Advancing the Catalogue of the World’s Natural History Collections

Hobern D, Asase A, Groom Q, Luo M, Paul D, Robertson T, Semal P, Thiers B, Woodburn M & Zschuschen E (2020) Advancing the Catalogue of the World’s Natural History Collections. v2.0. Copenhagen: GBIF Secretariat. https://doi.org/10.35035/p93g-te47.

The document Advancing the Catalogue of the World’s Natural History Collections is licensed under Creative Commons Attribution 4.0 Unported License.

https://doi.org/10.35035/p93g-te47

v2.0, March 2020

Updated from v1.0, published on 25 February 2020: Hobern D, Asase A, Groom Q, Paul D, Robertson T, Semal P, Thiers B & Woodburn M (2020) Advancing the Catalogue of the World’s Natural History Collections. v1.0. Copenhagen: GBIF Secretariat. https://doi.org/10.15468/doc-wnsx-ep77

The main changes from v1.0 are as follows:

Maryland sematophyllum moss (Sematophyllum marylandicum), collected by W.R. Buck in Ferncliff Natural Area, Ohiopyle State Park, Pennsylvania, United States. Photo 2018 New York Botanical Garden via The New York Botanical Garden Herbarium (NY), licensed under CC BY 4.0.

Collections staff and taxonomists collaborate as a truly global community. Valuable specimens are distributed between institutions in all parts of the world. Researchers visit these collections or borrow specimens as part of their work. Index Herbariorum (IH) is the directory of information on the world’s herbaria (addresses, contacts, specialties, size, etc.). It is a well-managed resource and highly regarded as a tool by the botanical community. No full equivalent exists globally for other natural history collections, although national/regional infrastructures such as the ALA collections pages, the iDigBio US Collections List, and the CETAF profiles serve similar roles. GBIF has recently integrated the Global Registry of Scientific Collections (GRSciColl) into its registry as a framework that can be extended with richer information curated by collections communities.

Taxonomic studies and other research projects normally depend on researchers (or their contacts) knowing which institutions hold relevant specimens or other materials. This is complicated by the history of expeditions and collecting activities. Specimens have been scattered across all continents. Only a small proportion of these specimens have been databased in forms that can be accessed through GBIF or other portals. A catalogue providing at least summary information on taxonomic and geographic scope for each collection could assist researchers in locating relevant materials.

The information needed to build the catalogue of collections closely matches the metadata required to publish a specimen dataset to GBIF and other portals. A record that describes a collection could be treated as a minimal first step, perhaps leading through processes such as Join The Dots and onwards to comprehensive digitisation. A comprehensive catalogue of such records could guide efforts to prioritise further digitisation, by highlighting collections with holdings of particular relevance or by assisting the development of collaborative digitisation networks like the ADBC Thematic Collection Networks.

Estimates of the number of specimens held by collections run into billions, but no definitive number exists. A catalogue could help to narrow these estimates and to assess the economic value of these irreplaceable holdings. This information may help to justify the scale of effort and funding needed to digitise collections and make their data accessible for universal, reliable and persistent use.

Accurate information on any collection can be used as a reference or as linked data associated with specimen records and other data objects. Users of specimen records need contextual information about the collection that holds the specimen, for example to communicate with collection managers about individual specimens, to offer corrections to specimen data, or simply to determine whether the collection is likely to hold quantities of similar specimens. It may be inefficient to embed all of this information within the specimen record. Holding a single authoritative copy assists with keeping the collection information current. The collection record may also contain information on taxonomic or geographic scope or other aspects that can resolve potential ambiguities within a specimen record. Links to current collection records will also enhance taxonomic publications referencing their materials. This is particularly important because catalogue numbers and other specimen identifiers used in publications may not link to digitised information on the specimens. Linking to the collection simplifies future access and may enable digital links to be inferred in future.

Although no complete catalogue of collections exists, the need for such information leads to such data repeatedly being published in different formats for different portals, project documentation, metadata for other data, etc. This duplication results in confusion as outdated information remains on the web. Mechanisms that always link to a single continuously updated version (and a version history) would address these issues.

