1. GBIF Program Officer for Data Access and Database Interoperability
Architecture and Standards for Global Biodiversity Informatics A GBIF and TDWG Perspective
Donald Hobern
GBIF Program Officer for Data Access and Database Interoperability
November 2004

2. TDWG and GBIF TDWG – Taxonomic Databases Working Group
Not-for-profit scientific and educational association
Affiliated to the International Union of Biological Sciences
Mission
To provide an international forum for biological data projects
To develop and promote the use of standards
To facilitate data exchange
Products
Standards/guidelines for recording/exchanging data about organisms
Promotion of use of these standards
Forum for discussion (especially annual meeting)
GBIF – Global Biodiversity Information Facility
Megascience activity involving 42 countries/economies and 28 international organisations
Secretariat based in Copenhagen, Denmark
Free and universal access to world’s biodiversity data via Internet
Sharing primary biodiversity data for society, science and a sustainable future
Registry of biodiversity data resources
Index of biodiversity data
Software tools
Web portals ( and data services

3. Primary biodiversity data
Class: Insecta
Taxonomic Names
Order: Lepidoptera
Sequence Data
Synonym: Pyralis nubilalis Hübner, 1796
Locus: AAL35331 Definition: acyl-CoA Z/E11 desaturase
1 mvpyattadg hpekdecfed...
Family: Pyralidae
Genus: Ostrinia Hübner, 1825
Species: Ostrinia nubilalis (Hübner, 1796)
Taxonomic Descriptions
Diagnosis: Wingspan 26-30mm; sexually dimorphic;male: forewings ochreous to dark brown; female: forewings pale yellow; …
Vernacular (EN): European Corn-borer
Vernacular (DE): Maiszünsler
Vernacular (ES): Piral del maíz
Vernacular (FR): Pyrale du maïs
Digital Literature
and Web Resources
Family: Gramineae
Pheromones of Ostrinia
Foodplant: Zea mais L. 1753
Ecological Interactions
Collection: DGH Lepidoptera
Record id: DGHEUR_003217
Country: France
Coordinates: ˚E ˚N
Date: 28 June 2003
Collector: Donald Hobern
Specimens and
Observations
Abiotic Data
Average Rainfall
Location: 48.82°N 2.29°E Jan Feb Mar Apr ...

4. Standardised structured data
<?xml version="1.0" encoding="UTF-8"?>
<response>
<record>
<darwin:DateLastModified> </darwin:DateLastModified>
<darwin:InstitutionCode>DGH</darwin:InstitutionCode>
<darwin:CollectionCode>DGH Lepidoptera</darwin:CollectionCode>
<darwin:CatalogNumber>DGHEUR_ </darwin:CatalogNumber>
<darwin:ScientificName>Dichomeris marginella (Fabricius, 1781)</darwin:ScientificName>
<darwin:BasisOfRecord>O</darwin:BasisOfRecord>
<darwin:Kingdom>Animalia</darwin:Kingdom>
<darwin:Order>Lepidoptera</darwin:Order>
<darwin:Family>Gelechiidae</darwin:Family>
<darwin:Genus>Dichomeris</darwin:Genus>
<darwin:Species>marginella</darwin:Species>
<darwin:ScientificNameAuthor>(Fabricius, 1781)</darwin:ScientificNameAuthor>
<darwin:IdentifiedBy>Donald Hobern</darwin:IdentifiedBy>
<darwin:Collector>Donald Hobern</darwin:Collector>
<darwin:YearCollected>2003</darwin:YearCollected>
<darwin:MonthCollected>06</darwin:MonthCollected>
<darwin:DayCollected>08</darwin:DayCollected>
<darwin:ContinentOcean>Europe</darwin:ContinentOcean>
<darwin:Country>Denmark</darwin:Country>
<darwin:County>Københavns Amt</darwin:County>
<darwin:Locality>Merianvej, Hellerup</darwin:Locality>
<darwin:Longitude>12.538</darwin:Longitude>
<darwin:Latitude>55.737</darwin:Latitude>
<darwin:CoordinatePrecision>100</darwin:CoordinatePrecision>
<darwin:IndividualCount>1</darwin:IndividualCount>
<darwin:Notes>1 in Skinner trap</darwin:Notes>
</record>
</response>
June 2003
S M T W T F S
29 30
Observation record formatted using the Darwin Core

5. TDWG Data Standards Darwin Core
Simple XML data model to represent taxon occurrence records (only core attributes)
Extensions to handle e.g. curation details, microbial data, image data
ABCD Schema – Access to Biological Collection Data
More complex XML data model to represent collection or observation data
Detailed document structure including features for different communities
DiGIR – Distributed Generic Information Retrieval
XML protocol for searching remote data resources
Suitable for use with a wide range of different data models
BioCASe Protocol
XML protocol for searching remote data resources with more complex schema (e.g. ABCD)
Derived from DiGIR – new unified DiGIR/BioCASe protocol being developed
Taxon Concept Schema
XML data model currently under development for exchange of nomenclatural/taxonomic data
First version to be used for implementation in 2005
SDD Schema – Structured Descriptive Data
XML data model for descriptive data relating to taxa or specimens (highly generalised)
Suitable for representation of character tables, diagnostic keys, etc.

