HISCOM AGM 2014 Adelaide
- 1 Meeting location and accommodation
- 2 Minutes
- 3 Welcome and housekeeping
- 4 eFlora Update
- 5 Names
- 6 Communicating feature requests and bug fix requests to ALA
- 7 NZVH update
- 8 HISPID
- 9 Dadswell Wood Collection
- 10 Demonstration of NSL
- 11 Data delivery
- 12 ALA/AVH Hub update
- 13 VicFlora and KeyBase
- 14 ASBS 2015
- 15 CHAH Website
- 16 AVH website
- 17 Feedback from conferences/meetings
- 18 Images
- 19 Sensitive Data Service
- 20 Annotation service
Meeting location and accommodation
Attendees: Ainsley Calladine (AD), Wayne Cherry (NSW), Eleanor Crichton (AD), Jim Croft (CANB), Anne Fuchs (CANB), Niels Klazenga (MEL), Donna Lewis (DNA), Rebecca Pirzl (ALA – Thursday morning), Nick dos Remedios (ALA), Alison Vaughan (MEL – Chair), Michelle Waycott (AD), Greg Whitbread (CANB), Aaron Wilton (CHR)
Apologies: Peter Bostock (BRI), Laurence Paine (HO), Ben Richardson (PERTH), Helen Thompson (ABRS)
For a summary of action items, see Action items 2014.
Welcome and housekeeping
Welcome, introductions and institution updates
- AD have funding to migrate their collections database from Texpress to Specify over the next 2.5–3 years, and have commenced work on this.
- DNA have incorporated the management of taxon names into their collections database, as well as working on the eFlora, which will be available next year.
- CANB have experienced savage budget cuts and are in a period of transition. They are losing a number of key staff from the Gardens and ABRS in the coming months, including Greg, who leaves in February 2015. CANB is now under the same management umbrella as the CSIRO collections. A science review resulted in very good outcomes for the collections.
HISCOM farewelled Greg and thanked him for his significant contributions over the years.
- NSW have had no major developments in the past year. NSW is still running their collections database in EMu, and have added HISPID ID qualifier fields. The merger with Centennial Parks is a big institutional change, but will supposedly not impact on the science area too much.
- MEL is continuing work on VicFlora; the census component is available now, and the first batch of descriptions will be published by the end of the year. A Science restructure is pending.
- CHR have reworked their access portal for specimen data, and have continued work on the eBiota (will include fungi and insects as well as plants). They are currently going through a reorganisation and will be losing some contract staff.
- HO have moved to a new government agency and many services have been cut. Laurence was sitting in budget estimates, so was unable to attend the HISCOM meeting.
- BRI are losing several key staff in the next few months, including Peter Bostock (who is finishing up at the end of September). Alan Bolin (Collection Manager) is also retiring. There’s no certainty that these positions will be replaced. Ailsa is the best person for HISCOM to communicate with after Peter retires. BRI are looking into data delivery options, and working on a CSV extract in DwC format. Peter will provide an overview of the BRI collections management system and resource constraints for HISCOM reference.
- PERTH have had a major reduction in staffing across the whole Division, and Ben is now the only person employed in the Herbarium with IT skills and focus, so there are a lot of competing demands on his time.
Discussion about the value of herbaria in a time of significantly reduced resourcing.
Minutes and actions from the previous meeting
The Minutes of the last meeting were approved and the Action Items were reviewed (see updated list at http://hiscom.rbg.vic.gov.au/wiki/Action_Items_2013)
The following action items were carried over from the 2013 meeting:
Discussion of RAH, collector pages and partner profiles:
- Agreement that RAH should be retired and the ALA collectory pages used instead
- Need to consider how to incorporate this information into the CHAH website when it’s reviewed
- Institutional information on the collectory pages is on-provided to Research Data Australia
The elected positions discussed at the recent teleconference were endorsed at the meeting.
