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IST-Africa 2013 Conference Proceedings
Paul Cunningham and Miriam Cunningham (Eds)
IIMC International Information Management Corporation, 2013
ISBN: 978-1-905824-38-0
i4Life: Standardising the World’s
Biodiversity Catalogue
Alastair CULHAM1, Magdalena SITKO1, Yuri ROSKOV1, Viktoras DIDŽIULIS1,
Kwok CHEUNG1, Thomas KUNZE1, Peter SCHALK2,
Wouter ADDINK2, Markus DÖRING3, Guy COCHRANE4, Stéphane RIVIÈRE4,
Vincent ROBERT5, Wieslaw BOGDANOWICZ6, Craig HILTON-TAYLOR7,
Walter BERENDSOHN8, Anton GÜNTSCH8, Andrew JONES9,
Richard WHITE9, Thierry BOURGOIN10
1
University of Reading - UoR, Whiteknights Shinfield Rd, Reading, RG6 6UR, UK
Tel: +44 118 378 6466, Email: [email protected]
2
ETI BioInformatics, Van Steenisgebouw, Einsteinweg 2, Leiden, 2333 CC, Netherlands
Tel: +31 71 527 1350, Fax: +31 71 527 1351, Email: [email protected]
3
GBIF, Universitetsparken 15, Copenhagen, DK-2100, Denmark
Tel: +45 35 32 14 70, Fax: +45 35 32 14 80, Email: [email protected]
4
EMBL-EBI, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK
Tel: +countrycode localcode number, Fax: + countrycode localcode number, Email:
5
KNAW, CBS, Uppsalalaan 8, Utrecht, 3584 CT, Netherlands
Tel: +31 30 2122600, Fax: +31 30 2512097, Email: [email protected]
6
MIZ-PAS, Wilcza 64, Warsaw, 00-679, Poland
Tel: +48 22 629 32 21, Fax: + 48 22 629 63 02, Email: [email protected]
7
UICN Species Programme Office, 219c Huntingdon Road, Cambridge, CB3 0DL, UK
Tel: +44 1223 277966, Fax: +44 1223 277845, Email: [email protected]
8
FUB-BGBM, Königin-Luise-Straße 6-8, Berlin, 14195, Germany
Tel: +49 30 838-50166, Email: [email protected]
9
Cardiff University - CU, 5 The Parade, Cardiff, CF24 3AA, UK
Tel: +4429 20875537, Fax: +44 29 20874598, Email: [email protected]
10
MNHN, 45 rue Buffon, Paris, 75005, France
Tel: + 33 (0)1 40 79 53 92, Email: [email protected]
Abstract: i4Life provides linkages between the Catalogue of Life, an expert based
knowledge portal for living species on earth, and global partners (IUCN, GBIF, ENA
at EBI, BOLD, EoL, and Life Watch) providing data portals for distribution, genetic
diversity and conservation information. This novel e-infrastructure offers the only
single global consensus list of living species on earth and their associated data. This
structure uses custom services to cross-map, transfer, and make available subsets of
this global list to interested users. It facilitates both global and local understanding
of biodiversity, it’s distribution, variation and threats.
Keywords: e-infrastructure, biodiversity informatics, Catalogue of Life, species
lists, data portals, taxonomy
1.
Introduction
Degradation and loss of global biodiversity is one of the key issues of our time.
Conservation of biodiversity is key to human survival, food security and quality of life.
Climate change and population growth combine to worsen this threat. However we are still
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without a complete, comprehensive and global list of the Earth’s living species against
which to measure biodiversity change. The i4Life project (www.i4Life.eu) is a 3-year
European e-Infrastructure project, launched at the University of Reading on 1st November
2010 and it is a continuation and expansion of the 4D4Life project. The project has brought
together the Species2000 [1] and ITIS [2] Catalogue of Life [3], an index of almost 1.4
million species, with six global biodiversity portals together delivering around 700 million
data records to provide an accessible, cross referenced access service to species lists and
data associated with genetic diversity, conservation, identification and distribution to allow
a truly global understanding of life on earth. The Catalogue of Life is a clearing house for
databases covering some 70% of the world’s known species, and this catalogue is growing
steadily in quality and coverage. It represents common data from over 100 constituent
databases curated and reviewed by experts. Combining this knowledge infrastructure with
the data portals of GBIF [4], IUCN RedList [5], ENA at EBI [6], BOLD [7] and EoL [8]
gives unrivalled access to man’s knowledge of biodiversity allowing appropriate legislative
decisions, conservation planning and focusing research priorities.
