The Systematics Association Special Volume Series 73 Edited by Gordon B. Curry University of Glasgow Glasgow, Scotland Chris J. Humphries The Natural History Museum London, UK Biodiversity Databases Techniques, Politics, and Applications CRC Press is an imprint of the Taylor & Francis Group, an informa business Boca Raton London New York TF1756.indb 3 3/26/07 1:12:06 PM CRC Press Taylor & Francis Group 6000 Broken Sound Parkway NW, Suite 300 Boca Raton, FL 33487‑2742 © 2007 by Taylor & Francis Group, LLC CRC Press is an imprint of Taylor & Francis Group, an Informa business No claim to original U.S. Government works Printed in the United States of America on acid‑free paper 10 9 8 7 6 5 4 3 2 1 International Standard Book Number‑10: 0‑415‑33290‑7 (Hardcover) International Standard Book Number‑13: 978‑0‑415‑33290‑3 (Hardcover) This book contains information obtained from authentic and highly regarded sources. Reprinted material is quoted with permission, and sources are indicated. 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Visit the Taylor & Francis Web site at http://www.taylorandfrancis.com and the CRC Press Web site at http://www.crcpress.com TF1756.indb 4 3/26/07 1:12:06 PM Contents Preface................................................................................................................................ vii The.Editors.......................................................................................................................... ix Contributors........................................................................................................................ xi Chapter 1 The.Global.Biodiversity.Information.Facility.(GBIF)..........................................................1 Meredith A. Lane and James L. Edwards Chapter 2 The.European.Network.for.Biodiversity.Information...........................................................5 Wouter Los and Cees H.J. Hof Chapter 3 Networking.Taxonomic.Concepts.—.Uniting.without.‘Unitary-ism’.................................13 Walter G. Berendsohn and Marc Geoffroy Chapter 4 Networking.Biological.Collections.Databases:.Building.a.European.Infrastructure..........23 Malcolm J. Scoble and Walter G. Berendsohn Chapter 5 A Comparison between.Morphometric.and.Artificial.Neural.Network.Approaches.to. the.Automated.Species.Recognition.Problem.in.Systematics.............................................37 Norman MacLeod, M. O’Neill and Steven A. Walsh Chapter 6 Automated Extraction of.Biodiversity.Data.from.Taxonomic.Descriptions.......................63 Gordon B. Curry and Richard J. Connor Chapter 7 The.Grid.and.Biodiversity.Informatics...............................................................................83 Andrew C. Jones Chapter 8 LIAS.—.An.Interactive.Database.System.for.Structured.Descriptive.Data.. of.Ascomycetes...................................................................................................................99 Dagmar Triebel, Derek Peršoh, Thomas H. Nash III, Luciana Zedda and Gerhard Rambold TF1756.indb 5 3/26/07 1:12:06 PM i Contents Chapter 9 Linking.Biodiversity.Databases:.Preparing.Species.Diversity.Information.Sources. by.Assembling,.Merging.and.Linking.Databases.............................................................111 Richard J. White Chapter 10 Priority.Areas.for.Rattan.Conservation.on.Borneo...........................................................129 Jacob Andersen Sterling, Ole Seberg, Chris J. Humphries, F. Borchsenius and J. Dransfield Index.................................................................................................................................181 Systematics Association Publications............................................................................189 TF1756.indb 6 3/26/07 1:12:06 PM ii Preface