A comprehensive directory could serve as a foundation for new tools that enhance taxonomic efforts and cooperation between all collection holders. One example might be the development of distributed loans systems or on-demand digitisation, as planned for the DiSSCo European Loans and Visits System (ELViS). A catalogue could also serve as a showcase for institutions to highlight their holdings and unique features, as in the visual concept shared by GBIF for collection pages. GBIF tracking and reporting on the use of biodiversity data in research publications could feed into new services that provide standard metrics and help collections to measure and report their impact.

Research value is primarily measured in terms of visibility and impacts from published literature. Natural history collections are poorly recognised by such measures and their importance as foundational research tools is almost hidden. Users of collections are regularly urged to cite specimens examined and reference the collection. However, citation is often lacking, incomplete or ambiguous. Research infrastructures such as OpenAIRE in Europe increasingly map not only linkages between researchers and publications but also datasets, projects, content providers and organisations. A catalogue could help to standardise citation of collections, making their impact visible through such knowledge graphs. Journals and editorial boards could be encouraged to require standard collection identifiers wherever collections are referenced.

Although this consultation aims to encourage the development of standardised information for all collections globally, each country or region may have needs or uses for this same information to in local applications and services. It is important to identify a range of these needs and to make sure they are addressed as part of a collaborative solution. An inclusive approach will bring incentives to work together to make information on each catalogue as complete, current and accurate as possible. Requirements are relatively well understood from Europe (e.g. DiSSCo) and the United States (e.g. iDigBio), but other regions may have subtly or significantly different needs.

The scope for the catalogue needs to be defined. The core use case under consideration is the listing and description of collections holding preserved biological specimens, referred to here as "natural history collections". The consultation will focus on developing a solution that is robust and effective for natural history collections, but it is valuable to explore needs and opportunities around other types of natural science collection. Some of these may fit readily within the scope of the catalogue. In other cases, work on the catalogue may offer benefits to these other communities. Note in particular: 1) many institutions hold both biological and geological collections and may manage these as a unified whole; 2) DiSSCo includes geological collections within its scope, and other networks such as iDigBio include at least paleontological collections; 3) GRSciColl was established to hold records on any scientific collection; and 4) the TDWG Collection Description standard is extensible for different collection types.

Most collections are already identified by one or more collection codes and may have existing web identifiers (URLs, DOIs, etc.) in one or more databases. The catalogue may reuse one or other of these identifiers or may help to support a standardised scheme. GRSciColl exists to assist with standardisation of collection codes and machine-readable identifiers, but several other efforts are also in place. Unique identifiers for each collection will be important to maximise cross-linkage of information and standardise citation, but other existing identifiers should ideally resolve to the same information and be recognised as synonyms for the preferred identifiers.

Within IH, each herbarium record usually corresponds to an institution with its own unique collection code, street address, etc. Within zoology, museums are often structured as a set of collections with differing and possibly hierarchical taxonomic scope. Specimens collected on famous expeditions or by significant researchers may have their own identity and appear as special collections. As a result, curators and researchers may wish to refer to different (potentially overlapping) sets of specimens as separate collections with their own names, identifiers and descriptions.

The TDWG Collection Descriptions (CD) Interest Group is currently developing the CD standard for collection descriptions (evolving from the earlier TDWG Natural Collections Description (NCD) standard). Existing networks and institutional schemes use a variety of different formats or variants of metadata standards for their collection records, as a result of which interoperability between these resources (and hence data aggregation) is limited. To overcome this barrier, clarity is needed around factors such as preferred standards and vocabularies, mandatory fields and compatibility between information in different formats.

Information in the collection catalogue may be linked to a wide range of other biodiversity information (specimens, sequences, datasets, images, publications, etc.) to support information access and exploration.

The main value from the collection catalogue may appear in the information services that can be offered around the information managed. Considering these services may help to clarify the content requirements.

