HISCOM AGM 2015 Hobart

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Meeting Location

TMAG, Hobart, Centre for Learning and Discovery meeting room in Museum, access via Gallery. Entry via Watergate side, Dunn Street.

AGENDA

Attendees

Laurence Paine (HO), Clifford (HO), Aaron Wilton (CHR), Ben Richardson (PERTH), Anne Fuchs (CANB), Niels Klazenga (MEL), Donna Lewis (DNA - Chair), Wayne Cherry (NSW), Rebecca Pirzl (ALA), Nick dos Remedios (ALA), Ainsley Calladine (AD), Eleanor Crichton (AD)

Apologies

Ian Cowie (DNA), Michelle Waycott (AD)

Welcome and Institution Updates

Donna welcomed all.

  • PERTH: Perth database will soon be hosted in Sydney, including FloraBase. This was a Departmental wide decision due to current server issues. Currently 1 position dedicated to manage IT, specimen database and FloraBase. Ben 3 days ALA, 2 Herbarium.
  • ALA: Funded until end of 2015/2016 financial year. There has been recent approval to employ an additional 3 software developers. Strategic Planning process taking place which has identified 6 focus areas – biological collections being one of them. ALA’s current attention is on core activities to improve services to clients. Also undergoing a review process of where servers are hosted. CSIRO moving to Amazon, ALA is moving to AWS which is more has more flexibility, tools and services, and a reduction in cost.
  • HO: Dealing with ongoing maintenance and security of TMAG databases which were created in the 90’s. Working on enhancements, aiming for more accurate data entry eg taxonomic tools. Focus in past 12 months has been 12-14 chapters of the eFlora and Algae. Digitisation olf representative species ready to put up on image servers, then available to feed to the ALA.
  • MEL: In a good place with the database and Flora of Victoria. Changing to a new server, undergoing a data restructure. Niels 3 days ALA, 2 Herbarium.
  • DNA: Specimen database has been extended to incorporate the maintenance of the taxon table, flora descriptions, ecological attributes, conservation and ethnobotanical data. FloraNT was recently made publicly available which points to the specimen database. An Agile project is currently underway to extend FloraNT to include the MacDonnell Ranges LUCID key which includes approximately 80% of aridzone NT flora.
  • NSW: Ongoing data maintenance. Flora keys are now in KeyBase. Focusing on eFlora Platform work with Flora of NSW being one of the pilot projects. Looking into a replacement server to an IT Dept’s virtual environments, moving from solaris to lunix. Restructure at the Gardens has meant further budget cuts. Support around database maintenance has been reduced to 1 in-house position.
  • AD: Specimen database system migration to Specify6 progressing (grateful for MEL assistance). Making progress towards moving flora descriptions to the eFlora Platform which will influence future directions. Corporate IT environment - extended DMZ (part of state CIO directive). Scheduled departmental move significantly impacting on corporate IT capacity
  • CANB: Undergoing many staffing changes - Jim and Greg have left who were both members of HISCOM. This has meant a loss in infrastructure knowledge. FoA up as a pilot project on the eFlora Platform for the current testing phase (Phase 2). Other projects centred around collective access, NSL, CMS project, living collection (i.e. public facing map). Received Bush Blitz funding to image high res images of the seed bank collection.
  • CHR: Working on eFlora, 36 family treatments published and ½ dozen due for production run. Taken on a good PhD candidate for 3 years on a gazetteer related project for georeferenced and under-georeferenced localities. Responsible for NZOR which could be a good funding opportunity.

Minutes and actions from previous meetings

Actions carried over from previous teleconferences and 2014 AGM ....

Action 1: Document the requirements for images on the homepage (i.e. image quality, format?, caption, credits? Etc). Also the batch of images may include 1 specimen, 1 vault, 1 field, etc.. so there is variety. (Niels).
Action 2: Provide Ainsley access to WordPress to be able to add images to AVH homepage, AVH dev and prod servers. (Niels).
Action 3: Advise CHAH of HISCOM Action 1 from 2014 AGM. New page on wiki for presentations and documents promoting the value of herbaria (Donna).

RAH - collectory pages (written about 4 yrs ago, only minor updates since). Login, edit content - MAHC reps or CCC should be shown how to do it. NB need to ensure these pages and CHAH website are aligned (or that there is one point of truth). It was discussed that the Collectory should have web services so that WordPress can pull data from the ALA Collectory.