Vast areas of agricultural landscape are predicted to become desert and whole
ecosystems will disappear or be degraded by species loss due to climate change and human
impact. Through population growth, urbanisation, and changing land use, some of the
ecosystems richest in wild species will continue to become fragmented or degraded beyond
repair, leaving us with lost ecosystem services and lost species diversity. Internationally
there is a perception that many sectors of society, especially in urban and city landscapes
around the world, do not even appreciate our extreme dependence on biodiversity, or the
severe threats it brings to the livelihoods of the next generation. For scientists there remains
a more fundamental issue: we are still racing to explore the extent of the species present on
earth before extinctions wipe these records from our evolutionary history.
A key issue in global biodiversity science is how scientists are able to synthesize a
comprehensive view of what global biodiversity is [9] its myriad components, and an
understanding of how it functions, and be able to model and forecast how it will respond to
the pressures of urbanisation and climate change [10] [11] [12] [13] [14] [15]. Several
projects have attempted this previously and particular challenges have included lack of
complete data on a Global scale [16] and knitting together legacy software [17] [18].
Harmonising the differing catalogues of species around the world is a crucial part of this
synthesis and has enormous practical significance in indexing the knowledge needed to
protect biodiversity. The six ‘global biodiversity programmes’ in i4Life, the Global
Biodiversity Information Facility (GBIF), the European Nucleotide Archive (part of
INSDC), the Barcode of Life initiatives, the IUCN Red List, the new LifeWatch [19] [20]
programme, and the Encyclopedia of Life, are partners in i4Life and each currently has its
own taxonomy of species so making the cross referencing of species from different data
portals an unreliable process [21]. Through i4Life these portals are being cross referenced
to a standardised Catalogue of Life list so that searches for a named species will be searches
for the same thing in each place (fig 1). The target is to enable each programme to enhance
its taxonomic catalogue with the assistance of the others, and to create a harmonised list for
the entire set of organisms based around the expert-edited Catalogue of Life.
These key players present particular hurdles to Catalogue integration because they a)
have established their own architectures, standards and protocols, b) have special
requirements, and c) have their own partial catalogues that need to be integrated with the
Catalogue of Life in a two way flow. In each case i4Life has designed and implemented,
and is now testing the necessary special data pipelines, and contributing to enhancement of
the Catalogue of Life taxonomic coverage through input from the global partners. By
providing access to a common species catalogue within each organisation, we expect to
contribute a much needed level of knowledge integrity across the various scientific and
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community studies of the global biota. To make sense of global biodiversity it is vital that
these organisations can communicate through a unified view of the extent of life.
Figure 1 – The Six Global Biodiversity Partners in i4Life are Becoming Interlinked
with the Taxonomic Backbone of the Catalogue of Life
A host of independently-run and separately-funded programmes are making progress in
documenting specific dimensions of global and regional biodiversity. But progress is slower
in synthesising these data into more broadly coherent pictures of life on earth, its processes
of change, and opportunities for its sustainable management. Most such programmes are
“owned” by one country or regional authority: the Catalogue of Life is not – it provides free
access to data via a web portal. Across various data portals information on species, in
particular, is fragmented and confused, with different standards and cultural perspectives
persisting in each. The Catalogue of Life offers the opportunity to bridge those gaps and
through the i4Life project, is building the required linkage – an ecosystem of services for
standardised species naming and classification.
The Catalogue of Life is a long existing and widely used product. The community of
users of the Catalogue of Life is developing to encompass a wealth of public, scientific,
societal and commercial needs for a single, consistent and reliable index of the world’s
species (Figure 2)
Figure 2
Community of Users of the Catalogue of Life
Apart from its many individual users, the CoL provides services to global biodiversity
portals. GBIF has used the COL as its taxonomic backbone since 2007. The Encyclopaedia
of Life has used the CoL as its taxonomic backbone from the beginning. Thanks to the
i4Life project this cooperation is now strengthened.
