i4Life - Fourth International Barcode of Life Conference

INDEXING for LIFE
i4Life: Cross-referencing the world’s
major taxonomic catalogues
Frank Bisby, Magda Sitko, Alastair Culham & (Vincent Robert)
The Fourth International Barcode of Life Conference
University of Adelaide, 3 December 2011
INDEXING for LIFE
Project duration: November 2010 –October 2013
Project participants: 12 organisations from 8 countries
Project Co-ordinator: The University of Reading, UK
Global Biodiversity Programmes:
GBIF, EMBL-EBI, Barcode of Life, IUCN Red List, LifeWatch, Encyclopaedia of Life
Catalogue of Life Community :
University of Reading, ETI Bioinformatics, Sp2000, MNHN Paris, Cardiff University,
(ITIS)
i4Life Webpage: http://www.i4life.eu
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
i4Life Project Objectives
To establish a Virtual Research Community
to interlink and harmonise global
taxonomic catalogues.
This builds on the work of the 4D4Life
Project.
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
A Virtual Research Community
i4Life project partners are some of the
major global programmes exploring the
full extent of life on Earth.
i4Life will for the first time provide a
summary of all species known across
these programmes.
It is creating a global standard for
taxonomic data integration in electronic
infrastructures world-wide.
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
The Catalogue of Life
•
The goal of Sp2000 is to create a taxonomically validated checklist of all the world's
species (plants, animals, fungi and microbes). This is being achieved by bringing
together an array of global species databases (GSDs) covering each of the major
groups of organisms.
•
The programme in partnership with the Integrated Taxonomic Information System
(ITIS) of North America currently produces the Catalogue of Life.
Species 2000 and Catalogue of Life were started and developed by Professor Frank Bisby
(1945 – 2011)
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
The Catalogue of Life
Annual Checklist 2011
1,347,224 species from 99 databases
(animals, plants, fungi, microorganisms)
On DVD and on website:
http://www.catalogueoflife.org/annual-checklist/
The CoL quarterly edition
(intermediate updates)
Last update: 24th October 2011
1,370,276 species from 101
databases.
On website:
www.catalogueoflife.org
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
The i4Life Global
Partners
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
Global Biodiversity
Information Facility (GBIF)
Global Biodiversity Information Facility (GBIF) –
an international organisation based in
Copenhagen, DENMARK.
It enables free and open access to biodiversity
data online. The data provided by many
institutions from around the world is accessible
and searchable through a single GBIF portal.
Role in i4Life: GBIF Pipeline, GNA and
GSD-Piping.
The current version of the CoL is
incorporated into the GBIF platform.
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
The European Nucleotide
Archive at EMBL-EBI
The European Bioinformatics Institute – EBI
(Cambridge, UK) is a non-profit academic organisation,
part of the European Molecular Biology Laboratory –
EMBL (Germany).
ENA (The European Nucleotide Archive) project at
EMBL-EBI - provides a comprehensive record of the
world's nucleotide sequencing information. Amongst
EBI data services, it is the ENA that harbours data from
the largest range of organisms.
Role in i4Life: EBI Pipeline, Cross-map, and GSD Piping
ENA is being used for interfacing with the CoL.
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
IUCN Red Lists
The IUCN Red List of Threatened Species (also
known as the IUCN Red List or Red Data List) is
the world's most comprehensive inventory of
the global conservation status of plant and
animal species.
Working with i4Life the IUCN Red List goal is to:
1) receive taxonomic information from CoL into
the IUCN Red List;
2) use this to facilitate information retrieval on
the IUCN Red List website;
3) assist during the assessment process.
Role in i4Life: IUCN Red-Lists Pipeline, Crossmap, and GSD-Piping
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
LifeWatch
LifeWatch is a long-term, country-financed
project. Its goal is to create a portal to
present diversity information in a unified
way across multiple scales - genomic;
organism; habitat; ecosystem; landscape.
The EDIT Platform for Cybertaxonomy – is
expected to be a component of the
LifeWatch virtual laboratory. Core to the
platform - the EDIT Common Data Model
(CDM)
The main goal is to establish a LifeWatch
Pipeline for pulling the Catalogue of Life
synonymic species checklist, and its
taxonomic hierarchy into EDIT platform.
Role in i4Life: LifeWatch Pipeline
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
The Encyclopedia of Life
The Encyclopedia of Life (EOL) is a free
to
access,
online
collaborative
encyclopaedia.