Action 4: Inform ALA CCC role to be the conduit for the maintenance of the ALA Collectory pages. (Rebecca).

Elected Positions

  • Chair – Donna Lewis (endorsed to complete full 3 year term as Chair)
  • Assistant Chair - Ben Richardson (nominated)
  • Deputy Chair (and CHAH Rep.) – Ian Cowie
  • Technical Coordinator – Niels Klazenga (nominated to continue). Ben Richardson to assist when required
  • AVH User Liaison – Eleanor Crichton (nominated to continue)
  • ALA Collections Community Coordinator - CHAH to officially inform HISCOM of the appointment

HISCOM endorsed Donna to continue as Chair for a full term after replacing Alison.

Action 5: Recommend that CHAH approve the elected positions (Assistant Chair, Technical Coordinator, AVH User Liaison). (Donna).

SESSION 1 - ALA & AVH

ALA TaxonOverflow demonstration (Nick dos Remedios)

TaxonOverflow demonstration url taxonhelp.ala.org.au ('borrowed' from stackoverflow). Nick briefly demonstrated the ALA TaxonOverflow project. This project is currently on hold until more resources are available. A test version has not yet been released to the botanical or faunal communities. It’s similar to iNaturalist and iSpot (UK). HISCOM agreed it could be useful but needs to be tested rigorously. No suggestions at this point for potential ‘testers’. It could also create more work for Herbaria and more unidentified observations. More points below for future reference:

- hasn't progressed recently; want to consult with groups, get feedback before next changes.
- feedback has been 'average': too complex, not intuitive. 
- trying to take advantage of limited community resources that can ID species (currently only  a few, scattered, using different systems). act as central point. make it as easy as poss; incl 
- categories, digest (e/m, rss). flag 'experts', include confidence factor (?)
- could vote up/down on answers, but how to differentiate weightings for exp/non-exp voters
- will trial various methods, adjust.
- need 'expert' testers - Donna/Alexis were discussing circulating to FCIG/MAHC/HISCOM/CHAH re: recruiting testers
- initially narrow focus - internal ALA / ext /Bowerbird / fully ext - API
- been approached by NSW Env Dept & QUESTA Game developers
- may go out to commercial dev (they don't have resources currently to continue development)
- may filter by taxon hierarchy, or maybe common name groups
- could identify by rank first
- what about admin overhead? inappropriate comments, trolls etc 
  - need to be able to flag/remove v.fast, even if reinstated later
  - what time commitment may be required to do this

AVH update (Niels Klazenga)

Four new University data providers have come online including MELU, JCT, WOLL, LTB and BRI have started to deliver again. AD has a new BioCase Provider and DNA will be providing refreshed data soon.

NZVH update (Aaron Wilton)

Test environment soon to be available. HISCOM and MAHC members will be encouraged to test – allowing a 5 day period prior to moving to production. Seven of the 11 collections are providing data, 4 of which are outdated so they will require a refresh. Data from the collections are ready via IPT. The sensitive species lists are prepared and information has been sent to Niels on website changes (i.e. changing ‘Australia’ to ‘Australasia’). The taxon list needs to be loaded based on NZOR. Help pages have been amended to reflect NZ amalgamation and other bits.

AVH will support NZ geographic regions. Two additional facets have been added – 1. NZ Provinces (equivalent to Aust. States), and 2. Ecological Regions equivalent to IBRA. Contractor with ALA was extended until end of July (2015) and now well overdue. Aaron to get in touch with Michael Hope.

Media – 11 new providers, 300,000 currently digitised – contact Minky Faber, ALA CCC role to assist with articles.

Action 6: Recommendation to CHAH to officially thank the ALA for assisting the amalgamation of 2 countries herbarium collections once completed. (Donna).
Action 7: Prompt official launch of AVH and press release. (Donna).

Annotation Service

HISCOM agreed that annotation service is really valuable and needs to be improved. Currently the Annotation Service is not used much, but its usage is increasing. HISCOM need to think about some recommendations to put forward to the ALA through the Strategic Planning process on ideas as to what is required. The annotation service is only 1 example of future priorities to put forward. MAHC will need to be made aware of the Annotation Service as it will impact on Collection Management tasks (i.e. addressing and managing annotations). MAHC – what is the ALA providing and how can they help i.e. tools. Rebecca encouraged feedback from HSICOM as to recommendations on priorities (via HISCOM Chair). It was also advised that John la Salle will be coordinating requests from the collections community. Alexis (FCIG Chair) has been very involved.

