Cybertaxonomy as a new paradigm for documenting Cybertaxonomy as a new paradigm for documenting biodiversity: technological advances, opportunities biodiversity: technological advances, opportunities and the culture of taxonomyand the culture of taxonomy

Shaun L. WintertonShaun L. WintertonCalifornia State Collection of Arthropods, Sacramento, California, USACalifornia State Collection of Arthropods, Sacramento, California, USA

How to describe so many new species in face of a taxonomic impediment?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:

image and specimen databases, nomenclators, name registration, ontologies for standardized terminology, GUIDs.

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:

image and specimen databases, nomenclators, name registration, ontologies for standardized terminology, GUIDs.

•3 year project funded by Australian Biological Resource 3 year project funded by Australian Biological Resource Study (ABRS) to complete describing Australian Stiletto fly Study (ABRS) to complete describing Australian Stiletto fly faunafauna

•Revisions of species rich genera of Australasian therevids:Revisions of species rich genera of Australasian therevids:•AcraspisaAcraspisa Kröber (100+ new spp.) Kröber (100+ new spp.)•AgapophytusAgapophytus Guérin-Meneville (50+ new spp.) Guérin-Meneville (50+ new spp.)•ParapsilocephalaParapsilocephala Kröber (90+ new spp.) Kröber (90+ new spp.)

•Formal descriptions of 250+ spp. cannot be done using Formal descriptions of 250+ spp. cannot be done using current method of taxonomy; not business as usual.current method of taxonomy; not business as usual.

•Use of character matrices (e.g. Lucid Builder ver. 3.6; Use of character matrices (e.g. Lucid Builder ver. 3.6; mXmX)) •Integration of web resources in electronic descriptions (i.e. Integration of web resources in electronic descriptions (i.e. PDFs): PDFs):

•Online image databasesOnline image databases•Specimen databases Specimen databases •LSIDsLSIDs•Name registration (Zoobank)Name registration (Zoobank)

Project goals:Project goals:

2008–2010:… next steps 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.

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.

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.

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.

2008–2010:… next steps 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.

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.

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.

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. vSysLab DELTA Lucid mX …etc.

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. vSysLab DELTA Lucid mX …etc.

NeodialineuraNeodialineura Mann: complete revision of 13 Mann: complete revision of 13 spp. in approx. 1/3 time taken normally.spp. in approx. 1/3 time taken normally.

Register names in Zoobank:Register names in Zoobank:

Links from PDF to high resolution Links from PDF to high resolution images in Morphbankimages in Morphbank

Material examined lists:

• Specimen database

Material examined lists:

• Specimen database

Character matrix in Lucid Builder:Character matrix in Lucid Builder:

Character matrix in Lucid Builder:Character matrix in Lucid Builder:

Export of Natural Language Descriptions in XML to monographs and html fact sheets:Export of Natural Language Descriptions in XML to monographs and html fact sheets:

Interactive keys:Interactive keys:

NLD parsing of character matrices:NLD parsing of character matrices:•Nothing new, been around for long time, but adoption has not been Nothing new, been around for long time, but adoption has not been promoted or difficult to implement (e.g. DELTA)promoted or difficult to implement (e.g. DELTA)

•Highly standardized and frequently more concise.Highly standardized and frequently more concise.

•Atomized and thus machine readable.Atomized and thus machine readable.

•Greatest utility and power when used to describe large numbers of taxa Greatest utility and power when used to describe large numbers of taxa (single species descriptions vs. 100 species)(single species descriptions vs. 100 species)

•Data is stored well (SDD) and reusable multiple times (e.g. interactive keys, Data is stored well (SDD) and reusable multiple times (e.g. interactive keys, fact sheets, etc.), and updatable in non-original format.fact sheets, etc.), and updatable in non-original format.

•Character matrices: DELTA, LUCID, Character matrices: DELTA, LUCID, mXmX,… etc.,… etc.

High resolution images of specimens:High resolution images of specimens:

Are lengthy descriptions really Are lengthy descriptions really necessary?necessary?

Still not immediately clear what the organism looks like…Still not immediately clear what the organism looks like…

A picture tells a thousand A picture tells a thousand words, or more…words, or more…

Illustrators are expensive:Illustrators are expensive:-time consuming [days, weeks months per plate]-time consuming [days, weeks months per plate]-funds [salaries]-funds [salaries]

A picture tells a thousand A picture tells a thousand words, or more…words, or more…

……technicians with imaging systems are not:technicians with imaging systems are not:-rapidly produced [minutes,…hours per image]-rapidly produced [minutes,…hours per image]-very detail with no artistic license-very detail with no artistic license

ConclusionsConclusions

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

ConclusionsConclusions

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.

……

Mid-2009: Publication of Mid-2009: Publication of NeodialineuraNeodialineura revision in Zootaxa as revision in Zootaxa as empirical test case: what have we learned? empirical test case: what have we learned?

ProsPros•Increased speed to publication.Increased speed to publication.•Images are more detailed and provide much more information.Images are more detailed and provide much more information.•Use of diagnostic characters provides more focus on identification Use of diagnostic characters provides more focus on identification rather than morphological characterization rather than morphological characterization ad infinitumad infinitum..•Data is stored well and reused often in standard format normalized Data is stored well and reused often in standard format normalized across outputs.across outputs.

ConsCons•Some aspects cannot be more efficient without compromise of quality.Some aspects cannot be more efficient without compromise of quality.•Ontology lacking, so integration of datasets will remain problematic.Ontology lacking, so integration of datasets will remain problematic.•Permanent storage of high resolution images still has risks.Permanent storage of high resolution images still has risks.•Many journals are not set up yet to seamlessly generate html rich PDF Many journals are not set up yet to seamlessly generate html rich PDF documents.documents.•Editors are not familiar with techniques/tools yet, although many willing Editors are not familiar with techniques/tools yet, although many willing to learn.to learn.•Databases still ‘clunky’.Databases still ‘clunky’.•Uptake by taxonomic community patchy, sometimes highly resistant Uptake by taxonomic community patchy, sometimes highly resistant

Mid-2009: Publication of Mid-2009: Publication of NeodialineuraNeodialineura revision in Zootaxa as revision in Zootaxa as empirical test case: what have we learned? empirical test case: what have we learned?

Response by taxonomic community highly polarized Response by taxonomic community highly polarized

Mid-2009: Publication of Mid-2009: Publication of NeodialineuraNeodialineura revision in Zootaxa as revision in Zootaxa as empirical test case: what have we learned? empirical test case: what have we learned?

Where to now?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?

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?

Where to now?Where to now?

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.