Taxonomy and computers
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L. Shyamalmuscicapa @ crosswinds.net
http://www.crosswinds.net/~muscicapa/
Taxonomic databases - Some possibilities
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Database aimsWhat to store ? To what purpose ?
• Species information – Taxonomic - structure, naming, literature, identification
• Collection (Observations) information – identified (linked to species)
– unidentified (linkable )
• Analysis and reporting– searching
– identification-key generation (with geographic/taxonomic bounds)
– phylogenetic analyses
– biological studies
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The case for plain text• Knowledge level of an index-card user
• Not tied to software (applications / OS)
• Ease of conversion
• Searchable – with readily available tools and search engines
– Can be filtered in advanced ways
• usable with systems that extract data from natural language (eg: Finnish Lepidoptera database draws distribution maps based on country names)
• In the absence of entry tools - entry needs care
• greater storage
• the web is a text based database
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tagged fields - a taxonomic entry in HISPID format { CBG_NO 7702638, COLL_YEAR 1975, COLL_MONTH 'JUL', COLL_DAY 20, COLLECTOR 'Crisp, B.C.', FIELD_NUMBER '383', COUNTRY 'AUSTRALIA', REGION_CODE 'WHA', LOCALITY 'Great Sandy Desert; Wolf Creek Meteorite crater.', LAT_DEG 19, LAT_MIN 10, LAT_DIR 'S', LONG_DEG 127, LONG_MIN 48, LONG_DIR 'E', GEOCODE_SOURCE 1, HABITAT_A 'Red sand dune.', NOTES_A 'Shrub to 1 m.', HERBARIUM_ITEMS '1', HERBARIUM_MAT 'H', DETERMINED 'Crisp, M.D.', SUPRA_FAMILY 'PD', FAMILY 'FABACEAE', GENUS 'Jacksonia', SPECIES 'aculeata', SP_AUTHOR 'W.V. Fitzg.',}
Royal Botanic Gardens, Sydney
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Tagged Data<specimen id=“AB1001”>
<collector> X </collector>
<location latitude=“12.83N” longitude=“77.5S”date=“19DEC1999”>
Bangalore
</location>
<comments>feeding on ant pupae</comments>
<identification>
<determined> Y </determined>
<family>Calliphoridae</family>
<genus>Bengalia</genus>
<species>lateralis</species>
</identification>
<image href=“http://…”>wing image</image>
</specimen>
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Other Data ElementsLiterature
Descriptions - other notes, biology
links to pictures
links to sound
Maps - locations + time
Biochemical/sequence data
Cross references
to other species - hosts - predator - parasite, web sites, etc.
Other databases
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Extensible Markup Language
• XML - open specification (= ‘generic HTML’ )
• advantages of plain text + metadata
• checking and validation can be automated
• searching/querying/filtering the data is easy
• standard schema can be adopted
• can be used on the internet via browser
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DatabaseXML/text
Webserver
Web-browserApplets
internet
•Applets to render distribution maps•Applets to generate keys•Interactive identification programs•Applets to submit data
•Search•Query•Filter•Edit•Enter
Webserver
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• DELTA Description language for taxonomy– M. J. Dallwitz and T. A. Paine
• XDELTA (XML)
• Linnaeus II (ETI) UNESCO/University of Amsterdam
• TDWG - Taxonomic Database Working Group
• ITIS - USDA
• host-plant database NHM- public domain
• WCMC Red-data list
Current standards and models
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Available Systems Linnaeus II - ITIS - SpeciesAnalyst
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Character matricesautomated key generation
cladistic analysis
Character 1 Character 2 Character 3 Character 4 Character 5Species 1 1 1 0 1 -Species 2 1 2 1 2 1Species 3 1 2 0 2 -Species 4 0 1 1 2 -Species 5 1 2 1 2 -
Metadata - characters - states(ordinal/nominal), weightage
Weights c2 > c1 > c3 > c4 > c5
c2(s1,s4)
(s2,s3,s5)
c1s1
s4
c3
s3
(s2,s5) c5s2
s5
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DistributionDiversity
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http://www.wbrc.org.uk/general/maps.htm
Propylea 14-punctataThe 14-spot ladybird
Grid size 2x2Km
black dots represent records since 1995;
The hashed square is an older record given only to 10km by 10km accuracy.
