Difference between revisions of "CARO:Main Page"
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This is intended as a source of background reading material primarily for the workshop participants. Please help and add more! | 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. | ||
| + | |||
| + | 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== | ||
| + | 1. The neural tube develops from the neural plate in a generally anterior to posterior direction. At any given time during this transition, both exist. One would never specify the subparts any more, yet when we say the neural tube at the stage at which both exist, we mean the portion that has become the neural tube. | ||
| + | |||
| + | neural thingy st 1-8 | ||
| + | p neural plate st 1-5 | ||
| + | d neural tube st 3-8 | ||
| + | p neural tube st 3-8 | ||
| + | |||
| + | An annotation example: gene x is in neural tube but not neural plate at stage 4, gene y is in both at stage 4, and gene z is in neural plate but not neural tube at stage 4. The problem is, that we don’t really have a name for “neural thingy’. Maybe it could be presumptive nervous system? But then what is the relationship between plate and presumptive cns? Is it part_of or is_a? This is a big problem for many anterior to posterior developing structures for which we don’t (usually) specify individual names for individual parts, nor do we often know the exact state of the tissue at a given time and place (which may in fact be even more granular than our stages ontology allows anyway). A picture of this can be seen here: | ||
| + | http://www.sciencemuseum.org.uk/on-line/lifecycle/11.asp | ||
| + | |||
| + | |||
==Relations== | ==Relations== | ||
Revision as of 15:37, 8 August 2006
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
The following list may also be of interest
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.
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
1. The neural tube develops from the neural plate in a generally anterior to posterior direction. At any given time during this transition, both exist. One would never specify the subparts any more, yet when we say the neural tube at the stage at which both exist, we mean the portion that has become the neural tube.
neural thingy st 1-8
p neural plate st 1-5
d neural tube st 3-8
p neural tube st 3-8
An annotation example: gene x is in neural tube but not neural plate at stage 4, gene y is in both at stage 4, and gene z is in neural plate but not neural tube at stage 4. The problem is, that we don’t really have a name for “neural thingy’. Maybe it could be presumptive nervous system? But then what is the relationship between plate and presumptive cns? Is it part_of or is_a? This is a big problem for many anterior to posterior developing structures for which we don’t (usually) specify individual names for individual parts, nor do we often know the exact state of the tissue at a given time and place (which may in fact be even more granular than our stages ontology allows anyway). A picture of this can be seen here: http://www.sciencemuseum.org.uk/on-line/lifecycle/11.asp
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
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