NCBO Wiki - User contributions [en]

Hinxton meeting March 2008

2008-04-02T13:52:42Z

Helenp:

=== Attendees ===

* Michael Ashburner, Cambridge University
* Johnathan Bard, Edinburgh University
* Bernard de Bono, EBI
* Thorsten Henrich, EMBL
* Suzi Lewis, LBL
* Jane Lomax, EBI
* James Malone, EBI
* David Osumi-Sutherland, Cambridge University
* Helen Parkinson, EBI
* Monte Westerfield, Zfin

=== Agenda ===
* Johnathan Bard - Minimal Anatomy Ontology

* Thorsten Henrich - The Bilateria Ontology

* ftp://ftp-exchange.embl-heidelberg.de/pub/exchange/henrich/bilateria/2008_03_EBI.pdf

* David Osumi-Sutherland

http://www.bioontology.org/wiki/index.php/Image:DOS_caro-MRCA_080321.ppt

* Helen Parkinson

http://www.bioontology.org/wiki/index.php/Image:Caro_hinxton_2008.ppt#filelinks

* Bernard de Bono

=== Discussion ===

The presentations focussed on:

* the need and use cases for a cross species anatomy ontology for annotation and analysis purposes (Helen, Thorsten, Johnathan, Bernard).

These include:

* queries for gene expression (array and in situ) across gross shared anatomical structures in eg. human/mouse/rat and zebrafish/Drosophila developmental time
* need for pathway mapping and inference across species
* need for annotation source that's multispecies for use in submission tools
* need for validated mappings between ontologies that can be used by databases and applications that are not single species - MMIA currently provides these.

* CARO state of the art and experiences extending CARO (David, Thorsten)

CARO has been used successfully, but is not intuitive and could be improved with some small effort. This would promote the use of CARO and ease ontology building for other groups. Specific suggestions are listed in Action Items. A discussion on whether CARO itself should be modified at this point, or whether CARO2 was a preferable route as people are using CARO as a framework to develop other ontologies already. This needs to be discussed further with other interested parties

* Evaluation of CARO, Bilateria and MMIA against presented use cases (Helen, Johnathan, Thorsten, David)

CARO was not intended to solve the problem of multi-species anatomy annotation and representation, nor was it intended to hold maps between ontologies representing anatomy in individual species. The bilateria ontology and the MMIA both address these questions. Both have some relative strengths including the maps to other ontologies present in MMIA (which is not considered to be an ontology and uses only SKOS relationships, broader_than/narrower_than). Clearly building a multi species anatomy ontology is a huge project but work has been done already, there are some low hanging fruit and the use cases are not all anatomically complex.

=== Action Items ===

* 1. Generate a list of developmental process terms and submit these to the Gene Ontology for inclusion

E.g. delamination

AI:Johnathan, David, Thorsten

* 2. Development of a common methodology to represent (anatomical) homology groups a David and Thorsten have approached this in a similar way already. In consulatation with phenoscape and others, David has developed a system for representing homology groups using relations based on the "homologous_to" relation defined by phenoscape.

AI:David will generate an OBO file containing his modelling strategy for representing homology groups

AI: David and Thorsten will work together to produce a single system based
on their respective modelling approaches. This will include consultations with phenoscape to
ensure the new approach is compatible with theirs.

* 3. Development of a Most Recent Common Ancestor Anatomy (MRCA) Ontology

David, Thorsten, Johnathan all have ideas on how to do this, and some work has been done already. It's clear to do significant work there will need to be funding but preliminary work would be very useful and some compact MCRA ontology could be used now by several projects. This is likely a necessary pre-requisite for securing funding. see 6.

* 4. FMA update model.

AI: The conversion of the FMA to OWL format is non trivial and labour intensive. Suzi will contact Onard Medino to discuss this.

* 5. CARO improvements

Thorsten had successfully used CARO to build the bilateria ontology, but it was felt that the use of CARO by other groups would be improved if:

* all the definitions contained examples
* an example CARO should be available extended for an example species
* a manual on how to use CARO is needed (the paper helps)
* the FMA is a good example of definitions plus examples.
* synonyms would be useful
* epithelial cell could be removed - it's duplicate with the Cell Ontology
* CARO doesn't deal with function and therefore organ is not present. David suggested that an abstract class function could be added to help with refining the middle part of CARO
* DS and JB will work on defining differentia (labels that would want to attach to a tissue) such as the boundary types that could be included in CARO
* communication of any proposed changes should be done by the obo-anatomy list so that all are aware of proposed changes

Post workshop email discussion suggests that CARO is useful, with some more work it could be really useful and easier to use as a framework for development and used as a parent for the emerging cross species anatomy ontology.

