Difference between revisions of "CARO:Main Page"

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This wiki (hosted on the main NCBO public wiki) will contain information on the new CARO reference ontology of anatomy, combining FMA and model organism anatomical ontologies. How this will be achieved is yet to be decided...
 
This wiki (hosted on the main NCBO public wiki) will contain information on the new CARO reference ontology of anatomy, combining FMA and model organism anatomical ontologies. How this will be achieved is yet to be decided...
 +
 +
CARO is available from OBO
 +
 +
* http://obo.sourceforge.net/cgi-bin/detail.cgi?caro
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See Also
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* [http://research-service.com/custom-research-paper.html research paper]
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The OWL version is available at:
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* http://purl.org/obo/owl/CARO
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A chapter summarizing the current status of CARO and the conclusions drawn from the NCBO anatomy workshop in September, 06, is available here:
 +
 +
[[Media:CAROchapter.pdf|CAROchapter.pdf]]
 +
 +
This chapter is being published in a book on Anatomy Ontologies:
 +
 +
Anatomy Ontologies for Bioinformatics: Principles and Practice
 +
Albert Burger, Duncan Davidson and Richard Baldock (Editors)
 +
 +
Please email the anatomy listserve with suggestions and comments.
 +
 +
* [mailto:obo-anatomy@lists.sourceforge.net obo-anatomy@lists.sourceforge.net]
 +
 +
 +
== Draft Versions (previous) ==
 +
 +
[[Media:CAROtest.doc|CAROtest.obo]]
 +
 +
[[Media:CAROtest2.doc|CAROtest2.obo]]
 +
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[[Media:CAROtest3.doc|CAROtest3.obo]]
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Version below is being published in a book on Anatomy ontologies, edited by Richard Baldock, Duncan Davidson, and Albert Burger.
 +
[[Media:CAROtest8.doc|CAROtest8.obo]]
  
 
=Resources=
 
=Resources=
  
 
==Mail Lists==
 
==Mail Lists==
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- [http://listserv.buffalo.edu/archives/ontology-of-anatomy-list.html CARO] (not in use)
  
 
- [https://lists.sourceforge.net/lists/listinfo/obo-cell-type OBO Cell]
 
- [https://lists.sourceforge.net/lists/listinfo/obo-cell-type OBO Cell]
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http://www.bioontology.org/wiki/index.php/Anatomy_Ontology_Workshop
 
http://www.bioontology.org/wiki/index.php/Anatomy_Ontology_Workshop
  
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=Background Material=
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=Meeting presentations=
  
−
This is intended as a source of background reading material primarily for the workshop participants. Please help and add more!
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==Seattle 09/06 presentations==
 +
Please see the shared materials page for meeting minutes and presentations:
  
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==Anatomy working group discussion points - notes to follow soon==
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http://www.bioontology.org/wiki/index.php/hinxton_meeting_March_2008
  
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1. Integration of MOD-specific anatomy ontologies, the Cell Ontology, and the Gene Ontology Cellular Component into CARO. Use of taxonomy ontology to limit terms in CARO to specific organisms.
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http://www.bioontology.org/wiki/index.php/Shared_Materials#CARO_September_2006_meeting
  
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2. How MODs can use stages with anatomy ontologies.  Relations required for doing this. Rules for using these relations.
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=Background Material=
  
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3. The develops_from relationship.
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This is intended as a source of background reading material primarily for the workshop participants. Please help and add more!
  
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4. Axes of catagorization.  There could be three- functional, structural, and developmental.
 
  
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5. Spatial relations. Where do they live?  How can they be used?
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==Use cases==
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(posted by Melissa Haendel)
  
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6. Sex specific anatomical terms.
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Neural tube development:
  
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7. Requirements for ontology editing software.
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The vertebrate nervous system begins its development as a neural plate, which then "rolls up" into the neural tube (this is very simplified -there are a variety of mechanisms to get from a plate to a tube). The neural tube develops from the neural plate in a generally anterior to posterior direction. At any given time during this transition, both exist.  A picture of this can be seen here:
 +
http://www.sciencemuseum.org.uk/on-line/lifecycle/11.asp
  
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8. Genus differentia definitions.
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An annotation example could be that at a given stage, gene x is in neural tube but not neural plate, gene y is in both, and gene z is in neural plate but not neural tube.
  
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9. Homology.  No, we can't get away from it.  We don't have to deal with it now, but we do need a plan.
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[details of the problems of encoding this in an ontology of anatomical continuants to follow shortly (ds)]
  
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10. part_of and has_part.
 
