GBIF registry (GBRDS), at European Nodes meeting in Alicante, Spain (10 March 2010)

GBRDSGlobal Biodiversity Resources

Discovery System

European GBIF Nodes Meeting 2010, March 10th-12th Alicante, SpainDag Endresen, Nordiv Genetic Resources Center, NordGen

What is the Global Biodiversity Information Facility?

• GBIF enables free and open access to biodiversity data online.

• An international government-initiated and funded initiative focused on making biodiversity data available to all and anyone, for scientific research, conservation and sustainable development.

• GBIF’s Data Portal provides this infrastructure.

GBIF site :: http://www.gbif.org/index.php?id=269

http://www.gbif.org/index.php?id=269

GBIF from prototype to full operationGlobal informatics research infrastructure:•Global participation, a global network of partners•Enabling publishing of biodiversity data•Promoting development of data exchange standards•Building an informatics architecture•Capacity building•Catalysing development of analytical tools

•Data provider•Data aggregator

GBRDS :: Linking resources

• Who? (Institutions, Collections, Networks, ...)

• What? (Data sets, Services, Persistent Identifiers...)

• Where? (Locations, Service access points, ...)

• When? (Temporal scope)

• How? (Formats, protocols, ...)

As a distributed service

Available APIs (so far)

Question: Do we (the NODES) miss an important API here, or are these good to go?

Visit GBRDS at Google Code: http://code.google.com/p/gbif-registry/w/list

http://code.google.com/p/gbif-registry/w/list

At the core, a Discovery System

ConsumersDataPublishers

Discovering

SearchingRetrieving

DiscoverySystem

Registering

ServicePublishers Others…

Slide by Vishwas Chavan, GBRDS workshop September 2009

GBIF GBRDS

http://gbrds.gbif.org Slide prepared by GBIF (Samy Gaiji)

http://gbrds.gbif.org/





USE CASES & mock-up examples

• The same primary biodiversity data can be analyzed differently for different uses

Discussion: Do we the NODES, have other important use cases?

Discussion: Do we the NODES have other requirements for the GBRDS user interface?

What can you do with georeferenced biodiversity data?

Predict effects of climate change Analyse and predict spread of pests and diseases of humans, crops, livestock,

wildlife, etc. Predict best places to set up new protected areas Analyse invasive species and predict invasion pathways Provide policymaker-relevant data of all kinds Be a resource for biodiversity science communities

The same primary biodiversity data can be analyzed differently for different uses.

Uses cases primary biodiversity data

Modified from slide by Vishwas Chavan, GBRDS workshop September 2009

http://code.google.com/p/gbif-registry/wiki/UseCases

http://code.google.com/p/gbif-registry/wiki/UseCases

Moving towards… global integration

ThreatenedSpp.; Red List Spp.

Migratory Spp.

Invasives, crop wild relatives, medicinals, etc.

?


Global Biodiversity Resources Discovery Systemempowering discovery of biodiversity data

microhyla ornata western ghats 1980 Discover

About GBRDS Bug Report @ 2009, GBIF

1-5 of 351, <<Next>>Database of Frogs of Southern India..........(more)

AmphibiaWeb...................................................(more)

Fauna of India Database..................................(more)

Microhyla of the World....................................(more)

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779 resources in six categories discovered, with 428 accessible, 351 resources records

Names (82) Primary Biodiversity Data (200)Resources (351)

Multimedia (12) Maps (28) Literature (106)

Mock-up examples


Database of Frogs of Southern India: South Asian Centre for Biodiversity Monitoring, Kathmandu, NepalCDROM, published November 2006, ISBN-001-898-0788, [email protected] . <<Click here for complete metadata record>>

AmphibiaWeb: http://www.amphibiaweb.org/ Access point live as on 20th June 2009<<Click here for complete metadata record>>

Fauna of India Database: National Centre for Biodiversity Informatics, New Delhi, IndiaIn-house database, accessible through bi-lateral arrangement, [email protected] <<Click here for complete metadata record>>

Microhyla of the World: Smithsonian Institution, Washington DC, USA257 specimen records: 1700 – 2001: http://www.si.edu/amphibia/microhyla/ Access point live as on 12th Jan 2009 <<Click here for complete metadata record>>

Amphibian Collection of Raffles Museum: Raffles Museum, Singapore7004 specimens, non-digital: [email protected]. <<Click here for complete metadata record>>

Global Biodiversity Resources Discovery Systemempowering discovery of biodiversity data

microhyla ornata western ghats 1980 Discover

About GBRDS Bug Report @ 2009, GBIF

779 resources in six categories discovered, with 428 accessible, 351 resources records

Resources Names PrimaryBiodiversity Data Multimedia Maps Literature

Resources (351): 1-5 of 351 : Next : Previous : Last :

