Biodiversity Informatics at COMSC

Cardiff School of Computer Science & Informatics

Biodiversity Informatics at COMSCBiodiversity Informatics at

COMSC

Andrew Jones & Richard White

School of Computer Science & Informatics

[email protected]@cs.cf.ac.uk

2Cardiff School of Computer Science & Informatics

Richard White’s interests

• Design and construction of database systems to deliver biodiversity data

• Methods for making these systems – interoperable with other systems– adaptable for multiple uses– capable of following concept changes

• deducing and maintaining information on changes

• (Extracting numerical information from images, e.g. in “Morphidas” project, not described here)


Premise

• Bioinformaticians want to use information about the species whose genetic material is being studied to understand their development

• Biodiversity scientists (including taxonomists, ecologists, etc.) want to use molecular data to enhance their classifications, phylogenies and models


Biodiversity informatics

Therefore

• Bioinformatic and biodiversity data need to be linked together in many analyses

• Links often involve the species name as the key linking element


Species naming in a nutshell (Corylus avellana L.)

• Common (vernacular) names• Latin descriptive phrases• Linnaeus: binomial nomenclature• Adanson: rules for precedence etc. • Accepted names and synonyms• Checklists (e.g. the Catalogue of Life …)• Data (in different formats, e.g. Buffie …) is

usually linked to species names• Taxon concepts (including species and higher

taxa such as genera, families, etc.)• Tracking changes in taxon concepts …


Species 2000 & ITIS

• International programme to assemble data from “Global Species Databases” (GSDs) and deliver the Catalogue of Life (CoL)

• Authoritative up-to-date checklist of all the world’s species (1.3 out of 1.8m)

• Reference list of taxon concepts (with unique identifiers) to aid indexing and cross-referencing of species data sources

• Available on DVD, through the Web (www.sp2000.org) and by using electronic (“web”) services


The Catalogue of Life


4D4Life project

• “Distributed Dynamic Diversity Databases for Life”, EU project 2009 – 2012

• Carry the Catalogue of Life forward with improved sustainable infrastructure

• In COMSC we are designing a new architecture and will deliver a working prototype

• Service-oriented, re-usable components


Re-usable components

1. GSD editors create a data resource “GSD1”

2. CoL partners create the Catalogue of Life from such resources

3. A user creates a new product using the Catalogue of Life

1 2 3


Interoperability

• Catalogue of Life– GSDs are heterogeneous in

• Content

• Access methods

• More generally– Multiple data representations & exchange

formats– Changing concepts of taxa (and geography)


ENBI project and BUFFIE

• “European Network for Biodiversity Information”, EU project 2003-2006

• Mostly reporting on standards, practices and recommendations

• In COMSC, R. Sundaravadivelu developed a prototype interoperability demonstrator (BUFFIE, “Biodiversity Users Framework For Information Exchange”)

• Accepts data sources using different protocols and XML formats

• Provides a merged response in an XML format and protocol of the user’s choice


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A world of resources

• Imagine a digital world full of biodiversity data and analytical resources like these, just as there is in bioinformatics

• How will users be able to find out what resources there are and how to use them in combination to answer scientific questions?


The cross-mapping problem

Taxonomy 1

Vicia faba

Caesalpinia crista L.

Taxonomy 2

Faba faba

Caesalpinia crista L.

Caesalpinia bonduc (L.) Roxb.

Caesalpinia crista L., p.p.


i4Life

4D4Life


Constraints and checklists

• (From Litchi 1)

• “A full name which is not a pro-parte name may not appear as both an accepted name and a synonym in the same checklist”


Persistent identifiers and change

In i4Life we need to

• Use persistent identifiers for taxon concepts– (started in TDWG-TIP project)

• Link taxonomies and track change– create and maintain “cross-maps”


Joining things up: workflow systems



Workflow problems addressed

• Incorporation of biodiversity services in workflows (BiodiversityWorld)

• Authentication in a workflow environment (ASMIMA)

• Rich annotation of services; discovery (Ewen Orme’s PhD)

• Knowledge-based assistance for workflow creators (Russell McIver’s PhD)

• Improving the User Experience (ACJ’s main contribution to BioVeL proposal)


Andrew Jones’ interests

• Naming & concepts– Accurately identifying concepts– Tracking change

• Making scientific workflow systems usable by non-computer scientists– Hiding “programming” complexity– Helping to find resources & build workflows

• Environments to support collaborative scientific research– E.g. “doing” taxonomy


Future projects

• We research solutions for data-handling problems faced by biologists and bioinformaticians

• If you think you might have an interesting and challenging problem, please get in touch

• [email protected] [email protected]

Documents

Biodiversity Informatics at COMSC