  
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11. A proposal for CARO implementation (a many year plan):
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Lateral line development:
  
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Stage 1: generic CARO (no links to organisms). To be used by MODs to help organize their anatomies, and to begin synchronization across species.
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The lateral line placode gives rise to two entities, the lateral line ganglion and the lateral line primordium. A portion of cells in the placode move away posteriorly as the primordium, and the remaining portion of the placode will become the ganglion.  The primordium deposits neuromasts as it travels posteriorly. These neuromasts will eventually be connected together by way of the lateral line nerve, which has its cell bodies in the ganglion and sends signals to the brain.  The nerve and the neuromasts and the ganglion are are collectively referred to as the lateral line.  This term is often used before the process is complete. Here is a picture:
  
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Stage 2: have functional categories and link to taxonomy ontology.
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http://www.neurodvpmt.univ-montp2.fr/model/latline.html
  
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Stage 3: have homology tables between structures with evidence codes and citations. Slurp up all of the anatomy ontologies with dbxrefs.
 
  
  
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==Use cases==
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Early urogenital development (posted by MAH for Jonathan Bard and Stuart Aitken)
  
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Neural tube development:
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This informal text description of the early urogenital system tries to link the developmental
 +
anatomy (tissues) with their associated cell types to (1) the underlying processes
 +
underpinning development and (2) the changes in differentiation that give rise to new cells
 +
types. The description uses DEFINED TIME SLOTS (from Theiller stages (TS) = 12h here, partly
 +
for standardization and partly as this is the granularity of GXD, the mouse gene-expression
 +
database). A simplified graphical version is given at the end.
  
−
The neural tube develops from the neural plate in a generally anterior to posterior direction. At any given time during this transition, both exist...
+
It is also worth noting that, in principle at least, each time-dependent tissue, cell type and
 +
developmental process can be assigned an EMAP, CL or GO ID, and the tissues can be linked
 +
to the GXD database to give gene expression data. It is thus relatively straightforward to
 +
produce a complete systems description of the molecules, cell types, tissues and processes
 +
that enable the intermediate mesenchyme to produce the gonad and the metanephros.
  
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. A picture of this can be seen here:
 
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http://www.sciencemuseum.org.uk/on-line/lifecycle/11.asp
 
  
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(details of how to cope with this to follow)
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[[Media:CARO-UG-development-JB.pdf|mouse urogenital development pdf]]
  
 
==Relations==
 
==Relations==
  
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Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall CJ, Neuhaus F, Rector A, Rosse C
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[http://genomebiology.com/2005/6/5/R46 Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall CJ, Neuhaus F, Rector A, Rosse C.  Relations in Biomedical Ontologies Genome Biology, 2005, 6:R46]
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Relations in Biomedical Ontologies
 
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Genome Biology, 2005, 6:R46
 
 
   
 
   
 
[http://obo.sourceforge.net/relationship OBO Relations]
 
[http://obo.sourceforge.net/relationship OBO Relations]
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http://sigpubs.biostr.washington.edu/archive/00000135/
 
http://sigpubs.biostr.washington.edu/archive/00000135/
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 +
Mejino JLV Jr, Rosse C. 2004. Symbolic modeling of structural relationships in the Foundational Model of Anatomy. In Proceedings: First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004), Whistler Mountain, B.C., Canada; pp 48-62.
 +
 +
http://sigpubs.biostr.washington.edu/archive/00000155/
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Mejino, Jose L V, Agoncillo, Augusto V, Rickard, K. L. and Rosse, Cornelius (2003) Representing Complexity in Part-Whole Relationships within the Foundational Model of Anatomy. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 450-454.
 +
 +
http://sigpubs.biostr.washington.edu/archive/00000140/
  
 
Barry Smith, Jose L.V. Mejino Jr., Stefan Schulz, Anand Kumar and Cornelius Rosse, “Anatomical Information Science”, in A. G. Cohn and D. M. Mark (eds.), Spatial Information Theory. Proceedings of COSIT 2005 (Lecture Notes in Computer Science), Berlin/Heidelberg/New York: Springer, 149–164.
 