AI:David(?) will communicate these suggestions CARO improvements to the CARO team

* 6. Funding

There are two possible sources of funding identified
* an unsolicited R01
* EC funding. This will be conditional on use and implementation, rather than solely development of an ontology.
* Datasets that could be integrated include Zebrafish, Gene Expression in situ/array based, VPH

AI: Helen and Bernard will look into EC funding sources (ICAT)
AI: Suzi will look into submitting an R01 to develop the MCRA

* 7. MMIA ways forward

MMIA is a useful string matching tool, no ontological claims are made for it.

AI:Johnathan will work with Thorsten, David on a plan for a new CARO derived multi-species anatomy ontology MCRA. See 3. 

* 8. Annotation/curator tools

Much of the discussion covered the needs of those using anatomy ontologies rather than those building them. Suggestion that an annotation tool could use some 'lite' version of the MCRA and users could navigate to mapped species specific ontologies if these were needed.

* 9. Visualization

Use of ontologies in developing a visualization methodology/standard e.g. using a schematic body plan to present gene expression and maps to pathways was also discussed. Bernard in particular is interested in this. Stuart Aitken (Edinburgh) has a new grant to develop 2.5D visualization tools. Suzi is interested in generic visualizations that also work for environments.

AI:BdB to contact Stuart Aitken and Richard Baldock about visualization tools.

=== Shared Materials ===

Hinxton meeting March 2008

2008-03-31T12:44:49Z

Helenp: /* Action Items */

=== Attendees ===

* Michael Ashburner, Cambridge University
* Johnathan Bard, Edinburgh University
* Bernard de Bono, EBI
* Thorsten Henrich, EMBL
* Suzi Lewis, LBL
* Jane Lomax, EBI
* James Malone, EBI
* David Osumi-Sutherland, Cambridge University
* Helen Parkinson, EBI
* Monte Westerfield, Zfin

=== Agenda ===
* Johnathan Bard - Minimal Anatomy Ontology

* Thorsten Henrich - The Bilateria Ontology

* ftp://ftp-exchange.embl-heidelberg.de/pub/exchange/henrich/bilateria/2008_03_EBI.pdf

* David Osumi-Sutherland

http://www.bioontology.org/wiki/index.php/Image:DOS_caro-MRCA_080321.ppt

* Helen Parkinson

http://www.bioontology.org/wiki/index.php/Image:Caro_hinxton_2008.ppt#filelinks

* Bernard de Bono

=== Discussion ===

The presentations focussed on:

* the need and use cases for a cross species anatomy ontology for annotation and analysis purposes (Helen, Thorsten, Johnathan, Bernard).

These include:

* queries for gene expression (array and in situ) across gross shared anatomical structures in eg. human/mouse/rat and zebrafish/Drosophila developmental time
* need for pathway mapping and inference across species
* need for annotation source that's multispecies for use in submission tools
* need for validated mappings between ontologies that can be used by databases and applications that are not single species - MMIA currently provides these.

* CARO state of the art and experiences extending CARO (David, Thorsten)

CARO has been used successfully, but is not intuitive and could be improved with some small effort. This would promote the use of CARO and ease ontology building for other groups. Specific suggestions are listed in Action Items. A discussion on whether CARO itself should be modified at this point, or whether CARO2 was a preferable route as people are using CARO as a framework to develop other ontologies already. This needs to be discussed further with other interested parties

* Evaluation of CARO, Bilateria and MMIA against presented use cases (Helen, Johnathan, Thorsten, David)

CARO was not intended to solve the problem of multi-species anatomy annotation and representation, nor was it intended to hold maps between ontologies representing anatomy in individual species. The bilateria ontology and the MMIA both address these questions. Both have some relative strengths including the maps to other ontologies present in MMIA (which is not considered to be an ontology and uses only SKOS relationships, broader_than/narrower_than). Clearly building a multi species anatomy ontology is a huge project but work has been done already, there are some low hanging fruit and the use cases are not all anatomically complex.

=== Action Items ===

* 1. Generate a list of developmental process terms and submit these to the Gene Ontology for inclusion

E.g. delamination

AI:Johnathan, David, Thorsten

* 2. Development of a common methodology to represent (anatomical) homology groups a David and Thorsten have approached this in a similar way already. In consulatation with phenoscape and others, David has developed a system for representing homology groups using relations based on the "homologous_to" relation defined by phenoscape.

AI:David will generate an OBO file containing his modelling strategy for representing homology groups

AI: David and Thorsten will work together to produce a single system based
on their respective modelling approaches. This will include consultations with phenoscape to
ensure the new approach is compatible with theirs.