Since.the.first.desktop.computers.emerged.in.the.late.1970s.and.early.1980s,.the.power,. speed.and.storage.capacity.has.increased.radically,.especially.in.recent.years..Indeed,.the. whole.approach.to.computing.and.database.management.has.shifted.from.the.independent. researcher.keeping.records.for.a.particular.project.to.state-of-the-art.file.storage.systems,. presentation.and.distribution.over.the.World.Wide.Web..Taxonomists.are.natural.informa- tion.scientists.and.their.outputs.are.highly.desired.by.anyone.interested.in.biology.and. geology,.or.indeed.any.system.that.requires.retrieval.of.data..However,.to.make.systems. work.effectively,.it.is.necessary.to.bring.together.social.scientists,.programmers,.database. designers.and.information.specialists.to.achieve.the.right.political.setting.and.give.insti- tutions.the.right.platforms.for.dissemination.of.taxonomic.information..This.is.what.this. book.is.about. The.subject.matter.is.moving.at.a.very.fast.pace;.new.techniques.in.ways.of.recognition,. compilation.and.data.management.emerge.virtually.on.a.daily.basis..The.rules.are.chang- ing.and.moving.into.a.different.league..The.Intel.and.Motorola.chips.are.very.different. processors.compared.with.those.of.10.years.ago..Just.as.the.World.Wide.Web.gave.access. to.vast.amounts.of.information,.the.computing.community.is.changing.gear.and.raising.the. stakes.with.new.capabilities.for.storage.and.moving.information.around..New.initiatives.are. emerging.that.will.bring.together.new.agencies.in.the.world.of.bioinformatics..Chapter.1.by. Lane.and.Edwards.and.Chapter.2.by.Los.and.Hof.suggest.that.techniques.of.bioinformatics. should.be.upgraded.to.levels.achievable.at.global.and.European.standards..Those.chapters. by.Berendsohn.and.Geoffroy.and.Scoble.and.Berendsohn.suggest.that.networking.systems. are.trying.to.put.the.techniques.together. Within.biology,.computing.is.moving.to.a.new.generation.in.terms.of.function.and. phylo-informatics..Gone.are.the.days.of.looking.at.one.small.group.of.organisms;.molecu- lar.systematics,.sequence.storage.and.barcoding.of.all.major.groups.of.taxa.mean.that.sub- jects.such.as.blast.searching,.verification.and.delivery.systems.are.changing.the.language. of.databases..Coupled.with.the.notion.that.computers.are.far.more.useful.now.than.they. have.ever.been,.this.means.that.the.time.is.right.to.bring.together.a.group.of.professionals. in.the.field. Many.of.the.databases.dealt.with.are.still.handled.by.individual.taxonomists,.and.these. represent.the.cottage.industry.aspect.of.the.task..Therefore,.the.purpose.of.this.book.is.to. show.how.we.might.turn.the.cottage.industry.into.a.major.enterprise..At.the.same.time,.we. acknowledge.that.the.principles.of.database.design.were.created.by.the.pioneers.and.that. what.is.needed.is.evolution.rather.than.revolution.in.the.field.of.development..At.the.end. of.the.day,.we.want.to.be.able.to.have.access.to.the.materials.and.methods.without.neces- sarily.knowing.where.the.original.information.comes.from..This.has.been.referred.to.as. the.industrialization.of.information.amongst.Australian.colleagues..In.Australia,.there.is.a. checklist.of.angiosperms.online.(a.topic.we.had.hoped.to.cover),.but.nobody.really.knows. who.is.holding.the.record;.we.just.know.that.it.is.agreed.upon.throughout.Australia. TF1756.indb 7 3/26/07 1:12:07 PM ix The Editors Gordon B. Curry is.currently.reader.in.earth.sciences.in.the.Department.of.Geographi- cal.and.Earth.Sciences.at.the.University.of.Glasgow,.Scotland..Prior.to.joining.the.staff.at. the.University.of.Glasgow.in.1992,.he.was.a.Royal.Society.of.London.University.research. fellow.for.8.years..His.interests.include.palaeo-environmental.reconstruction.(in.particular. using.stable.isotopes),.taxonomy.and.computing..He.was.project.manager.for.the.UK’s.Nat- ural.Environment.Research.Council’s.Centre.of.Research.and.Training.in.Taxonomy.in.the. University.of.Glasgow.for.5.years,.until.1999..He.acted.as.tutor.for.the.Open.University’s. evolution.course.from.1985.to.2003.and.as.associate.lecturer.of.the.university.for.the.earth. and.life.course.in.Scotland.from.1996.to.2004. Dr..Curry.served.on.the.Council.of.the.Systematics.Association.from.1993.to.2005,. and.was.treasurer.from.1996.to.2005..He.also.served.as.the.Systematics.Association’s. representative.on.the.Council.of.the.Linnean.Society,.London,.from.1999.to.2003..In.1985. Dr..Curry.received.the.President’s.Award.of.the.Geological.Society.of.London.and.the. Clough.Award.from.the.Edinburgh.Geological.Society..In.1989.he.was.awarded.the.Wol- laston.Fund.from.the.Geological.Society.of.London. To.date,.Dr..Curry.has.prepared.over.120.publications.and.written.or.edited.five.books.. He.has.worked.with.seven.postdoctoral.research.fellows.and.research.assistants.and.super- vised.19.Ph.D..projects,.all.successfully.completed..Dr..Curry.has.organized.nine.interna- tional.conferences.in.Scotland,.England,.France,.Japan.and.Ireland..His.research.has.been. carried.out.primarily.across.Europe.and.in.New.Zealand. Christopher J. Humphries.is.merit.researcher.at.the.Department.of.Botany.at.the.Natural. History.Museum,.London,.and.visiting.professor.at.the.University.of.Reading..He.received. his.Ph.D..from.the.University.of.Reading..Dr..Humphries’s.interests.are.in.systematic.theory,. angiosperms,.historical.biogeography.and.area.selection.techniques.in.conservation.biol- ogy..Among.the.honours.and.awards.that.he.has.received.are.the.Bicentenary.Silver.Medal. 