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Although the majority of visits to the Catalogue of Life portal are from North America
and Europe, the Catalogue of Life has is widely used in African countries as well. The map
below provides information about the distribution of visits to the CoL by country in Africa
(fig 3). There is no indication of direct use of the Catalogue of Life web portal so far from
following countries: Chad, Equatorial Guinea, Eritrea, Guinea-Bissau, Sierra Leone,
Western Sahara and South Sudan. However in addition to online functionality, the
Catalogue of Life Annual Edition is distributed in DVD form to many places around the
world including many African countries. We have sent DVDs directly on individual request
to 16 African countries including most of the countries listed above, with exception of
Western Sahara and South Sudan. We also send DVDs to GTI/CHM Focal Points which
send out DVDs to 49 countries in Africa; and to GBIF and GBIF Node Managers covering
16 African countries.
Figure 3 Distribution of online visits from Africa to CoL; by country (Google statistics 2013).
2.
Objectives
The principle goal if i4Life has been to establish the Virtual Research Community that will
interlink and harmonise the global taxonomic catalogues presently developed by each of the
global partners. The existing Catalogue of Life has been used as a backbone.
1. The project has conducted gap analysis in our knowledge and to facilitate
communication among scientists and among all people with an interest in life on earth.
2. It has enabled the programme of each global partner to enhance its catalogue with the
assistance of the others, and to create a harmonised list for the entire set of organisms.
3. i4Life will for the first time provide a summary of all species known across these
programmes.
4. It is creating a global standard for taxonomic data integration in electronic
infrastructures world-wide.
5. It has built on the work of the 4D4Life Project that presently supports the internal
‘service ecosystem’ of the Species 2000 Catalogue of Life database networks.
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3.
Methodology
The global programme partners are exploring or aggregating knowledge on the extent of
species diversity on earth as a part of their scientific work on different aspects of global
biodiversity: global species distribution modelling, genome and sequence diversity, species
identification using DNA Barcodes, conservation etc. Several of these programmes use and
publish well-developed and widely used taxonomic catalogues – for instance the IUCN Red
List, and the NCBI Taxonomy displayed in EBI. This project is to take the first steps
towards a global virtual research community working with these leading global
organisations (the five global programmes plus the CoL) to share some of the responsibility
for exploring and cataloguing the extent of species diversity, making use where appropriate
of the CoL as a common base, alongside their own catalogues (fig 5).
It includes both practical installations and informatics:
1. Installing the Catalogue of Life within each global partner’s informatics platform,
and making it available for comparison with its own taxonomy and, where
appropriate, for that organisation’s user interface.
2. Establishing maintained cross-maps at the taxonomic concept level, so that internal
staff and external users of each organisation can, where appropriate, see the
relations between their own taxonomy and that of the CoL.
3. Establishing a workflow by which each organisation can make contributions of
missing taxa and names to the CoL. Although large and growing, the CoL remains
patchily incomplete. Data flow from partners can provide both additional names and
taxa encountered in their present system, and the ongoing inflow of new taxa for
reasons related to their own business. Because the CoL is a federated system with
taxonomic expert responsibilities taken by an array of 115 organisations, this
exercise also requires an extensive new workflow within the CoL organisation. In
some cases adding the precise taxa or names used by one of the global partner
organisations will add significantly to the usability of the CoL within that
community.
Figure 5
4.
Technology Description
The Virtual Research Network established by i4Life has the largest direct impact on the
working process, on the standardisation, and on the coherent outcomes for those working
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on species explorations and documentation within the Global Programmes.
To fulfil goals of the project, three workflows have been established:
1. The Download Tools Workflow - the purpose of this workflow is to deliver the
download tool. The download format for data exchange across the project is the
Darwin Core Archive format (DwC-A) [22] [23]. Download service is operational.
2. The Cross-mapping Tools Workflow - the purpose of this workflow is to deliver the
cross-mapping tool. The development version of the tool is operational.
3. The CoL Piping Tools Workflow - the purpose of this workflow is to deliver the
Piping tool. The development version of the tool is operational.
These tools provide a web-accessible route to connect data among the partners and to
deliver output in Darwin Core Archive format to users. Development is through an
international partnership lead by Reading University with collaborators at ETI
Bioinformatics (Netherlands) and Cardiff University (UK).
The overview of the Workflow is given in the diagram below (Figure 6).
Fig. 6 – The i4Life systems diagram. GBPs – Global Biodiversity Programmes, GSDs
– the Catalogue of Life source databases called Global Species Databases.
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5.
Developments
One of the tasks in the project was to establish a workflow that delivers refreshed instances
of the Catalogue of Life taxonomy within the very heterogeneous working platforms and
portals of the global programme partners (GBIF, EBI, ECBOL, IUCN and LifeWatch),
using a CoL download service developed by ETI as its base. The i4Life project has
designed and implemented the enhanced download service of the Catalogue of Life which
serves all global partners. This service is currently available only within the project, but the
next stage of development will be to open the service more widely.