HISCOM will also need to address how the Annotation Service will affect our data delivery (HISPID Specific fields). ALA is still in the process of shaping a mechanism for input into the strategic planning process – focus area being Biological Collections. The initial contact will be through HISCOM Chair and ALA CCC position. HISCOM/MAHC/CHAH needs to identify what the community needs to fit into the ALA Strategic Plan. ALA priorities are the core activities on existing products. They are working on consolidating issues to be addressed. ALA Strategic Planning with HISCOMs input:

  • Coherent set of work activities;
  • Project delivery plans;
  • Identify areas of opportunity.
Action 8: Make the ‘annotations document’ available on the wiki. (Niels).
Action 9: Advice to CHAH that HISCOM sees improving the Annotation Service to be a priority and to be included as part of the ALA Strategic Planning process. (Donna).
Action 10: Document requirements of the annotations service. (Ben).

NB: David Cantrill mentioned during the CHAH AGM 2015 (MEL) an Annotations Service out of Berlin. He believes it is open source...something to be aware of to avoid 'reinventing the wheel'.

SESSION 2 - HISPID Review

HISPID 3 was more about Herbarium specimens and could accommodate living collections. The HISPID review has refined the terms and concepts to be more Herbarium Specimen centric. It will however be more observations focused, especially when images come online. HISPID Terms were agreed upon by HISCOM members and the issues flagged in GitHub by the HISPID Review working group were worked through and either dealt with or recorded for action prior to publication. HISPID is management brought into line with TDWG standards (esp. DarwinCore). Wherever possible existing terms in DarwinCore, ABCD and Audubon Core have been adopted, although a number of new terms have been added and vocabularies provided. The new terms may be nominated for inclusion into other standards, for example terms that support transfer of consent/permit information. HISPID will be published at http://hiscom.github.io/hispid/terms/ and http://hiscom.github.io/hispid/vocabulary/. The HISPID Issues can be found at https://github.com/hiscom/hispid/issues.

  • HISPID Review implementation

Steps forward to complete and implement HISPID:

  • Establish the number of new terms (i.e. not Darwin Core) once they are all in rdf.
  • Propose terms for other standards (i.e. Darwin Core). There is a process for this through TDWG.
  • Create 2 rdf documents 1. old version, 2. currently accepted terms.
  • Create a style sheet to put into PDF.
  • cmf template – extend it to incorporate new terms etc.

Aim for completion of HISPID standard will be end of 2015. Processes and convention document is in GitHub which will be expanded on.

Action 11: Provide Niels vocabulary for Fungi. (Tom).
Action 12: Follow up with Bush Blitz on how to ID each expedition so they can be differentiated in AVH/ALA. (Anne).
Action 13: Recommend CHAH supports the proposal for Bush Blitz to create a unique ID for each expedition. (Donna).

EVENT Class – habitat, topography, aspect, geological substrate, substrate, soil, vegetation Leaving as free text fields at present but to be reviewed over the next 12 months. Determine what the ecological community would like to see?

Action 14: Review data in these fields to determine potential vocabularies or to leave as free text fields. (ALL).
Action 15: Contact TERN EcoInformatics to determine if there are already vocabularies for the following terms: habitat, topography, aspect, geological substrate, substrate, soil, vegetation. (Donna).
Action 16: Expand the HISPID Review processes and convention document. (HISPID Review working group).
Action 17: Advice to CHAH that the new version of HISPID was ratified by HISCOM, and that only “mechanical” changes are now required for publication. (Donna).

SESSION 3

National Species List (Anne Fuchs)

ANNE'S NOTES: Technical documentation: https://biodiversity.org.au on the ‘docs’ link. Source code available at https://github.com/bio-org-au https://github.com/bio-org-au/nsl-documentation

Action 18: Provide feedback and suggestions on the NSL either through the feedback link or email. (ALL).

Ways of using the NSL within other institutions:

  • Call services within applications (see a list of available services in the documentation)
  • Extract data and load in own institutions databases.
  • IBIS is going to extract the NSL and load into our database. Use this as the basis of a local name table which will also include names not in the NSL. Maintain a link to the NSL provided data and use services to sync to the NSL (ingest new records, changes to existing records, flag soft deletes etc). The system to maintain this local table will hopefully be made available via github as well.
  • Aaron flagged the need to do periodic ‘pull’ processes to ensure there is no missing data.