* 3. Development of a Most Recent Common Ancestor Anatomy (MRCA) Ontology

David, Thorsten, Johnathan all have ideas on how to do this, and some work has been done already. It's clear to do significant work there will need to be funding but preliminary work would be very useful and some compact MCRA ontology could be used now by several projects. This is likely a necessary pre-requisite for securing funding. see 6.

* 4. FMA update model.

AI: The conversion of the FMA to OWL format is non trivial and labour intensive. Suzi will contact Onard Medino to discuss this.

* 5. CARO improvements

Thorsten had successfully used CARO to build the bilateria ontology, but it was felt that the use of CARO by other groups would be improved if:

* all the definitions contained examples
* an example CARO should be available extended for an example species
* a manual on how to use CARO is needed (the paper helps)
* the FMA is a good example of definitions plus examples.
* synonyms would be useful
* epithelial cell could be removed - it's duplicate with the Cell Ontology
* CARO doesn't deal with function and therefore organ is not present. David suggested that an abstract class function could be added to help with refining the middle part of CARO
* DS and JB will work on defining differentia (labels that would want to attach to a tissue) such as the boundary types that could be included in CARO
* communication of any proposed changes should be done by the obo-anatomy list so that all are aware of proposed changes

AI:David(?) will communicate these suggestions CARO improvements to the CARO team

* 6. Funding

There are two possible sources of funding identified
* an unsolicited R01
* EC funding. This will be conditional on use and implementation, rather than solely development of an ontology.
* Datasets that could be integrated include Zebrafish, Gene Expression in situ/array based, VPH

AI: Helen and Bernard will look into EC funding sources (ICAT)
AI: Suzi will look into submitting an R01 to develop the MCRA

* 7. MMIA ways forward

MMIA is a useful string matching tool, no ontological claims are made for it.

AI:Johnathan will work with Thorsten, David on a plan for a new CARO derived multi-species anatomy ontology MCRA. See 3. 

* 8. Annotation/curator tools

Much of the discussion covered the needs of those using anatomy ontologies rather than those building them. Suggestion that an annotation tool could use some 'lite' version of the MCRA and users could navigate to mapped species specific ontologies if these were needed.

* 9. Visualization

Use of ontologies in developing a visualization methodology/standard e.g. using a schematic body plan to present gene expression and maps to pathways was also discussed. Bernard in particular is interested in this. Stuart Aitken (Edinburgh) has a new grant to develop 2.5D visualization tools. Suzi is interested in generic visualizations that also work for environments.

AI:BdB to contact Stuart Aitken and Richard Baldock about visualization tools.

=== Shared Materials ===

Hinxton meeting March 2008

2008-03-31T12:27:29Z

Helenp:

=== Attendees ===

* Michael Ashburner, Cambridge University
* Johnathan Bard, Edinburgh University
* Bernard de Bono, EBI
* Thorsten Henrich, EMBL
* Suzi Lewis, LBL
* Jane Lomax, EBI
* James Malone, EBI
* David Osumi-Sutherland, Cambridge University
* Helen Parkinson, EBI
* Monte Westerfield, Zfin

=== Agenda ===
* Johnathan Bard - Minimal Anatomy Ontology

* Thorsten Henrich - The Bilateria Ontology

* ftp://ftp-exchange.embl-heidelberg.de/pub/exchange/henrich/bilateria/2008_03_EBI.pdf

* David Osumi-Sutherland

http://www.bioontology.org/wiki/index.php/Image:DOS_caro-MRCA_080321.ppt

* Helen Parkinson

http://www.bioontology.org/wiki/index.php/Image:Caro_hinxton_2008.ppt#filelinks

* Bernard de Bono

=== Discussion ===

The presentations focussed on:

* the need and use cases for a cross species anatomy ontology for annotation and analysis purposes (Helen, Thorsten, Johnathan, Bernard).

These include:

* queries for gene expression (array and in situ) across gross shared anatomical structures in eg. human/mouse/rat and zebrafish/Drosophila developmental time
* need for pathway mapping and inference across species
* need for annotation source that's multispecies for use in submission tools
* need for validated mappings between ontologies that can be used by databases and applications that are not single species - MMIA currently provides these.

* CARO state of the art and experiences extending CARO (David, Thorsten)

CARO has been used successfully, but is not intuitive and could be improved with some small effort. This would promote the use of CARO and ease ontology building for other groups. Specific suggestions are listed in Action Items. A discussion on whether CARO itself should be modified at this point, or whether CARO2 was a preferable route as people are using CARO as a framework to develop other ontologies already. This needs to be discussed further with other interested parties

* Evaluation of CARO, Bilateria and MMIA against presented use cases (Helen, Johnathan, Thorsten, David)

CARO was not intended to solve the problem of multi-species anatomy annotation and representation, nor was it intended to hold maps between ontologies representing anatomy in individual species. The bilateria ontology and the MMIA both address these questions. Both have some relative strengths including the maps to other ontologies present in MMIA (which is not considered to be an ontology and uses only SKOS relationships, broader_than/narrower_than). Clearly building a multi species anatomy ontology is a huge project but work has been done already, there are some low hanging fruit and the use cases are not all anatomically complex.

