Existing collaborations and project plans

Alliance for Biodiversity Knowledge
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The alliance proposed at GBIC2 should serve as a mechanism for international stakeholders to cooperate in proposing, refining, agreeing and implementing shared projects. An open forum for such planning would increase opportunities for collaboration and sustainable development of tools and infrastructure. A key priority for the alliance should be to establish an effective model for supporting such project planning and implementation.

Although no such model is in place, biodiversity informatics initiatives are already partnering together on a range of projects that aim to expand cooperation and deliver solutions that can be adopted by all partners. It would be valuable to capture information on these activities to bring them to the attention of other parties that would benefit from a joint solution. Such projects may also serve as early candidates for wider adoption and support as proofs-of-concept for the alliance.

This thread is to highlight existing collaborative projects that aim to increase standardization and progress towards interoperability between stakeholders in biodiversity informatics. Please provide information on such collaborations, including goals, current partners, proposed deliverables and timelines, and pointers to other web resources.

Comments in questions other than English are welcome.

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Catalogue of Life Plus project

The Catalogue of Life has the mission to catalogue all known species as an authoritative consensus taxonomy produced by the global taxonomic community. Up to now it has completed peer-reviewed inclusion of nearly all extant species.

Many large institutional users (i.e. GBIF, EOL, ALA, Lifewatch) extend their copy of the catalogue with additional names and species to complete it to serve their own specific purpose. These disconnected efforts result in ‘taxonomic inconsistencies’ and cause confusion amongst users.

The CoL+ project seeks to replace these efforts with a shared, extended catalogue and complete the reviewed name coverage without sacrificing quality. Creating an open, shared, and sustainable consensus taxonomy to serve the proper linking of data in the global biodiversity information initiatives is the ultimate goal the project contributes to.

The goals for the Catalogue of Life Plus (CoL+) project are:

  1. creating both an extended and a strictly scrutinized taxonomic catalogue to replace the current GBIF Backbone Taxonomy and Catalogue of Life
  2. separating nomenclature (facts) and taxonomy (opinion) with different identifiers and authorities for names and taxa for better reuse
  3. providing (infrastructural) support to the completion and strengthening of taxonomic and nomenclature content authorities
  4. ensuring a sustainable, robust, and more dynamic IT infrastructure for maintaining the Catalogue of Life.

Specifically the project will establish a clearinghouse for taxonomy and nomenclature and rebuild all existing infrastructure of the Catalogue of Life including webservices, the portal and the software for the assembly of the catalogue and its editorial work.

Current partners

Catalogue of Life Plus is a collaboration between the Catalogue of Life, the Global Biodiversity Information Facility Secretariat,Naturalis Biodiversity Center and partners with financial support by the Netherlands Biodiversity Information Facility and the Netherlands Ministry of Education, Science, and Culture.

Relevance to alliance for biodiversity knowledge

Catalogue of Life Plus could be adopted as an alliance project (rather like the GA4GH “Driver Projects” with relevance to many of the components of the GBIO framework, in particular as the optimal area in which to develop models for the international Biodiversity Knowledge Network to develop a shared knowledge product, and of course the actual delivery of the central Taxonomic Framework.

The Catalogue of Life Plus project wishes to engage with national efforts to develop species lists and with other projects and institutions mobilising information on species names and treatments.

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Integrated Occurrence Data

The GBIO identified Integrated Occurrence Data as one of the components of the Evidence layer. This component recognises that different user communities, including taxonomists, biogeographers, ecologists, conservationists, and policymakers among others, need comprehensive access to all available evidence for the occurrence, and abundance, of any species in time and space. This need exists for studies at local or national scale just as much as for global analyses, since relevant data sources may be distributed anywhere.

Many data infrastructures (e.g. GBIF, ALA and other Living Atlas instances, iDigBio, OBIS, GGBN) harvest data frrom many relevant sources to build different indexes of species occurrence data. None of these is comprehensive - they each include a different subset of available data). They all process the data in different ways, so that the same underlying data may be represented with different identifiers, different flags and inconsistent interpretation in multiple indexes. Data publishers have difficulty tracing the use of their data through all these networks, and end users are unable easily to combine data indexed by different networks. Curation of data is hampered because so many incompatible versions are accessible.

GBIF, ALA, iDigBio and other infrastructures responsible for indexing occurrence data have started discussions to reduce variation between their processes and to explore unifying some or all steps. The ideal scenario is for every record of a specimen or other evidence of species occurrence to have a stable and unique identifier, a consistent interpretation at the global scale in terms of geography, taxonomy, etc., and additional properties relevant to the country, taxon, type of evidence, biome, etc., and for all communities to be able to use, reference and annotate this shared version of the data. If it is possible to deliver a consistent data management model of this kind, it will open the door for increased standardisation and functionality both in software for those who manage and publish data and in workbenches for accessing and analysing data.

Current partners

GBIF, the Atlas of Living Australia, iDigBio and DiSSCo have started to explore ways to align and possibly integrate their data processing pipelines. These partners are also exploring sources of funding to expand this effort.

Relevance to alliance for biodiversity knowledge

Delivering a consistent global approach to Integrated Occurrence Data would increase efficiency, transparency and sustainability for the partner institutions and simplify work on many other components identified in the Data and Understanding layers of the GBIO framework.

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International Committee on Taxonomy of Viruses (ICTV)

This recent Nature commentary from the organisers of the International Committee on Taxonomy of Viruses (ICTV) covers much of the same ground that discussions around the alliance have traced regarding both the need for ongoing support of the taxonomic endeavour as well as the importance of establishing effective incentives for expert contributions to the same. The classification and nomenclatural challenges they describe for viruses mirror those across other kingdoms, which is why we’re so keen to build on the collaboration between GBIF and UNITE on eDNA-based occurrences by extending it across other infrastructures with the help of ELIXIR, EBI-EMBL, SILVA and MGnify.

The call for “funders to give more priority to projects based on evolutionary biology and discovery…[to] harness the rapidly developing analytical tools and get involved in taxonomy.” This need is as just as urgent for other kingdoms as for viruses, highlighting how we may benefit from laying out a consolidated road map for larger, more interoperable and interdependent targets, even when efforts in individual domains remain of necessity more limited in scope.

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Sounds like an interesting part of the puzzle, but the webpage it links to went the way of the Dodo. Is there a new page?

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Thanks, @earthdoc - The only link I could find that had gone away was the one for the GBIO, which I’ve now corrected and repeat here:

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Hello Donald,

Yes, that is the one! Sorry for not specifying. Great looking plan. I’m beginning to see the arc of where you all have been and where you are now. I suspect that the Stakeholders Ontology in the other discussion might be a sweet spot for collaboration at the moment. More soon I hope.

Thanks!

John

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