Joint HISCOM/MAHC 2016 Brisbane

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Meeting Location

FM Bailey Room, Queensland Herbarium, Mount Coot-tha Botanic Gardens, Mount Coot-tha Road, Toowong.

AGENDA

Attendees

  • HISCOM - Gillian Brown (BRI-MAHC/HISCOM), Aaron Wilton (CHR), Ben Richardson (PERTH), Anne Fuchs (CANB), Niels Klazenga (MEL), Donna Lewis (DNA-Chair), Wayne Cherry (NSW), Michael Hope (ALA), Ainsley Calladine (AD), Eleanor Crichton (AD), Ryonen Butcher (ALA CCC)
  • MAHC - Helen Vonow (AD), Carolyn Ricci (AD), Dhahara Ranatunga (AK), Gillian Brown (BRI), Lorna Ngugi (BRI) (observer), Ailsa Holland (BRI) (observer), Helen Cole (BRI) (observer), Bronwyn Collins (CANB), Deb Bisa (DNA), Frank Zich (CNS) (chair), Lyn Cave (HO), Pina Milne (MEL), Karen Marais (MQU), Jo Birch (MELU), Katherine Downs (NSW), Karina Knight (PERTH) (minutes), Jeremy Bruhl (NE), Frank Hemmings (UNSW), Anthony Kusabs (WELT)
  • Teleconference - Anthony Whalen (ABRS), Russell Barrett (ABRS), Alison Vaughan (MEL- HISCOM)
  • Other (selected sessions) - Peter Bostock (ex BRI), Will Smith (BRI - botanical illustrator), Paul Robins (BRI - observer)

Apologies

  • MAHC - Peter Jobson (NT)
  • HISCOM - Laurence Paine (HO), Ian Cowie (Deputy Chair - CHAH)

Welcome - Mark Jacobs, Executive Director

Welcome from Mark Jacobs, Executive Director of the Science Delivery group of Department of Science, Information Technology and Innovation (DSITI). Mark acknowledged the traditional owners of the land. Mark stated that he is impressed with the expertise that is intrinsically linked to the collections. He recognises MAHC collectively have responsible for up to 5 million specimens across Australasia. The Queensland government values and appreciates the work that these groups do. Mark recognised the 45 year CHAH collaboration. “It is impressive to see the work MAHC and HISCOM does (including the AVH and GPI initiatives) which informs CHAH and demonstrates impressive collaborative problem solving. HISCOM data standards/systems allowing for free exchange of data and information in line with best practice. Herbaria are needed to supply the scientific data and information to inform leading science. Mark encourages MAHC and HISCOM to refine and promote what we do. Promoting is important because as we get further away from this group the understanding about what we do drops away.

Introductions - Frank Zich (MAHC Chair) and Donna Lewis (HISCOM Chair)

Donna Lewis facilitated a quick round table where everyone introduced themselves from MAHC and HISCOM.

Minutes and Actions from 2015 MAHC/HISCOM meeting

Donna summarised 2015 minutes. Minutes accepted as true and correct. No comments or questions. Actions carried forward will be covered throughout the course of the joint meeting and HISCOM meeting. Donna had summarised the ALA community project with the MAHC group on Tuesday. Michael Hope (ALA) explained that the funding to support the recent round of ALA Community projects was opportunistic. Action 1 carried over and to be followed up by Ryonen Butcher (ALA-CCC) to produce articles for the AVH news feds in consultation with the project managers and ALA Communications Officer Hannah Scott.

Action 1: ALA Herbarium community projects managers to write an article for the AVH/ALA news feeds. Ryonen Butcher to coordinate this with Hannah Scott where required (Project Managers, Ryonen).

SESSION 1

eFlora Platform demonstration (Anthony Whalen (ABRS), Russell Barrett (ABRS) Michael Hope (ALA))

Teleconference presentation with Anthony Whalen and Russell Barrett, in coordination with Michael Hope. Anthony, Russell and Michael presented information and demonstration of the eflora platform. Anthony and Russell have been with the project for a number of months. The project has been running since 2014. Collaboration between ALA, Advisory group, CHAH. Anthony acknowledged the support from NZ through advisory group and CHAH and “the great work” by Michael Hope of building the platform. Also acknowledge the support of Kevin Thiele. Volume 47 was the final hardcopy of Flora of Australia. Anthony stated delays in waiting for latest updates will be a thing of the past. Individual treatments will be published very quickly. The eflora will provide functionality for botanists to publish straight onto the eflora platform. Advisory Group is guiding this ‘Flora of Australia’ transition. Authors will be given assistance with publishing.