One of the crucial things needed for comparison between differing catalogues and for
the partners to be able to share species information, is a tool allowing taxonomic crossmapping between lists of names present in each of them. This will enable identification of
how taxonomy differs from one organisation to another. The cross-mapping tools have been
developed by the team from Cardiff University and the first phase of development has
finished. Establishing the relationships among names and actual species is a complex
process usually requiring experience and knowledge however a large element of the work
can be entirely or partially automated. However the software has to cope with relationships
as simple as “equal to” and as complex as “partially included in” or “overlaps with”. These
can be very challenging to work out.
The piping tools are designed to improve quality of the taxonomic backbone of the
i4Life partner’s databases. The piping tools workflow developed at Reading University
accepts submission of lists of species names that are not in the CoL database and then
assigns them to the relevant GSDs for inclusion into their taxonomic databases. This has
been achieved by providing a web based user interface for name-list uploads, downloads,
reporting placement status, commenting on species and taxa names, and displaying workflow statistics and progress. The piping tools are operational and were already in use to
serve data distribution for the i4Life pilot projects.
A key to achieve project objectives was a transformation of the Catalogue of Life data
to a common, internationally recognised data exchange format. The initial specification of a
reduced DwC-A format agreed in the first year of the project was enhanced and refined
during the second year into a document called ‘The i4Life DwC-A profile’ (www.i4life.eu).
This document forms the basis for a common checklist exchange format.
6.
Results
A project specific version of the DwC-A format has been specified and is in use across the
project for exchanging information between the partners and the Catalogue of Life.
The initial implementation of tools in Global Partner Organisations has started.
The GBIF data portal has now upgraded from the 2007 Catalogue of Life with 1 million
species to current version of the Catalogue containing almost 1.4 million species. This
increased coverage by the Catalogue of Life has already helped to resolve some of the
problematic taxonomic records in the GBIF data portal making searches more successful.
The DNA database at EBI now has a public taxon portal available in prototype and EBI
are currently engineering a more robust backend data warehouse to support this. There are
more than 800000 species (and infraspecies) in the EBI database.
The first implementation linking the IUCN Red List web site to the CoL using the CoL
webservice has been completed and allows outside users to get information that a species
name they have searched for is not in IUCN but is in CoL. The fundamental importance of
that is that the user is reassured they have searched for a real species with a recognised
spelling and is not tempted to try other name spellings or to just give up their search.
The specification of how the Catalogue of Life will cooperate with the Barcode
community was discussed and agreed. A connection with the BOLD database will be done
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through the BOLD European Mirror based in Utrecht (KNAW). The first stage of the
process in which the Catalogue of Life will be incorporated into the BOLD platform was
achieved.
The pipeline between the Catalogue of Life and the EDIT platform (part of the
LifeWatch project) has been implemented. The specification addresses both the data flow
between the two platforms and the element mapping between concepts of the DwC-A
format and the EDIT-CDM.
The i4Life download service has been successfully used for data quality measures in the
OpenUp! (http://open-up.eu/ ) project. The service is part of the “Data Quality Toolkit”
used by curators of specimen databases to check names associated with zoological objects.
In the first 6 months of deployment of the Data Quality Toolkit already 220,000 zoological
metadata records have been checked. With this, the i4Life download services contributes
significantly to the quality and retrievability of collection data provided by European
Natural History collections.
The Cross-mapping tools have also been adopted by the related EC-funded EU-Brazil
OpenBio (http://www.eubrazilopenbio.eu/Pages/Home.aspx ) project, and adapted for use
within the GCUBE high-performance computing environment, and the cross-mapping
software design is being incorporated as a service within the EC-funded BioVeL
(http://www.biovel.eu/) project. It is therefore becoming recognised as a product which can
contribute to the scientific infrastructure of a number of biodiversity initiatives, helping to
support inter-operation at the taxonomic level between heterogeneous data sets.
7.
