1. EDIT
ZooBank and EDITZooBank and EDIT
Towards a Business Model for ZooBankTowards a Business Model for ZooBank
ZoologicalZoological
MuseumMuseum
AmsterdamAmsterdam
Yde de Jong &Yde de Jong & Dave RobertsDave Roberts

2. EDITEU 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

3. EDIT
EDITEDIT
Toward the EEuropean DDistributed Institute of TTaxonomy
Network of Excellence on TaxonomyNetwork of Excellence on Taxonomy
http://www.e-taxonomy.net

4. EDITNetwork 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

5. EDIT
The expert basis
The infrastructure basis
Coordinating research
Internet platform
for cybertaxonomy
Web-based
taxonomy
Application in
conservation
Training and
public awareness
ProductsResourcesCoordination
and integration
1
2
3
4
5
6
7
8
Making EDIT
Scheme of the WP relationsScheme of the WP relations

6. EDIT
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

7. 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

8. 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
♀
♂
ö
œ
oe
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 $ £ €
FinancialFinancial
profitsprofits
FundingFunding
modelsmodels
Financial modelFinancial model
Cost recoveryCost recovery
ExploitationExploitation
modelmodel

9. 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 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

10. EDIT
© Frank van Harmelen
contentcontent
referencereference
applicationsapplications
usersusers
Semantic Web Application - architectureSemantic Web Application - architecture
HOW
TO
CONNEC
T
IT
ALL
?

11. EDIT
contentcontent
referencereference
applicationsapplications
usersusers
contentcontent
referencereference
applicationsapplications
usersusers
open standards
open standards
open standards
open standards
© Frank van Harmelen
Open Reference Networks ArchitectureOpen Reference Networks Architecture
Role of
ZooBank
as a
'nomenclator'
for referencing

12. 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) 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

13. EDIT
ZOBODAT
Fauna Europaea
Example of taxonomic ambiguity:Example of taxonomic ambiguity:
Sphex domesticaSphex domestica (splitter / lumper case)(splitter / lumper case)

14. EDIT
Fauna Europaea
TITAN
?
nomen oblitum
Example of taxonomic ambiguity:Example of taxonomic ambiguity:
Musaria affinisMusaria affinis (complex case)(complex case)

15. EDIT
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

16. EDIT
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

17. EDIT
Catalogue
of Life
ZooBankZooBank
INDEXINDEX
Expert networkExpert networkSocietiesSocietiesResourcesResources
Backwards indexing - Social modelBackwards indexing - Social model

18. 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-lab
facilities
DNA
storage
Digital infrastructure
(Databases; linkage to other
collection data sources)
Physical Infrastructure
(Collections)
Specimen data
Digitalisation
(Digitalisation of specimen info)
Genetic
resources
Specimen
databases
db content
db content
ECAT
Phylogenetic /
PhyloInformatics
Deep-morphology
& Evo-Devo
MorphoBanks
Data integration
Names
Names Identification Marshaller
Names
O
t
h
e
r
O
t
h
e
r
Linking to otherLinking to other
resourcesresources

19. EDITEDIT 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.

20. 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 experts
Is ZooBank scientifically feasible?Is ZooBank scientifically feasible?

21. 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