HISCOM AGM 2017 Melbourne
- 1 Meeting Location
- 2 MONDAY combined CHAH / CHAFC / HISCOM / FCIG / MAHC
- 3 TUESDAY HISCOM General Business
- 3.1 Attendees
- 3.2 Apologies
- 3.3 SESSION 1: Welcome and Institution Updates
- 3.4 Minutes and actions from previous meetings
- 3.5 SESSION 2: Elected Positions
- 3.6 HISCOM ToR
- 3.7 Email lists, HISCOM wiki, HISCOM GitHub
- 3.8 AVH Technical Addendum
- 3.9 SESSION 3: Australasian Virtual Herbarium
- 3.10 HISPID
- 3.11 NSL
- 3.12 SESSION 4
- 4 THURSDAY HISCOM /CHAH
- 4.1 SESSION 1: Welcome
- 4.2 HISCOM/CHAH Update/Recommendations
- 4.3 SESSION 2: National Species List
- 4.4 HISCOM Future Directions
University of Melbourne, Biosciences Building
MONDAY combined CHAH / CHAFC / HISCOM / FCIG / MAHC
Welcome and Committee Introductions (Michelle & Leo)
SESSION 1: Sharing Our Collections and Taxonomic Resources
- Atlas of Living Australia (John La Salle & Michael Hope)
- National Species List (Anne Fuchs)
- ABRS (AFD and eFlora) (Anthony Whalen)
- Biodiversity Heritage Library (Ely Wallis)
SESSION 2: Future of Managing and Digitising Our Collections
- Nagoya - a case study from Queensland Herbarium (Gill Brown)
- Biosecurity for international shipments (Frank Zich)
- Tissue collections, genomics and the future (Michael Hope & Margaret Cawsey)
- Citizen Science (Paul Flemons)
- National digitisation strategy discussion (Andrew Young)
SESSION 3: Upcoming Events
- Decadal plan discussion (Decadal plan working group members)
- 2018 NZ SPNHC &TDWG meeting http://spnhc-tdwg2018.nz/
- Wrap-up and closing remarks, CHAH and CHAFC Chairs (Michelle Waycott & Leo Joseph)
TUESDAY HISCOM General Business
Location: Royal Society of Victoria, Meeting Room 2
Anne Fuchs (CANB), Niels Klazenga (MEL), Donna Lewis (DNA - Chair), Wayne Cherry (NSW), Michael Hope (ALA), Ainsley Calladine (AD), Nimal Karunajeewa (MEL), Greg Clarke (CANB)
Ben Richardson (PERTH), Laurence Paine (HO), Gillian Brown (BRI), Aaron Wilton (CHR), Eleanor Crichton (AD), Simon Checksfield (CSIRO)
SESSION 1: Welcome and Institution Updates
Got a model for Collective Access - migrating data to it.
The State Herbarium of South Australia continues to progress its herbarium information system transition from an historic TexPress database (ADHERB) to Specify. The underpinning technical work continues however delivery by the Department of Environment, Water and Natural Resources technology infrastructure staff of a critical component has delayed the completion of phase 2 of the project - where data from the established Specify Concepts can be delivered to corporate systems (internal to South Australian Government) and external systems (AVH). In addition, the South Australian Government has required whole of Government changes to underlying infrastructure leading to a serial collapse of our resources due to the out of date platforms being unable to run with updated system software. The has diverted effort to 'rescuing' core resources including taxonomic infrastructure (Flora of South Australia 4th End) and developing ongoing plans for future downgrades in functionality. In addition, bespoke functionality to build Flora of South Australia 5th Edition chapters via a TWIKI has become unusable. Eleanor Crichton and I have been required to conduct ongoing, emergency, analysis and problem solving to keep systems functional. The State Herbarium has been involved in a significant restructure within DEWNR, coinciding with the arrival of a new Director for the Botanic Garden and State Herbarium, Dr Lucy Sutherland. The Herbarium is now the lead team in the Science and Conservation group, within Botanic Gardens and State Herbarium Branch, which is part of Economic and Sustainable Development directorate. Chief Botanist Michelle Waycott is a member of the BG&SH executive group, and has been involved in the recruitment of the other two deputy Director positions (still to start). There has been extensive staff involvement in the development of a new 5-year strategic plan, and the consequent business and master planning. Technological development has been identified as a critical underpinning requirement to progress the strategic plan however DEWNR is unable to provide adequate support.