Michael: Results and feedback from user testing analysed. Work on improving navigation around platform. Focus on editing profiles and getting data in. Map enhancements (eg filtering dots on map out) can filter down to individual herbaria (similar to AVH). Layout improvements – tabbed layout so you can break down to individual pages. Names hierarchy functionality needs improving – looking at hooking into NSL tree builder capability. Profile platform not only being used in ALA for eflora. Also being used for Indigenous knowledge (2 software development sprints have focused on this alone) but improvements can be used across the platform. The upcoming December sprint will focus on public interface, page layout design enhancements. ‘Profiles’ platform is a high priority on ALA agenda.

Russell highlighted the attribution of authorship for different parts of content. So each attribute for different parts of profile can have separate authorship. It is now easier for individual to input small amounts of info and be acknowledged. So then how do you cite a treatment? Working through how to manage this. The group is confident of a first launch next year. Import test soon to ensure that the import of the hard copy html is working.

Anthony: Where no content exists for a taxon, funding is required for treatments from authors. Legacy of names which are not current. Working through how many are current. Engaging more with the botanical community. Work out a way of filling gaps (once identified) by potential contracts with authors. Building a large group of authors over time to complete the eflora.

Michael, Russell and Anthony gave a live demo of the site including content that Russell has been working on recently. This covered profile searches at genus and sup-species level and creating a new profile. Taxa are matched to parent taxa on a hierarchy. Necessary to attribute authorship and editorship. We saw that each profile stands alone as a full profile (even at sub-species level). Functionality around comparing diagnostic features between taxa. Also looking at linking threatened species info, other info.

NSL demonstration and update (Anne Fuchs)

AusMoss and Lichen data now loaded and have now started on APC Orchid taxonomy. There are new and improved features including:

  • Name check - in APNI and asks if they are in APC. http://www//biodiversity.org.au/nsl/services/apni
  • Improvement - output names now parsed, Family, Genus, species etc.
  • Export Name and Taxon - CSV, names, accepted taxonomy.
  • Instance editor improvements include rules are ICN adherence, workflow improvements - i.e. warnings, user interface, bug fixes.
  • Data queries including data cleaning and quality checks and handling requests.
  • Search interface includes cleaner and more compact list of names without all of the details.
  • The tree editor is in the early phase of testing, and maintains taxonomic hierarchy's.
  • Other tasks for NSL include an overall model for flora and fauna feed (Australian Faunal Directory), conversations are happening around governance.
  • There is a move towards CSIRO hosting, extension of editors to ICZN.
  • Integration with eFlora Platform project and FoA data.
  • NEXT governance model, tree editor to production, new search functionality to production, manage APC workflow rather than using a word doc, documentation (citations, technical, governance), protologue data (BHL).
  • Other tasks: Overall model for all datasets, interface needs to be consistent across all flora and fauna and sub-grouping. Approached by dept. of Agriculture and Resources to maintain taxonomic lists of taxa on interest. Hosting their lists incl. viral and bacterial nomenclature.
  • QUESTIONS - How do we get data into APNI in a better way? Department of Ag and Water work.

How do we do citations with NSL? Issues around governance. Q. Aaron Wilton: Name list matching service an exact match or is there fuzziness within it? A. Anne Fuchs: Pretty sure this is an exact match. Michael agrees. Search, includes ‘not found’ (illegitimate) taxa. Q. Frank Zich: Have you looked a linking type images in JSTOR? A. Anne Fuchs: No, but easy to add once you have the data.