=== Action Items ===

* 1. Generate a list of developmental process terms and submit these to the Gene Ontology for inclusion

E.g. delamination

AI:Johnathan, David, Thorsten

* 2. Development of a common methodology to represent (anatomical) homology groups a David and Thorsten have approached this in a similar way already. In consulatation with phenoscape and others, David has developed a system for representing homology groups using relations based on the "homologous_to" relation defined by phenoscape.

AI:David will generate an OBO file containing his modelling strategy

AI: David and Thorsten will work together to produce a single system based
on their approaches. This will include consulations with phenoscape to
ensure the new approach is compatible with theirs.

* 3. Development of a Most Recent Common Ancestor Anatomy (MRCA) Ontology

David, Thorsten, Johnathan all have ideas on how to do this, and some work has been done already. It's clear to do significant work there will need to be funding but preliminary work would be very useful and some compact MCRA ontology could be used now by several projects. This is likely a necessary pre-requisite for securing funding. see 6.

* 4. FMA update model.

AI: The conversion of the FMA to OWL format is non trivial and labour intensive. Suzi will contact Onard Medino to discuss this.

* 5. CARO improvements

Thorsten had successfully used CARO to build the bilateria ontology, but it was felt that the use of CARO by other groups would be improved if:

* all the definitions contained examples
* an example CARO should be available extended for an example species
* a manual on how to use CARO is needed (the paper helps)
* the FMA is a good example of definitions plus examples.
* synonyms would be useful
* epithelial cell could be removed - it's duplicate with the Cell Ontology
* CARO doesn't deal with function and therefore organ is not present. David suggested that an abstract class function could be added to help with refining the middle part of CARO
* DS and JB will work on defining differentia (labels that would want to attach to a tissue) such as the boundary types that could be included in CARO
* communication of any proposed changes should be done by the obo-anatomy list so that all are aware of proposed changes

* 6. Funding

There are two possible sources of funding identified
* an unsolicited R01
* EC funding. This will be conditional on use, rather than solely development of an ontology.
* Datasets that could be integrated include Zebrafish, Gene Expression in situ/array based, VPH

AI: Helen and Bernard will look into EC funding sources (ICAT)
AI: Suzi will look into submitting an R01 to develop the MCRA and do some work on CARO to support this.

* 7. MMIA ways forward

MMIA is a useful string matching tool, no ontological claims are made for it.

AI:Johnathan will work with Thorsten, David on a plan for a new CARO derived multi-species anatomy ontology MCRA. See 3.

* 8. Annotation/curator tools

Much of the discussion covered the needs of those using anatomy ontologies rather than those building them. Suggestion that an annotation tool could use some 'lite' version of the MCRA and users could navigate to mapped species specific ontologies if these were needed.

* 9. Visualization

Use of ontologies in developing a visualization methodology/standard e.g. using a schematic body plan to present gene expression and maps to pathways was also discussed. Bernard in particular is interested in this. Stuart Aitken (Edinburgh) has a new grant to develop 2.5D visualization tools. Suzi is interested in generic visualizations that also work for environments.

AI:BdB to contact Stuart Aitken and Richard Baldock about visualization tools.

=== Shared Materials ===

File:DOS caro-MRCA 080321.ppt

2008-03-31T12:25:25Z

Helenp: David Osumi-Sutherland meeting presentation CARO March 2008

David Osumi-Sutherland meeting presentation CARO March 2008

Hinxton meeting March 2008

2008-03-31T11:07:02Z

Helenp:

=== Attendees ===

* Michael Ashburner, Cambridge University
* Johnathan Bard, Edinburgh University
* Bernard de Bono, EBI
* Thorsten Henrich, EMBL
* Suzi Lewis, LBL
* Jane Lomax, EBI
* James Malone, EBI
* David Osumi-Sutherland, Cambridge University
* Helen Parkinson, EBI
* Monte Westerfield, Zfin

=== Agenda ===
* Johnathan Bard - Minimal Anatomy Ontology

* Thorsten Henrich - The Bilateria Ontology

* ftp://ftp-exchange.embl-heidelberg.de/pub/exchange/henrich/bilateria/2008_03_EBI.pdf

* David Osumi-Sutherland

* Helen Parkinson

http://www.bioontology.org/wiki/index.php/Image:Caro_hinxton_2008.ppt#filelinks

* Bernard de Bono

=== Discussion ===

The presentations focussed on:

* the need and use cases for a cross species anatomy ontology for annotation and analysis purposes (Helen, Thorsten, Johnathan, Bernard).