1980.(scientist.of.the.year.under.40.years),.the.Linnean.Society.of.London’s.OPTIMA.Sil- ver.Medal.for.1979.for.best.paper.on.European.taxonomy,.1979–1980,.and.the.gold.medal. for.botany.awarded.by.the.Linnean.Society.of.London.in.2001.. A.few.of.the.many.positions.held.by.Dr..Humphries.include.head.curator.of.the.Euro- pean.herbarium,.British.Museum.(natural.history),.London,.1974–1980;.principal.scientific. officer,.general.herbarium,.British.Museum.(natural.history),.1980–1990;.and.president.of. the.Systematics.Association,.2000–2003..He.has.served.as.associate.editor.of.the.Botani- cal Journal of the Linnean Society..Dr..Humphries.was.founder.and.editor.of.Cladistics,. the.journal.of.the.Willi.Hennig.Society,.and.he.is.on.the.editorial.board.of.the.Journal of Comparative Biology.. TF1756.indb 9 3/26/07 1:12:07 PM xi Contributors Walter G. Berendsohn Botanic.Garden.and.Botanical.Museum. Berlin–Dahlem Freie.Universität.Berlin Berlin,.Germany. F. Borchsenius Department.of.Biological.Sciences Ny.Munkegade Aarus,.Denmark Richard J. Connor Department.of.Computer.Science University.of.Strathclyde Glasgow,.Scotland Gordon B. Curry Department.of.Geographical.and.. Earth.Sciences University.of.Glasgow Glasgow,.Scotland J. Dransfield The.Herbarium Royal.Botanic.Gardens,.Kew Richmond,.Surrey,.UK James L. Edwards GBIF.Secretariat Copenhagen,.Denmark Marc Geoffroy Botanic.Garden.and.Botanical.Museum. Berlin–Dahlem Freie.Universität.Berlin Berlin,.Germany Cees H.J. Hof Institute.for.Biodiversity.and.Ecosystem. Dynamics.and.Zoological.Museum University.of.Amsterdam Amsterdam,.The.Netherlands Chris J. Humphries Department.of.Botany The.Natural.History.Museum London,.UK Andrew C. Jones School.of.Computer.Science Cardiff.University Cardiff,.Wales,.UK Meredith A. Lane GBIF.Secretariat Copenhagen,.Denmark Wouter Los Institute.for.Biodiversity.and.Ecosystem. Dynamics.and.Zoological.Museum University.of.Amsterdam Amsterdam,.The.Netherlands Norman MacLeod Department.of.Palaeontology The.Natural.History.Museum London,.UK Thomas H. Nash III School.of.Life.Sciences Arizona.State.University Tempe,.Arizona TF1756.indb 11 3/26/07 1:12:07 PM xii Contributors Jacob Andersen Sterling The.Natural.History.Museum.of.Denmark Botanical.Garden.and.Museum Copenhagen,.Denmark Dagmar Triebel Botanische.Staatsammlung.München Department.of.Mycology Munich,.Germany Steven A. Walsh Department.of.Palaeontology The.Natural.History.Museum London,.UK Richard J. White School.of.Computer.Science Cardiff.University Cardiff,.Wales,.UK Luciana Zedda Universität.Bayreuth Bayreuth,.Germany M. O’Neill Oxford.University.Museum.of.Natural. History Oxford,.UK Derek Peršoh Universität.Bayreuth Bayreuth,.Germany Gerhard Rambold Universität.Bayreuth Bayreuth,.Germany Malcolm J. Scoble Department.of.Entomology The.Natural.History.Museum London,.UK Ole Seberg The.Natural.History.Museum.. of.Denmark Botanical.Garden.and.Museum Copenhagen,.Denmark TF1756.indb 12 3/26/07 1:12:07 PM 1 The Global Biodiversity Information Facility (GBIF) Meredith A. Lane and James L. Edwards Contents Abstract.................................................................................................................................1 1.1. What.Is.GBIF?...........................................................................................................1 1.2. Why.Was.GBIF.Established?.....................................................................................3 1.3. The.GBIF.Contribution.to.Interoperability................................................................3 AbstrACt In.very.broad.strokes,.as.indicated.by.the.International.Union.for.the.Conservation.of.Nature. and.Natural.Resources.(IUCN).in.1980,.biology.can.be.thought.of.at.three.levels.of.organiza- tion:.molecular/genetic,.species.and.ecosystem..The.raw.data.of.the.molecular.level.are.nearly. all.digital,.as.are.many.of.those.at.the.ecosystem.level..However,.the.raw.data.of.the.species. level.