The past year has been an eventful one at BRI, with both exciting and distressing events, as well as business as usual chugging along in the background. The two main activities the collections team at BRI have been involved in since our last meeting have been the DAWR incident and the Biodiversity Systems Modernisation (BSM) Project. DAWR incident · Specimens from Paris destroyed. Working with DAWR and MAHC working group, Brisbane Gateway facility biosecurity team, as well as departmental internal audit team. International loans program reopened October 2017 with first request to SING. · Changes as a result of the incident: o Complete overhaul of loans manual o Developed and implemented escalation procedures, as well as JIRA task allocation and tracking tool. Biodiversity Systems Modernisation (BSM) Project · Project within larger IT program (ASDI) in the department. Aim to consolidate and modernise all our biodiversity databases, including HERBRECS, WIldNet, vegetation site survey data and regional ecosystem data. As well as herbarium staff we have a dedicated project manager, two business analysts (BA), program developers, and a systems architects. · This is year 1 of a 5 year proposed project. Main objective of this year is to identify future state and develop detailed business case to obtain funding for years 2-5, as well as some remediation to HERBRECS to mitigate risk due to unsupported, end of life technology. · Outcomes so far: o Documented other jurisdictions and undertaken initial request for information to obtain possible vendors and systems available. Identified need for separate CMS and site data systems that are interoperable. Demos of suitable systems being organised. o Mapped HERBRECS fields to HISPID6. Programmer working on data transformations required to migrate data to new system. o All collections processes mapped by BA, which has helped us identify many places to implement efficiencies. Has provided evidence to get support from Director and staff to trial changes to processes (e.g. ID room processes) o Imaging trial has resulted in a massive increase in imaging capacity. Latest trial took photos of 120 specimens in just under 4 hours, up from c. 20-30 previously. Other activities · Developed and implemented bulk upload of data from .csv files for staff, regular collectors and other collections (e.g. exchange data). · Started to gather and document (in spreadsheet) the various stashes of silica gel around the herbarium and linking with AQ numbers. Will incorporate into new HERBRECS as currently unable to make changes to our tables and forms without large expense.
It has been business as usual with databasing and curation of the backlog (mainly cryptograms), photography of historical specimens, flora updates for the annual release of the census and ongoing identifications and documentation for Bush Blitz taxonomy grants being major activities. A bequest will enable the first Algae of Tasmania publication to be released in the last quarter of 2017.
TMAG currently has its focus on the passage of new legislation to establish it as a statutory authority with a modern governance arrangement. The new framework will finally balance the responsibilities and accountabilities between the Crown and Trustees. It is hoped the new arrangements will receive the royal ascent and commence from 1 January 2018.
TMAG has received funds from the State Government to undertake options work on future collections and research facilities, which will include a solution for the replacement or development of the current Herbarium facility.
TMAG have made a major structured infrastructure investment bid to the State Government for the replacement of the collection management system, web content management systems, digital storage and digital preservation platforms to support the institution moving forward. TMAG, through the GLAM Peak alliance, are investigating the feasibility of moving data network services to AARnet infrastructure and establishing a cultural platform solution through their services. This would provide the statutory authority with a level of autonomy outside the current whole-of-government services.
The Collection Management System (CMS) project is underway. A data model which combines the requirements for the Herbarium, Insect and Wildlife collection has been prepared and reviewed by the Fish Collection. Data migration is currently underway. Imaging of specimen sheets is underway with approximately 35,000 to date. These images will be linked to the ANHSIR specimen record. The Living Collections system is being redeveloped in PostgreSQL and services implemented to supply provenance and specimen data from the CMS. The NSL development continues with improvements in the name editor, a refactor of the tree editor to improve performance and simplify maintenance. APNI Community editing was undertaken.
