Yde de Jong & Dave Roberts - ZooBank and EDIT: Towards a business model for ZooBank
EDITZooBank and EDITZooBank and EDITTowards a Business Model for ZooBankTowards a Business Model for ZooBankZoologicalZoologicalMuseumMuseumAmsterdamAmsterdamYde de Jong &Yde de Jong & Dave RobertsDave Roberts
EDITEU Networks of Excellence (NoE)EU Networks of Excellence (NoE)NoE objectives• Strengthen and spread excellence– Strengthening excellence by tackling the fragmentation ofEuropean research– Strengthen scientific and technological excellence gathering the expertise needed to provide Europeanleadership gathering the critical mass of resources– Spread excellence beyond the boundaries of its partnership
EDITEDITEDITToward the EEuropean DDistributed Institute of TTaxonomyNetwork of Excellence on TaxonomyNetwork of Excellence on Taxonomyhttp://www.e-taxonomy.net
EDITNetwork of Excellence on TaxonomyNetwork of Excellence on TaxonomyEDIT objectives• To prepare the building stones of a new researchinfrastructure• To coordinate institutions policies, and to integratetheir research activities– to improve delivery of taxonomy to its users, and– to transform the way how taxonomists work throughdevelopment of shared informatics tools, in order• To improve the quality and quantity of taxonomicresults
EDITThe expert basisThe infrastructure basisCoordinating researchInternet platformfor cybertaxonomyWeb-basedtaxonomyApplication inconservationTraining andpublic awarenessProductsResourcesCoordinationand integration12345678Making EDITScheme of the WP relationsScheme of the WP relations
EDITApplication of Taxonomy &ConservationInfrastructure basisExpert and Expertise basisManagement ActivitiesTraining & Capacity BuildingJoint Research ActivitiesMaintaining IntegrationEDIT integration schemeEDIT integration scheme
EDITZooBank within EDITZooBank within EDIT• WP 6 – Unifying revisionary taxonomy– establish prototype for web taxonomy (focused on some test-groups)– Implement light version of ZooBank• WP 3.2 – The taxonomic information infrastructure network– set up business model for ZooBank– write proposals for external funding of a full-implementation• Collaboration between WP 3.2 and WP 6– definition of requirements (scope and specs)– experimenting with aspects of ZooBank, like implementation of nomenclatural acts procedures and routines (=tools) for data submission data validation (quality checks) and standardization backwards indexing
EDIT• Investments in cyber-infrastructurecyber-infrastructure (IT-based infrastructure)increasingly essential for science and web-engineering– optimal cross-referencingcross-referencing: "biological information at your fingertips"– efficiencyefficiency: reducing the number of chains from describing a species toits (final) digitization– web-publishingweb-publishing: Godfray’s “unitary taxonomy”– web-taxonomyweb-taxonomy: collaborative revisionary work• Use of Semantic Web ApplicationSemantic Web Application as IT-based infrastructureThe Need of ZooBank - science caseThe Need of ZooBank - science case
EDIT• Species names are keywords information in biology is linked to,however, species names are not stable:– species concepts change through time– different species concepts are concurrently used between specialists– species concept can differ because of the observational context• How to prevent wrong or ambiguous returns (of data objects) whensearching on names?– how unambiguously interlink taxonomic concepts and classifications?– how effectively link species names to other data sources?• How to establish an objective (=stable) layer of name-objects toserve as unique and persistent identifiers (= critical meta-data)?– proceed from nominal taxa (+/- ZooBank model)– proceed from authoritative checklistsThe Need of ZooBank -The Need of ZooBank -stable name objects for referencingstable name objects for referencing
EDITZOBODATFauna EuropaeaExample of taxonomic ambiguity:Example of taxonomic ambiguity:Sphex domesticaSphex domestica (splitter / lumper case)(splitter / lumper case)
EDITFauna EuropaeaTITAN?nomen oblitumExample of taxonomic ambiguity:Example of taxonomic ambiguity:Musaria affinisMusaria affinis (complex case)(complex case)
EDITSplitting names from concepts for cross-referencing:• ZooBank taking care of the nomenclature• Other resources (ZooRec, CoL, ITIS, FaEu, FishBase, etc.) takingcare of the taxonomic concepts and classifications• However, taxonomic resources are relevant for initial uploading(backwards indexing)Subjective versus Objective referencingSubjective versus Objective referencing
EDITTaxonomic concepts & names merged withinZoological Record, CoL and other resources......Catalogueof LifeSet up of central name repository......:ZooBank- supervised by ICZN- standard for GUIDsuploadingCatalogueof LifeZool Record, CoL, etc. dealing with taxonomicconceptsconcepts and classificationsclassificationsNomenclator dealingwith namesnamesnames as criticalmetadata for conceptmapping andcross-linkingCatalogueof LifeBackwards indexing - Scientific modelBackwards indexing - Scientific model
EDITCatalogueof LifeZooBankZooBankINDEXINDEXExpert networkExpert networkSocietiesSocietiesResourcesResourcesBackwards indexing - Social modelBackwards indexing - Social model
Taxonomic Name ServerClassifications(SubjectiveSubjective reference totaxonomic concepts throughtime and among taxonomist)Names(ObjectiveObjective reference to names)Taxonomic indexingNomenclators& GSD’sSpecies check-lists & catalogsTaxon concept mappingDigital infrastructure(Databases; linkage to othergenetic data sources)Physical InfrastructureDNA bar-codingDNA-labfacilitiesDNAstorageDigital infrastructure(Databases; linkage to othercollection data sources)Physical Infrastructure(Collections)Specimen dataDigitalisation(Digitalisation of specimen info)GeneticresourcesSpecimendatabasesdb contentdb contentECATPhylogenetic /PhyloInformaticsDeep-morphology& Evo-DevoMorphoBanksData integrationNamesNames Identification MarshallerNamesOtherOtherLinking to otherLinking to otherresourcesresources
EDITEDIT WP 6 – Web based taxonomyEDIT WP 6 – Web based taxonomyEDIT WP6 is committed to making revisions (more thanthe names) available on the web.ZooBank will provide the taxonomic framework for theserevisions.EDIT will cover animals, plants and microbes.EDIT will work towards summary data extraction frompublished work without breach of copyright.
EDIT• Presumably yes:– considerable number of high quality resources exists• From Fauna Europaea it appeared that:– zoologists can be organized (positive social model)– zoological data show relatively few nomenclatural complications like:homonyms, duplicates, pro-parte synonymy, etcetera– there is wide acceptance for the web as a taxonomic medium– funding of a large, web-based taxonomic project is possible• However:– large numbers of species– decreasing number of expertsIs ZooBank scientifically feasible?Is ZooBank scientifically feasible?
EDITFunding ModelFunding Model• European Sciences Foundation– ESF Research Conferences - New call for Proposals in about April 2006 Single events (one or a few conferences) Topics at forefront of scientific research Interdisciplinary when appropriate Informal discussion of leading scientists and other participants• Dutch Science Foundation– Middle-Large Scale Research Facilities - Deadline September 2006– Large Scale Research Facilities - Deadline September 2007– Several other programs• National Science Foundation (USA)– Cyberinfrastructure (OCI) - NSF 05-625, November 30, 2006– Biological Infrastructure (DBI) - NSF 05-577, July 10, 2006
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