Community model for APNI/APC:

  • Discussed options that are being presented in the APNI paper to CHAH
  • General agreement that a reasonable way to go was:

1. Herbaria provide APNI entry for the own institutions journals and publications their botanists publish in 2. Will require training for editors, user guide, help with work flow and a means of reviewing entries to ensure consistency of treatment 3. APC coordination retained by CANBR 4. Discussed ingesting electronically published journals into the NSL. The main issue is considered to be the lack of consistency in publication. This is space that is worth watching but was considered low priority.

State Checklists and the NSL:

  • Require the ability to both

1. House the checklists as a ‘tree’ in the NSL and use services to present the checklist in the own institutions web site. 2. Services to link/push/pull NSL data to locally maintained databases to reduce duplication of effort in maintaining the names. This model is required as state checklists may also include faunal names and rare/threatened status etc.

ADDITIONAL NOTES

Current Status: There are three main outputs of the NSL.

  • Nomenclatural file – similar to APNI names output including name, code, where it was published i.e. essentially all components of a name.
  • APC output – same as APC data output. This needs to be available for/to the ALA.
  • Just the APC.

Needs to be mapped to DarwinCore where possible. Discussed output of 6 fields which include the URI’s. Names are stored which are out into a tree and can go back to the tree at any point in time – name stays the same. Taxon instance also stays the same. New instance is the usage of a name. Every record has a unique ID across the whole system.


Outstanding Work: Bringing in other datasets i.e. fungi and mosses (AusMoss) using an integer number series. State and Territory trees will be separate and ability to download or via web services. Each institution has different issues in light of using the NSL for State and Territory Censuses. For example Perth has different curatorial staff that edit and maintain their State Census. This point requires further discussion.


Editing and Maintenance: CANB are currently preparing a paper to address:

  • No change
  • Editing of a name (APNI)
  • Name – herbaria to edit APNI based on house journals and CANB to pick up the rest

APC accepted taxonomy will continue to be maintained by CANB. Discussed the possibility of “community editing” and the resources required and services required to do this. HISCOM recommend APC to be maintained by CANB and APNI opened to institution delegates for editing. This would require running an ‘editing workshop’ so the delegates are consistent in editing and maintaining APNI. State and Territory herbaria – edit APNI based on House Journals CANB – continue to edit APNI based on ASB and other journals (national and international).

Action 19: Provide a summary of NSL workflows for editing etc. (Anne).
Action 20: Recommend that CHAH support ‘open editing’ to institution delegates for APNI and APC continues to be edited by CANB. (Donna).
Action 21: Recommend that CHAH funds a workshop for APNI and APC editors. (As response to Action 15.) (Donna).

SESSION 4

GPI and Images

Discussed during the joint HISCOM/MAHC meeting. See http://hiscom.rbg.vic.gov.au/wiki/Joint_HISCOM/MAHC_2015_Hobart_minutes for minutes and corresponding actions.

eFlora Platform Images

Currently images are sourced from the ALA plant index etc. Images are included to a new profile where they match to a name as default. An editor can exclude any images from a profile. HISCOM suggested that this mechanism for image inclusion to a profile is ‘switched’, so essentially an editor has to select which images to include. Rebecca has noted this change and will look into implementing it in the eFlora Platform. New images can be added to the ALA image repository. An editor can request these images not to be shown anywhere other than for a profile on the eFlora. HISCOM discussed other attributes for multimedia which Rebecca has noted.

Action 22: Follow up API for image service for eFlora Platform. (Rebecca).

HISCOM mailing list (Donna Lewis/Ben Richardson)

The HISCOM list is reviewed on a needs basis, essentially annually. HISCOM agreed new members are added who are officially involved in data delivery to the AVH/ALA. There are of course exceptions to this rule. This generally includes people that may be able to contribute to HISCOM relating to standards or projects regarding collections data management. MAHC members in the past have been encouraged to join the list. This is not a requirement as anything MAHC related is forwarded to the group.

Action 23: Provide names and email addresses to Ben to be added to the HISCOM list. (Donna).

MAHC Draft Standards (Donna Lewis)

The Draft Standards were reviewed by HISCOM for MAHC. They are based on museum standards 2013 - general, overarching policy document. Makes reference to HISCOM group as responsible for data delivery standards.

