Cardiff School of Computer Science & Informatics Biodiversity Informatics at COMSC Andrew Jones & Richard White School of Computer Science & Informatics

Cardiff School of Computer Science & Informatics 2 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)

Cardiff School of Computer Science & Informatics 3 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

Cardiff School of Computer Science & Informatics 4 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

Cardiff School of Computer Science & Informatics 5 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 …

Cardiff School of Computer Science & Informatics 6 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 ( and by using electronic (“web”) services

Cardiff School of Computer Science & Informatics 7 The Catalogue of Life

Cardiff School of Computer Science & Informatics 8 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

Cardiff School of Computer Science & Informatics 9 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 123

Cardiff School of Computer Science & Informatics 10 Interoperability Catalogue of Life –GSDs are heterogeneous in Content Access methods More generally –Multiple data representations & exchange formats –Changing concepts of taxa (and geography)

Cardiff School of Computer Science & Informatics 11 ENBI project and BUFFIE “European Network for Biodiversity Information”, EU project 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

Cardiff School of Computer Science & Informatics 12 THIS SLIDE INTENTIONALLY LEFT NOT QUITE BLANK

Cardiff School of Computer Science & Informatics 13 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?

Cardiff School of Computer Science & Informatics 14 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.

Cardiff School of Computer Science & Informatics 15 i4Life 4D4Life

Cardiff School of Computer Science & Informatics 16 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”

Cardiff School of Computer Science & Informatics 17 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”

Cardiff School of Computer Science & Informatics 18 Joining things up: workflow systems

Cardiff School of Computer Science & Informatics 19

Cardiff School of Computer Science & Informatics 20 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)

Cardiff School of Computer Science & Informatics 21 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

Cardiff School of Computer Science & Informatics 22 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