)


5.1 HISPID schema

  • Need to get HISPID5 schema somewhere accessible so that it can be validated against; could be hosted on the AVH site
  • Jim pointed out that we own taxonomy.org.au and biodiversity.org.au; it was agreed that it would be better on biodiversity.org.au
Action 17: Put the HISPID5 schema on the biodiversity.org.au site (Ben and Greg)

5.2 Structural review of HISPID

  • Agreement that we need to review HISPID and add new concepts that have been identified
  • Also need to extend the content to include some other information types (e.g. images)
  • If a module has already been described and has a generic standard that suits our needs, we will use that. So we might, for example, use DwC fields for the specimens module, Audobon Core fields for the images etc.
  • We need to undertake a documentation exercise first, in order to better inform how HISPID should be reviewed
  • There is a need for a workshop around standards at some point, but the timing and structure will be dependent on the outcomes of the documentation exercise

Documentation exercise

  • It was agreed that it would be helpful to have a review of all the fields and concepts being used in herbaria so we can highlight areas where there is confusion, and which fields are or are not being used
  • It’s important to know the current state of play in order to make good decisions that factor in all herbaria, regardless of their different levels of resourcing or technical expertise
Action 18: Herbaria to provide information on the data concepts used and delivered (All, coordinated by Michelle and Aaron)

5.3 Images

  • We need clarity about how to deliver images to AVH (see notes from Dave below)
  • We need to decide on image metadata standards for image sharing within HISCOM/AVH
  • MEL is currently dealing with hundreds of specimen images provided by collectors
  • All herbaria are also dealing with GPI images, which should be made available on AVH
  • There needs to be a related discussion about how to attach unique identifiers to images and other types of collection data

Delivering images to AVH

  • Dave says that the simplest way to deliver images is to include a URL for the image location on the local web server; otherwise herbaria can send them an export of images with a table that includes file name, catalogue number or specimen GUID, and image metadata
  • ALA can deal with multiple images per specimen
  • When images are harvested, derivatives are created (thumbnail and smaller image)
  • JPEG, PNG and TIFF currently supported, but JPEG preferred (it is the most web-friendly)
  • ALA will be working on a large image viewer (the Morphbank solution is not working very well)
  • Image metadata is being embedded in specimen data
  • Ben has been working with Gaia Resources on Imagebank; which might work for images in ALA
Action 19: Provide the ALA image fields, and examples of image metadata being sent by other providers to HISCOM (Dave)
Action 20: Put MEL’s current image metadata discussions on the HISCOM list (Alison)
Recommendation: Herbaria should deliver GPI images to ALA via protocol developed with Dave; there is no impediment to ALA accepting images from herbaria, and no changes to the AVH site is needed to make the images display

(In the joint CHAH/HISCOM meeting, it was noted that the Darwin Core fields for delivering type information are limited, which will need to be addressed when we start delivering type images to ALA.)

6. AVH

6.1 ALA update

Dave provided an update on ALA architecture and work programs, which framed the following discussions.

ALA architecture overview

  • See: http://crawler.gbif.org/dataset/ddfca596-41db-475c-b1ad-c1a77d20e133
  • The overarching principle is separate components communicating through web services
  • There are four layers in the architecture:
    • Front-end apps (species pages, occurrence searching, spatial portal, AVH, OZCAM etc.) – don’t actually have DBs underneath, they instead call to other underlying web services
    • Web services (national species lists, occurrence data, environmental layers etc.)
    • DBs, Indexes, Filesystem storage
    • Offline processing
  • Two download types when AVH went live:
    • Cassandra database had detailed downloads working from it, but it was impacting other users and has been disabled for now
    • Fast downloads running from SOLR

Coming work

  • ALA is currently on a recruitment drive. They currently have a director, two project managers and seven developers. One project manager is working on field data capture software and the other project manager is working on recruitment.
  • Working on expansion of the PhyloJive function (see http://www.ala.org.au/blogs-news/phylojive-integrating-biodiversity-data-with-phylogenies/)
  • Recruiting a project manager and a developer for VTI (virtual taxonomic infrastructure); HISCOM would like to be more engaged in this work (it hasn’t really started yet due to project managers being otherwise occupied)
Action 21: Express interest to John La Salle and/or Peter Doherty in HISCOM being stakeholders in the development of the VTI (Aaron and Michelle)
Action 22: Keep HISCOM updated on VTI developments (Dave, Greg and Jim)
Recommendation: There is going to be an active virtual taxonomic infrastructure program in the ALA, and the most appropriate way to respond to the NSL document is to be part of the VTI program work with ALA.