6. BioCASe-ABCD
<?xml version='1.0' encoding='UTF-8'?>
<response xmlns=' xmlns:xsi=' xsi:schemaLocation='
<header>
<version software='Python Interpreter'>2.3 (#46, Jul , 18:54:32) [MSC v bit (Intel)]</version>
<sendTime> T22:22:40+02:00</sendTime><source> </source><destination> </destination><type>search</type>
</header>
<content recordDropped='0' recordCount=‘1' recordStart='0' totalSearchHits=‘1'>
<DataSets xmlns='
<DataSet>
<OriginalSource><SourceInstitutionCode>BGBM</SourceInstitutionCode><SourceName>Bridel Herbar</SourceName><SourceLastUpdatedDate> </SourceLastUpdatedDate></OriginalSource>
<DatasetDerivations>
<DatasetDerivation>
<DateSupplied> </DateSupplied>
<Supplier>
<Organisation><OrganisationName>Botanic Garden and Botanical Museum Berlin-Dahlem</OrganisationName></Organisation><Person><PersonName>Andrea Hahn</PersonName></Person>
<TelephoneNumbers><TelephoneNumber><Number>+49 (0) </Number></TelephoneNumber></TelephoneNumbers><URLs><URL>
</Supplier>
<Rights>
<TermsOfUse>The use of the data is allowed only for non-profit scientific use and for non-profit nature conservation purpose.</TermsOfUse>
<LegalOwner>
<Organisation>
<OrganisationName>Botanic Garden and Botanical Museum Berlin-Dahlem</OrganisationName>
<OrganisationCodes><OrganisationCode>BGBM</OrganisationCode></OrganisationCodes>
</Organisation>
</LegalOwner>
<CopyrightDeclaration>No part of this data base may be copied or reproduced without written permission from the legal owner.</CopyrightDeclaration>
<IPRDeclaration>The Intellectual Property Rights are held by the legal owner or, in case of living persons, by the collector or determinator.</IPRDeclaration>
</Rights>
<Statements><Disclaimer>No responsibility is accepted for the accuracy of the information in this data base.</Disclaimer></Statements>
</DatasetDerivation>
</DatasetDerivations>
<Units>
<Unit>
<UnitID>Bridel-1-362</UnitID>
<Identifications>
<Identification PreferredIdentificationFlag='0'>
<TaxonIdentified>
<HigherTaxa><HigherTaxon TaxonRank='Family'>Pottiaceae</HigherTaxon><HigherTaxon TaxonRank='Kingdom'>Plantae</HigherTaxon></HigherTaxa>
<NameAuthorYearString>Leucophanes octoblepharioides Brid. 1827</NameAuthorYearString>
<ScientificNameString>Leucophanes octoblepharioides</ScientificNameString>
<AuthorString>Brid. 1827</AuthorString>
</TaxonIdentified>
<Identifier><IdentifierPersonName><PersonName>Allen, Noris Salazar</PersonName></IdentifierPersonName></Identifier>
<IdentificationDate><ISODateTimeBegin> </ISODateTimeBegin></IdentificationDate>
</Identification>
</Identifications>
<Gathering><GatheringSite><ContinentOrOcean>Asia</ContinentOrOcean><Country><CountryName>NP</CountryName></Country><AreaDetail>Nepal</AreaDetail></GatheringSite></Gathering>
</Unit>
</Units>
</DataSet>
</DataSets>
</content>
<diagnostics><diagnostic>OK</diagnostic></diagnostics>
</response>
PROTOCOL
COLLECTION (INCLUDING METADATA)
Note that structure of record elements is part of the content schema (ABCD), not part of the protocol
SPECIMEN
PROTOCOL

