Our Discovery Mission
Our mission, should we choose to accept it, is to discover and document all remaining Australian species of plants, animals, fungi and other organisms ... in a generation.
Part 3 - Whiteboards
The ideas below have been contributed to the whiteboard for discussion during the roundtable breakouts. You can add to them on the Whiteboard ideas page
Roundtable 5: What informatics structures, processes and programs do we need to support our mission?
Taxonomy and informatics are no longer separable. Almost all traxonomists now use a wide range of informatics tools in their day-to-day work, including online taxonomic checklists and nomenclators such as are provided by ABRS, occurrence records in the ALA and GBIF, online repositories of type images and information, and online sequence repsoitories and analysis tools. This workshop will examine the informatics toolkit available to taxonomists and ask the questions:
What more do we need?
Are our exisitng tools comprehensive enough, and integrated enough?
What's the next big thing we need to be aware of (or perhaps build)?
A tool for compiling a synonymy for taxa at every level in a family or genus I am revising. This is a "full synonymy" in the sense of Hj. Eichler's manuals for Contrib. Herb . Australiensis and Brunonia and Leenhouts's Guide to Practice of Herbarium Taxonomy. For vascular plants we have the
Austrtalian Plant Names Index APNI developed out of Aust National Herbarium which feeds into the international equivalent IPNI. From that the Australian Plant Census sources much of its data.
APNI has been compiled from scanning all references to taxa across the Australian literature. A huge task.
As a specialist compiling revisions I want a web space or app with a facile front end in which I can create a revised full synonymy for each genus, species and subspecies or variety. A drag and drop approach from APNI would be ideal.
Outputs provided (1) that can be pasted en bloc for each taxon into my ms for publication of my new taxonomy (versatile arrangement and formatting obviously desirable, but not essential in first instance)m, and (2) enabling upload to APNI (via admin review no doubt) once the taxonomy has been published.
We need born-digital, born-public specimens: born with a unique identifier at time of collection (e.g., through an app as simple as iNaturalist), georeference, photograph, standardized trait annotations, and current (temporary) physical location, (and Nagoya compliance information), independently of identification / name concept.
Ability to consistently link and discover data
Greater community understanding of biodiversity data and its limitations
Open data (not redacted information which causes more issues...)
Up-to-date authority lists
Funding for imaging of specimens and coordinated online repository
Tools for efficient collections management and sharing data
All the whiteboards present handy ideas to make info more accessible. To add to that, how about we enliven taxonomic info by routinely incorporatiing it into databases which can project the info graphically? For example, I have been doing that via pop-ups attached to digital phylogenetic trees.
3D scans of type material (at appropriate resolution) & experts or simple tools/programs we can access to manipulate the scans, zoom in to features, quickly measure specimens.
Is it possible to scan new specimens & use AI/machine learning to compare new unidentified specimens with scans of type material and spit out differences & similarities? Then taxonomist evaluates result.Currently scans are expensive & steep learning curve for processing scans. Limited experts available?
A database of holotype images would be very beneficial. With some international collections being severely short-staffed, it can take more than six months to obtain images of a holotype or paratype. Travelling to locations where holotypes are housed can be costly and time inefficient. By having a database with holotypes and associated close up images would save lots of precious time.
Two things that would really help me in my work now (which is related to indexing names and publication details on behalf of the botanical community):
(1) Being able to harvest the necessary parts of taxonomic publications (i.e. names and their statuses, authors, bibliographic details, type and etymological information) for electronic ingestion into the National Species List;
(2) Automated notification of changes to state/territory censuses when a taxon is added, deleted or changed in status. (Note that this is distinct to notifications based on raw specimen records; censuses represent a curated and considered list of the taxa that a given jurisdiction regards as being present, which is important for legislation relating to threatened species, weeds etc.)
1. Online depositories of type images and historical texts would be incredibly valuable.
2. National database of current 'authorized/approved' taxonomic experts to fast-track finding relevant species experts and to highlight knowledge gaps.
3. Providing a TA SOP for uploading annotated sequence data to Genbank as this is often completing this task is way harder than it should be.
More (or better) ideas? Add them here.