- Chair – Alison
- User Liaison – Alison to continue
- Technical Coordinator – Niels to continue
- Deputy Chair (and CHAH Rep.) – Michelle
- Assistant Chair – Donna (proposed)
Discussion of possible industry participation in HISCOM:
- Jim raised possibility of inviting non-HISCOM members to meetings, e.g. Alex Chapman (formerly of WA Herbarium and now at Gaia Resources). The potential for a conflict was interest was raised, especially if inviting people when the state representative can not attend. It was decided that it would be more appropriate to invite industry guests to participate in individual meetings or individual agenda items after consultation with HISCOM, rather than extending a blanket invitation for participation.
Rebecca led a discussion and update on eFlora and VTI:
- included the relationship and interaction between VTI and eFlora
- Attribution and citation – need a small working group to progress this
- need to liaise with the university sector regarding requirements for flora chapters being credited
- do have opportunity to influence, but this means we have to think about this now
- flora descriptions are also data
- looking to get input on VTI from CABC
- eFlora tools are a way of delivering outcomes of work that might be undertaken within a VTI
- modularity is important so you’re not dictating certain workflows or products on people: need to allow people to interact with the tools any way they want
- the first phase of work (through to June 2015) will develop a prototype using Flora of Australia data
Key points of contact with HISCOM during eFlora development:
- in addition to institutional contact
- Alison and Aaron are on working group
- input to technical architecture, standards, editing and attribution.
- Need some clarity around goals
- Gather, verify requirements; determine and develop the modules (dependant upon getting the programming resources)
- Commence further discussion around citation and attribution
Greg provided an update on WFO:
- workshops held, Use Cases documented, trial projects underway using eBiota software, Common Data Model
- MO see the lack of a WFO as the single greatest obstacle to global plant conservation
- eMonocot has been developed, trial underway to import data (the Flora of Australia data will be provided for this)
- key points of interaction for eFlora –
- discussion around the minimum number elements, how many levels deep
- review DwC elements
- different levels of sophistication – locals have more complexity but consolidate to ‘lowest common denominator’
- aiming for a plant list assembled by experts.
See more detailed discussion below.
Request from CHAH
Need for broader management model for ongoing maintenance for APNI/APC – ref value proposition (refer to CHAH request for action: APNI/APC, 26 September 2014)
- If the herbaria adopt APNI/APC for the management of state censuses, then they could justify contributing resources to help maintain APNI/APC
- would need sufficient offset
- what architecture, services would be needed?
- need to broaden the base
- Other requirements around effort to apply updates within the institutions
- needs discussion at each institution re workflow implications
- want APNI/APC developed as a collaborative, distributed model
- web services and option to install a local copy
- need to streamline processes eg taxonomic update process.
Communicating feature requests and bug fix requests to ALA
Alison reported on the proposed system for the Collections Community Coordinators to document feature requests and bug fixes for ALA (there’s a spreadsheet of Collections Tasks and Issues maintained by both CCC’s (for flora and fauna), which includes priorities and focus on coming year’s work), and discussed potential overlap with existing communication methods:
- this approach allows us to see where our requests and issues fit with other issues, and to see what’s been prioritised and what’s currently being worked on
- this method doesn’t need to preclude any individual contact with developers
- it provides formality to facilitate prioritisation and consistency in direction
- there’s value in collecting and filtering locally (i.e. within HISCOM) first – some issues are temporary or can be addressed locally
- it was suggested that the GitHub issue tracker might be more appropriate to use.
Aaron provided an update on NZVH
- included discussion on status, next steps, AVH/NZVH merge
- working on new cache, structured around a flattened DwC. Harvest via csv/DwC archives/IPT
- a test archive was sent to Dave Martin a few weeks ago (all looked good)
- IPT is easy to work with – the hard part is getting people to provide updates
- has graphic designer working on new logo for the Australasian Virtual Herbarium
- next step – start sourcing additional spatial layers to provide to ALA
- AVH "Home" map needs re-centering on initial page load (keep same zoom and shift centre so that both Australia and NZ are visible)
There’s a need to separate the standard (HISPID) from the delivery format (XML/CSV), and agree on their mappings:
- think about vocabulary restrictions and documentation.
