GBIF Data Access and Database Interoperability

2003 Work Programme Overview

Donald Hobern, GBIF Programme Officer for Data Access and Database Interoperability

dhobern@gbif.org

Indaiatuba, Brazil, 19 October, 2002

GBIF Node Responsibilities

GBIF Portal

Data Node

Participant

1. Network2. Standards3. Tools

1. Encourage participation2. Manage registration of

Data Nodes

1. Network2. Standards3. Tools4. Consolidated Data

1. Data2. Metadata

1. Identify (local) Data Nodes2. Forward registration

metadata from Data Nodes3. National Language

Interfaces

GBIF Data Access and Database Interoperability

Node Architecture

Collection Data Node

Collection Database

Node Data ServicesPresentation

Service

HTML

Collection Database Adaptor

Collection Database

Collection Database Adaptor

…

…

Metadata Services

WSDL Service

Descriptions

Specimen Index Data (3-5 fields)

Specimen Summary Data (20-30 fields)

Specimen Detail

(full data)

Data Repository

General Resource Node

Resource Database

Node Data ServicesPresentation

Service

HTML

Resource Database Adaptor

Resource Database

Resource Database Adaptor

…

…

Metadata Services

WSDL Service

Descriptions

General Resource Data

Data Repository

GBIF Aggregated Data Portal

UDDI Service Registry

Specimen Index

General Resource

Index

WSDL Service Descriptions

Specimen Index Data (3-5 fields)

General Resource Index Data

Indexing Service

Data Aggregation ServicesPresentation

Service

Specimen Summary Data (20-30 fields)

Index Requests

Aggregated Specimen DataHTML

Name Services (ECAT)

Name DataAggregated General

Resource Data

Geographic Service Data

Name Data

Participant Node

Data Services from GBIF Portal

Portal ServicesPresentation

Service

Specimen Data from Collection

Data Nodes

UDDI Service Registry

WSDL Service Descriptions

Registry Management

WSDL Service Descriptions

SpecimenDataHTML

Name Data

General Resource Data

Data Flow within GBIF Network

Collection Node Collection Nodes

GBIF PortalParticipant

Node

Service Metadata

Participant Node

Service Metadata

Service Metadata

Specimen Index Data

Detailed Specimen

Data

Aggregated Data

Detailed Specimen Data

Aggregated Data

User Browser

HTML Data HTML Data

Service Metadata

Example Interactions: Collection View

Collection Node

User Browser

HTML Data

Example Interactions: Global View

Collection Node Collection Node

GBIF Portal

Specimen Summary

Data

User Browser

HTML Data

Example Interactions: Participant View

Collection Node Collection Node

GBIF Portal

Participant Node

Aggregated Specimen Index

Data

Specimen Summary Data

User Browser

HTML Data

Example Interactions: Participant Network

GBIF Portal

Specimen Summary Data

User Browser

HTML Data

Network Collection Nodes

Participant Network Node

Specimen Data (Network-specific

Format) Collection Node

Specimen Summary Data

Example Interactions: Duplicated Node

GBIF Portal

Specimen Summary Data

User Browser

HTML Data

Collection Node

Specimen Summary Data

Participant Network Collection Nodes

Specimen Data (Network-specific

Format)

One of the Collection Nodes is linked to the GBIF portal by multiple paths. The intervening nodes must retain all attribution details from the original provider to ensure that duplicate records may be recognised.

GBIF Data Access and Database Interoperability

Walkthrough of Registration for new Data Node

1. Data Node submits Metadata

Data Node

Participant Node

User Browser

The Node Manager uses the Metadata Services component to define the data held by the node and to submit this data to a Participant Node (either the Country Node for the Data Node or a Node with related interests.

WSDL description of the Data Node’s holdings, registered via UDDI

GBIF Portal

2. Participant Node authorises Metadata

Data Node

Participant Node

User Browser

The Participant Node Manager uses the Registry Management component to define the data held by the node and to submit this data to a Participant Node (either the Country Node for the Data Node or a Node with related interests.

WSDL description of the Data Node’s holdings, propagated to GBIF Portal Registry

GBIF Portal

3. GBIF Portal indexes Data Node

Data Node

Participant Node

User Browser

The GBIF Portal requests the Index data required to use the Data Node when processing user requests, and the Data Node responds with Index data

DiGIR Scan request to retrieve index data

DiGIR Response containing index data

GBIF Portal

GBIF Data Access and Database Interoperability

Walkthrough of User Request for Data

1. User submits Query to Participant Node

Data Node

Participant Node

User Browser

The User completes a form on the Participant Node web site (or, alternatively on the GBIF Portal). The request is handled by a Java servlet in the Participant Node.

Request for Specimen data for given species (HTML form submission)

GBIF Portal

2. Participant Node queries GBIF Portal

Data Node

Participant Node

User Browser

The Participant Node Services component adds any parameters specific to the Node (e.g. to filter to records specific to a given country) and forwards a DiGIR request to the GBIF Portal. The request is handled by a Java servlet in the Portal Services component

DiGIR Request for ABCD Specimen data for given species within geographic scope of Participant Node

GBIF Portal

3. GBIF Portal returns Matches

Data Node

Participant Node

User Browser

The Portal Services component searches the Index data to determine the locations of all matching Specimens held by Data Nodes. The results are returned in XML as a DiGIR response.

DiGIR Response containing summary detail and access information for all Specimen records matching request.

GBIF Portal

4. Participant Node returns Matches

Data Node

Participant Node

User Browser

The Presentation Services component transforms the XML response into HTML for the user, including URLs to access the detailed data from the Data Nodes.

HTML Response containing summary detail and URLs to access detailed information for all Specimen records matching request.

GBIF Portal

5. User requests Detailed Data

Data Node

Participant Node

User BrowserThe User selects a URL to access detailed data for a Specimen.

HTML Request for detail for a Specimen record.

GBIF Portal

6. Data Node returns Detailed Data

Data Node

Participant Node

User Browser

The Data Node processes the request (and produces an XML response) and formats the XML into HTML using the Presentation Services component.

HTML Response with detailed data formatted for browser.

Note: The requests for detail could alternatively be directed to either the Participant Node or the GBIF Portal, either of which could then format XML into HTML appropriately. The model illustrated is the simplest.

GBIF Portal

GBIF DADI Work Programme

1. Establish the data standards and interchange mechanisms required to integrate species-level and specimen-level data within the GBIF Network - $90,000

2. Identify and develop the foundational components of the network as early as possible - $70,000

3. Provide tool kits to assist node managers to bring their databases online as rapidly as possible - $140,000

4. Promote a community (and open-source) development model for GBIF components

GBIF Standards Requirements

Requirements for 2003

• Federated Data Access (DiGIR)

• Collection Data Exchange Schema (ABCD)

• Name Data Exchange Schema (Taxonomic Names)

• Geographical Services (Spatial Data)

Future requirements:

• Structured Descriptive Data (SDD)

Also required:

• Description of user requirements for GBIF network