6.2 AVH harvesting

  • The occurrence processing stage (see ALA architecture document) is where AVH data is harvested, processed, sampled and indexed
  • Harvesting protocols: mostly pulling in DwC archives (can support DiGIR, Tapir, BioCASe etc., but it’s a very slow, problematic and complex way to harvest the data)
  • Community is moving away from XML data delivery. Ebird in US (80 million records, 25% of what’s in GBIF) shifted from BioCASe to DwC archives, which means data can be harvested in minutes instead of weeks, also freed up a server
  • DwC archives are not limited to DwC: you can use your own vocabulary and schema
  • ALA supports deletes in two ways:
    • it can support a file that lists which records have been deleted (museums do this, i.e. provide IDs of records that need to be deleted)
    • the other way is to get full DwC archive and delete existing records that aren’t in the new archive
Action 23: Get clarification and agreement around future harvesting plans, i.e. plans to harvest directly from herbaria (Niels and Miles)

6.3 Unique identifiers

  • ALA sees it as not their role to mint identifiers (cf. GBIF, who do)
  • There was discussion on the suitability of DOIs given the commercial model and the number that we’d have to deal with
  • There was agreement that GUIDs or UUIDs should be implemented for multiple concepts in herbarium management systems
  • We don’t see resolvability as being essential at this point; the most important thing is to be able to uniquely identify records in a practical and sustainable way
  • GUIDs should never be reused for a different object
  • There was agreement that there is no need to apply a new GUID to a new version of a record that relates to the same collection object

6.4 Institutional metadata harvesting

  • If we deliver institutional metadata, it can be harvested by ALA to populate and maintain the collectory pages
  • The collectory schema is an amalagation of different schemas (BCI, EML etc.)-
  • There is equivalence with the GRBio standard, so the same metadata can be delivered to both
  • The collectory can also be edited directly by people with editing rights
Action 24: Provide HISCOM with the collectory schema (Dave)
Advice to CHAH: Individual herbaria can start editing their own collectory page. Each institution can decide who has access, and should ask Alison to add the necessary permissions to their ALA account.
Recommendation: Ask ALA to deliver collectory data to GRBio on our behalf.
Action 25: Decide if there is additional metadata that should be captured and let ALA know (All, via HISCOM-l)

7. NZVH status

  • Contracts are still being signed by the different NZ stakeholders; this needs to be completed before a contract between NZVH and ALA can be prepared
  • The aim is to have a joint Australasian Virtual Herbarium by the end of June
  • Harvesting in NZ will be similar to how it’s currently done in Australia (i.e. central cache)
  • The following changes to the AVH interface were discussed:
    • Spatial layers: limit to individual country, or display them both at the same time? It was agreed to add whatever NZ layers we can, add see if a need for a combined layer view arises
    • The home page design will need to be modified, as there will be 11 new providers
    • Map default: should be centred on distribution, but set at a minimum scale (i.e. so you can always tell what country you’re looking at, even if the distribution is very localised)
    • Collectory (management will be straightforward now that we can edit own sites)
    • We need to decide how NZ records from non-NZ collections will be processed (i.e. matched against APC/CoL process or NZOR?)
    • The advanced query options are populated by the data, so they don’t need to be changed (but some facet labels might need to be modified)
    • Query assertions would have to be developed for NZ region, but this isn’t a lot of work – ALA just need the right environmental layers
    • Sensitive data service – ALA need the listing for NZ taxa
    • URL: Aaron says the .au is not going to be a problem. nzvh.co.nz will be redirected to ala.chah.org.au

8. Extra-state records

See Request for Action from CHAH, Dealing with non-state records in AVH.