Recently appointed permanent Collections Manager and Technician (Facility Manager). Business Case was approved to upgrade the Taxon Table in HOLTZE and dynamically link it to the Departments Vegetation Site Database (VSD), the work was undertaken and is now in production (July 2017). This means names are all maintained in HOLTZE and dynamically updated against HOLTZE specimens and VSD plot data which flows into the Departments NT Flora Atlas, Flora NT website, and NR Maps. Both specimen data and plot data are visible on the Flora NT website. There has been ongoing population of data to flora, conservation and ethno-botany modules in the HOLTZE Specimen Database. Keys have also been prepared and uploaded to KeyBase. Images stored on a Doc repository and are linked to a Taxon ID and visible through Flora NT fact sheets and images continue to be prepared and uploaded by Herbarium staff and volunteers. The recently appointed Collections Manager is gradually developing a more structured volunteer program and this will mature over the next 12 months. The NT Herbarium has been involved in various Departmental projects, including being more heavily involved in development assessments (species modelling), the national assessment for threatened species and a Bush Blitz survey to Bradshaw Field Training Area in May 2017, final report submitted October 2017, with 815 specimens collected adding 194 species to the previously know list. Data management is an ongoing task and we now have an annual budget for IT support which comprises ongoing enhancements to our database systems through external programmers.
Restructure at RBGV, 2 new flora writers. Alisons' position has now become 'Digital Collections Adviser' - Nimal is acting in this position currently. Niels' position is Biodiversity Informatics. Secured 3 years of funding for VicFlora to hire 2 botanists part time. Work on VicFlora will also include easy ID systems i.e. based on flower colour, growth form etc. and extra funding for images. Implementing permits within Specify - permits table is linked to accessions in preparation for Nagoya by documenting permit information.
Recently 4 positions have been filled including Russell Barrett, Shelley James (Collections Manager). Current project is to combine the living and Herbarium specimens into the one database (EMU) - currently they are 2 separate systems (living collections is IRIS - off the shelf).
Our department's name was changed to Biodiversity, Conservation and Attractions and email addresses to email@example.com as of the start of the financial year. The Herbarium has completed a major thinning operation on its collection and is now part way through a similarly extensive cleaning operation. Karina will no doubt discuss these at MAHC. The Herbarium's server migration was completed around mid-year, with the result that 10-15 services and applications are now running on modern hardware and operating systems. This work paves the way for future major upgrades to PERTH applications, including FloraBase and WAHerb.
Recent projects include AVH release in June 2017, eFlora Platform. More recent focus has been on infrastructure upgrades that were 6 years old. Moving from single servers to cluster servers - 6 servers close to 100% success. By adding more servers to the cluster can therefore add additional fields to the index. New positions include project manager (Hamish), Peter Brenten (BioCollect) and new business analyst, Communications Manager appointed (Larissa Cordner) whilst Hannah Scott is on secondment.
Minutes and actions from previous meetings
Worked through the HISCOM issues and updated / closed where relevant. Five issues remain open as they have been carried over or are ongoing.
SESSION 2: Elected Positions
- Chair: Ben Richardson elected (to transition to Chair at first 2018 teleconference)
- Assistant Chair: Anne Fuchs elected
- Deputy Chair (and CHAH Rep.): No longer exists. Refer to HISCOM ToR
- Technical Coordinator: Niels Klazenga
- AVH User Liaison: Niels Klazenga & Nick dos Remedios (technical support), Eleanor Crichton & Nimal Karunajeewa (data support), Aaron Wilton (NZ data support), Anne Fuchs & Michael Hope (also receive firstname.lastname@example.org emails). ALA Support email is likely to change to an open source help desk ticketing system. The AVH User Liaison role should be reviewed when this change is implemented.
NOTE: it was discussed having another NZ rep for Data Support other than Aaron - see Action 2.
HISCOM ToR were amended at the 2016 AGM, however were never endorsed by CHAH. The same changes were put forward again and have now been endorsed with some minor changes since 2016. The changes include the new role of CHAH Liaison to replace the Deputy Chair role (which was an elected CHAH member). The CHAH Liaison can be any member from the CHAH Executive to attend the 2-3 HISCOM teleconferences a year. The local CHAH representative will be invited to attend HISCOM AGMs. Remove mention of technical environment statements from the ToR.