7. DiGIR-Darwin Core
<?xml version='1.0' encoding='utf-8' ?>
<response xmlns='
<header>
<version>$Revision: 1.14 $</version>
<sendTime> T13:48: </sendTime>
<source resource="martius_munchen_infocomp">
<destination> </destination>
<type>search</type>
</header>
<content xmlns:darwin=' xmlns:xsd='
<record>
<darwin:DateLastModified> </darwin:DateLastModified>
<darwin:InstitutionCode>Botanische Staatssammlung München</darwin:InstitutionCode>
<darwin:CollectionCode>Infocomp</darwin:CollectionCode>
<darwin:CatalogNumber>010702P1</darwin:CatalogNumber>
<darwin:ScientificName>Wedelia longifolia Mart. ex Baker</darwin:ScientificName>
<darwin:BasisOfRecord>Label</darwin:BasisOfRecord>
<darwin:ScientificNameAuthor>Baker, J.G.</darwin:ScientificNameAuthor>
<darwin:TypeStatus>Holotypus</darwin:TypeStatus>
<darwin:CollectorNumber>s.n.</darwin:CollectorNumber>
<darwin:Collector>Martius, C.F.P. von</darwin:Collector>
<darwin:ContinentOcean>South America</darwin:ContinentOcean>
<darwin:Country>Brazil</darwin:Country>
<darwin:Locality>' ... in prov. S. Paulo, inter herbas locis irriguis ad Lorena ... ' (op. cit.)</darwin:Locality>
<darwin:Notes>Tribe: Heliantheae,
Reference protologue: Martius, C.F.P. von: Flora Brasiliensis 6(3): ,
</darwin:Notes>
</record>
</content>
<diagnostics>
<diagnostic code="STATUS_INTERVAL" severity="info">3600</diagnostic>
<diagnostic code="STATUS_DATA" severity="info">79,5,2</diagnostic>
<diagnostic code="MATCH_COUNT" severity="info">1</diagnostic>
<diagnostic code="RECORD_COUNT" severity="info">1</diagnostic>
<diagnostic code="END_OF_RECORDS" severity="info">true</diagnostic>
</diagnostics>
</response>
Note that structure of record elements is part of the protocol – the content schema (Darwin Core) only defines the attributes describing the record
PROTOCOL
SPECIMEN
PROTOCOL

8. BioCASe-ABCD compared to DiGIR-Darwin Core
BioCASe-ABCD model
Document-based (response document includes metadata and records as a structured package)
Strengths
No problem with modelling complex nested structures and repeating elements
Fits perfectly with UBIF proposal – ABCD DataSet elements and ABCD Metadata could readily be standardised with the DataSet/Metadata structures from other TDWG standards such as Structured Descriptive Data (SDD) and Taxon Concept Schema (TCS) – with rather little work. DataSets from all three of these could be combined to form a single document with cross-references between sections.
Possible weaknesses
Not simple for specialist networks to extend the structure with additional elements of their own (requires well-planned open extension points to be designed into the schema), especially if a provider wishes simultaneously to be part of more than one such specialist network .
(At present) all elements in the ABCD schema are versioned together. Handling an updated version of the schema requires significant additional effort on the part of providers and users. For example, adding new elements to support plant genetic resource data – without changing the elements for museum/herbarium specimens – requires all users to handle a new version of the schema.
DiGIR-Darwin Core model
Record-based (response returns a set of records which may contain descriptor elements from any schema)
Massively flexible and extensible model allowing different networks to use a common protocol and shared core elements alongside their own network-specific extensions.
(In integrated protocol version) could return ABCD elements as part of response records. If ABCD is treated as a library of elements, this fits even better.
Model maps well to supporting a flexible object-oriented data model for biodiversity informatics.
(In existing version) cannot readily handle complex data structures with nested repeating elements.
Records have no intrinsic data type – currently relies on an implicit understanding between user and data provider.

9. Exchange via web services
Standardised
Structured Data
Heterogenous Databases
Web Services
Internet
Users
<request>
<response>
<record> …
<request>
<response>
<record> …
<response>
<record> …
<request>

10. GBIF network of biodiversity data nodes
Specimens:
Flowering Plants of Africa
Observations:
Birds of Central America
DiGIR-DarwinCore
Specimens:
Proteaceae of the World
Museum A
Observations:
Butterflies of Belize
BioCASe-ABCD
Observer
Network B
Taxon Names:
Proteaceae of the World
DiGIR-DarwinCore
BioCASe-ABCD
Checklist:
Birds of Belize
GBIF
Network
Taxon Concept Schema
Taxon Concept Schema
DiGIR-DarwinCore
BioCASe-ABCD
Specimens:
Bacteria Cultures
Specimens:
Mammals of North Europe
Taxon Concept Schema
Taxon Concept Schema
Taxon Names:
Mammals of the World
Taxon Names:
Bacteria
Further Links:
Mammals
Further Links:
Bacteria
Museum C
University D

11. Central GBIF registry of data nodes
Type of data
Taxon
Region
Records
Museum A
Specimen/Observation
Flowering Plants
Africa
327000
Proteaceae
World
23000
Taxonomic Names
1500
Observer Network B
Birds
Central America
68500
Butterflies
Belize
4200
Name List
587
Museum C
Mammals
North Europe
1800
8000
General Resources
600
University D
Bacteria
1200
5000
400

