Difference between revisions of "Teleost Anatomy Ontology"

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The Teleost Anatomy Ontology (TAO) is a multi-species anatomy ontology for ostariophysan fishes. Growth of the TAO is enabled by contributions from data curators and the ichthyological community (see [[#Anatomy Term Trackers|Anatomy Term Trackers]]). The TAO can be browsed by using the [http://bioportal.bioontology.org/visualize/38362 NCBO BioPortal].
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==Summary==
  
===TAO and ZFA synchronization===
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The Teleost Anatomy Ontology (TAO) is a multi-species anatomy ontology for teleost fishes. The TAO uses terms from the Common Anatomy Reference Ontology [http://code.google.com/p/caro2/ (CARO)] as a template for its upper level nodes, and the Vertebrate Skeletal Anatomy Ontology [http://www.obofoundry.org/cgi-bin/detail.cgi?id=vertebrate_skeletal_anatomy (VSAO)] for general skeletal anatomy classes. Growth of the TAO is enabled by contributions from data curators and the ichthyological community (see [[#Anatomy Term Tracker and Teleost-discuss Mailing List|Anatomy Term Trackers]]). The TAO can be browsed by using the [http://bioportal.bioontology.org/visualize/38362 NCBO BioPortal] and data annotated using TAO terms can be queried using the [http://kb.phenoscape.org/ Phenoscape Knowedgebase]. Details about the development and use of TAO can be found in [http://sysbio.oxfordjournals.org/cgi/content/abstract/syq013/ Dahdul et al. 2010]
The TAO was initialized with terms from the ZFA, and we currently maintain manual synchronization of the two ontologies.  A synchronization tool (in development) will help automate this process.
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The current release may be found [http://purl.obolibrary.org/obo/tao.obo here].
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== TAO and ZFA synchronization ==
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The TAO was initialized with terms from the Zebrafish Anatomical Ontology (ZFA), and we currently maintain manual synchronization of the two ontologies.  We developed the [http://phenoscape.org/wiki/Synchronization_Tool Synchronization Tool] as an Obo-Edit plug-in to help automate this process.
  
 
One of the challenges in synchronzing the two ontologies involves the addition of terms to the TAO that are not required for the ZFA.  The addition of these terms to the TAO may require the creation of additional intermediate terms that are redundant for the ZFA.  For example, zebrafish have only one type of tooth (ceratobranchial 5 tooth).  Other teleost species have teeth on the jaw bones and other branchial arch and  oral cavity bones.  Because of this, the term ‘tooth’ is needed in the TAO as a parent to all tooth types:
 
One of the challenges in synchronzing the two ontologies involves the addition of terms to the TAO that are not required for the ZFA.  The addition of these terms to the TAO may require the creation of additional intermediate terms that are redundant for the ZFA.  For example, zebrafish have only one type of tooth (ceratobranchial 5 tooth).  Other teleost species have teeth on the jaw bones and other branchial arch and  oral cavity bones.  Because of this, the term ‘tooth’ is needed in the TAO as a parent to all tooth types:
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**ceratobranchial 5 tooth is_a multi-tissue structure
 
**ceratobranchial 5 tooth is_a multi-tissue structure
  
===Genus-differentia definitions===
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== Anatomy Term Tracker and Teleost-discuss Mailing List ==
Term definitions in the teleost anatomy ontology (TAO) take the form of genus-differentia definitions:  B is an A that has X.
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The term B is defined by its membership in higher category A and distinguished from its sibling terms by characteristic X. The following are examples of genus-differentia definitions in the TAO:
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The anatomy ontology is regulary updated to include new terms and developed based on feedback from the community. Requests for changes are submitted to the anatomy term tracker and a summary is forwarded to the teleost-discuss mailing list for community discussion (see [[Term Requests | instructions on requesting terms]] for details). Terms are added to the TAO usually within one week, with any comments or suggestions from  teleost-discuss incorporated. We invite you to join the [https://lists.sourceforge.net/lists/listinfo/obo-teleost-discuss teleost-discuss mailing list] and contribute to the discussion of terms. [http://sourceforge.net/mailarchive/forum.php?forum_name=obo-teleost-discuss Archives] of teleost-discuss are also available.
#''Antorbital:'' Dermal bone that is located on the anterior margin of the infraorbital series, dorsal to the first infraorbital and lateral to the nasal bone.
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#''Dentary:'' Dermal bone that forms the anterolateral part of the lower jaw.
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In example 1, the definition mentions the parent dermal bone of the term antorbital, followed by the characteristics that differentiate antorbital from all other dermal bones.
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== Homology ==
 
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Post-composed terms (terms created on-the-fly at the time of annotation) take the form of genus-differentia definitions.
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===Anatomy Term Tracker===
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The anatomy ontology is regulary updated to include new terms and developed based on feedback from the community.  Requests for changes are submitted to the anatomy term tracker and a summary is forwarded to the teleost-discuss mailing list for community discussion (see [[Term Requests | instructions on requesting terms]] for details). Terms are added to the TAO usually within one week, with any comments or suggestions from  teleost-discuss incorporated. We invite you to join the teleost-discuss mailing list and contribute to the discussion of terms.
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===Homology===
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Homology links are important in the use of multi-species ontologies to define homology relations between different terms in the ontology, and because homology is not implied if the same term is used in annotations for different species. Terms in the anatomy ontology are defined based on structural similarity, and it cannot be assumed that this similarity is due to common ancestry.  For example, zebrafish and humans both possess a frontal bone; however, there is evidence that the zebrafish frontal bone is homologous to the human parietal bone. Our use of the homologous_to relation between entities that are homologues will help clarify the identity of such similarly named but nonhomologous bones.
 