Digital, Offline

Digital, Free, Online

Digital, Restricted Access

Digital, Free, Online

Non- Digital


Mock-up examples

mailto:[email protected]

http://www.amphibiaweb.org/


http://www.si.edu/amphibia/microhyla/


Online demo (pre-alpha)

GBRDS? What’s that?

eBiosphere resolution recommendation:“Complete durable global registries of biodiversity informatics resources”

Slide by Samy Gaiji, GBRDS workshop September 2009

Is this the GBRDS?The GBRDS is 1) a Registry of resources and services and 2) a set of discovery services interacting with existing infrastructure such as GBIF to facilitate the discovery of biodiversity information. The most important component, the Registry would facilitate the inventory of information resources by creating a single annotated index of publishers, institutions, networks, collections (datasets), schema repository and services. The envisaged GBRDS is not conceived to be designed as simply a collection of centralized indexes but much more as an integrated ‘Yellow Pages’ reference of all biodiversity information resources, reconciling all distributed resources and providing a meaningful way to discover them in a distributed manner.Slide by Samy Gaiji, GBRDS workshop September 2009

Registry: The past…Universal Description Discovery and Integration

(UDDI)

“…XML-based registry for businesses worldwide to list themselves on the Internet …”

UDDI GBIF

Businesses Institutions

+ Services + Collections

+ Service Bindings + Endpoints (DiGIR etc)

+ TModels + Application Schemas (DwC etc)

Modified from slide by Tim Robertson, GBRDS workshop September 2009

NB! Capitalise on resources (investments) till date, re-use previous solutions.

Technical specifications• Re-use of registry for your own purposes, and thematic

networks (model sub networks)• Identification of duplicate datasets / records• Scalable, up-time (24/7/365)• How to build relations between resources (Perhaps

FaceBook style: “Institution X requests to be associated with you. Would you like to accept this association?”)

• Central curation, or distributed community curation?• Allow the tagging of resources (human, machine)

• Discussion: Any additional specifications to add from the NODES?

Source: slides by Tim Robertson, GBRDS workshop September 2009

GBRDS Planning: Some issues to

consider

GBIF Network: The real scenario

Challenge #1:

Model the true nature of the network makeup.

A graph and not a tree Multiple entity types

Institutions, networks, collections, GBIF Nodes

Many relationship types

Slide by Tim Robertson, GBRDS workshop September 2009

Slide by Samy Gaiji, GBRDS workshop September 2009

GBRDS scalability/portability to other communities/locations will be critical!

Where metadata fits in ...

Modified from slide by Éamonn Ó Tuama, GBRDS workshop September 2009

NB! Remember import / compatibility with other metadata catalogues / systems

• The Persistent Identifier is a digital name tag• Also called Global Unique Identifiers (GUID)• Life Science Identifiers (LSID) is one example• Digital Object Identifier (doi) is another example

• The Persistent Identifier concept introduces a straightforward approach to naming and identifying data resources stored in multiple, distributed data stores.

• Persistent Identifiers provides a naming standard to support interoperability.

GBRDS : Persistent Identifiers

Discussion: Are Persistent Identifiers an important task for the GBRDS? (From NODES view-point)

LSID-GUID Task Group: summaryEffective identification of data objects is essential for linking the world’s biodiversity data. If GBIF is to enable the exchange of biodiversity data it must promote identifier adoption through:

- education, training, outreach- leadership- practical services

Source: slides by Éamonn Ó Tuama, GBRDS workshop September 2009

Recommendation 10: GBIF should provide services to support identifier resolution, redirection, metadata hosting, and caching.

Endpoint monitoring http://bioguid.info/status/ (Rod Page)

GBRDS : Provider monitoring

Modified from slide by Tim Robertson, GBRDS workshop September 2009

http://bioguid.info/status/

Endpoint monitoring http://bigdig.ecoforge.net/ (David Vieglais, Kansas University, 2006)

GBRDS : Provider monitoringDate Last Updated: 2010-03-08 08:15:01+0000


Endpoint monitoring http://chm.grinfo.net/ (Bioversity, Dag Endresen, March 2006)

GBRDS : Provider monitoring



Long tail or Dark Data is economically and ecologically very critical

Most of existing and future data would be hold by Small Data Publishers

The early focus of GBIF was the low hanging fruits – the LARGE datasets

Further expansion of the GBIF data network should struggle to include the small datasets

Source: Curating the Dark Data in the Long tail of science by P. Bryan Heidorn (Google Tech Talk, August 28, 2008, http://www.youtube.com/watch?v=mgN74bR57i0

REMEMBER : the small data providers

Source: slides by Vishwas Chavan, GBRDS workshop September 2009

http://www.youtube.com/watch?v=mgN74bR57i0

Thanks for listening

GBIF registry (GBRDS), at European Nodes meeting in Alicante, Spain (10 March 2010)

Technology

Transcript of GBIF registry (GBRDS), at European Nodes meeting in Alicante, Spain (10 March 2010)