SESSION 2

ALA Update (Michael Hope)

63 mil data records, 8.5 billion records downloaded since inception. 1. Engagement: Biggest thing in atlas – making inroads into these groups. TERN/ Biodiversity Climate Change Virtual Laboratory (NeCTAR) use the atlas data for their means. So working closely with nectar; Working closely (eflora) with NSL ABRS ACSA citizen science – also a key focus are Bio connect – a community group can create a landing page in the atlas and space for their people to record observations. NGO’s resource management groups are all using bio connect. The project finder links you with interests of similar (ACSA) CSIRO/BPA – genomic data projects – improved visualisation tools. Eg Aus mammals – genome maps for all species across Australia. Improved visualisation tools. Looking at developing the Atlas data searching capabilities. Let you do enough analysis to identify the data you need and then pull it out (download). 2. Collection Community Workshops:

  • Image voting capability.
  • Annotations – flagging issues (now implemented). Improvement around the response when somebody flags an issue. The owner can now check and verify, record.
  • Updated names infrastructure – update has been achieved. Improvements include a larger range of names (mosses, lichens, APC, AFD, NZOR, and Catalogue of life). Watch this space for WORMS, others. Almost a push-button capability to update names in the database – 1 month process. Two days process (automated) – to retrieve the names. Probably do this 6 monthly.
  • 180 000 tissue records in the atlas (another 30000 coming shorty) Marked as tissues. Upload records that are marked as samples – linked to the original specimen. Link is not the other way – reasons: Host parasite data will be linked to host specimen in the same way.
  • Download functionality (improved) eg track downloads to individual user.
  • Current Work: ALA mobile apps have failed – needs works; Spatial portal upgrade – backend code clean-up.

Sensitive data enhancements – if somebody reported a sensitive; Work around New Zealand data import. All data is pre-searched. Every time we add another layer, new index field / spatial layers. Reaching the limits of the hardware – breaking system across multiple servers may solve this problems. Globalisation – 8 countries using the Atlas infrastructure. Up to a dozen on cards for development. Charge a cost recovery to develop the sites. Data backlog – takes the same amount of time no matter how big the set is, so larger ones talked first.

  • Bio collect: ALA citizen science – growing at 6 a week. Linked to USA ‘science starter’
  • Indigenous knowledge: Capturing knowledge. Dealing with non-western taxonomy. Privacy - releasing only those records approved by the community.
  • ALA hubs: ZoaTrack – separate app ALA have agreed to host. AVH. Australian Plant Pest Database Upgrade to be released – improvements including updated data. Searching on host fields, Integration with Murray Darling Basin Authority website.
  • Communication: Symposium (Perth). Hannah Scott – new communications officer. CHECK WITH PREVIOUS Comms strategy under development. Impact review – measuring ALA impact in terms of delivering our success to NCRIS (National Collaborative Research Infrastructure Services) – body providing infrastructure for research purposes.

ALA considered one of the most successful NCRIS facilities. ALA is quite certain the funding will be maintained.

  • User Experience review – identifying what problems need to be addressed. Kick off with a workshop which some of this group have been invited to. Separate Expert review.
  • QUESTIONS Q. Gill Brown: Genome. We have data in genbank with link back to collections. Is there a way that can be linked in the ATLAS. Pick up links from Genbank when they are not supplied. A. Michael Hope: can certainly have a look at this (pulling the data through).

AVH Update (Ryonen Butcher)

  • New test page Australasian Virtual Herbarium http://avh-test.ala.org.au/ – since July 2016 incorporates the new improved names indexing ALA improvements. Test environment ready to go to production soon.
  • Display of filter searches. Eg NZ ecological district, specimen types, conservation status, multimedia, location ID, record type (human observations, specimens), presence absence, institution.
  • Most new fields in advanced search.
  • Map Zoom extent is defaulted to Australasia (OZ & NZ). All requested that there is a 'zoom to extent' button in order to zoom to the maximum extent of the distribution for a species search i.e. Nothofagus.
  • Important information is now available at the top of the specimen page.
  • Corrections can be flagged by any registered user.

QUESTIONS Q. Deborah Bisa: Who’s the recipient for AVH flags at herbaria? A. Each institution has somebody who receives the AVH flags. If, upon receiving a flag, the record at the herbarium is found to be correct. Inform the IT expert at your institution to see if it is a fault at the database end. If okay, they can alert Aaron. Collection Managers are encouraged to subscribe to receive annotations on specimens from their herbarium.

  • Collection number appears in the main record window.
  • Issue/ Improvement: At bottom of main specimen page where representative and related records are shown, registration number and institution should be shown.