Action 24: Notify Pina (MAHC Chair) that HISCOM supports the Draft Standards and do not have any recommended changes at this stage. (Donna).

SESSION 5

CHAH correspondence (Donna Lewis)

  • AVH MoU: With CHAH to provide feedback. Terms of inclusion will be reflected in MoU.
  • AVH Terms of Inclusion: Waiting for CHAHs response. One of the datasets has been incorporated in the ALA but not AVH. Alison replied to herbarium rep in interim. Groups in contact with Miles (ALA). This aspect is covered by the MoU.
  • AVH ToR: Has been endorsed. Final version needs to be reflected on the wiki – still draft.
Action 25: Check the ToR are updated on the wiki (Donna).

AVH Social Media (Donna Lewis)

  • AVH news feeds (newsletter)

HISCOM and MAHC jointly agreed to encourage ALA Herbarium Community Projects to write articles for the AVH news feeds. See HISCOM/MAHC joint minutes for details and action items at http://hiscom.rbg.vic.gov.au/wiki/Joint_HISCOM/MAHC_2015_Hobart_minutes.

  • Facebook

Current FB administrators are Alison Vaughan, Gillian Brown, and Jim Croft. Alison handed it over to another colleague in MEL (NAME???) whilst on maternity leave. With Jim retired we have included another FB administrator (Anne Fuchs).

Action 26: Add Anne Fuchs as an administrator to AVH FB page. Check Gillian Brown is still OK to continue being AVH admin once she has commenced at BRI (Donna/Anne).
  • AVH/NZVH amalgamation

HISCOM agreed a media release would be appropriate when the Australasian Virtual Herbarium goes to production.

Action 27: CHAH support a media release for the AVH launch. (Donna).

AVH Website

  • Hosting

To be discussed in line with the CHAH website hosting and leading up to the launch??

  • Content

Necessary changes have been made to AVH pages in light of the amalgamation and need to be implemented prior to the test site being circulated to HISCOM/MAHC for testing. See NZVH Update for more details.

CHAH Website and Email List

  • Hosting, Content, Development

HISCOM agreed this was CHAH business that did not need discussion at HISCOM AGM. All agreed that hosting will need to be discussed at a later stage when the site has been developed with content.

  • CHAH Email List

Currently only Anne Fuchs, Alison Vaughan and Michelle Waycott can administer the CHAH list. Anne proposed another administrator should be added. HISCOM agreed Donna Lewis should be added as another administrator.

Action 28: Set up rights for Donna Lewis to help administer the CHAH email list. (Anne).

HISCOM Wiki

It was proposed to use GitHub for HISCOM business instead of the wiki. It was also discussed whether GitHub would be appropriate for MAHCs needs.

Action 29: Determine the process and requirements of using GitHub and redirects to the wiki for future HISCOM business. (Niels).
Action 30: Advice to CHAH of HISCOMs intention to manage projects in GitHub rather than the wiki. HISCOM advise that this may also accommodate MAHCs needs (Donna).

HISCOM Future Directions

HISCOM discussed future projects once the HISPID Review is completed and implemented. HISCOM agreed the NSL is an important project that requires HISCOM’s input regarding the services required. Also, the ALA is undergoing a strategic planning process which identifies 6 focus areas, biological collections being one of them. The ALA requires input from HISCOM 1. to provide recommendations on core activities i.e. future functionality of the AVH, 2. identify areas of opportunity. We need to be ready to give our priorities eg to John la Salle, otherwise others' priorities will drive future developments. Also need to reiterate importance of AVH, current initiatives & tools etc.

It may be advisable to have teleconference before Christmas, to cover all above and outstanding HISPID Review issues etc.


Action 31: HISCOM require a clear strategic direction from CHAH. (Donna).

Next HISCOM AGM

HISCOM discussed joint meeting with CHAH/MAHC, but with CHAH likely to meet in NZ felt it may be difficult to get travel approvals. HISCOM discussed the next AGM should be located in BRI, if not then CNS. There were also discussions around meeting with FCIG, especially with the completion and implementation of the HISPID Review. Clifford from HO will discuss this at FCIG AGM 2015 to determine whether FCIG see the value of meeting with HISCOM again.

Action 32: Liaise with CHAH/MAHC re: next AGM. (Donna).