These include:

* queries for gene expression (array and in situ) across gross shared anatomical structures in eg. human/mouse/rat and zebrafish/Drosophila developmental time
* need for pathway mapping and inference across species
* need for annotation source that's multispecies for use in submission tools
* need for validated mappings between ontologies that can be used by databases and applications that are not single species - MMIA currently provides these.

* CARO state of the art and experiences extending CARO (David, Thorsten)

CARO has been used successfully, but is not intuitive and could be improved with some small effort. This would promote the use of CARO and ease ontology building for other groups. Specific suggestions are listed in Action Items. A discussion on whether CARO itself should be modified at this point, or whether CARO2 was a preferable route as people are using CARO as a framework to develop other ontologies already. This needs to be discussed further with other interested parties

* Evaluation of CARO, Bilateria and MMIA against presented use cases (Helen, Johnathan, Thorsten, David)

CARO was not intended to solve the problem of multi-species anatomy annotation and representation, nor was it intended to hold maps between ontologies representing anatomy in individual species. The bilateria ontology and the MMIA both address these questions. Both have some relative strengths including the maps to other ontologies present in MMIA (which is not considered to be an ontology and uses only SKOS relationships, broader_than/narrower_than). Clearly building a multi species anatomy ontology is a huge project but work has been done already, there are some low hanging fruit and the use cases are not all anatomically complex.

=== Action Items ===

* 1. Generate a list of developmental process terms and submit these to the Gene Ontology for inclusion

E.g. delamination

AI:Johnathan, David, Thorsten

* 2. Development of a common methodology to represent (anatomical) homology groups a David and Thorsten have approached this in a similar way already. David suggested that the FMA relations be condensed and used.

AI:David will generate an OBO file containing his modelling strategy

* 3. Development of a Most Recent Common Ancestor Anatomy (MRCA) Ontology

David, Thorsten, Johnathan all have ideas on how to do this, and some work has been done already. It's clear to do significant work there will need to be funding but preliminary work would be very useful and some compact MCRA ontology could be used now by several projects. This is likely a necessary pre-requisite for securing funding. see 6.

* 4. FMA update model.

AI: The conversion of the FMA to OWL format is non trivial and labour intensive. Suzi will contact Onard Medino to discuss this.

* 5. CARO improvements

Thorsten had successfully used CARO to build the bilateria ontology, but it was felt that the use of CARO by other groups would be improved if:

* all the definitions contained examples
* an example CARO should be available extended for an example species
* a manual on how to use CARO is needed (the paper helps)
* the FMA is a good example of definitions plus examples.
* synonyms would be useful
* epithelial cell could be removed - it's duplicate with the Cell Ontology
* CARO doesn't deal with function and therefore organ is not present. David suggested that an abstract class function could be added to help with refining the middle part of CARO
* DS and JB will work on defining differentia (labels that would want to attach to a tissue) such as the boundary types that could be included in CARO
* communication of any proposed changes should be done by the obo-anatomy list so that all are aware of proposed changes

* 6. Funding

There are two possible sources of funding identified
* an unsolicited R01
* EC funding. This will be conditional on use, rather than solely development of an ontology.
* Datasets that could be integrated include Zebrafish, Gene Expression in situ/array based, VPH

AI: Helen and Bernard will look into EC funding sources (ICAT)
AI: Suzi will look into submitting an R01 to develop the MCRA and do some work on CARO to support this.

* 7. MMIA ways forward

MMIA is a useful string matching tool, no ontological claims are made for it.

AI:Johnathan will work with Thorsten, David on a plan for a new CARO derived multi-species anatomy ontology MCRA. See 3.

* 8. Annotation/curator tools

Much of the discussion covered the needs of those using anatomy ontologies rather than those building them. Suggestion that an annotation tool could use some 'lite' version of the MCRA and users could navigate to mapped species specific ontologies if these were needed.

* 9. Visualization

Use of ontologies in developing a visualization methodology/standard e.g. using a schematic body plan to present gene expression and maps to pathways was also discussed. Bernard in particular is interested in this. Stuart Aitken (Edinburgh) has a new grant to develop 2.5D visualization tools. Suzi is interested in generic visualizations that also work for environments.

AI:BdB to contact Stuart Aitken and Richard Baldock about visualization tools.