ANNOTATIONS. Aaron Wilton: Need to make a distinction between ‘verified’ versus ‘inferred’ duplicates. Ben Richardson: Some alerts need removing when they don’t make a lot of sense. If there are discrepancies in data records / duplicates.

  • Improved download functionality. Select a reason for download to help with uses of data. Customised download. Select categories/layers that you need.

DISCUSSION. Alison: We do have a page which explains the column headings - see http://data.rbg.vic.gov.au/avh/index.php/help/download-fields/ and http://data.rbg.vic.gov.au/avh/index.php/help/data/. It was encouraged to keep AVH functionality in line with ALA to reduce complexities. Discussion around ‘suggested fields’ for downloading of beneficial fields.

  • Spatial Search Demo: Import an existing GIS area. Download a species list. Field guide. Family distribution.
  • ALA can edit which species gets assigned to each taxon.
  • Voting on images, affects all images shown with a taxa.
Action 2: In AVH test Advanced Search the look up table for 'Botanical Group' includes animals and this needs to be fixed before it goes to production (Michael Hope).
Action 3: Add functionality to the AVH to be able to zoom to the extent of records after searching on a taxon or multiple Taxa (Michael Hope).
Action 4: Collections Managers to look to see they are registered with ALA and are receiving alerts, or that a similar relevant person at their institution is (MAHC Collection Managers).
Action 5: Annotations - check Collectory Institutions contacts plus Collection Managers are signed up for alerts and both are receiving alerts (Michael Hope).
Action 6: From Ben Richardson's suggestion, add HISPID 6.0 as a download option from the Downloads page (Michael Hope).
Action 7: Weed alerts - Use QLD weeds lists as a test case for weed alerts. This involves adding a weeds list to http://lists.ala.org.au/public/speciesLists and setting up the alerts (Gill, Ryonen, Michael Hope).

AVH/NZ amalgamation (Aaron Wilton, Michael Hope)

It was discussed if there were any additions required to finalise the Australasian Virtual Herbarium. Aaron: The name was already agreed and ratified by CHAH 'The Australasian Virtual Herbarium'. Ratification to go live as soon as possible. NZ organism data is a few years old (funding has been awarded for a major update). This can be picked up automatically from NZOR. The sooner the better. Michael: Yes, ready to go.

HISPID Update (HISCOM)

HISPID Terms http://hiscom.github.io/hispid/terms/ Largely discussed the fact it was finalised and loose ends needed tidying up by HISCOM this year. Outstanding GitHub issues will be addressed at HISCOM as well as the format and content of the PDF version. Two formats XML and PDF for date stamping and publishing. MAHC and HISCOM members agreed the PermitOrConsent Class included the relevant Terms to satisfy Nagoya. This was decided following the MAHC agenda item regarding the Nagoya Protocol.

Host/parasite interactions

Michael Hope (ALA): How do we link organisms that are related to each other? Associated occurrences vs associated organism (name only). Niels: Have it as a related resource. Talk to FCIG about this. Aaron: Work through some examples that we can then provide to FCIG (as long as ALA confirm they can do what is proposed).

Action 8: Work up some examples on host/parasite interactions and how HISPID 6.0 handles it (Niels? I can't recall who put their hand up for this?).

Tissue Data (destructive sampling)

Q. Gill Brown: Do we want to discuss tissue data? A. Michael Hope: Demonstration of Tissue Data on ALA. Currently the tissue data in OZCAM are treated as separate records. Locality info (standalone record). Click on source specimen. Test phase – next step ask all museums to supply there tissue data. Discussion around how herbaria register and store their tissue specimens. Most institutions seem to have adequately stored their material. Q. Gill Brown: Can the ALA automatically link the Genbank URL to the specimen record in ALA/AVH? A. Aaron Wilton: Jerry Cooper may have incorporated this functionality. Aaron to check. Aaron Wilton: recent audit produced numerous data (eg. 5000 plant records) that CHR didn’t know about.

Action 9: Check if Jerry Cooper incorporated the functionality of linked genbank URL to specimens (Aaron).
Action 10: Explore how genbank data can be linked to specimens in the AVH, and what field it should be linked on i.e. catalogue number, or a sweet of fields (Ben Richardson, Jo Birch).