Business Benefits
Given the huge societal, political, and economic interest in global biodiversity, these six
global biodiversity data organisations (with their network partners) thus find themselves the
bearers of a significant world responsibility, both in enumerating the extent of species
diversity and in the assembly of an electronic taxonomic backbone that can serve society’s
needs all around the world. The UN Convention on Biological Diversity has clearly
recognised the significance and urgency of this task.
i4Life is projected to make significant impact in five key areas:
1. The single largest impact will be to put in place the process of integration between the
major global biodiversity programmes, so that those in molecular biology, biodiversity
science, ecology and conservation can co-operate in the creation of a single
authoritative catalogue showing the detail and extent of species on earth.
2. Opening up a range of electronic e-taxonomy services as infrastructure that can be built
into the main global biodiversity information portals: GBIF, EBI, Barcode initiative,
IUCN, LifeWatch, EoL.
3. Opening up the same range of electronic e-taxonomy services as infrastructure that can
become part of the seamless architecture of biodiversity informatics, and available to be
built into the much wider range of national local and NGO portals in Europe and around
the world, and into novel experimental systems subject of a growing research and
development community. This will provide a significant contribution to the connected
structures needed for the global virtual biodiversity analysis laboratory prioritised and
endorsed by the e-Biosphere 09 ‘Roadmap’ planning group of June 4/5 2009.
4. Opening up the same range, plus additional specially tailored e-taxonomy services to
certain scientific communities, such as the biodiversity and climate change modelling
community, the oceanographic community, and the genomics community.
5. And finally, simply by enhancing Catalogue of Life content and services for global
biodiversity partners we anticipate significant impact on the wider user community.
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8.
Conclusions
This project is providing a vital and significant improvement to the provision of a world
species list and, co-working with the global programmes, as a vital first step to facilitate
many future improvements. The technology is now in place to deliver an enhanced
Catalogue of Life via a dedicated data portal (www.catalogueoflife.org) with associated
services and archived annual checklists. It also develops a range of additional services
which are planned to serve the global biodiversity community in its common goal to
enhance data quality and harmonise the species catalogues worldwide.
List of Terms Used in the Text
The Catalogue of Life - The Catalogue of Life, started in June 2001 by Species 2000 and
Integrated Taxonomic Information System (ITIS), is becoming a comprehensive catalogue
of all known species of organisms on Earth. The Catalogue currently compiles data from
115 peer-reviewed taxonomic databases that are maintained by specialist institutions around
the world. The twelfth annual edition of the catalogue (May 2012) included 1,404,038
species.
Species2000 - Species 2000 is a federation of database organizations across the world that
compiles the Catalogue of Life, a comprehensive checklist of the world's species, in
partnership with the Integrated Taxonomic Information System (ITIS). Species 2000 was
initiated by Frank Bisby and colleagues at the University of Reading in the UK in 1997 and
the Catalogue of Life was first published in 2001.
ITIS - The Integrated Taxonomic Information System (ITIS) is a partnership designed to
provide consistent and reliable information on the taxonomy of biological species. ITIS was
originally formed in 1996 as an interagency group within the U.S. federal government,
involving several US Federal agencies and has now become an international body, with
Canadian and Mexican government agencies participating.
GBIF - The Global Biodiversity Information Facility (GBIF) - an international organisation
that focuses on making scientific data on biodiversity available via the Internet using web
services.
IUCN RedList - Provides taxonomic, conservation status, and distribution information on
taxa that are facing a risk of global extinction.
ENA at EBI - The European Nucleotide Archive (ENA) captures and presents information
relating to experimental workflows that are based around nucleotide sequencing.
INSDC - International Nucleotide Sequence Database Collaboration. The International
Nucleotide Sequence Databases (INSD) have been developed and maintained
collaboratively between DDBJ, ENA, and GenBank for over 18 years.
NCBI - National Center for Biotechnology Information. U.S. government-funded national
resource for molecular biology information.
BOLD - The Barcode of Life Database is designed to support the generation and
application of DNA Barcode data.
EoL - The Encyclopedia of Life, a free, online collaborative encyclopedia intended to
document all of the 1.9 million living species known to science.
LifeWatch
is
a
European
research
infrastructure
in
development
http://www.lifewatch.eu/en_GB
DwC-A - Darwin Core Archive is a Biodiversity informatics data standard that makes use
of the Darwin Core terms to produce a single, self-contained dataset for species occurrence
or checklist data (http://www.gbif.org/informatics/standards-and-tools/publishing-data/datastandards/darwin-core-archives/ )
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Acknowledgement
Indexing for Life (i4Life) is a European e-Infrastructure project co-funded by the European Commission’s
Seventh Framework Programme for Research and Technological Development.
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