(where.they.are.found,.the.physiology,.morphology,.etc.).are.almost.all.entirely.analogue. and.descriptive..However,.developments.in.informatics.at.each.of.these.levels.can.be.of.service. to.the.others..The.Global.Biodiversity.Information.Facility.(GBIF).was.established.to.enable. the.digital.capture.and.dissemination.of.data.related.to.natural.history.specimens.(includ- ing.those.in.culture.and.other.living.collections),.of.which.there.are.an.estimated.1.5.billion. in.at.least.6000.collections.worldwide..Another.of.GBIF’s.tasks.is.to.generate.an.electronic. catalogue.of.names.of.known.organisms,.which.is.the.element.required.to.enable.data.mining. across.all.three.levels.in.a.single.query..GBIF’s.work.at.the.species.and.specimen.levels.of. biological.organization.can.be.thought.of.as.unifying.the.biological.information.domain..In. addition,.it.provides.worldwide.coordination.among.the.many.ongoing.digitization.projects,. standards.development.and.networking.efforts.within.biodiversity.informatics. . WhAt Is GbIF? The.Global.Biodiversity.Information.Facility.has.a.mission.to.make.the.world’s.species’.biodi- versity.data.freely.and.universally.available.via.the.Internet..It.is.a.megascience.facility.—.in. part.because.the.GBIF.concept.was.developed.by.a.working.group.formed.by.the.Mega- .Science.Forum.(now.the.Global.Science.Forum).of.the.Organisation.for.Economic.Coop- eration.and.Development..More.importantly,.it.is.megascience.because.it.is.a.worldwide. endeavour.that.is.challenging.in.the.several.areas.of.information.science,.technology.and. sociology.as.well.as.biology. GBIF’s.efforts.are.focused.on.primary.scientific.biodiversity.data.at.the.specimen.and. species.levels.because.these.data,.unlike.most.molecular/genetic.and.much.ecological.data,. TF1756.indb 1 3/26/07 1:12:08 PM Biodiversity Databases are.not.in.digital.form..Nonetheless,.primary.biodiversity.data.of.these.types.are.critically. important.for.society,.science.and.a.sustainable.future. The.kinds.of.data.and.services.that.the.activities.of.GBIF.and.its.participants.around.the. world.will.provide.to.the.Web.over.the.next.few.years.include:. georeferenced.specimen.data; an.electronic.index.to.scientific.names.and.thus.to.the.scientific.literature.and.data- bases;.and a.means.to.link.together.data.from.disparate.sources.(e.g.,.DNA.sequences,.speci- men.illustrations,.morphological.characters,.species.observations.and.ecosystem. data).to.answer.complex.questions. Among.other.things,.georeferenced.species.occurrence.data.allow.for better.prediction.of.areas.most.suitable.for.wildlife.reserves; rapid.identification.of,.and.information.about,.control.of.invasive.species; prediction.of.patterns.of.spread.of.new.diseases; correlation. of. species. occurrence. with. ecological. parameters. and. therefore. the. ability.to.understand.effects.of.ecological.change;.and repatriation.of.biodiversity.information.to.countries.of.origin. Examples.of.the.many.sorts.of.applications.and.analyses.that.will.be.able.to.make.use. of.these.data.include: systematic,.taxonomic,.ecological.and.environmental.research; policy.and.decision.making;. natural.resource.management; conservation;.and bioprospecting.and.biotechnology. GBIF.is.a.distributed.facility,.comprising.a.network.of.participant.nodes.that share.biodiversity.data.openly.and.freely; use.common.standards.for.data.and.metadata; encourage.generation.of.additional.data;. ensure.that.data.providers.retain.control.of.their.data;.and share.a.common.philosophy. The.GBIF.philosophy.is.that.primary.scientific.data.should.be.available.to.all.the.dif- ferent.kinds.of.users,.no.matter.where.in.the.world.they.may.be.located..Analyses.can.be. applied.to.the.same.data.sets.to.answer.different.kinds.of.questions..By.reusing.data,.dupli- cation.of.effort.is.avoided..GBIF.is.also.working.towards.the.time.when.biological.data.and. information.from.all.levels.of.organization.(molecular/genetic,.species.and.ecosystems).can. be.interoperable.and.complex.questions.requiring.information.from.all.of.those.levels.can. be.asked.via.single.queries.through.a.single.Internet.portal..Furthermore,.different.portals. to.the.same.data.can.be.constructed,.depending.on.the.needs.of.particular.users. • • • • • • • • • • • • • • • • • • TF1756.indb 2 3/26/07 1:12:08 PM