SESSION 3

AVH Social Media

  • AVH promo material (Alison Vaughan)

Thinking about what we want in association with the AVH launch. Which audience to promote AVH to - Indigenous rangers, students (primary, secondary, tertiary), consultants, ethno-botany, inter-agency (weeds, parks etc), rangers, conferences, international meetings. QUESTIONS. Alison: Do people see a need for this? A. Everyone - Yes. Diverse in terms of the amount of information necessary. Need to focus in on two or three different groups. Consultants, regional herbaria would require more info on the data itself (info heavy). Primary school groups – may be enough to have book marks, post cards. Discussion around grouping resources around different groups versus more generic materials. Taren Johnson: is education officer at ALA – K12 – developed ALA educational resources. Aaron: More comprehensive Electronic resources are on the website, so the focus could be around delivering the URL in some way – postcard, business card, and sticker. Helen: More modern way of supplying URL to interest groups? Ryonen: simplicity is key. The group considered brochures too complicated, busy. Bookmarks were okay. USB credit card stick were highly regarded by the group. URL on the USB with greater educational resources inside it, logo, branding. Alison: Posters could support this. Frank Z: More versatile if also printable at A4, then the poster could have two functions. Ainsley: The poster needed to be informative “have a couple of key things to intrigue people” Other ideas: Collectible cards to showcase different plant groups, link to that plant group in the AVH. Book mark or card would be interchangeable. Avantcards.com.au - Pop-up cards also received the thumbs up. Need a catch to tell people what is in AVH - discover your biodiversity. Helen: What is around my area? Jo Birch: Need to be a very generic design. Alison: No herbarium logos on the thing - too cluttered. Focus on promoting the AVH. Quantity: ?

Action 11: Provide a recommendation to CHAH to form a sub-group (MAHC/HISCOM members) to develop/coordinate the production of AVH promotional materials (Alison Vaughan, Donna Lewis).
  • AVH news feeds

ACTION carried forward from Joint HISCOM/MAHC AGM 2015 - see ACTION 1 above.

  • AVH FB
Action 12: Circulate email to AVH FB administrators to discuss a systematic approach for getting more regular posts on the AVH FB page (Gill).
  • CHAH website

Ben – Suggest that CHAH employ someone to design the website. Providing the content is most critical. Ainsley (HISCOM) is on the committee - set up a trial site. Donna: CHAH Chair (Michelle) would like two CHAH, MAHC and HISCOM members to coordinate the development of the CHAH website. Alison Vaughn (HISCOM) volunteered (nominated) Anne Fuchs seconded. Dhahara Ranatunga (MAHC) – volunteered. Pina was nominated and accepted. CHAH website working group comprises Pina Milne and Dhahara Ranatunga (MAHC), Alison Vaughan and Ainsley Calladine (HISCOM), CHAH reps ?

Most agree that MAHC just needs a place where we can put resources – eg best practice documents. Some content will need to come from institutions. Neils: cut down to something feasible eg no flora treatments. Link to eflora and other resources.

Action 13: Circulate the CHAH website 'mind map' to MAHC and HISCOM members (Ainsley).

Images - Progress on their access via AVH/ALA (Michael Hope)

Michael provided a brief demonstration on image voting in the ALA. Anybody who is registered can vote, but only one vote per image. The results of the voting sort the priority of images in the gallery to determine the default image to display. The ALA will use that as the representative image. Michael suggests supplying images for representative taxa as a community action. Aaron suggested that ideally we would have representative [hero] images which are linked to specimens so that taxonomy was more likely to stay current.[Hero] images supplied by herbaria should focus on those linked to specimens. NB: In order to upload updated metadata for existing images, the image needs to be reloaded.

QUESTIONS: Q. Ailsa: [If not linked to a specimen] is there a way of verifying that an image is what it states to be. A. Michael: Yes, if incorrect, use the ‘flag an issue’ process and it will go to the person who submitted the record. Discussion around [hero] images and the problem with verification of images if not vouchered.

Botanical community is keen to see that images supplied as hero images for taxa are linked to specimens, although recognise that unvouchered images are often better quality. Jeremy suggested weighting vouchered images up and un-vouchered images down in the ALA. Ainsley commented that people have higher confidence with vouchered images. Ben raised an important issue that we need to be able to avoid the problem of orphaned images once image data becomes lost.