12. DiGIR-BioCASe Protocol and Nested Networks
Get DiGIR-style records each with a set of Darwin Core descriptors and a complete ABCD Unit
Get full set of Soy Bean crop descriptors.
User
Get standard plant genetic resource Passport data for all crop types.
Get complete ABCD documents from each BioCASe provider
Get Darwin Core records where darwin:ScientificName equals Puma concolor from any provider.
BioCASe Provider
Darwin Core
ABCD
Taxon Occurrence
BioCASe Provider
Darwin Core
ABCD
Taxon Occurrence
MaNIS Provider
Darwin Core
Curatorial
Taxon Occurrence
OBIS Provider
Darwin Core
Marine
Taxon Occurrence
IPGRI Banana Provider
Darwin Core
IPGRI Passport
Banana Descriptor
Taxon Occurrence
IPGRI Soy Bean Provider
Darwin Core
IPGRI Passport
Soy Bean Descriptor
Taxon Occurrence

13. GBIF index to biodiversity data
User
requests
GBIF Data Nodes
Biodiversity Data Access
Specimen Data
DiGIR/BiOCASe
Biodiversity
Data
Index
Taxonomic Name Service (ECAT)
Catalogue of Life
Specimen Data
Observation Data
DiGIR/BiOCASe
Specimen Data
Name Lists
Taxon Concept
Specimen Data
Links to other data

14. GBIF data index

15. Central portal to biodiversity data
6 records
Show specimen records for Erinaceus europaeus
35 records
GBIF
Portal
17 records
58 records:
Museum A Paris
Museum A Nice
Museum A Avignon
Museum A Marseille
Observer B Norwich
Observer B Southampton
. . .
0 records

16. GBIF Data Portal

17. GBIF Data Portal

18. Participant Nodes with tailored information
Show specimen records for Erinaceus europaeus
from France
Geographic Services
GBIF
Portal
Show occurrence of Hérisson d’Europe
GBIF
France
26 records:
Museum A Paris
Museum A Nice
Museum A Avignon
Museum A Marseille
23. Observer B Calais
29. Observer B Paris
. . .
58. Museum C Toulouse
58 GBIF records:
Museum A Paris þ
Museum A Nice þ
Museum A Avignon þ
Museum A Marseille þ
Observer B Norwich ý
Observer B Southampton ý
. . .
58. Museum C Toulouse þ

19. Flexible applications
A customs official discovers specimens of a possible pest species of weevil (Curculionidae) on a consignment of agricultural produce at a port of entry.  The GBIF Network generates an identification key to support identification of pest weevil species to allow the official to determine appropriate response. This application requires access to data from a wide range of sources, including those GBIF participants that are organisations.
WANTED
Provide key to identify reportable Curculionidae
GBIF
List of names of reportable pest species
Elytra brown 2
Elytra not brown 5
Thorax black
Thorax brown 3
Hind tibia black Non-pest
Hind tibia brown 4
Hind femur brown
Hind femur black Non-pest
. . .
Descriptive data

20. Monitoring of data usage
81 records:
Museum A Paris
Museum A Nice
. . .
GBIF Usage: Museum A
16 August 2003
Search: Upupa epops
5 records returned
18 Augúst 2003
Search: Birds from Nice
16 records returned
Show specimen records for Upupa epops
GBIF
Portal
Data
Usage
Logs
Data Usage Reports
GBIF Usage: Observer B
16 August 2003
Search: Upupa epops
2 records returned
Show bird specimen records from Nice
126 records:
Museum A Upupa epops
Museum A Apus apus
Museum A Athene noctua
. . .

21. Future activity Globally unique identifiers Schema repository
TDWG-GBIF collaboration to develop models to allow data providers to attach persistent identifiers to their data records
Allow software to detect multiple instances of the same record
Allow users to save resolvable references to specimens, collections, taxon concepts, etc.
Schema repository
Central library of information on data models
Resource for discovering documentation or mappings between different schemas
Better support for intelligent software applications
Data validation tools
Framework for running sets of validation tests against XML data (content values, controlled vocabularies, relating georeference data to named localities, etc.)
Support different uses (data providers to locate possible problems in data; users to assure themselves of suitability of data; GBIF to provide metadata on data completeness/coherence)
Access to a wide range of taxonomic name data
Taxonomic/nomenclatural authorities (nomenclators, global species databases, revisions, etc.)
Lists used by different communities/organisations (red lists, pest species, regional checklists, etc.)
Customised portals
Organised according to taxon lists used by each user
Notifications of new data based on user profiles (taxonomic, geographic, etc.)

22. Taxonomic Databases Working Group
Links
Taxonomic Databases Working Group
Including access to working groups
Global Biodiversity Information Facility
Communications Portal
Data Portal
Architecture documents