USE CASE ChecklistBank

Background Information:
ChecklistBank is a core infrastructure of Catalogue of Life (COL) and the Global Biodiversity Information Facility (GBIF). It has been co-developed and is governed jointly by COL and GBIF. It was launched in December 2020 after an extensive roadmap development phase. This was prior to the start of the BiCIKL project. During the BiCIKL project enhancements were made to ChecklistBank in relation to expanding the data pipelines, and developing tooling for users to map and harmonise taxonomic datasets to one another. ChecklistBank is a publishing platform and repository focused on taxonomic checklist and nomenclatural datasets including TreatmentBank datasets, classifications, species hypotheses, (M)OTUs and BINs from e.g. Barcode of Life, NCBI Taxonomy/ENA, UNITE/PlutoF. Data and tooling are also used to create custom taxonomic data products by COL and GBIF.

Context of Use of the service:

All information related to a biological species is tied to its name. Combining information from different sources about a species is impossible without the unification of taxonomic names across various information sources. ChecklistBank offers access to authoritative taxonomic information, and provides avenues for harmonizing this information. ChecklistBank offers open access to taxonomic, nomenclatural, and species checklist datasets as well as mapping and harmonization tools and species list building functionalities for authoritative taxonomic products, such as the Catalogue of Life Checklist.

The Need:

ChecklistBank responds to the following needs:

• ChecklistBank provides an open data platform for the publishing and sharing of taxonomic checklist data, nomenclatural datasets, as well as policy relevant species and taon data sets, including TreatmentBank datasets, classifications, species hypotheses, (M)OTUs and BINs from e.g. Barcode of Life, NCBI Taxonomy/ENA, UNITE/PlutoF, amongst others;
• ChecklistBank offers a standardised interpretation of data. This facilitates the unification, comparison and harmonisation of taxonomic datasets;
  
• All datasets can be searched, browsed, downloaded or accessed programmatically via the ChecklistBank API;
  
• Data and tooling are also used to create custom taxonomic data products by COL and GBIF, such as the Catalogue of Life Checklist
  
• ChecklistBank is open for others to add data and use.

Added Value:

Having a global service for unifying and harmonizing taxonomic names is a very cost efficient activity not only for the scientific community, but also for policymakers, nations, multilateral policy initiatives, data infrastructures, and experts involved in nature conservation and management.

Competitive Advantage:

ChecklistBank is the single global open data repository covering all life on earth with a focus on publishing and sharing taxonomic checklist data, nomenclatural datasets, and other species/taxon related data in existence to date. It is meant to be a collaborative effort and supports the vision that major biodiversity data initiatives and infrastructures should revolve around a common and shared taxonomic service.

A qualitative upgrade on the current use of biodiversity data:

A common problem for users of biodiversity data is to combine data from different sources, such as literature, DNA sequences, Natural history collections, species occurrences and to be absolutely confident the information relates to the same biological group of organisms. ChecklistBank, and its authoritative taxonomic data products such as the Catalogue of Life Checklist, provides an avenue for a global quality assurance and quality control mechanism for species checklist building. Such a QA/QC mechanism is a much needed and fundamental function in order to gain trust in scientific data and results.

Exemplary Use of the Service:

The ChecklistBank tutorial provides 4 exercises to explore these tools: 

1. Explore the ChecklistBank repository: search, inspect and download checklists. 

2. Cross dataset search tool: look up the appearance of a particular scientific name in all data sources available in ChecklistBank. 

3. Name match tool: enables comparison of the COL Checklist with one or two other datasets in ChecklistBank in terms of taxon name matching. 

4. Dataset comparison tool: allows for comparison of two taxonomic datasets in ChecklistBank on a scientific name by scientific name basis.

Competencies and Skills that are needed to use the Service:

All data and functionalities of ChecklistBank are available through an API that supports machine to machine communication. At the same time, users can also use the API as well as a user interface to this functionality. ChecklistBank is oriented at users that are accustomed to working with biodiversity and species data. The Catalogue of Life public portal, https://catalogueoflife.org is more focused on a wider public of users.

Challenges for the Users:

As with any new development there is a small learning curve with ChecklistBank. For this reason we have developed and continue to develop detailed training material to aid users. In addition, we recognise different types of users. For those that are willing to share data to ChecklistBank we offer helpdesk support. We also offer different data standards and various formats in which data can be shared. In some cases we do offer assistance and custom scripts to transform data in the appropriate data standard. For users that are interested in getting data we do provide several helpdesk functions to assist (see below). For users that need custom data products, we can offer custom assistance in species list building services, taxonomic data mapping and harmonisation.

Users Role in the Service Development

Research Infrastructures are invited to join ChecklistBank governance to influence and fund the development roadmap. Individual user feedback is welcomed via support@catalogueoflife.org, can become a member of the API user email list (https://lists.gbif.org/mailman/listinfo/col-users), or can report bugs, provide comments and suggestions through Github: https://github.com/CatalogueOfLife/backend/issues/new. Occasionally workshops on ChecklistBank are also organised.