The best way to provide images to the ALA/AVH is via a URL for each image. Note that there is a minimum requirement of metadata associated with each image. ALA should be able to harvest from BioCASe Providers via MediaItem Class in HISPID 6.0? Thumbnails can also be delivered, large rather than small. Large images are tiled. Anything above 10MB the detail is wasted.

Action 14: Formulate a way to supply vouchered [hero] images against taxa (MAHC and HISCOM).
Action 15: Provide a means of deleted images that are incorrectly assigned to a name (Michael Hope).
Action 16: Provide a list of the minimum metadata data required to provide images to the ALA/AVH (Michael Hope).

Image Survey Results (Donna Lewis)

Donna summarised the results of the image survey conducted mid 2016 to identify the current status of images maintained in herbaria -

  • GPI

Project completed – type images available via JSTOR – subscription required. PERTH GPI images available on AVH test site. Multimedia facet for filtering type images in the AVH http://avh-test.ala.org.au/occurrences/search?q=collection_uid%3Aco75&qc=data_hub_uid:dh9&fq=multimedia%3A%22Image%22

  • ALA Biological Collections Community Workshop Feb 2016

Delivery of images to the ALA/AVH were identified as a priority (3 year priority) including images associated with vouchered specimens, historical images (imaged over time), derived images (i.e. slides, SEMs etc.), field images.

  • 12 questions were addressed:

1. All herbaria maintain images 2. Array of image types from specimens, field photos, illustrations, artworks, derived images…. 3. Internal and external servers and hard drives, web accessible servers 4. All herbaria can link to specimens but not all can link to images of unvouchered specimens MOSTLY all herbaria have their own conventions for naming images 6. Images mainly JPEG and TIFF format, size variable from 250KB to 180MB for GPI images 7. Images already exposed in existing platforms - APII, Rainforest Key, NSW Flora, VicFlora, FloraNT, FloraBase, NZFlora, AVH/ALA, eFlora Platform (APII), some specimen databases (i.e HO, DNA) 8. Ease of exposing images – technical support, funding, license conditions, IP range, copyright. Some are already exposed (i.e. APII) or could be exposed easily to AVH. 9. Copyright issues – various issues….. 10. Metadata storage – various including databases (MS Access, MS Excel, institution databases i.e. EMU), web service. Some have intention to extract (or already are) EXIF (other) if available. 11. Mostly all herbaria have illustrations, slides, other images etc that require digitising. Funds are required and the work is mostly achieved by volunteers. 12. Herbaria either have no program or ad-hoc programs for imaging non-type specimens. Priorities include threatened species, exemplars, historic collections, endemics.

Items identified from MAHC Meeting

  • Pina Milne: map zoom. Problematic for Europe records. Full extent button needed (Michel likes this). See ACTION 3
  • Gill Brown: BRI obliged to notify 296 weed species. Is there a way to better share these data alert notifications from the specimen record? A. Aaron Wilton: Should be able to subscribe to the weed species off the AVH list. See ACTION 7
  • Aaron Wilton: Nagoya issues – eg visibility of the status of material under Nagoya on the AVH. ACTION: TEST this in AVH
  • Aaron Wilton: New information class/grouping in HISPID ‘Permit of Consent’ type of consent from verbal through to permit. Ref number. Who issued it, dates. Range of permit. Permit status vocabulary – these can be expired.

Response to collectors need to be the same from all herbaria.

  • ACTION: MAHC to draft a notice that herbaria can provide to regular collectors which informs them of the legal obligation for them to supply evidence of authorised collections. NB: check if this is already covered in MAHC actions*********

Next AGMs 2017 and 2018

Possibility of meeting with HISCOM, FCIG and MAHC in Melbourne next year. FCIG are interested in meeting with MAHC to get an idea about what MAHC do.

Action 17: Recommendation to CHAH that MAHC and HISCOM meet at CHR in 2018 to coordinate with the SPNCH (The Society for the Preservation of Natural History Collections) and TDWG (Taxonomic Database Working Group) conference in Dunedin from 25th August to 2nd September 2018 (Donna, Frank)