=== Shared Materials ===

Hinxton meeting March 2008

2008-03-31T11:03:06Z

Helenp: /* Action Items */

=== Attendees ===

* Michael Ashburner, Cambridge University
* Johnathan Bard, Edinburgh University
* Bernard de Bono, EBI
* Thorsten Henrich, EMBL
* Suzi Lewis, LBL
* Jane Lomax, EBI
* James Malone, EBI
* David Osumi-Sutherland, Cambridge University
* Helen Parkinson, EBI
* Monte Westerfield, Zfin

=== Agenda ===
* Johnathan Bard - Minimal Anatomy Ontology

* Thorsten Henrich - The Bilateria Ontology

* ftp://ftp-exchange.embl-heidelberg.de/pub/exchange/henrich/bilateria/2008_03_EBI.pdf

* David Osumi-Sutherland

* Helen Parkinson

http://www.bioontology.org/wiki/index.php/Image:Caro_hinxton_2008.ppt#filelinks

* Bernard de Bono

=== Discussion ===

The presentations focussed on:

* the need and use cases for a cross species anatomy ontology for annotation and analysis purposes (Helen, Thorsten, Johnathan, Bernard).

These include:

* queries for gene expression (array and in situ) across gross shared anatomical structures in eg. human/mouse/rat and zebrafish/Drosophila developmental time
* need for pathway mapping and inference across species
* need for annotation source that's multispecies for use in submission tools
* need for validated mappings between ontologies that can be used by databases and applications that are not single species - MMIA currently provides these.

* CARO state of the art and experiences extending CARO (David, Thorsten)

CARO has been used successfully, but is not intuitive and could be improved with some small effort. This would promote the use of CARO and ease ontology building for other groups. Specific suggestions are listed in Action Items. A discussion on whether CARO itself should be modified at this point, or whether CARO2 was a preferable route as people are using CARO as a framework to develop other ontologies already. This needs to be discussed further with other interested parties

* Evaluation of CARO, Bilateria and MMIA against presented use cases (Helen, Johnathan, Thorsten, David)

CARO was not intended to solve the problem of multi-species anatomy annotation and representation, nor was it intended to hold maps between ontologies representing anatomy in individual species. The bilateria ontology and the MMIA both address these questions. Both have some relative strengths including the maps to other ontologies present in MMIA (which is not considered to be an ontology and uses only SKOS relationships, broader_than/narrower_than). Clearly building a multi species anatomy ontology is a huge project but work has been done already, there are some low hanging fruit and the use cases are not all anatomically complex.

=== Action Items ===

* 1. Generate a list of developmental process terms and submit these to the Gene Ontology for inclusion

E.g. delamination

AI:Johnathan, David, Thorsten

* 2. Development of a common methodology to represent (anatomical) homology groups a David and Thorsten have approached this in a similar way already. David suggested that the FMA relations be condensed and used.

AI:David will generate an OBO file containing his modelling strategy

* 3. Development of a Most Recent Common Ancestor Anatomy (MRCA) Ontology

David, Thorsten, Johnathan all have ideas on how to do this, and some work has been done already. It's clear to do significant work there will need to be funding but preliminary work would be very useful and some compact MCRA ontology could be used now by several projects. This is likely a necessary pre-requisite for securing funding. see 6.

* 4. FMA update model.

AI: The conversion of the FMA to OWL format is non trivial and labour intensive. Suzi will contact Onard Medino to discuss this.

* 5. CARO improvements

Thorsten had successfully used CARO to build the bilateria ontology, but it was felt that the use of CARO by other groups would be improved if:

* all the definitions contained examples
* an example CARO should be available extended for an example species
* a manual on how to use CARO is needed (the paper helps)
* the FMA is a good example of definitions plus examples.
* synonyms would be useful
* epithelial cell could be removed - it's duplicate with the Cell Ontology
* CARO doesn't deal with function and therefore organ is not present. David suggested that an abstract class function could be added to help with refining the middle part of CARO
* DS and JB will work on defining differentia (labels that would want to attach to a tissue) such as the boundary types that could be included in CARO
* communication of any proposed changes should be done by the obo-anatomy list so that all are aware of proposed changes

* 6. Funding

There are two possible sources of funding identified
* an unsolicited R01
* EC funding. This will be conditional on use, rather than solely development of an ontology.
* Datasets that could be integrated include Zebrafish, Gene Expression in situ/array based, VPH

AI: Helen and Bernard will look into EC funding sources (ICAT)
AI: Suzi will look into submitting an R01 to develop the MCRA and do some work on CARO to support this.

* 7. MMIA ways forward

MMIA is a useful string matching tool, no ontological claims are made for it.

AI:Johnathan will work with Thorsten, David on a plan for a new CARO derived multi-species anatomy ontology MCRA. See 3.

* 8. Annotation/curator tools

Much of the discussion covered the needs of those using anatomy ontologies rather than those building them.