  • It was agreed that we need to do a preliminary analysis of the data to see if there is any truth to the hypothesis that state-based data is of a higher quality than extra-state records
  • We also need to find out what curatorial standards each herbarium applies to extra-state records
  • There are several issues around this that need further consideration
  • Dave said it was technically possible to create a facet for extra-state records, but it would require some work:
    • When indexing, look at where record comes from and compare that with the georeference to identify extra-state records
    • Some additional institutional metadata would need to be recorded
    • Dave estimated that it would be about one week’s work to implement these changes
Action 26: Test assertion by analysing AVH data using ALA data quality tools and circulate to HISCOM and CHAH for discussion (Alison)
Recommendation: That HISCOM and MAHC document the approach each herbarium takes to curating extra-state records (particularly georeferencing and identification)
Recommendation: The general principle is that AVH is a summation of the collective holdings of the Australian herbaria. It is preferable to fix errors rather than remove them from view. We suggest that CHAH strongly endorses the principle of all herbaria providing all records.
Advice to CHAH: It is currently possible to do filter out extra-state records on a state-by-state basis. It would be technically possible to add a facet to filter out extra-state records for the whole country at once. This would require about one week’s development work from ALA.

9. EWS/Weed alert functionality

  • ALA could consume species distribution polygons, but, for weed alerts, it would be more appropriate to use a dynamic approach that compares new records to existing records
  • It would be good to be able to define an area and be alerted when a record of a new species is reported for that area; this way it would not be limited to weeds
  • To get this on to the list of development, it would need to be properly scoped and agreed upon by the ALA management committee
  • It would be fairly easy to implement something for a small number of taxa (such as weeds of national significance) that reports new records that fall outside a static polygon that represents the current known range (this wouldn’t need to go past the AVH management committee)
  • A more dynamic and flexible approach would be possible, but would be a significant amount of work
Recommendation: That CHAH communicate with weeds people to that they know about current alerts functionality in ALA, and to discuss ideas about enhancing the alert functionality.
Action 27: Write a news item about creating alerts in AVH (Alison)

10. KeyBase

See Request for Action from CHAH, AVH-ALA taxon listing for KeyBase.

  • The KeyBase requirements can be met by the area report tool in the spatial portal. It will include all ALA records, not just AVH records, but it doesn’t sound like that will be a problem for what it’s going to be used for.
Advice to CHAH: This functionality is already available.

11. AVH user feedback and change requests

  • The main feedback in the past few months has been people asking about when the detailed downloads will be available again. ALA has ordered some new hardware that will be used to make detailed downloads available.
  • The main improvements requested by users are:
    • Add a facet on subclass so that mosses can be filtered.
    • Include a facet for determination uncertainty.
    • Add a bounding box/WKT/KML query options to AVH (probably one to two weeks of development time).
    • The ability to download any field (and to customise which fields are in the download).
Advice to CHAH: These are the priorities for development of AVH from our users.
Action 28: Liaise with ALA about implementing these features (Niels)

12. New GBIF site

13. Election of roles

  • Aaron was re-elected in the role of Chair of HISCOM
  • Alison was re-elected in the role of User Liaison
  • Michelle was re-elected in the role of CHAH representative
  • Niels was re-elected in the role of Technical Coordinator
Action 29: Circulate the description of the roles (Michelle)
Recommendation: That CHAH endorse these re-appointments

14. Presentations

  • Aaron gave a presentation of the Flora of New Zealand (slides will be made available online). Aaron wants to collaborate with HISCOM/ALA communities about applying standards to descriptions. File:NZ EFlora HISCOM AGM 2013.pdf
  • Michelle demonstrated the open-source Leaflet image viewing software:http://images.ourplants.org/leaflet/AD256558.html
  • Dave showed us the Biodiversity Volunteer Portal, which now has a herbarium expedition (from the Smithsonian); this template might work well for other herbarium collections: http://volunteer.ala.org.au/project/index/2834239
  • Ian talked about the extended HOLTZE specimen and the NT flora online (slides will be put on the wiki)

Appendix 1: DRAFT Technical Schedule for MoU


Ideally HISPID5/ABCD, DwC if not possible.