Existing information on collections is edited and maintained in different ways. IH allows herbaria to provide or edit their records and offers support for herbaria to provide updates via email or other channels. Other communities such as national portals have other pathways for collections to provide or update information. Several tools help data publishers to create EML metadata for publishing data to GBIF and elsewhere. These could evolve to deliver collection records in preferred formats. The Integrated Publishing Toolkit (IPT) could be enhanced to offer collection records as one of the core record types that can be shared. This would allow collections either to publish one or more collection records as a small standalone dataset or collection networks to manage and publish a dataset comprising many collection records. Wikidata could also serve as a tool or platform for editing catalogue information and making it widely accessible and reusable.

IH is the best established catalogue servicing a large community of collections, but many other communities are important, including regionally or nationally focused efforts, such as CETAF’s institutional profiles, the web portals of iDigBio and the ALA, and the One World Collection initiative, and thematically aligned efforts, such as the World Directory of Culture Collections and the Global Genome Biodiversity Network portal. A comprehensive global catalogue should ensure that the needs of these different communities are met and support their continued operation and independence wherever is valued by collections. Understanding these requirements is essential in planning the technical implementation and governance of the catalogue.

GBIF has the mission to provide global-scale support for biodiversity informatics solutions and has expanded its Registry to host the data historically maintained as GRSciColl. GRSciColl content is incomplete and is best seen as a framework for expansion with richer collection metadata that properly represents the needs and interests of collections. GBIF can serve as the context for integration and deduplication of collection information from different sources and for interlinking this information for other biodiversity data. GBIF requires guidance on the best way to support the needs and branding of collections and their communities as it develops such services.

Most natural history collections maintain data on their specimens in a collection management system (CMS) such as Specify, Symbiota, EMu, DarWIN or BRAHMS. Some of these tools could develop to interface directly with the collection catalogue, providing up-to-date metadata and metrics.

The value of a shared commons-based resource can be maximised by ensuring that interfaces and APIs support the needs of all key stakeholder groups, including addressing issues around content delivery to the fullest extent possible in multiple languages. Some needs may be addressed by offering reusable client components that can be embedded in other applications.

The basic assumption is that each institution should have primary responsibility and control for information on its collections. However, it may be appropriate to delegate full or partial responsibility to thematic, regional or national communities that have data curators able to ensure the quality and standardisation of collection records. In some contexts, where institutions have for any reason not provided authoritative information, or do not have the resources to do so, there may be reason to allow or encourage a wider user base to contribute and improve collection records. In all cases, a version history is required for the information, so that users can understand and respond to changes made by others.

Communities such as IH, CETAF, ALA, iDigBio, etc. play an important role supporting collections and promoting standards-based practices. In many cases, these communities have a high level of understanding and participate closely in the development of biodiversity informatics solutions. Their roles and rights need to be well defined and supported in any integrated solution.

Biodiversity information infrastructures such as GBIF, DiSSCo, iDigBio and other national and regional platforms are usually funded in the context of broader open science goals for research infrastructures. Their participation can provide an important bridge between the needs of the collection communities and funding and expertise for informatics solutions. Roles and responsibilities must however be well defined to ensure that the needs of researchers and user communities are central. It is important to define clearly how these technical infrastructures can best participate in the overall solution, including demonstrating the benefits required to secure sustained funding for an integrated catalogue and for all the component parts.

A complex, commons-based solution will depend for its long-term success on a governance model that provides confidence to all parties that their interests are served and protected. The model should find the right balance between ensuring the health of the collaboration and minimising associated overheads in terms of meetings, reporting, etc.

Relatively little effort may be required for each institution to register and manage its own collection records. However, the stability of the system will depend on continued effort from these institutions or from other parties to correct errors and outdated information. There should be clear benefits or incentives encouraging stakeholders to contribute this effort. A key goal should be to ensure that the catalogue contributes usefully for the work of collection managers and taxonomists. Acknowledgement of contributions may also be valuable.

Funding needs will depend on other aspects of the approach adopted to build the catalogue. Costs will be higher if more central support is required to maintain the content. Even if the content is largely managed for free by the international community, sustaining a reliable infrastructure requires effort and long-term investment (see for example the CoreTrustSeal model for trusted repositories).