Local Distributions
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Adsavakulchai ,S., V. Baimai, W. Prachyabrued, P. J.Grote and S. Lertlum (1998) Morphometric study using wing image analysis for identification of the
Bactrocera dorsalis complex (Diptera : Tephritidae).
The World Wide Web Journal of Biologyhttp://www.epress.com/w3jbio/vol3/Adsavakulchai/index.html
Automated Identification
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Automated Data acquisition
• optical character recognition (OCR)• extraction of species and character information
from well-structured descriptions in old literature (eg. Fauna of British India)
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Remote access
• Databases as well as collections• Remote examination of specimens
– web cams - manual / robotic
– field / lab
• Sharing and copyright issues• Quality control
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Online references
Digital Taxonomy Resources ( http://www.geocities.com/RainForest/Vines/8695/ )
ITIS -USDA Taxonomists workbench ( http://itis.usda.gov/ )
SpeciesAnalyst XML ( http://habanero.nhm.ukans.edu/ )
ETI, University of Amsterdam – World Biodiversity Database ( http://www.eti.uva.nl )
DELTA ( http://www.keil.ukans.edu/delta/, http://www.biodiversity.uno.edu/delta/ )
XDELTA ( http://www.bath.ac.uk/~ccslrd/delta/index.html )
Software for Field biologists ( http://www.euronet.nl/users/mbleeker/prog/soflis_e.html )
Key generation ( http://prod.library.utoronto.ca/polyclave/, http://www.lucidcentral.com )
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Data Standards
Conn, B. (ed.). (1996). HISPID3. Herbarium information standards and protocols for interchange of data. Version Three. Sydney: Royal Botanic Gardens. 126 pp.
Dallwitz, M.J., T.A. Paine & E.J. Zurcher. (1993). DELTA user's guide. A general system of processing taxonomic descriptions. Fourth ed.,Canberra CSIRO Division of Entomology. 136pp.
Dallwitz, M. J. (1980). A general system for coding taxonomic descriptions. Taxon 29, 41–6.
Dallwitz, M. J. (1980). User’s guide to the DELTA system. A general system for coding taxonomic descriptions. CSIRO Aust. Div. Entomol. Rep. No. 13, 71 pp.
Dallwitz, M. J. (1984). User’s guide to the DELTA system: a general system for coding taxonomic descriptions. 2nd edition. CSIRO Aust. Div. Entomol. Rep. No. 13, 1–93.
Dallwitz, M. J., and Paine, T. A. (1986). User’s guide to the DELTA system: a general system for
processing taxonomic descriptions. 3rd edition. CSIRO Aust. Div. Entomol. Rep. No. 13, 1–106. Pankhurst, R. J. (1986). A package of computer programs for handling taxonomic databases.
CABIOS 2, 33–9.
Watson, L., Dallwitz, M. J., Gibbs, A. J. and Pankhurst, R. J. (1988). Automated taxonomic descriptions. Pp. 292-304 in: Hawksworth, D. L., Davies, R. G. & Bisby, F. A. (eds.), Prospects in Systematics. Clarendon Press, Oxford.
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Automated identification
• Yu, D.S., Kokko, E.G., Barron, J.R., Schaalje, G.B. & Gowen, B.E. (1992). Identification of ichneumonid wasps using image analysis of wings. Systematic Entomology, 17, 389-395.
• White, I.M. & Scott, P.R. (1994). Computerized information resources for pest identification : a review, pp.129-137 in : Hawksworth, D.L. (ed.), The Identification and Characterisation of Pest Organisms.. CAB International, Wallingford, UK.
• Howell, V.D., Hoelmer, K., Norman, P. &Allen, T.(1982) Computer-assisted measurement and identification of honey bees (Hymenoptera : Apidae). Annals of the Entomological Society of America, 75, 591-594.
• Frampton, E.R., Fry, J., Stephenson, B.P. & Cowley, J.M. (1991). A Computerised system for data management during a fruit fly outbreak. The International Symposium on the Biology and control of fruit flies.