L. Shyamalmuscicapa @ crosswinds.net

http://www.crosswinds.net/~muscicapa/

Taxonomic databases - Some possibilities

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

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

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

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>

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

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

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

• 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

Available Systems Linnaeus II - ITIS - SpeciesAnalyst

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

DistributionDiversity

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

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

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)

Remote access

• Databases as well as collections• Remote examination of specimens

– web cams - manual / robotic

– field / lab

• Sharing and copyright issues• Quality control

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 )

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.

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.