Report from FCIG 2014

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The annual FCIG meeting was held on October 1–2 at the Queen Victoria Museum and Art Gallery in Launceston. The meeting was attended by representatives from all the state and territory museums, as well as representatives from ABRS and ALA. Items of discussion relevant to the botanical community are outlined below.

Communication with ALA

The need for ALA to produce release notes when changes are implemented was identified, so we have clear information about new developments and bug fixes.

TDWG

Paul Flemons (one of the Oceania TDWG representatives, along with Aaron Wilton) expressed concern at the lack of representation from the Australasian community at TDWG meetings. The work of the TDWG community underpins the information management and data sharing work of both the zoological and botanical communities, and it’s important that we both support TDWG financially via institutional membership, and remain engaged in TDWG work by attending meetings and participating in discussions around standards development. Some museums are having trouble receiving budget approval for the annual TDWG membership, and it was suggested that CHAFC takes out an institutional membership on behalf of the zoological community. Individual institutions will remain TDWG members where they can.

The proposed location for TDWG meetings in the next few years is:

  • 2015 – Africa (though this may need to be reviewed, depending on security and health concerns)
  • 2016 – South America (probably Costa Rica)
  • 2017 – Canada
  • 2018 – Australia (probably Cairns or Townsville).

It is hoped that there is strong representation from the zoological and botanical communities when TDWG is in Australia.

FCIG also recommend that each institution is a member of the Society for the Preservation of Natural History Collections (SPNHC); SPNHC memberships are 75 USD per year.

Action for HISCOM: Determine which herbaria are TDWG and/or SPNHC members, and consider whether we would benefit from a CHAH membership to TDWG. If not all institutions are members of these organisations, do we want to assign someone to report back on relevant activities?

Download field names

The field names in the ALA downloads are not Darwin Core (DwC) terms. Although the README.txt file shows the mapping between the column headers and DwC, FCIG would prefer the column headers were DwC. FCIG also want detailed downloads available again.

ALA response: CSIRO has a couple of data centres and ALA are looking at putting virtual machines in Canberra for redundancy. They are also looking at beefing up the system to support better download options.

Action for HISCOM: Document HISCOM’s preferences for download options and share with FCIG

Accessibility

Morgan Strong (Western Australian Museum) did a high-level accessibility audit of the ALA website. While many of the recommendations are things that ALA need to fix, it is also important that data providers deliver data that allows the ALA to meet accessibility guidelines, such as alt text with images.

ALA are planning a review of the website design, and suggested that the accessibility issues could be addressed as part of the redesign. However, the view from FCIG was that there are many simple fixes that should be addressed as a matter of priority, rather than being delayed until the site is redesigned.

See the audit documentation for more information (note that the reference to the WA Museum website in the References tab is erroneous – the audit is of the ALA site).

Action for HISCOM: Review the audit and endorse the recommendations to ALA (if deemed appropriate)

Biodiversity Heritage Library

During 2014–2016, Museum Victoria (MV) will continue to act as the lead agency for the Biodiversity Heritage Library (BHL) in Australia. One area of work is to provide external advocacy, training and support to any ALA participant organisation who is committed to starting a literature digitisation project. They cannot provide equipment or staff, but can provide advice and training on getting scanned literature into BHL. They can also provide advice and assistance to organisations who already have digitised literature that can be contributed to ALA. Other developments include:

  • ‘Collections’ are being set up within BHL so you can see what has been contributed by a particular institution
  • BHL-Europe has set up Biodiversity Library Exhibitions on different themes (e.g. spices, poisonous nature) and the Australian node will do something similar
  • ‘article-isation’ of BHL has been done to the extent it can be (Rod Page has been working on this).

See this one-page document for more information about BHL work in the next two years.

The new BHL project manager, Nicole Carney, will be in contact soon regarding engagement with the herbarium community.

