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ZooBank and EDITZooBank and EDIT

Towards a Business Model for ZooBankTowards a Business Model for ZooBank

Zoological Zoological MuseumMuseum

Amsterdam Amsterdam

Yde de Jong & Yde de Jong & Dave RobertsDave Roberts

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EU Networks of Excellence (NoE)EU Networks of Excellence (NoE)

NoE objectives

• Strengthen and spread excellence

– Strengthening excellence by tackling the fragmentation of

European research

– Strengthen scientific and technological excellence

gathering the expertise needed to provide European

leadership

gathering the critical mass of resources

– Spread excellence beyond the boundaries of its partnership

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Toward the EEuropean DDistributed Institute of TTaxonomy

Network of Excellence on TaxonomyNetwork of Excellence on Taxonomy

http://www.e-taxonomy.net

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Network of Excellence on TaxonomyNetwork of Excellence on Taxonomy

EDIT objectives

• To prepare the building stones of a new research infrastructure

• To coordinate institutions policies, and to integrate

their research activities– to improve delivery of taxonomy to its users, and

– to transform the way how taxonomists work through development of shared informatics tools, in order

• To improve the quality and quantity of taxonomic

results

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The expert basis

The infrastructure basis

Coordinating research

Internet platform for cybertaxonomy

Web-basedtaxonomy

Application inconservation

Training and public awareness

ProductsResourcesCoordinationand integration

1

2

3

4

5

6

7

8

Making EDIT

Scheme of the WP relationsScheme of the WP relations

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Application of Taxonomy & Conservation

Infrastructure basis

Expert and Expertise basis

Management Activities

Training & Capacity Building

Joint Research Activities

Maintaining Integration

EDIT integration schemeEDIT integration scheme

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ZooBank 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

Business Model - elements (draft)Business Model - elements (draft)

System modellingSystem modelling(data integrity, rules)(data integrity, rules)

InterconnectivityInterconnectivity(infrastructure & LSIDs)(infrastructure & LSIDs)

Database contentDatabase content(long-term maintenance)(long-term maintenance)

Expert accessExpert access(on-line registry, roles)(on-line registry, roles)

Technical modelTechnical model Scientific modelScientific model

ICZN re-definitionICZN re-definition(electronic application)(electronic application)

Resource identificationResource identification(backwards indexing)(backwards indexing)

Catalogue

of Life

StandardisationStandardisation(authorship, spelling, gender)(authorship, spelling, gender)

Expert networkExpert network(validation, consensus)(validation, consensus)

Social modelSocial model

♀♂

öœoe

End-user applicationsEnd-user applications

Web publishingWeb publishing

Web-based taxonomyWeb-based taxonomy

Dissemination modelDissemination model

Publication modelsPublication models

Electronic resourceElectronic resource

Copyright & citationCopyright & citation

© ® ℗

ƒ $ £ €

FinancialFinancialprofitsprofits

Funding Funding modelsmodels

Financial modelFinancial model

Cost recoveryCost recovery

Exploitation Exploitation modelmodel

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• 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 to

its (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 infrastructure

The Need of ZooBank - science caseThe Need of ZooBank - science case

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© Frank van Harmelen

contentcontent

referencereference

applicationsapplications

usersusers

Semantic Web Application - architectureSemantic Web Application - architecture

HOW

TO

CONNECT

IT

ALL

?

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contentcontent

referencereference

applicationsapplications

usersusers

contentcontent

referencereference

applicationsapplications

usersusers

open standardsopen standards

open standardsopen standards

© Frank van Harmelen

Open Reference Networks ArchitectureOpen Reference Networks Architecture

Role of ZooBank

as a 'nomenclator'for referencing

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• 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) when searching 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 to

serve as unique and persistent identifiers (= critical meta-data)?– proceed from nominal taxa (+/- ZooBank model)

– proceed from authoritative checklists

The Need of ZooBank - The Need of ZooBank - stable name objects for referencingstable name objects for referencing

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ZOBODAT

Fauna Europaea

Example of taxonomic ambiguity: Example of taxonomic ambiguity: Sphex domestica Sphex domestica (splitter / lumper case)(splitter / lumper case)

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Fauna Europaea

TITAN

?

nomen oblitum

Example of taxonomic ambiguity:Example of taxonomic ambiguity:Musaria affinis Musaria affinis (complex case)(complex case)

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Splitting names from concepts for cross-referencing:

• ZooBank taking care of the nomenclature

• Other resources (ZooRec, CoL, ITIS, FaEu, FishBase, etc.) taking

care of the taxonomic concepts and classifications

• However, taxonomic resources are relevant for initial uploading

(backwards indexing)

Subjective versus Objective referencingSubjective versus Objective referencing

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Taxonomic concepts & names merged within Zoological Record, CoL and other resources......

Catalogue

of Life

Set up of central name repository......:

ZooBank- supervised by ICZN- standard for GUIDs

uploadingCatalogue

of Life

Zool Record, CoL, etc. dealing with taxonomic conceptsconcepts and classificationsclassifications

Nomenclator dealing with namesnames

names as critical

metadata for concept

mapping and

cross-linking

Catalogue

of Life

Backwards indexing - Scientific modelBackwards indexing - Scientific model

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Catalogue

of Life

ZooBankZooBankINDEXINDEXExpert networkExpert networkSocietiesSocietiesResourcesResources

Backwards indexing - Social modelBackwards indexing - Social model

Taxonomic Name Server

Classifications(SubjectiveSubjective reference to

taxonomic concepts through time and among taxonomist)

Names(ObjectiveObjective reference to names)

Taxonomic indexing

Nomenclators& GSD’s

Species check-lists & catalogs

Taxon concept mapping

Digital infrastructure(Databases; linkage to other

genetic data sources)

Physical Infrastructure

DNA bar-coding

DNA-labfacilities

DNAstorage

Digital infrastructure(Databases; linkage to other

collection data sources)

Physical Infrastructure(Collections)

Specimen data

Digitalisation(Digitalisation of specimen info)

Genetic resources

Specimendatabases

db content

db content

ECAT

Phylogenetic /PhyloInformatics

Deep-morphology& Evo-Devo

MorphoBanks

Data integration

Names

Names Identification Marshaller

Names

Other

Other

Linking to other Linking to other resourcesresources

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EDIT WP 6 – Web based taxonomyEDIT WP 6 – Web based taxonomy

EDIT WP6 is committed to making revisions (more than the names) available on the web.

ZooBank will provide the taxonomic framework for these revisions.

EDIT will cover animals, plants and microbes.

EDIT will work towards summary data extraction from published work without breach of copyright.

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• 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 experts

Is ZooBank scientifically feasible?Is ZooBank scientifically feasible?

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Funding 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