Delivery format

XML, Darwin Core Archive. Other formats (e.g. csv) may be negotiated if absolutely necessary.

Delivery mechanism

Delivery mechanisms will ideally be one BioCASe 3.0 (or higher), IPT, or existing (but no new) Tapir providers. A single CSV format is an acceptable delivery mechanism if they are unable to implement one of the preferred mechanisms.

For initial uploads and re-indexing a Darwin Core Archive (or similar) may be required.

Delivery frequency

The ideal frequency of delivery will be daily. We will accept periodical uploads if harvesting is problematic.

For providers who can only deliver data periodically, the ideal delivery frequency is at least quarterly, with a minimum delivery frequency of yearly.

Where required, re-indexing will be conducted yearly.

Data quality

Herbaria will endeavour to respond to annotations and verify specimen data, especially in relation to the identifications and georeferencing.

For initial uploads and re-indexing a Darwin Core Archive may be sent back to the provider for checking.


Herbaria should deliver all available fields from those listed below. The minimum set of fields that constitute an AVH record are marked with an asterisk.

Names starting with a lowercase letter are Darwin Core terms; these fields form the core BioCache record. Names starting with a capital indicate ABCD and HISPID elements that are not in DwC or had to be manipulated to fit them into a DwC concept.

o   [1]Collection Object group

§ [2]institutionCode *

§ [3]collectionCode *

§ [4]catalogNumber *

§ [5]occurrenceID

§ [6]basisOfRecord

§ [7]preparations

§ [8]modified *

o   [9]Collecting Event

§ [10]recordedBy

§ [11]AdditionalCollectors

§ [12]recordNumber

§ [13]eventDate

§ [14]verbatimEventDate

§ [15]country *

§ [16]countryCode

§ [17]stateProvince *

§ [18]locality *

§ [19]GeneralisedLocality

§ [20]NearNamedPlaceRelationTo

§ [21]decimalLatitude *

§ [22]verbatimLatitude

§ [23]decimalLongitude

§ [24]verbatimLongitude *

§ [25]verbatimCoordinates

§ [26]verbatimCoordinateSystem

§ [27]verbatimSRS

§ [28]geodeticDatum

§ [29]coordinateUncertaintyInMeters

§ [30]coordinatePrecision *

§ [31]georeferencedBy *

§ [32]georeferenceProtocol *

§ [33]georeferencedDate

§ [34]georeferenceSources

§ [35]georeferenceVerificationStatus

§ [36]georeferenceRemarks

§ [37]minimumElevationinMeters

§ [38]maximumElevationinMeters

§ [39]verbatimElevation

§ [40]minimumDepthInMeters

§ [41]maximumDepthinMeters

§ [42]verbatimDepth

§ [43]locationRemarks

§ [44]habitat

§ [45]associatedTaxa

§ [46]HispidHabitat

§ [47]locationRemarks

§ [48]Aspect

§ [49]Substrate

§ [50]Soil

§ [51]Vegetation

§ [52]occurrenceRemarks

o   [53]Current Determination

§ [54]nomenclaturalCode

§ [55]scientificName *

§ [56]kingdom

§ [57]phylum

§ [58]class

§ [59]order

§ [60]family *

§ [61]genus

§ [62]specificEpithet

§ [63]taxonRank

§ [64]infraspecificEpithet

§ [65]CultivarName

§ [66]scientificNameAuthorship

§ [67]nomenclaturalStatus

§ [68]ABCD IdentificationQualifier

§ [69]ABCD IdentificationQualifierInsertionPoint

§ [70]identificationQualifier

§ [71]NameAddendum

§ [72]DeterminerRole

§ [73]identifiedBy

§ [74]dateIdentified

§ [75]VerbatimDeterminationDate

§ [76]identificationRemarks

o   [77]Identification history

§ [78]previousIdentifications

o   [79]Type status designations

§ [80](ABCD) TypeStatus

§ [81]TypifiedName

§ [82]DoubtfulFlag

§ [83]Verifier

§ [84]VerificationDate

§ [85]VerificationNotes

§ [86]typeStatus

o   [87]Exchange

§ [88]ExHerb

§ [89]ExHerbCatalogNumber

§ [90]DuplicatesDistributedTo

o   [91]Loans

§ [92]LoanNumber

§ [93]LoanDestination

§ [94]LoanForBotanist

§ [95]LoanDate

§ [96]LoanReturnDate

o   [97]Denormalised Named Areas

§ [98]Australian Herbarium Region

§ [99]IBRARegion

§ [100]IBRASubregion

o   [101]Denormalised Measurement or Facts