Email lists, HISCOM wiki, HISCOM GitHub
The HISCOM List was reviewed and 'cleaned up'. The new Email lists include CHAH, HISCOM, MAHC, AVH, APC, APNI Editors. Other lists can be easily added. Its a Google account that CHAH pay for $10 per month (Google Groups are free). There is 1 administrator per account.
AVH Technical Addendum
The Technical Addendum was reviewed and all agreed only minor changes were required. Niels to provide an itemised list of these changes - useful to outline preferred workflow and all agree on the current status of having at least yearly re-indexing and data being updated at a minimum frequency of every three months. Some providers would like to see an automated approach to nightly updates rather than manual updates as it currently is.
SESSION 3: Australasian Virtual Herbarium
UNSW is ready to provide but waiting on legal approval and pending the updated MOU from CHAH. Currently AD and UNE providers not working. AD is due to database change over. Other than this 10 BioCAse Providers are working and BRI delivers DwCA directly to the ALA. There are 11 NZ providers which deliver via CHR through the GBIF IPT.
Discussion of facets
Niels raised the AVH facets and the proposed changes in the document provided. ALL encouraged to review and provide comment and if agreement to implement.
Delivery of data to GBIF
GBIF pull data from the ALA from an ALA monthly archive. BasisofRecord is required for GBIF as a DwC archive.
Worked through the AVH GitHub issues and confirmed that mostly all are DONE. Discussion around provided/processed name in search result. Currently in production it is searching on both. Proposed that a toggle in the advanced search to enable searching on either provided name OR processed/matched name. Simple Search = text string search - searches on both provided and processed name Advanced Search = toggle to select the search on provided OR processed/matched name. Matched name is the default.
Data Management Issues ALA GitHub
PERTH GPI images are unlinked. Locality information is not being downloaded from AVH (locality is not being populated). Locality is currently provided as verbatum. Botanical Group still displays animals BUT ALA hide it from the look up table in AVH. AFD is overwriting NZ data which is why animal names are appearing. This is a short term fix, which works at present. DwC does not handle typified names - Type Status TypeOfType i.e. 'Holotype'
- Implementation of vocabularies (i.e. LifeForm)
It was agreed the GBIF vocabulary for LifeForm was not appropriate thus updated in GitHib HISPID repo https://github.com/hiscom/hispid/issues/122
- Bush Blitz - HISCOM use CollectingTrip , FCIG use DataSet Name. ALA don't mind what is used..The wildcard field was turned off so Bush Blitz expedition cannot be searched on. Providers are encouraged to deliver Bush Blitz. The list is still loaded on the Bushblitz website: http://bushblitz.org.au/resources/. Under the resources heading, bottom of the list is “Bush Blitz Point data name formats”
Report on NSL developments
- Changes to the names editor before and after APNI training. Included additional work flow requirements to review instances, audit report, improvements in consistency of the interface.
- Tree editor being refactored for performance and maintenance. Requirements documented at https://github.com/bio-org-au/services/blob/new-tree/doc/NewTreeStructure.adoc. Implementation and testing currently in progress.
- Advanced search feature being developed based on feedback on current search and prototype developed in 2016. Advanced search to be written with services so that other applications can use the same services. Initial development focused on experimenting with these services, presentation on multiple devices and richness of the search capability. Interested and available users for providing requirements and testing are welcome.
- CHAH discussing governance of ICN datasets (Vascular, Lichen, Algae, Fungi and Bryophytes). ABRS prepared dashboard for the status of Algae datasets.
- DAWR (Dept. of Agriculture and Water) adopting the open source NSL software for management of their names and taxonomy for their in-house systems.
Herbaria of Australasia Website
HISCOM agreed that this conversation required the appropriate direction from CHAH especially when the website working group had been proposed at the 2016 AGM and comprised of Gintaras, Michelle (CHAH), Ainseley, Niels (HISCOM), Pina, Dahara (MAHC). HISCOM agreed it was sensible to build on the current AVH website to be hosted on an ALA server. Further discussed CHAH/HISCOM meeting below (Thursday).