The goal of the EoL is to compile and
make available over the Internet as
much information as possible about the
world’s species of plants, animals and
microorganisms.
Encyclopedia of Life already uses the
Catalogue (since its launch in 2008).
The Encyclopedia of Life is a ‘sixth’ global
programme, without a Workpackage in
the Research Activities. EoL does not have
a clear European base, and cannot be
included in the funding.
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
The Barcode of Life Initiatives
i4Life is cooperating with two Barcoding Laboratories in Europe:
CBS-KNAW (Netherland) managing the European BOLD mirror.
MIZ-PAS (Poland) uploading and downloading from to the Nematode
taxonomy barcode system
Role in i4Life: Barcode Pipeline, Cross-map and GSD-Piping
Barcode CoL - interested in the taxonomic tree and hierarchy from the CoL
COL  Barcode- potentially new species from BOLD.
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
Progress:
KNAW
•
•
Specification agreed and available for CoL to BOLD/ECBOL pipeline:
the European BOLD mirror (managed by CBS-KNAW using the BioloMICS
software) will create the needed interface (as web services) to extract data from
the Catalogue of Life and possibly feed all BOLD mirrors (Canada, China and
associates, Australia and Europe).
It was also decided to create another web service which will allow i4Life
partners to get taxonomic data deposited in BOLD systems.
Preliminary website at the European BOLD Mirror portal where some CoL data
(only fungal data at this stage) are visible.
MIZ-PAS
•
Specification agreed for CoL to MIZ-PAS Nematode database pipeline
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
i4Life workflows
Download Tools
Piping Tools
Cross-mapping Tools
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
The i4Life Download Tools
The i4Life download service:
provides data to partner organisations - now fully operational.
It is accessible via i4Life website: www.i4Life.eu (password protected)
DwC-A is agreed as an official i4Life format for exchanging information between the
CoL and Global Partners.
The specification is agreed and mapping between the CoL DwC–A and partners’ data
is being completed.
Developed by:
ETI Bioinformatics, Netherlands
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
The i4Life Cross-mapping Tools
•
•
For partners to be able to share species information
For comparing how taxonomy differs from one organisation to another
The cross-map can be used to support user interfaces which show the relationships
between the taxonomies and allow users to switch between them.
The tools are being planned to be delivered in a few stages:
First stage – mapping catalogues to obtain taxa not present in the CoL. –
COMPLETED.
Next stages – other rules revealing the relationships between taxa listed in
differing species/names catalogues
Developed by:
The University of Cardiff. UK
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
The i4Life Piping Tools
Pulling “batches of names” from i4Life providers (taxa not present in CoL as
identified by the Cross-mapping tools).
Distributing names to the right Catalogue of Life Global Species Databases (an array
of more then 100 Global Species Databases).
Expected results:
– Providing updates from GSDs “batches of names” in the CoL – filling gaps in the
CoL
– Providing comments from GSDs back to the global partner – enhancing the
global partners’ catalogues
Developed by:
The University of Reading, UK
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
i4Life project progress so far
GOAL: Designing and implementing a pipeline for transmitting CoL and CoL updates to
the global partners informatics platform
GBIF – already completed
BOLD European Mirror – prototype portal already present
ENA at EMBL-EBI – first stage completed: taxon-centric portal is operational
GOAL: Designing and implementing a regular cross-mapping process between the CoL
taxonomy and the global partners, using the CoL cross-mapping tools
The First version of the Cross-mapping tool is operational (new taxa rule), next
version (advanced rules) planned to be delivered this December
GOAL: Establishing the workflow by which each partner organisation can make
contributions of missing taxa and names to the CoL, using the CoL piping tools
Data already obtained from GBIF, UICN, Barcode Nematode Database
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
i4Life Workshops
Networking workshops on policy and planning issues relating to the taxonomic
catalogues of the six organisations:
 The role and organisation of this work within the Global Names Architecture
community
COMPLETED. 8-10 November 2011, Paris. The report in progress
PLANNED FOR 2012:
 The taxonomic cataloguing of clusters of DNA sequences repeatedly detected
in environmental metagenomic studies.
 The classification of cryptic species detected in DNA Barcoding.
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011
INDEXING for LIFE
Thank you!
The Fourth International Barcode of Life Conference, University of Adelaide, 3 December 2011