§ [102]reproductiveCondition

§ [103]CultivatedOccurrence *

§ [104]NaturalOccurrence

§ [105]establishmentMeans

Deaccession mechanism

Records to be deleted will be delivered in an extension in the DwC Archive. This CSV file only needs to have institutionCode and catalogNumber. A deaccession vocabulary will be added to allow deaccessioned specimen records that still constitute a valid occurrence record to be retained in the ALA.

Appendix 2: Workshop discussion

Questions raised overall:

  • Should HISCOM meet annually? Or should we meet every couple of years and have working meetings to get stuff done or help other herbaria in the interim?
    • an option was suggested that we meet as HISCOM biannually with smaller working groups meeting in between. Perhaps the face to face bi-annual meeting could involve presenting work to stakeholders and partners eg ALA, MAHC
  • Need to work more closely with MAHC?
  • Yes, a number of projects have been discussed. Need to elaborate in discussion with MAHC.

Area Opportunities/items needed Specific actions
Super wish list * How to effectively depict uncertainty
  • fully engaged with ALA decision making
  • build organisational resilience

Aspirational * Modularisation
  • Web services; distributed design

Knowledge sharing * Transition
  • Mentoring, upskilling -> change of staff
  • training and advice
  • share experience/advice, system solutions
  • integration with MAHC

* use HISCOM-L more for discussion, problem solving
  • Training/consultation between institutes (?$)
  • invite more to the list
  • Run meetings to enhance exchange and participation

Standards * standards (incl.content)
  • clear standards and guidelines (specimens, names, descriptive content)

* engage with MAHC (ensure implications of their work consistent/understood)
  • Future of HISPID -> flexibility and manage transition
  • Engage with FCIG (new analyses possible)

Standards 2` * Provide clear and understandable field definitions
  • guids
  • Standards: cultivated plants; hybrids; sensitive taxa
  • Standards around

* create when no other options (e.g., descriptive)
  • Adopt or create
  • Image metadata
  • Collaboration to adpot image metadata (ALA, ? etc)

eFlora * sharing of flora descriptions (and images)
  • AVH still not fulfilling original vision of being a tool for herbaria
  • nomenclatural update tools (not just NSL; Virtual Taxonomic Infrastructure)   

* Find engagement model for national initiatives
  • CHAH - How to recognise inputs from institutions
  • Thinking beyond specimen

* Annotation service
  • Understanding the amount of filtering/dithering of data for sensitive species (Metadata service)
  • Facilitate the transfer of data to AVH/annotation back to host institute
  • Engage with ALA

* Engage with ALA
  • To ALA - APD:  use cases
  • full circle feedback
  • How to implement and identif projects with MAHC   

Tools * Data validation tools (geocode)
  • Autogeocoding infrastructure
  • Improve duplicate detection
  • Better duplicate specimen data exchange   
  • Data processing tools: in/out (e.g., transformation)

* workshop with MAHC [on duplicates]
    • identify how each herbarium deals with duplicates: curation and data
    • Identify what needs to be done to resolve duplicate data issue
    • All add fields to db

Images * GPI and other images

* [deliver:  standards and methods]       

* cloud-based database for small collections
  • software obsolescence & redevelopement

* Give CHAH state of each institutes system
  • Support need for small collections beyond current
  • find core similarities to build on
  • develop strategies for upgrade and support

Barriers 1 Role of CHAH * PR- value of members individually as part of a collective
  • www PR

Barriers 2 * CHAH vision and support
  • www pr
  • state/province vs country with delivery needs
  • centralised $ not distributed