CARO:Main Page

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...

Resources

Mail Lists

- 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

Background Material

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

Anatomy working group discussion points - notes to follow soon

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. Each MOD can make a cell type slim, and add it to their own AO, giving the terms organism specific IDs. It is implied that these terms have an is_a relationship to the terms in the CL, and they can be referenced using the dbxref field. Please see the following email thread for some discussion on this issue: http://sourceforge.net/mailarchive/forum.php?thread_id=20469590&forum_id=48471 This method may be too complex to integrate the cellular component ontology in any given MOD's AO. These terms can be post-composed.

2. How MODs can use stages with anatomy ontologies. Relations required for doing this. Rules for using these relations.

3. The develops_from relationship.

4. Axes of catagorization. There could be three- functional, structural, and developmental.

5. Spatial relations. Where do they live? How can they be used?

6. Sex specific anatomical terms.

7. Requirements for ontology editing software.

8. Genus differentia definitions.

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.

10. part_of and has_part.

11. A proposal for CARO implementation (a many year plan):

Stage 1: generic CARO (no links to organisms). To be used by MODs to help organize their anatomies, and to begin synchronization across species.

Stage 2: have functional categories and link to taxonomy ontology.

Stage 3: have homology tables between structures with evidence codes and citations. Slurp up all of the anatomy ontologies with dbxrefs.

Use cases

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

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/

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

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