Transcript 8 Winterton[cybertaxonomy]

Cybertaxonomy as a new paradigm for documenting
biodiversity: technological advances, opportunities
and the culture of taxonomy
Shaun L. Winterton
California State Collection of Arthropods, Sacramento, California, USA
How to describe so many new species in face of a
taxonomic impediment?
 Need: Increased speed of taxonomic description via semi-automating the more
tedious and redundant aspects of species description.
 Need: Paradigm shift away from traditional hand crafted taxonomic descriptions
towards character matrices.
 Need: Proliferation of use of web-based information from distributed databases in
species descriptions:
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image and specimen databases,
nomenclators,
name registration,
ontologies for standardized terminology,
GUIDs.
Project goals:
•3 year project funded by Australian Biological Resource
Study (ABRS) to complete describing Australian Stiletto fly
fauna
•Revisions of species rich genera of Australasian therevids:
•Acraspisa Kröber (100+ new spp.)
•Agapophytus Guérin-Meneville (50+ new spp.)
•Parapsilocephala Kröber (90+ new spp.)
•Formal descriptions of 250+ spp. cannot be done using
current method of taxonomy; not business as usual.
•Use of character matrices (e.g. Lucid Builder ver. 3.6; mX)
•Integration of web resources in electronic descriptions (i.e.
PDFs):
•Online image databases
•Specimen databases
•LSIDs
•Name registration (Zoobank)
 2008–2010:… next steps
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Pyle, R.L., Earle, J.L. & Greene, B.D. (2008) Five new species of the damselfish genus Chromis (Perciformes: Labroidei:
Pomacentridae) from deep coral reefs in the tropical western Pacific. Zootaxa 1671, 3–31.
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Johnson, N.F., Masner, L., Musetti, L., Van Noort, S., Rajmohana, K., Darling, D. C., Guidott, A., & Polaszek, A. (2008) Revision
of world species of the genus Heptascelio Kieffer (Hymenoptera: Platygastroidea, Platygastridae). Zootaxa 1776, 1–51.
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Deans A.R. & Kawada R. (2008) Alobevania, a new genus of neotropical ensign wasps (Hymenoptera: Evaniidae), with three
new species: integrating taxonomy with the World Wide Web. Zootaxa 1787: 28-44.
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Miller, J. A., Griswald, C.E. & Yin, C.M. (2009) The symphytognathoid spiders of the Gaoligongshan, Yunnan, China (Araneae,
Araneoidea): Systematics and diversity of micro-orbweavers. Zookeys, 11, 9–195.
 Lyubomir et al. (2010) Semantic tagging of and semantic enhancement to
systematics papers: Zookeys working examples. Zookeys 50: 1–16.
 Populating species descriptions with web resources by embedding PDFs with
html and LSIDs.
 Still hand crafted descriptions in a word processor!
 Data is not atomised, SDD compliant and is of limited use
without subsequent legacy XML mark-up.
 Natural Language Parsing of character matrices into taxon
descriptions.
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vSysLab
DELTA
Lucid
mX
…etc.
Neodialineura Mann: complete revision of 13
spp. in approx. 1/3 time taken normally.
Register names in Zoobank:
Links from PDF to high resolution
images in Morphbank
Material examined lists:
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Specimen database
Character matrix in Lucid Builder:
Character matrix in Lucid Builder:
Export of Natural Language Descriptions in XML to monographs and html fact sheets:
Interactive keys:
NLD parsing of character matrices:
•Nothing new, been around for long time, but adoption has not been
promoted or difficult to implement (e.g. DELTA)
•Highly standardized and frequently more concise.
•Atomized and thus machine readable.
•Greatest utility and power when used to describe large numbers of taxa
(single species descriptions vs. 100 species)
•Data is stored well (SDD) and reusable multiple times (e.g. interactive keys,
fact sheets, etc.), and updatable in non-original format.
•Character matrices: DELTA, LUCID, mX,… etc.
High resolution images of specimens:
Are lengthy descriptions really
necessary?
Still not immediately clear what the organism looks like…
A picture tells a thousand
words, or more…
Illustrators are expensive:
-time consuming [days, weeks months per plate]
-funds [salaries]
A picture tells a thousand
words, or more…
…technicians with imaging systems are not:
-rapidly produced [minutes,…hours per image]
-very detail with no artistic license
Conclusions
Continued societal need for biodiversity discovery (a.k.a. taxonomic
description).
Needed paradigm shift away from traditional hand-crafted taxonomic
descriptions towards more efficient methods.
Move towards wider usage of high resolution color images in publications,
focusing on diagnostic features and keys rather than lengthy descriptions.
Increased usage of web-based information from online distributed databases
in species descriptions
Conclusions
The individual parts are not novel, just integrating them in a seamless
way to increase efficiency in taxonomy is.
Most difficult part maybe presenting them in a convincing way that
taxonomists will want to use them.
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Mid-2009: Publication of Neodialineura revision in Zootaxa as
empirical test case: what have we learned?
Pros
•Increased speed to publication.
•Images are more detailed and provide much more information.
•Use of diagnostic characters provides more focus on identification
rather than morphological characterization ad infinitum.
•Data is stored well and reused often in standard format normalized
across outputs.
Mid-2009: Publication of Neodialineura revision in Zootaxa as
empirical test case: what have we learned?
Cons
•Some aspects cannot be more efficient without compromise of quality.
•Ontology lacking, so integration of datasets will remain problematic.
•Permanent storage of high resolution images still has risks.
•Many journals are not set up yet to seamlessly generate html rich PDF
documents.
•Editors are not familiar with techniques/tools yet, although many willing
to learn.
•Databases still ‘clunky’.
•Uptake by taxonomic community patchy, sometimes highly resistant
Mid-2009: Publication of Neodialineura revision in Zootaxa as
empirical test case: what have we learned?
Response by taxonomic community highly polarized
Where to now?
Journals need to focus more on enabling and facilitating web resources in their publications.
Scientific community is eager, but adoption will require further cases of successful empirical
use and actual guidance [no ‘how-to’ manuals for this stuff]…lots of activity analyzing
taxonomic process analyses, but no simple guides to aid transition.
Platform used is not the issue, rather it is seamless integration of data between platforms
essential through adoption of universal languages (e.g. SDD, Darwin core)
Any cybertaxonomic effort should intermittently self assess:
Is process efficient as far as time and quality?
Is data stored only once and then able to be reused as metadata (integration and lexicons)?
Does it value add to product by making use of web-based informatics resources?
Where to now?
Changes needed to codes to facilitate electronic descriptions?
How can we develop and implement (community agreed) standardized morphological
ontologies to speed process further?
Can a species description be simply a series of high resolution images of primary
type and diagnostic features maintained in a character matrix?
Acknowledgements
Funding support by National Science Foundation grant (DEB 0614213), the
Australian Biological Resource Study (ABRS).
Thank you to Rich Pyle (Zoobank), Debbie Paul (Morphbank), Matt Taylor
(CBIT), Gary Jolley-Rogers (TRIN), Gail Kampmeier (U of I) and Donald
Hobern (ALA) for their assistance.