Barry Smith, Jose L.V. Mejino Jr., Stefan Schulz, Anand Kumar and Cornelius Rosse, “Anatomical Information Science”, in A. G. Cohn and D. M. Mark (eds.), Spatial Information Theory. Proceedings of COSIT 2005 (Lecture Notes in Computer Science), Berlin/Heidelberg/New York: Springer, 149–164.
  
 
http://ontology.buffalo.edu/anatomy_GIS/FMA-AIS.pdf
 
http://ontology.buffalo.edu/anatomy_GIS/FMA-AIS.pdf
 +
 +
Michael, J. and Mejino, Jose L V and Rosse, Cornelius (2001) The Role of Definitions in Biomedical Concept Representation. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 463-467.
 +
 +
http://sigpubs.biostr.washington.edu/archive/00000148/
  
 
Ingvar Johansson, Barry Smith, Katherine Munn, Nikoloz Tsikolia, Kathleen Elsner, Dominikus Ernst, and Dirk Siebert, "Functional Anatomy: A Taxonomic Proposal”
 
Ingvar Johansson, Barry Smith, Katherine Munn, Nikoloz Tsikolia, Kathleen Elsner, Dominikus Ernst, and Dirk Siebert, "Functional Anatomy: A Taxonomic Proposal”
Line 102: Line 158:
 
Pierre Grenon, Barry Smith and Louis Goldberg, “Biodynamic Ontology: Applying BFO in the Biomedical Domain”, in D. M. Pisanelli (ed.), Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies, Rome October 2003 (Studies in Health and Technology Informatics, 102 (2004)), Amsterdam: IOS Press, 2004, 20–38.
 
Pierre Grenon, Barry Smith and Louis Goldberg, “Biodynamic Ontology: Applying BFO in the Biomedical Domain”, in D. M. Pisanelli (ed.), Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies, Rome October 2003 (Studies in Health and Technology Informatics, 102 (2004)), Amsterdam: IOS Press, 2004, 20–38.
 
http://ontology.buffalo.edu/medo/biodynamic.pdf
 
http://ontology.buffalo.edu/medo/biodynamic.pdf
−
 
−
 
  
 
==Model Organisms==
 
==Model Organisms==
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==Formal Ontology==
 
==Formal Ontology==
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==Uberon==
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 +
[[UBERON:Main_Page]]

Latest revision as of 12:50, 6 October 2009

CARO

Welcome to CARO!

This wiki (hosted on the main NCBO public wiki) will contain information on the new CARO reference ontology of anatomy, combining FMA and model organism anatomical ontologies. How this will be achieved is yet to be decided...

CARO is available from OBO

See Also

The OWL version is available at:

A chapter summarizing the current status of CARO and the conclusions drawn from the NCBO anatomy workshop in September, 06, is available here:

CAROchapter.pdf

This chapter is being published in a book on Anatomy Ontologies:

Anatomy Ontologies for Bioinformatics: Principles and Practice Albert Burger, Duncan Davidson and Richard Baldock (Editors)

Please email the anatomy listserve with suggestions and comments.


Draft Versions (previous)

CAROtest.obo

CAROtest2.obo

CAROtest3.obo

Version below is being published in a book on Anatomy ontologies, edited by Richard Baldock, Duncan Davidson, and Albert Burger. CAROtest8.obo

Resources

Mail Lists

- CARO (not in use)

- OBO Cell

- OBO Anatomy

The following list may also be of interest

- OBO CrossProduct

Meetings

http://www.bioontology.org/wiki/index.php/Anatomy_Ontology_Workshop

Meeting presentations

Seattle 09/06 presentations

Please see the shared materials page for meeting minutes and presentations:

http://www.bioontology.org/wiki/index.php/hinxton_meeting_March_2008

http://www.bioontology.org/wiki/index.php/Shared_Materials#CARO_September_2006_meeting

Background Material

This is intended as a source of background reading material primarily for the workshop participants. Please help and add more!


Use cases

(posted by Melissa Haendel)

Neural tube development:

The vertebrate nervous system begins its development as a neural plate, which then "rolls up" into the neural tube (this is very simplified -there are a variety of mechanisms to get from a plate to a tube). The neural tube develops from the neural plate in a generally anterior to posterior direction. At any given time during this transition, both exist. A picture of this can be seen here: http://www.sciencemuseum.org.uk/on-line/lifecycle/11.asp

An annotation example could be that at a given stage, gene x is in neural tube but not neural plate, gene y is in both, and gene z is in neural plate but not neural tube.