Banks and Solander Collection - Cooks first Voyage
CHAH and CHAFC propose promoting the Banks and Solander Collection late 2019 - using both Museum and Herbarium collections. HISCOM did not discuss as very little information was required and what HISCOM's role in this would be. Noting it in the minutes so there is a record of it for future reference.
Next HISCOM AGM NZ (SPNHC & TDWG)
2018 HISCOM AGM to be a 1 day meeting in NZ day prior to the TDWG Conference
THURSDAY HISCOM /CHAH
Location: Eastern Transit Room, Royal Botanic Gardens Victoria
SESSION 1: Welcome
- HISCOM: Anne Fuchs (CANB), Niels Klazenga (MEL), Donna Lewis (DNA - Chair), Wayne Cherry (NSW), Michael Hope (ALA), Ainsley Calladine (AD), Nimal Karunajeewa (MEL), Greg Clarke (CANB)
- HISCOM: Ben Richardson (PERTH), Laurence Paine (HO), Gillian Brown (BRI), Aaron Wilton (CHR), Eleanor Crichton (AD), Simon Checksfield (CSIRO)
- Chair: John Huisman (PERTH) for next 12 months.
- NEW CHAH Liaison Officer: Aaron Wilton (proposed). This is a new position in order to maintain better communication lines and would be a member of the CHAH executive. This position would sit on teleconferences and the local CHAH rep would be invited to attend HISCOM AGMs.
- CHAH Executive: John, Michelle, Darren, Aaron.
- HISCOM ToR were reviewed and updated as per above heading in these minutes - CHAH endorsed - not yet updated on wiki.
- 2018 HISCOM AGM to be a 1 day meeting in NZ day prior to the TDWG Conference - CHAH supported and has travel funds allocated.
- 2019 HISCOM AGM to be in PERTH due to newly elected Chair only able to attend alternate years - CHAH supported the idea
- should HISCOM meetings warrant a 1 day meeting going forward - a suggestion was to align the AGMs with ASBS - CHAH noted.
- ALA CCC role - consensus from joint HISCOM/MAHC/FCIG meeting was 2 part-time positions for the botanical and faunal communities and the position be framed around a 'science communicator' type role who understands our business, and can promote it. The person in the position would ideally sit on both HISCOM and MAHC sub-committees as observers. The position would also be responsible for social media (i.e. AVH FB) and potentially coordinate the development of the new Australasian herbaria website. CHAH agreed on the same role....in addition to liaison within our community, outreach focus is important; a greater focus on this could make a difference in making the role more broadly known. Social media outreach would be a strong focus as well as engaging in the community. The position would be funded by the ALA for 18 months. Michelle is preparing the JD with Michael Hope.
- HISCOM suggested presenting 'names' and NSL at TDWG - CHAH supported
- Review and update AVH Technical Addendum, recognised MoU is out of date and needs to be amended with NZ data being online, remove technical environment statements - CHAH agreed. Each institution to be sent a copy of the MoU for legal review and sign off prior to continue negotiating a data agreement with the ALA.
- AVH Launch - It is anticipated to have a launch at the Systematics conference in November. CHAH would like to have some promotional material; it was noted that HISCOM had proposed a number of these last year and CHAH had decided against hard copy material such as bookmarks. HISCOM noted that suggestions had been made earlier and had awaited feedback. Moving forward, in preparation for a virtual Australia/NZ launch CHAH wanted to see a 'new' AVH look. It was also agreed that images on the carousel change, and the news items down the right pane are new and current. The Help Pages need to be updated especially the Downloads - CHAH encouraged HISCOM to progress.
- Collections Community Resources - at the joint HISCOM/MAHC/FCIG meeting it was discussed that a central repository was required for all groups CHAH/CHAFC/HISCOM/FCIG/MAHC where the 'final' version of documents can be located. HISCOM argues that we have our systems in place regarding the HISCOM wiki and GitHub repos. However, CHAH supported the idea to investigate options and thought it was logical to host something on the ALA - Nicole (FCIG), Gill & Frank (MAHC), Donna (HISCOM) to further investigate and circulate a scoping document to the CHAH list. https://github.com/hiscom/business/issues/65.
- Bush Blitz Data - can now be delivered to the AVH. Only impediment may be technical constraints at various herbaria.
- Email lists evaluation - all agreed was working really well.