Homology links are important in the use of multi-species ontologies to define homology relations between different terms in the ontology, and because homology is not implied if the same term is used in annotations for different species. Terms in the anatomy ontology are defined based on structural similarity, and it cannot be assumed that this similarity is due to common ancestry.  For example, zebrafish and humans both possess a frontal bone; however, there is evidence that the zebrafish frontal bone is homologous to the human parietal bone. Our use of the homologous_to relation between entities that are homologues will help clarify the identity of such similarly named but nonhomologous bones.
  
 
We have developed a method for homology designation by recording homology statements outside of the ontology, as an annotation with attribution and evidence codes.  Homology statements are hypotheses, and users of our database will have the option of viewing competing hypotheses of homology when they occur.
 
We have developed a method for homology designation by recording homology statements outside of the ontology, as an annotation with attribution and evidence codes.  Homology statements are hypotheses, and users of our database will have the option of viewing competing hypotheses of homology when they occur.
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==License==
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<span class="plainlinks">[http://creativecommons.org/publicdomain/zero/1.0/ http://i.creativecommons.org/l/zero/1.0/80x15.png]</span>
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To the extent possible under law, Wasila M. Dahdul has waived all copyright and related or neighboring rights to the Teleost Anatomy Ontology (TAO). This work is published from  the United States.
  
 
[[Category:Ontology]]
 
[[Category:Ontology]]
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[[Category:Curation]]
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[[Category:Anatomy]]

Latest revision as of 01:37, 15 August 2012

Summary

The Teleost Anatomy Ontology (TAO) is a multi-species anatomy ontology for teleost fishes. The TAO uses terms from the Common Anatomy Reference Ontology (CARO) as a template for its upper level nodes, and the Vertebrate Skeletal Anatomy Ontology (VSAO) for general skeletal anatomy classes. Growth of the TAO is enabled by contributions from data curators and the ichthyological community (see Anatomy Term Trackers). The TAO can be browsed by using the NCBO BioPortal and data annotated using TAO terms can be queried using the Phenoscape Knowedgebase. Details about the development and use of TAO can be found in Dahdul et al. 2010

The current release may be found here.

TAO and ZFA synchronization

The TAO was initialized with terms from the Zebrafish Anatomical Ontology (ZFA), and we currently maintain manual synchronization of the two ontologies. We developed the Synchronization Tool as an Obo-Edit plug-in to help automate this process.

One of the challenges in synchronzing the two ontologies involves the addition of terms to the TAO that are not required for the ZFA. The addition of these terms to the TAO may require the creation of additional intermediate terms that are redundant for the ZFA. For example, zebrafish have only one type of tooth (ceratobranchial 5 tooth). Other teleost species have teeth on the jaw bones and other branchial arch and oral cavity bones. Because of this, the term ‘tooth’ is needed in the TAO as a parent to all tooth types:

  • TAO:
    • ceratobranchial 5 tooth is_a tooth
    • premaxillary tooth is_a tooth
    • tooth is_a multi-tissue structure

The term ‘tooth’ is redundant for the ZFA because zebrafish have only one type of tooth:

  • ZFA:
    • ceratobranchial 5 tooth is_a multi-tissue structure

Anatomy Term Tracker and Teleost-discuss Mailing List

The anatomy ontology is regulary updated to include new terms and developed based on feedback from the community. Requests for changes are submitted to the anatomy term tracker and a summary is forwarded to the teleost-discuss mailing list for community discussion (see instructions on requesting terms for details). Terms are added to the TAO usually within one week, with any comments or suggestions from teleost-discuss incorporated. We invite you to join the teleost-discuss mailing list and contribute to the discussion of terms. Archives of teleost-discuss are also available.

Homology

Homology links are important in the use of multi-species ontologies to define homology relations between different terms in the ontology, and because homology is not implied if the same term is used in annotations for different species. Terms in the anatomy ontology are defined based on structural similarity, and it cannot be assumed that this similarity is due to common ancestry. For example, zebrafish and humans both possess a frontal bone; however, there is evidence that the zebrafish frontal bone is homologous to the human parietal bone. Our use of the homologous_to relation between entities that are homologues will help clarify the identity of such similarly named but nonhomologous bones.

We have developed a method for homology designation by recording homology statements outside of the ontology, as an annotation with attribution and evidence codes. Homology statements are hypotheses, and users of our database will have the option of viewing competing hypotheses of homology when they occur.

License

80x15.png To the extent possible under law, Wasila M. Dahdul has waived all copyright and related or neighboring rights to the Teleost Anatomy Ontology (TAO). This work is published from the United States.