HISCOM AGM 2014 Adelaide

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Meeting location and accommodation

http://know.ourplants.org/mahc-hiscom-2014/

Minutes

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.

Action 1: Share documentation/presentations that include value of herbarium collections and associated use of the data (Jim, All)

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:

Action 2: 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. Herbaria to provide information on the data concepts used and delivered. (All)
Action 3: Write a news item about collections management and data delivery in a university herbarium and communicate to the university herbaria. (Alison, Gill Brown (MELU))
Action 4: ALA to provide collectory schema to HISCOM (Nick)
Action 5: Provide ALA image fields, and examples of image metadata being sent by other providers (Nick)
Action 6: Send MEL image metadata fields and descriptions to HISCOM (Alison)
Action 7: Write a news item about creating alerts in AVH (Alison)
Action 8: Liaise with ALA about implementing the features listed in item 11 in the minutes (from 2013) (Niels)

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
Action 9: Compare content of RAH with collectory pages (Alison)
Action 10: Review CHAH partner page format – consider how to make more engaging (Alison and Aaron with Fiona Brown (ALA) and Alexis Tindall (SAMA))

Elected Positions

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)
Action 11: Notify CHAH of HISCOM’s decision to implement the Assistant Chair role (Alison)

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.

eFlora Update

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.

Next steps:

  • 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
Action 12: Contact Ilse re attribution paper, then discuss with Rebecca (Alison)

WFO update

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.
Action 13: Circulate the WFO model to HISCOM (Greg)

Names

NSL update

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
Action 14: Identify who needs to be in the conversation (e.g. herbarium staff responsible for their census) (All)
  • 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.
Action 15: Respond to request for advice from CHAH (Alison, Michelle)

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.
Action 16: HISCOM to determine and document their processes for prioritising and submitting feature requests and bug fixes (Alison)
Action 17: Ascertain what issue tracking system is currently in use and what ALA would recommend (Rebecca)

NZVH update

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)

HISPID

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.
Action 18: Define the objectives and scope of the HISPID review (HISPID Review Working Group)
Action 19: Schedule a HISPID review workshop (HISPID Review Working Group)

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).

Recommendation to CHAH: All plant groups (including mosses) should be presented as part of APNI.
Recommendation to CHAH: NSL is critical infrastructure underpinning all the work we do and should continue to be supported.

Data delivery

Background:

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.

Action 20: Create a table in the AVH help pages that shows which herbaria deliver which fields (Alison, Niels)
Action 21: Talk to Peter Bostock about BRI data delivery to see if HISCOM can help with a workaround (Greg)

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.

Maps:

  • 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
Action 22: Decide which layers need to be available in the AVH hub, considering that the list will be twice as long once NZ data is in there (All)

Spatial search:

  • 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
Action 23: Provide feedback on the grouping of the facets (particularly the ones currently listed under ‘Miscellaneous’) and decide on which facets should be displayed by default in AVH (including any that needn’t ever be displayed) (All)

Downloads:

  • disabled detailed download option about 12 months ago
  • can modify download to add back in fields.
Action 24: Ensure that the requirement for detailed downloads is documented and has been adequately communicated to ALA (Alison)

Duplicates:

  • ALA has algorithms to detect ‘associated records’
  • It works reasonably well, but sometimes results in false matches, and sometimes doesn’t match true duplicates
Action 25: Provide guidance around which fields to use, and provide examples of false positives, to improve the duplicate detection algorithms (All)

User assertions:

  • 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)
Action 26: Provide short-term guidance on how the annotation service could be improved in the short-term (Alison)
Action 27: Redesign home page to allow for news/blog roll and subscription service (Niels)

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:

Metrics:

  • 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
Action 28: Review AVH documentation and modify it in preparation for NZVH/AVH merge (Alison, Niels and Aaron)
Action 29: Add links to context-sensitive help from the Advanced Search page (Niels, Alison)

Jim discussed with Nick the possibility of annotation service that works both ways (send/receive).

VicFlora and KeyBase

Niels demonstrated VicFlora and KeyBase:

VicFlora (http://data.rbg.vic.gov.au/vicflora)

Keybase (http://keybase.rbg.vic.gov.au)

ASBS 2015

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.

CHAH Website

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
Action 30: Establish a working group to scope and plan new website (Michelle, Alison, Anna Munro (CANB))
Action 31: Prepare a briefing note for, and arrange a teleconference with Ilse, Darren and Kevin (and website working group) (Michelle)

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.

Action 32: Circulate the Communication Plan to HISCOM and MAHC (Alison)

AVH 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
Action 33: Decide on, and implement, layout of new AVH homepage, and make it responsive to different screen sizes (Niels)
Action 34: Provide images to Alison (All)

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.
Recommendation to CHAH: Encourage and support attendance at the annual ALA Science Symposium by research and technical staff within the herbarium community.

Images

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

Metadata vocabularies:

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.

Action 35: Provide feedback around auto extract/inclusion of EXIF data (who?)

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.

Action 36: Provide all GPI metadata files (to who?) so we can collate GPI data in one place (All)

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.

Annotation service

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.