* 9. Visualization

Use of ontologies in developing a visualization methodology/standard e.g. using a schematic body plan to present gene expression and maps to pathways was also discussed. Bernard in particular is interested in this. Stuart Aitken (Edinburgh) has a new grant to develop 2.5D visualization tools. Suzi is interested in generic visualizations that also work for environments.

AI:BdB to contact Stuart Aitken and Richard Baldock about visualization tools.

=== Shared Materials ===

Hinxton meeting March 2008

2008-03-31T10:58:43Z

Helenp:

=== Attendees ===

* Michael Ashburner, Cambridge University
* Johnathan Bard, Edinburgh University
* Bernard de Bono, EBI
* Thorsten Henrich, EMBL
* Suzi Lewis, LBL
* Jane Lomax, EBI
* James Malone, EBI
* David Osumi-Sutherland, Cambridge University
* Helen Parkinson, EBI
* Monte Westerfield, Zfin

=== Agenda ===
* Johnathan Bard - Minimal Anatomy Ontology

* Thorsten Henrich - The Bilateria Ontology

* ftp://ftp-exchange.embl-heidelberg.de/pub/exchange/henrich/bilateria/2008_03_EBI.pdf

* David Osumi-Sutherland

* Helen Parkinson

http://www.bioontology.org/wiki/index.php/Image:Caro_hinxton_2008.ppt#filelinks

* Bernard de Bono

=== Discussion ===

The presentations focussed on:

* the need and use cases for a cross species anatomy ontology for annotation and analysis purposes (Helen, Thorsten, Johnathan, Bernard).

These include:

* queries for gene expression (array and in situ) across gross shared anatomical structures in eg. human/mouse/rat and zebrafish/Drosophila developmental time
* need for pathway mapping and inference across species
* need for annotation source that's multispecies for use in submission tools
* need for validated mappings between ontologies that can be used by databases and applications that are not single species - MMIA currently provides these.

* CARO state of the art and experiences extending CARO (David, Thorsten)

CARO has been used successfully, but is not intuitive and could be improved with some small effort. This would promote the use of CARO and ease ontology building for other groups. Specific suggestions are listed in Action Items. A discussion on whether CARO itself should be modified at this point, or whether CARO2 was a preferable route as people are using CARO as a framework to develop other ontologies already. This needs to be discussed further with other interested parties

* Evaluation of CARO, Bilateria and MMIA against presented use cases (Helen, Johnathan, Thorsten, David)

CARO was not intended to solve the problem of multi-species anatomy annotation and representation, nor was it intended to hold maps between ontologies representing anatomy in individual species. The bilateria ontology and the MMIA both address these questions. Both have some relative strengths including the maps to other ontologies present in MMIA (which is not considered to be an ontology and uses only SKOS relationships, broader_than/narrower_than). Clearly building a multi species anatomy ontology is a huge project but work has been done already, there are some low hanging fruit and the use cases are not all anatomically complex.

=== Action Items ===

* 1. Generate a list of developmental process terms and submit these to the Gene Ontology for inclusion

E.g. delamination

AI:Johnathan, David, Thorsten

* 2. Development of a common methodology to represent (anatomical) homology groups a David and Thorsten have approached this in a similar way already. David suggested that the FMA relations be condensed and used.

AI:David will generate an OBO file containing his modelling strategy

* 3. Development of a Most Recent Common Ancestor Anatomy (MRCA) Ontology

David, Thorsten, Johnathan all have ideas on how to do this, and some work has been done already. It's clear to do significant work there will need to be funding but preliminary work would be very useful and some compact MCRA ontology could be used now by several projects. This is likely a necessary pre-requisite for securing funding. see 6.

* 4. FMA update model.

AI: The conversion of the FMA to OWL format is non trivial and labour intensive. Suzi will contact Onard Medino to discuss this.

* 5. CARO improvements

Thorsten had successfully used CARO to build the bilateria ontology, but it was felt that the use of CARO by other groups would be improved if:

* all the definitions contained examples
* an example CARO should be available extended for an example species
* a manual on how to use CARO is needed (the paper helps)
* the FMA is a good example of definitions plus examples.
* synonyms would be useful
* epithelial cell could be removed - it's duplicate with the Cell Ontology
* CARO doesn't deal with function and therefore organ is not present. David suggested that an abstract class function could be added to help with refining the middle part of CARO
* DS and JB will work on defining differentia (labels that would want to attach to a tissue) such as the boundary types that could be included in CARO
* communication of any proposed changes should be done by the obo-anatomy list so that all are aware of proposed changes

* 6. Funding

There are two possible sources of funding identified
* an unsolicited R01
* EC funding. This will be conditional on use, rather than solely development of an ontology.
* Datasets that could be integrated include Zebrafish, Gene Expression in situ/array based, VPH

AI: Helen and Bernard will look into EC funding sources (ICAT)
AI: Suzi will look into submitting an R01 to develop the MCRA and do some work on CARO to support this.