Time-frame for doing this – preliminary work prior to TDWG because there will be workshops there on ABCD and DwC that potentially could help address any issues/questions we have.
Need to be able to provide detailed documentation – both for small herbaria and also for the larger ones as in-house expertise is lost and there would be more reliance on external contractors.
Where concepts are missing, identify and have them added
- typified names, type images, spatial fields (these in DwC but not hispid)
It was agreed that a core working group would facilitate the review process, do preparatory work and distribute documentation for feedback, then meet for a workshop to finalise the work (est. 3-day workshop).
- A working group for the HISPID review (comprising Ben, Aaron, Anne and Niels) was established
- All interested parties are welcome to engage with the process and provide feedback.
- There was discussion about whether or not the review should include data requirements for DNA samples, images etc.
- Need to consult with MAHC about their standards and procedures and identify areas where HISCOM need to have input on data standards.
Dadswell Wood Collection
Jim reported that the Dadswell Wood Collection (see http://www.eoas.info/bib/ASBS03460.htm) has been moved from CSIRO to CANB. Jim wanted to know whether HISCOM knew of anyone working in the area who might be interested in the collection. If there’s no pressing need to digitise the collection soon, it will remain in the CANB backlog.
Demonstration of NSL
Greg discussed the status of NSL:
- test NSL editor is operational and being regularly updated
- APNI data is migrated daily (it takes about 35–40 minutes each time)
Relationship between APNI and NSL:
- APNI is a nomenclator with a taxonomic layer on top, which captures synonymies etc; APNI is a product that sits on top of the NSL
- NSL is infrastructure that can store all that taxonomic information, but not just for plants: it can be used for anything (not just taxonomic concepts), i.e. a very complex thesaurus
The demonstration of NSL and presentation of process diagrams was very valuable in helping HISCOM understand the necessary complexity of the NSL (incl example diags from Greg’s NSL demo if available).
- Data delivery report: http://bit.ly/1usgPlN
- AVH fields (who is currently delivering what): http://bit.ly/1rtKGX9
Niels demonstrated the BioCASe provider and the GBIF Integrated Publishing Toolkit (IPT), with discussion around their differences, and when/how each may be of benefit:
- BioCASe better suited for data delivery to AVH, particularly for the larger herbaria
- 100+ concepts are delivered to AVH at the moment, but only 67 of those can be mapped in IPT
- can use extensions to IPT (write them and submit them for inclusion)
- IPT may be a tool for university and other small herbaria
- IPT is okay for ad hoc data delivery and re-indexing, but it can't do dynamic data delivery, so is not an alternative for a BioCASe provider and is not appropriate for data delivery to AVH (This is not a minor issue that can be easily glossed over. We have said for the last ten years (at least) that data delivery to AVH should be dynamic.)
- In the end the most important thing is that the right concepts are provided and both the BioCASe provider and IPT can do that.
HISCOM discussed what options might be available to help BRI with their data delivery.
ALA/AVH Hub update
Brazil, Spain, Costa Rica, France and Argentina are looking to use the ALA infrastructure, and there’s been a rewrite of the hubs in Grails to cater for this.
- ALA is now using Leaflet for mapping
- The background map is greyscale by default, but you can add roads, terrain and/or satellite layers
- There’s an opacity slider that allows you to make the dots opaque so you can view details of the underlying layer
- Can also display maps by record density grid, rather than individual dots
- The environmental layers aren’t in yet (do people still want them?)
- Can we determine how much they’re used?
- Do we want to revisit which if any? (initially nominated a subset)
- NZVH will be providing some spatial layers - their community use them
- A WKT search box has been added
- Users can now also query AVH by drawing a polygon on the map, and can also do this to refine results of a query
Current AVH (http://avh.ala.org.au) not yet updated, but will happen very soon
- Trying to keep differentiation between hub and spatial portal
- There was general agreement that AVH should be used for querying, but the spatial portal should be used for detailed analysis
- However, have incorporated capability to import an existing GIS area
- Would be of benefit to be able to save, export a GIS shape
- Fields delivered, default values can be configured – can be different for AVH from the rest of ALA
- Facets will be grouped – the display of facets can be customised for AVH
- disabled detailed download option about 12 months ago
- can modify download to add back in fields.