SESSION 2: National Species List
- CHAH identified the future need to align APC/State Censuses and the EPBC taxon on this list. Requested update on how this may be achieved technically and what the Department of Environment is planning.
- State censuses - discussed State/Territory censuses and how we want to use the NSL (maintain list in the NSL, linked services, export) and what data is required to transition a census to the NSL if it is to be used (taxonomic coverage, attributes attached, regulatory group i.e. EPBC). State censuses will have implications for Biosecurity. NSL to continue discussions with state herbaria on requirements.
- Dynamic electronic publications, discussion on how to handle new APNI instances with are "born-APNI" ie. they are not published externally of APNI. Need for a reference using a permanent ID/URL/DOI.
- Migration of data that already exists in electronic form - short discussion on extracting metadata from electronic publications. Ongoing requirement that requires suitable standards.
- Governance model - the model proposed by ABRS to CHAH using the algae as a case study was adopted by CHAH. This will allow different governance models for different 'national' taxon lists with a different visual presentation in the NSL. eg. concept endorsed by consensus model ie. APC tick or by specialist group and CHAH endorsed ie. CHAH tick.
HISCOM Future Directions
Herbaria of Australasia Website
ALA agreed on the original mind-map concept and both committees agreed to build on the AVH pages rather than a separate website. Hosting on ALA is free for now and have already agreed to this and liked the idea that their community used their infrastructure. ZOO (company) helped with Flora of Aust design and were suggested as a company to do the new web page. Since they have worked with ALA and now have a good working relationship with them and no the issues this could be an advantage for us to use them - they have a flavour for the community. Working group Niels, Ainsley (both have access to the Wordpress site), Pina, Gintaras, John, Dahara to commence work 2018. Actions –support for getting a design done, Action support for movement for other resources into one web presence; maintenance? CHAH have allocated $5K to redevelopment and graphic design. ALA CCC could potentially coordinate website development with the working group (once appointed) - work to commence 2018.
Image Delivery to AVH
Ongoing see https://github.com/hiscom/business/issues/62. At the joint HISCOM/CHAH meeting it was apparent images of vouchered specimens should be linked to accessions - there were concerns raised should images be directly provided to the ALA and the AVH providers are going via MEL. Niels is currently preparing to provide the GPI images to AVH and generated a survey to acquire info on how many type images per Herbarium acronym, format and ability to transform to JPEG, and if they were available via URL. Once the GPI images are loaded then the same template will ideally be used for images associated with vouchered specimens. CHAH supports unvouchered images to be provided directly to ALA based on the list of top 200 taxa Michael is to provide. NOTE: ALA can now deliver full resolution images.
- APII still not linked through to specimens where images are of the plants which were picked and pressed again linked through unique identifier of specimen.
- Universities do not have to pay for large uploads to ALA.
- Copyright for images. In order for these to be in ALA needs to be CC-BY. You still have the copyright, still have it but just giving up the exclusive rights to control it.
One of the issues is that it’s all fine if we import the data ourselves but with information that comes from others we have to track it all down in publications. Genbank has a catalogue field but not easy to search for it and people skip this field and can be filled in varying formats. Continue to have this on the HISCOM agenda with MAHC and FCIG contributing to investigate linking to genbank using GGBN standards. In order to do this form a working group comprising Jo Birch, Margaret Cawsey, Shelley James. Shelley has followed up https://github.com/hiscom/business/issues/53. Existing 2016 AGM Action left open https://github.com/hiscom/business/issues/44. Other contacts may include Ed Baffin (AD), Sarah Matthews (CANB).
- DISCUSSION - ALA is thinking of this in terms of taxa but we record trait data at an individual level (there is real power for specimens if we can tie the data to them). Multiple measurements for single specimens may not be capable of being recorded in HISPID fields for now but could be incredibly important. This could be tied into a goal in the decadal plan - we can aim to have all available trait and genomic data tied to specimen data and be readily available.
- CHAH encouraged HISCOM to progress the trait data space and what this would look like for the botanical community. Some ideas included phenology, flora writing scoring sheets (traits scored off a specimen), Delta, Lucid character sets. HISCOM to discuss from this point forward.