Action for HISCOM: Each institution to consider whether they want assistance or advice about digitising literature or providing already-digitised literature to BHL

Data delivery

IPT is working well for many zoological collections, and some are looking into using IPT to deliver images (it already includes links to specimens etc). There was a suggestion that the ALA could fund IPT workshops for the community.

Discussions about data delivery with Michael Hope and Mahmoud Sadeghi identified issues with the delivery of updated records where a null field was previously populated. If a field was previously populated, but is now delivered as null, the ALA interprets it as meaning that there is no change to the field, rather than deleting the previous value. This was identified as being a bigger issue for FCIG than the deletion of entire records (which is also an issue).

Input from Niels: This issue has been noted in AVH very early on and that Natasha put a process in place that removes obsolete columns (which are really more like key–value pairs in the BioCache) from AVH records after they have been updated, meaning that columns that are delivered with no value or are not delivered at all will be removed from the AVH record. This process only works if all fields – or at least all the fields that should still have data in them – are delivered with each update (quite possibly in a single CSV row and not partly in the Core and partly in various extensions) and not just the updated fields. This is the case for AVH records, but not necessarily for other ALA providers.

This process worked very well when it was implemented, but we haven’t checked on it for a long time and it is quite possible that it has been turned off accidentally some time after Natasha and Miles left and not turned back on, as nobody else knew it existed (we have proof that it does).

AVH has several fields that frequently change from having data to having no data, such as loans that have been returned, or old identifications that have identification remarks (or, worse, an identification qualifier) and new identifications that do not, and we have also had various re-mappings of fields, so when it was discovered what was happening, we didn’t even feel that HISCOM needed to be consulted and that it was a no-brainer that this should be resolved, so that’s what Natasha did and we accepted the consequences this would have for data delivery.

Implementing the Nagoya Protocol in Australia

The Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization (the Protocol) is a global agreement that implements the access and benefit-sharing obligations of the Convention on Biological Diversity (CBD). Australia is a signatory to the Protocol. As of the 14th of October this year, researchers must be able to demonstrate that any genomic data used in research was legally obtained, and that the source material was legally collected. The Protocol does not apply retrospectively; it only applies to material collected after the 14th of October.

A CHAH/CHAFC meeting in 2011 acknowledged that the Protocol will have some ramifications for the mechanisms around sharing, exchanging and collecting specimens. The main impact of the Protocol on collections is that permits will have to be tracked and locatable. The state and territory museums and herbaria will be granted ‘trusted institution’ status, but it is unclear how the Protocol will apply to collections from other countries; it seems that we are obliged to demonstrate that material from other countries was collected legally and has known provenance. It is also unclear how quarantine seizures will be treated. There were plans for the tracking of international trade of biological materials to be managed at the national level, but it seems that this is no longer going to happen. CHAFC submitted a response to the Department of Environment’s Consultation on ‘A Model for Implementing the Nagoya Protocol in Australia’ in May this year.

Action for HISCOM: Include permit in HISPID so that we can exchange permit numbers with duplicates

Global Genome Biodiversity Network

Margaret Cawsey attended the Global Genome Biodiversity Network (GGBN) Conference on Biodiversity Biobanking in London earlier this year.

GGBN membership and fees

An organisation that signs the Memorandum of Understanding becomes an associate member of GGBN. Once you start delivering data to GGBN, you become a full member, and have to pay fees. At the GGBN meeting, it was proposed that the annual fee would be $10,000 per institution, but the response was that this is completely untenable.

GGBN standard

The GGBN has published an international standard for sharing tissue data, DNA sequences etc., which will probably be ratified by TDWG at this year’s meeting. The Australian National Wildlife Collection, the Australian Museum and Museum Victoria are trying to implement the GGBN standard in their collections management systems, but have run into various issues. Some notes on the standard:

  • permit – relates to collecting permit, not state/territory import/export permit (i.e. it appears that within GGBN, proof of legality relates only to the collection of the original specimen, and you don’t need to prove the legality of transferring material derived from the specimen between different jurisdictions)
  • permitType – the vocabulary needs to be clarified
  • preparationDate – required, but it’s okay to record it as ‘not recorded’
  • preparationType – this field currently conflates preservation materials and vessel (i.e. dried, silica, alcohol, tube)
  • there is no field for preservation temperature, despite this being useful information for freeze-dried material.
  • the GGBN standard and GenBank are really set up for traditional sequencing, not for next-gen sequencing.