- ALA has algorithms to detect ‘associated records’
- It works reasonably well, but sometimes results in false matches, and sometimes doesn’t match true duplicates
- providers need to be able to import assertions into their databases (long-term aim)
- the ability for providers to deliver an assessment of how fit for spatial analysis particular records are would be good in the long-term (consider this for HISPID review)
HISCOM is responsible for keeping AVH documentation up to date. Feedback from MAHC – it would be good to have links to context-sensitive help on search pages. Nick indicated that this is possible:
- Code is in GitHub: https://github.com/Atlasoflivingaustralia/avh-hub
- Wiki is in wordpress
- Is it possible to get more refined user metrics (not just number of records downloaded)
- tracking query patterns?
- number of record views?
- These statistics are very useful for business cases etc
- Dave is still looking into usage statistics
Jim discussed with Nick the possibility of annotation service that works both ways (send/receive).
VicFlora and KeyBase
Niels demonstrated VicFlora and KeyBase:
ASBS 2015 will be in Canberra.
Topics to be discussed:
- eFloras, ID keys, species profiles
- innovative ways collections can be used for systematics research
Jim suggested that we should present the eFlora at ASBS, assuming that a prototype is available.
Identified a need for a new (over-arching) framework/website – Herbaria of Australasia, rather than branding it as CHAH. The AVH concept is broader than specimen mapping, and includes eFlora, VTI, images and curation tools. Need to keep the ‘Virtual Herbarium’ concept at higher level
- ALA part of supporting infrastructure
- Revamped website is not just about branding, but also outreach
Michelle developed an information architecture model (Michelle to circulate?)
- Urgent to consider this within the time-frame for AVH-NZVH merge
- Aaron has graphic designer available for new logo
- Identify currrent resources, content location – ANBG, collectory, other (out of date) websites
- Identify content gaps, and who/where to source/write it
- MAHC to review current institutional ‘how to’ guides
Tasks for the working group:
- design, refine architecture
- application/recommendation to CHAH for funding
- initiate discussions with ALA re hosting
- start compiling a list of resources and content for the new website.
A communications plan is being developed by the Collections Community Coordinators, which may have some relevance to the new website.
Some changes to the AVH home pages are required:
- Requirement for flexible display on wide range of screen sizes from large down to mobile phone.
- Need to accommodate newsfeed and subscribe option on homepage
- Need new images
Feedback from conferences/meetings
ALA Science Symposium
Alison’s attendance was supported by the ALA as part of the Collections Community Coordinator role
- very good symposium, lots of presentations showcasing uses of the data
- also provides good insights into ALA activity and strategic directions
- bias to zoological community, needs more representation from botanical collections community
- there is no conference fee, so only transport and accommodation costs need to be covered.
MAHC are discussing image licensing
- want input but don’t know what current ‘rules’/conditions are
- Michelle has discussed this with them, including GPI, institution IP, CC BY
- Audubon Core: http://vocabularies.gbif.org/node/126782
- subject category vocabulary is required
ALA have separated images out into 3 groups (types, specimens, other (including ‘snaps’)), and ranks within these, i.e. types, vouchered specimens are given more weight than others, and appear first in results.
Concerns were expressed about the extraction of EXIF data, as it may infringe privacy and may not be accurate.
There was a view among HISCOM that image management at ALA is too big to be dealt with as just one part of someone’s job, but that it needs a dedicated role, i.e. a national curator of images.
Sensitive Data Service
Time constraints meant that this could only be touched on briefly. Details of the SDS are on http://lists.ala.org.au.
Previous discussions about the need for an annotation service were revisited. HISCOM emphasised that a functional annotation service that works both ways (i.e. can send and receive annotations between collections databases and ALA) will make the ongoing maintenance of ALA absolutely essential for the herbarium community. Alison intends to start documenting requirements for an annotation service as part of her Collections Community Coordinator role.