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Taxonomy and computers

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Presentation made in 2001 at the pre-Association of Tropical Biology meet in Bangalore. Main suggestion is for biologists to just contribute to the web at least in free text without needing to be …

Presentation made in 2001 at the pre-Association of Tropical Biology meet in Bangalore. Main suggestion is for biologists to just contribute to the web at least in free text without needing to be burdened by technology oor knowledge of computers

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  • 1. L. Shyamal muscicapa @ crosswinds.net http://www.crosswinds.net/~muscicapa/ Taxonomic databases - Some possibilities
  • 2. Database aims What 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
  • 3. 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
  • 4. 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
  • 5. 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>
  • 6. Other Data Elements
    • Literature
    • 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
  • 7. 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
  • 8. Database XML/text Webserver Web-browser Applets internet
    • Applets to render distribution maps
    • Applets to generate keys
    • Interactive identification programs
    • Applets to submit data
    • Search
    • Query
    • Filter
    • Edit
    • Enter
    Webserver
  • 9.
    • 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
  • 10. Available Systems Linnaeus II - ITIS - SpeciesAnalyst
  • 11. Character matrices automated key generation cladistic analysis Metadata - characters - states(ordinal/nominal), weightage Weights c2 > c1 > c3 > c4 > c5 c2 (s1,s4) (s2,s3,s5) c1 s1 s4 c3 s3 (s2,s5) c5 s2 s5
  • 12. Distribution Diversity
  • 13. Propylea 14-punctata The 14-spot ladybird http://www.wbrc.org.uk/general/maps.htm 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
  • 14. 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 Biology http://www.epress.com/w3jbio/vol3/Adsavakulchai/index.html Automated Identification
  • 15.  
  • 16. 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)
  • 17. Remote access
    • Databases as well as collections
    • Remote examination of specimens
      • web cams - manual / robotic
      • field / lab
    • Sharing and copyright issues
    • Quality control
  • 18. 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 )
  • 19. 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 .
  • 20. 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.