See Margaret Cawsey’s presentation and overview of the GGBN fields for more information.

GGBN and ALA

The zoological community wants to be able to easily identify specimens and tissues, and want to share data with the GGBN via ALA. The ALA have indicated that they’re happy to serve data to the GGBN on behalf of the community.

FCIG have requested guidance from ALA about how to deliver tissue data, particularly around defining relationships between the principle record (i.e. the original specimen) and sample record(s) (e.g. tissue collection(s)). Some museums register individual tissue samples as separate records, and some as one record, with the different types of tissue sample listed within the record.

Action for HISCOM: Consider the implementation of GGBN within the botanical community. Do we need to be more closely engaged with GGBN standards development?

Relationships between records

As well as relationships between specimen records and tissue records, ALA also needs to help resolve issues with the delivery of multiple images per specimen record and images that relate to more than one specimen record. ALA are currently working on a project called AusTrack, which is looking at linking associated records in time and space (e.g. tracking data for animals). There is an AusTrack workshop on the 16th and 17th of October to look at how best to link this data. It would be useful for FCIG and HISCOM to provide examples of relationships between collection-based records, so that our needs can be factored into the discussions.

Action for HISCOM: Provide Michael Hope with clear examples of relationships between specimen records (e.g. duplicates) and between specimen records and images

BushBlitz identifier

Pam Beesley (ABRS) spoke about implementing an identifier for BushBlitz so that records of specimens collected on BushBlitz expeditions can be easily queried in ALA. The formatting of the BushBlitz name will be specified in contracts, so it is consistent across collections. The current idea is to use the DwC datasetName to record the BushBlitz name, but this might have implications for the chain of attribution. I think we also need to consider this in terms of collecting trips or expeditions more widely. While it might make sense to have records from a particular BushBlitz as a discrete data set, I don’t think this makes sense for other collecting trips, such as exploring expeditions or research trips, which we would presumably want to record using the same DwC concept. ABRS might have some funds available to help institutions implement a new field, if required. The current idea is that the BushBlitz identifier will only be recorded in future, and not retrospectively, but I don’t think it would be much more work to implement it retrospectively, given that there is already a record of which specimens were collected on BushBlitz trips.

ABRS haven’t yet been in contact with the herbarium community about this, but will be soon.

(As an aside, informal names are an issue for the zoological community, as they can’t be delivered to ALA due to potential confusion arising from, e.g. ‘Genus sp. 1’ being delivered by different providers. There was some discussion about implementing phrase names for informal zoological names.)

Action for HISCOM: Consider whether datasetName is the most appropriate concept to use. Determine how much work it would be for each institution to implement a collecting trip/expedition field.

‘Club view’ in AVH

Unlike HISCOM, FCIG don’t currently have a method for giving people access to full locality data for taxa listed on the sensitive data service. In looking at the AVH model, we realised that anyone who gets access to full locality information in AVH also gets access to full locality details for everything in ALA, so AVH users with ‘club view’ can see more detail about museum records than the museum curators themselves. ALA have identified a need to overhaul the user management system so that privileges can be assigned at different scales.

Club view also gives the option to verify a record that has been annotated, whereas users without club view can only make another annotation; this also applies across ALA as a whole, not just to AVH.

Collective Access

Western Australian Museum is migrating their collections database to Collective Access, an open-source, relational collections management system. Morgan Strong reports that the developers are very responsive; if you put an issue on the forum you’ll hear back from lead developers within a day. It uses an elastic search, which is super fast and will use spare resources on other servers in the same network if available.

Action for HISCOM: Consider whether Collective Access is worth investigating for herbarium data management