* 7. MMIA ways forward

MMIA is a useful string matching tool, no ontological claims are made for it.

AI:Johnathan will work with Thorsten, David on a plan for a new CARO derived multispecies anatomy ontology MCRA. See 3.

* 8. Annotation/curator tools

Much of the discussion covered the needs of those using anatomy ontologies rather than those building them.

=== Shared Materials ===

Hinxton meeting March 2008

2008-03-31T10:42:53Z

Helenp: /* Discussion */

Hinxton meeting March 2008

2008-03-31T10:33:09Z

Helenp: /* Discussion */

Hinxton meeting March 2008

2008-03-31T10:31:50Z

Helenp:

Hinxton meeting March 2008

2008-03-31T10:27:13Z

Helenp:

Hinxton meeting March 2008

2008-03-31T09:59:00Z

Helenp:

File:Caro hinxton 2008.ppt

2008-03-31T09:57:41Z

Helenp: Presentation by Helen Parkinson. Anatomy Ontology meeting, Hinxton March 2008.

Presentation by Helen Parkinson. Anatomy Ontology meeting, Hinxton March 2008.

Hinxton meeting March 2008

2008-03-31T09:56:13Z

Helenp: /* Agenda */

Hinxton meeting March 2008

2008-03-31T09:53:04Z

Helenp: /* Attendees */

Hinxton meeting March 2008

2008-03-31T09:52:12Z

Helenp:

=== Attendees ===

Michael Ashburner, Cambridge University
Johnathan Bard, Edinburgh University
Bernard de Bono, EBI
Thorsten Henrich, EMBL
Suzi Lewis, LBL
Jane Lomax, EBI
James Malone, EBI
David Osumi-Sutherland, Cambridge University
Helen Parkinson, EBI
Monte Westerfield, Zfin

=== Agenda ===
Johnathan Bard - Minimal Anatomy Ontology

Thorsten Henrich - The Bilateria Ontology

ftp://ftp-exchange.embl-heidelberg.de/pub/exchange/henrich/bilateria/2008_03_EBI.pdf

David Osumi-Sutherland

Helen Parkinson

Bernard de Bono

=== Action Items ===

=== Shared Materials ===

Hinxton meeting March 2008

2008-03-31T09:33:09Z

Helenp: New page: === Present == Michael Ashburner, Cambridge University Bernard de Bono, EBI Thorsten Henrich, EMBL Suzi Lewis, LBL Jane Lomax, EBI James Malone, EBI David Osumi-Sutherland, Cambridge Univ...

=== Present ==

Michael Ashburner, Cambridge University
Bernard de Bono, EBI
Thorsten Henrich, EMBL
Suzi Lewis, LBL
Jane Lomax, EBI
James Malone, EBI
David Osumi-Sutherland, Cambridge University
Helen Parkinson, EBI
Monte Westerfield, Zfin

=== Agenda ===

=== Presentations: ===

=== Action Items ===

=== Shared Materials ===

CARO:Main Page

2008-03-31T09:29:47Z

Helenp: /* Seattle 09/06 presentations */

=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

* http://obo.sourceforge.net/cgi-bin/detail.cgi?caro

The OWL version is available at:

* http://purl.org/obo/owl/CARO

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]]

[[Media:CAROtest3.doc|CAROtest3.obo]]

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=

==Mail Lists==

- [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-anatomy OBO Anatomy]

The following list may also be of interest

- [https://lists.sourceforge.net/lists/listinfo/obo-crossproduct 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.

[[Media:CARO-UG-development-JB.pdf|mouse urogenital development pdf]]

==Relations==

[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]

[http://obo.sourceforge.net/relationship 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==

CARO:Main Page

2008-03-31T09:27:13Z

Helenp: /* Meeting presentations */

=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

* http://obo.sourceforge.net/cgi-bin/detail.cgi?caro

The OWL version is available at:

* http://purl.org/obo/owl/CARO

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]]

[[Media:CAROtest3.doc|CAROtest3.obo]]

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=

==Mail Lists==

- [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-anatomy OBO Anatomy]

The following list may also be of interest

- [https://lists.sourceforge.net/lists/listinfo/obo-crossproduct 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:

HinxtonAnatomyDiscussion

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.

[[Media:CARO-UG-development-JB.pdf|mouse urogenital development pdf]]

==Relations==

[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]

[http://obo.sourceforge.net/relationship 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==