A%20Systematic%20Nomenclature%20for%20Embryo%20Anatomy

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A Systematic Nomenclature for Embryo Anatomy
Albert Burger

• MRC, Human Genetics Unit
• Heriot-Watt University, Dept. of Comp EE,

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Overview

• MRCs Mouse Atlas project
• Anatomy Hierarchies
• EdAMS
• XSPAN
• Conclusion

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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

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EMAP Spatio-Temporal Framework for Developmental
Biology
Space
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EMAP Anatomy Browser
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Anatomy Hierarchies
Stage i
A
B
C
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Anatomy Hierarchies
Stage i
A
B
C
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Anatomy Hierarchies
Stage i
A
B
C
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Abstract Mouse
A
Stage i
A
B
D
C
B
C
C
E
or
Stage j
A
A
B
D
C
B
D
E
C
E
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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

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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

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• 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. )

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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.
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String Matching (applied to name)

• 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).

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Path Matching (applied to path)

• 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.

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Transitivity Matching

• X in species S1 has been mapped to Y in species
  S2
• Y in species S2 has been mapped to Z in species
  S3
• --------------------------------------------------
  -------------
• X in species S1 is mapped to Z in species S3

X in S1
Y in S2
Z in 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.
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Lineage Matching

• 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
  S2
• --------------------------------------------------
  -------------
• X2 in species S1 is mapped to Y2 in species S2

X1 in S1
X2 in S1
Y1 in S2
Y2 in S2
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Spatial Matching

• 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
  S2
• --------------------------------------------------
  -------------
• X2 in species S1 is mapped to Y2 in species S2

X1 in S1
X2 in S1
Y1 in S2
Y2 in S2
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EdAMS Software Architecture
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XSPAN

• Cross-Species Anatomy Network
• Joint project between Heriot-Watt University and
  Edinburgh University
• Funded under BBSRCs e-Science Bioinformatics
  initiative
• Two phases
• XSPAN core
• XSPAN ontology
• To be hosted at MRC HGU, Edinburgh
• Datasets Mouse, Human, Zebrafish, Drosophila, C.
  elegans

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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

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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

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XSPAN ontology

• Formalisation of embryo anatomy ontologies
• Use of DAMLOIL, OWL,
• Additional reasoning capabilities (FaCT)
• To be integrated with XSPAN-core

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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?

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Conclusion

• Systematic nomenclature for mouse embryo anatomy
  as part of MRC Mouse Atlas project
• Cross-Species Embryo Anatomy
• EdAMS
• XSPAN