[details of the problems of encoding this in an ontology of anatomical continuants to follow shortly (ds)]


Lateral line development:

The lateral line placode gives rise to two entities, the lateral line ganglion and the lateral line primordium. A portion of cells in the placode move away posteriorly as the primordium, and the remaining portion of the placode will become the ganglion. The primordium deposits neuromasts as it travels posteriorly. These neuromasts will eventually be connected together by way of the lateral line nerve, which has its cell bodies in the ganglion and sends signals to the brain. The nerve and the neuromasts and the ganglion are are collectively referred to as the lateral line. This term is often used before the process is complete. Here is a picture:

http://www.neurodvpmt.univ-montp2.fr/model/latline.html


Early urogenital development (posted by MAH for Jonathan Bard and Stuart Aitken)

This informal text description of the early urogenital system tries to link the developmental anatomy (tissues) with their associated cell types to (1) the underlying processes underpinning development and (2) the changes in differentiation that give rise to new cells types. The description uses DEFINED TIME SLOTS (from Theiller stages (TS) = 12h here, partly for standardization and partly as this is the granularity of GXD, the mouse gene-expression database). A simplified graphical version is given at the end.

It is also worth noting that, in principle at least, each time-dependent tissue, cell type and developmental process can be assigned an EMAP, CL or GO ID, and the tissues can be linked to the GXD database to give gene expression data. It is thus relatively straightforward to produce a complete systems description of the molecules, cell types, tissues and processes that enable the intermediate mesenchyme to produce the gonad and the metanephros.


mouse urogenital development pdf

Relations

Smith B, Ceusters W, Klagges B, Kohler J, Kumar A, Lomax J, Mungall CJ, Neuhaus F, Rector A, Rosse C. Relations in Biomedical Ontologies Genome Biology, 2005, 6:R46

OBO Relations

See also RO:Main_Page, the main RO wiki

Fiat Boundaries

As we're in the business of carving up reality, this paper of Barry's might be useful:

http://wings.buffalo.edu/philosophy/faculty/smith/articles/fiatobjects.pdf

FMA

A Reference Ontology for Bioinformatics: "The Foundational Model of Anatomy" Rosse, Cornelius and Mejino, Jose L V (2003) A Reference Ontology for Bioinformatics: The Foundational Model of Anatomy. Journal of Biomedical Informatics 36:pp. 478-500

http://sigpubs.biostr.washington.edu/archive/00000135/

Mejino JLV Jr, Rosse C. 2004. Symbolic modeling of structural relationships in the Foundational Model of Anatomy. In Proceedings: First International Workshop on Formal Biomedical Knowledge Representation (KR-MED 2004), Whistler Mountain, B.C., Canada; pp 48-62.

http://sigpubs.biostr.washington.edu/archive/00000155/

Mejino, Jose L V, Agoncillo, Augusto V, Rickard, K. L. and Rosse, Cornelius (2003) Representing Complexity in Part-Whole Relationships within the Foundational Model of Anatomy. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 450-454.

http://sigpubs.biostr.washington.edu/archive/00000140/

Barry Smith, Jose L.V. Mejino Jr., Stefan Schulz, Anand Kumar and Cornelius Rosse, “Anatomical Information Science”, in A. G. Cohn and D. M. Mark (eds.), Spatial Information Theory. Proceedings of COSIT 2005 (Lecture Notes in Computer Science), Berlin/Heidelberg/New York: Springer, 149–164.

http://ontology.buffalo.edu/anatomy_GIS/FMA-AIS.pdf

Michael, J. and Mejino, Jose L V and Rosse, Cornelius (2001) The Role of Definitions in Biomedical Concept Representation. In Proceedings, American Medical Informatics Association Fall Symposium, pages pp. 463-467.

http://sigpubs.biostr.washington.edu/archive/00000148/

Ingvar Johansson, Barry Smith, Katherine Munn, Nikoloz Tsikolia, Kathleen Elsner, Dominikus Ernst, and Dirk Siebert, "Functional Anatomy: A Taxonomic Proposal” Acta Biotheoretica, 53(3), 2005, 153–166. http://ontology.buffalo.edu/medo/Functional_Anatomy.pdf

also on the static versus dynamic see:

Pierre Grenon, Barry Smith and Louis Goldberg, “Biodynamic Ontology: Applying BFO in the Biomedical Domain”, in D. M. Pisanelli (ed.), Ontologies in Medicine: Proceedings of the Workshop on Medical Ontologies, Rome October 2003 (Studies in Health and Technology Informatics, 102 (2004)), Amsterdam: IOS Press, 2004, 20–38. http://ontology.buffalo.edu/medo/biodynamic.pdf

Model Organisms

SAEL

Formal Ontology

Uberon

UBERON:Main_Page

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