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1 A Systematic Nomenclature for Embryo Anatomy MRC, Human Genetics Unit Heriot-Watt University, Dept. of Comp & EE, Albert Burger.

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Presentation on theme: "1 A Systematic Nomenclature for Embryo Anatomy MRC, Human Genetics Unit Heriot-Watt University, Dept. of Comp & EE, Albert Burger."— Presentation transcript:

1 1 A Systematic Nomenclature for Embryo Anatomy MRC, Human Genetics Unit Heriot-Watt University, Dept. of Comp & EE, Albert Burger

2 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop2 Overview MRC’s Mouse Atlas project; Anatomy Hierarchies; EdAMS; XSPAN; Conclusion;

3 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop3 MRC Mouse Atlas and Gene Expression Project EMAP: Edinburgh Mouse Atlas Project: Anatomy Reconstructions; Anatomy Domains; Systematic Nomenclature; EMAGE: Edinburgh Mouse Atlas Gene- Expression Database; Project leaders: Richard Baldock and Duncan Davidson;

4 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop4 EMAP: Spatio-Temporal Framework for Developmental Biology Iconic Symbolic Space

5 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop5 EMAP: Anatomy Browser

6 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop6

7 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop7 Anatomy Hierarchies A BC Stage i A BC DEFG Stage j

8 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop8 Anatomy Hierarchies A BC Stage i A BC DEFG Stage j H

9 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop9 Anatomy Hierarchies A BC Stage i A BC DEFG Stage j H

10 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop10 Abstract Mouse A BC Stage i A BD CE Stage j A BD CE C A BD E C or

11 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop11 EdAMS Edinburgh Anatomy Mapping System: a first attempt to deal with cross-species embryo anatomy; Collaboration between MRC, Heriot-Watt University and Edinburgh University; CORBA-based system to interoperate between embryo anatomy databases;

12 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop12 Basic Approach use of a mapping database that stores confirmed mappings between tissues of different species; database editor(s) control content of mapping database; mapping rules are used to suggest possible mappings to editor(s); confirmation, rejection and annotation stored in database;

13 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop13 A mapping query can be based on mapping database only; original anatomy databases plus a set of mapping rules; combination of both; (In case a rule has applied, but the same mapping has previously been explicitly rejected by an editor, the mapping is not shown to the user. )

14 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop14 Mapping Rules Given a term such as /embryo/branchial arch/1st arch/branchial groove we refer to /embryo/branchial arch/1st arch as being the path and branchial groove as the component name or simply the name.

15 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop15 Exact String Matching: A component maps to another if their names match exactly. Substring Matching: A component maps to another if their names have a common substring of a user-defined length. Character Matching: A component maps to another if the letters of their names are the same for a user-defined percentage (for example over 70%). String Matching: (applied to name)

16 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop16 Exact Path Matching: A component maps to another if their paths are exactly the same. Sub Path Matching: A component maps to another if a user-defined number of components of their paths match. Parent Matching: A component maps to another if the last part of their paths is identical. Path Matching: (applied to path)

17 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop17 X in species S1 has been mapped to Y in species S2 Y in species S2 has been mapped to Z in species S X in species S1 is mapped to Z in species S3 The rule is only applied to mappings confirmed in the mapping database to avoid large result sets which contain a high proportion of unwanted entries. X in S1Y in S2Z in S3 Transitivity Matching

18 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop18 X1 in species S1 gives rise to X2 in S1 Y1 in species S2 gives rise to Y2 in S2 X1 in species S1 has been mapped to Y1 in species S X2 in species S1 is mapped to Y2 in species S2 X1 in S1X2 in S1 Y1 in S2Y2 in S2 Lineage Matching

19 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop19 X1 in species S1 is spatially connected to X2 in S1 Y1 in species S2 is spatially connected to Y2 in S2 X1 in species S1 has been mapped to Y1 in species S X2 in species S1 is mapped to Y2 in species S2 X1 in S1X2 in S1 Y1 in S2Y2 in S2 Spatial Matching

20 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop20 EdAMS Software Architecture:

21 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop21

22 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop22

23 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop23

24 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop24 XSPAN Cross-Species Anatomy Network; Joint project between Heriot-Watt University and Edinburgh University; Funded under BBSRC’s e-Science Bioinformatics initiative; Two phases: XSPAN core; XSPAN ontology; To be hosted at MRC HGU, Edinburgh; Datasets: Mouse, Human, Zebrafish, Drosophila, C. elegans;

25 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop25 XSPAN: People Heriot-Watt Uni. Albert Burger Werner Nutt Patrick Holt Gus Ferguson Kenneth McLeod Aba-Sah Dadzie Edinburgh Uni. Jonathan Bard Bonnie Webber Stuart Aitken …

26 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop26 XSPAN core: Make use of existing datasets; Distributed approach vs central data warehouse approach; Developing a generic XML Schema for embryo anatomy (for interoperability); Graphical User Interfaces and program level access (Web Service?); To include heuristics (as in EdAMS), natural language processing techniques and confirmed and rejected mappings database;

27 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop27 XSPAN ontology Formalisation of embryo anatomy ontologies; Use of DAML+OIL, OWL, … ; Additional reasoning capabilities (FaCT); To be integrated with XSPAN-core;

28 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop28 XSPAN Issues Update problem: underlying embryo databases can/will change; XSPAN-ontology to eventually replace XSPAN-core or co-exist? How to make use of XSPAN-core to provide semi- automatic support for the creation of XSPAN- ontology? How to make XSPAN available to maximise interoperability with other bioinformatics resources (not just other ontologies)? What software support can be given to make building XSPAN a community effort?

29 A Systematic Nomenclature for Embryo Anatomy 24 March 2002Manchester Bioinformatics Week: Ontology Workshop29 Conclusion Systematic nomenclature for mouse embryo anatomy as part of MRC Mouse Atlas project; Cross-Species Embryo Anatomy: EdAMS; XSPAN;


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