Difference between revisions of "Anatomy Ontology Development Plan"

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The Phenoscape project is coordinating the integration and development of multispecies and single species  vertebrate ontologies for teleosts, zebrafish, amphibians, frog, amniotes, and mouse.  The focus of ontology development in year 1 is the limb/fin skeletal branch.
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#REDIRECT [[Ontologies]]
  
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The development of these ontologies follows OBO Foundry principles. Importing or MIREOTing ontology terms is the preferred mechanism for using shared terms and VAO will be imported into TAO, AAO, and AMAO. However, the existing model organism databases are largely hardcoded and a move toward importing terms from external ontologies will take time to implement. Because of this, some of the existing MOD vertebrate ontologies will instead duplicate shared terms with cross-references to equivalent terms in external ontologies.
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The Phenoscape project is coordinating the development and integration of multispecies and single species anatomy ontologies for vertebrates, with taxonomic focus on teleosts, zebrafish, amphibians, Xenopus, amniotes, and mouse.  The limb/fin branch is the focus of ontology development in year 1.
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The development of these ontologies follows [http://obofoundry.org/ OBO Foundry principles]. Reusing ontology terms (by import or MIREOT) is the preferred mechanism for using shared terms and VAO will be imported into TAO, AAO, and AMAO. However, the existing model organism databases are largely hardcoded to reference identifiers for their own ontologies (e.g., MGI database reads MA term identifiers). In the long term, we will be exploring how to import terms into these ontologies. In the interim, the existing MOD vertebrate ontologies will continue to duplicate equivalent terms from other ontologies, with cross-references to the external ontology identifiers.
  
 
== Year 1 Development Plan ==
 
== Year 1 Development Plan ==
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See [[Ontologies#Release_Schedules_and_Features | ontology release schedule]] for detailed implementation schedule.
 
  
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=== Vertebrate Anatomy Ontology (VAO) ===
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=== Vertebrate Musculoskeletal Anatomy Ontology (VAO) ===
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VAO will be expanded to include skeletal terms shared by two or more multispecies ontologies. These shared terms will be obsoleted from and subsequently imported into the multispecies ontologies. For example, ‘femur’, a term applicable to AAO and AMAO, will be added to VAO and imported into AMAO (Year 1) and AAO (Year 2). However, terms shared by a multispecies ontology and its corresponding single-species ontology (e.g., AAO and XAO) will not be added to VAO. These terms should ideally be imported from the multispecies ontology into the single species ontology (or rather, a single ontology for that taxonomic group should be used). However, because MODs currently cannot import terms, single species ontologies will instead duplicate shared terms and cross-reference the external ontology. For example, because XAO and AAO both contain the term ‘radio-ulna’, XAO will cross-reference the AAO ID for this term.
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VAO will be expanded to include terms in the muscular and skeletal systems that are shared by two or more multispecies vertebrate ontologies. These shared terms will be imported into the multispecies ontologies. For example, ‘femur’, a term applicable to AAO and AMAO, will be added to VAO and imported into AMAO (Year 1) and AAO (Year 2). Shared terms that already exist in multispecies ontologies will be obsoleted, given a "replaced_by" relationship to the relevant VAO term, and the shared term subsequently imported into the ontology. Terms shared by a multispecies ontology and its corresponding single-species ontology (e.g., AAO and XAO) would also ideally be imported from the multispecies ontology into the single species ontology (or rather, a single ontology for that taxonomic group could be used). However, because MODs currently cannot import terms, shared terms will instead be duplicated in single species ontologies and cross-referenced to the term in the external ontology. For example, because XAO and AAO both contain ‘radio-ulna’, the term XAO term will cross-reference the AAO ID for radio-ulna.
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'''Next target release date:''' Late August 2011
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'''Features:'''
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*New skeletal terms for the limb/fin and cranial skeleton will be added based on work done at the Phenotype RCN Vertebrate Working Group meeting in Boulder, CO (June 1-3, 2011)
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*Relationships to terms from external ontologies (GO, PATO, CL) will be included
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=== Teleost Anatomy Ontology (TAO) ===
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'''Next target release date:''' Late August 2011
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'''Features:'''
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*VAO musculo-skeletal terms will be imported, and existing TAO terms applicable outside of Teleostei will be obsoleted and added to VAO for subsequent import
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=== Amphibian Anatomy Ontology (AAO) ===
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'''Next target release date:''' Late August 2011
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'''Features:
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*children of "unclassified anatomical entity" will be given appropriate is_a parents
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*add VAO xrefs
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As a long term goal, AAO and XAO will be aligned, XAO terms will cross reference their AAO parents, and these ontologies will be regularly synchronized. However, because AAO development is not scheduled for the first year (whereas XAO will be adding many new non-skeletal terms), an initial synchronization at the beginning of year 1 will take place, followed by cloning AAO from XAO at the beginning of year 2. Specifically, AAO terms applicable to Xenopus will be added to XAO and given an AAO xref. If AAO xrefs VAO, then the VAO ID should be used preferentially over the AAO ID. Relationships for xrefed terms will be the same as those in AAO. AAO terms not applicable to Xenopus won't be added or cross-referenced in XAO. In Year 1, XAO will continue to add new terms whereas AAO development will be frozen.
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In Year 2, AAO will be cloned out from XAO, with AAO xrefs converted into primary AAO IDs and new AAO identifiers created for terms added to XAO in year 1. The non-Xenopus AAO terms that weren't added to XAO will then be added to the newly cloned AAO. XAO will retain xrefs to AAO terms.
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=== Amniote Anatomy Ontology (AMAO) ===
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'''Next target release date:'''
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'''Features:
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*In the initial release, musculo-skeletal terms from VAO and non-skeletal terms from the amniote subset of the Uber Anatomy Ontology [http://obofoundry.org/cgi-bin/detail.cgi?id=uberon (Uberon)] will be imported into AMAO
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=== Zebrafish Anatomical Ontology (ZFA) ===
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ZFA terms are cross referenced to TAO terms, and these cross references will be maintained and updated as needed. In addition, cross references to VAO musculo-skeletal terms will be added.
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'''Next target release date:'''
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'''Features:'''
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=== Xenopus Anatomy Ontology (XAO) ===
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(see desciption of XAO/AAO merge above)
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'''Next target release date:'''
  
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====Implementation of taxonomic constraints in VAO====
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'''Features:'''
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Taxonomically constrained subsets of VAO will be generated so that the terms imported into a subontology include only those designated as applicable to the taxonomic group of interest (e.g., TAO would import VAO using the "teleost" subset). This can be accomplished by using either taxonomically-defined subsets or never_in_taxon/only_in_taxon links to generate taxonomic slims of VAO.
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* Cross references to AAO and VAO musculo-skeletal terms will be added
  
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=== Zebrafish (ZFA) ===
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=== Mouse Adult Gross Anatomy (MA) ===
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Will add VAO xrefs; will update term relationships
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'''Next target release date:'''
  
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=== Teleost (TAO) ===
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'''Features:
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TAO will import only teleost applicable VAO terms. For example, ‘femur’ would not be imported.
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* Cross references to VAO musculo-skeletal terms will be added
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Will import teleost subset of VAO.
 
  
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=== Xenopus (XAO) ===
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[[Category:Anatomy]]
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[[Category: Ontology]]

Latest revision as of 21:17, 26 March 2012

Redirect to:

The Phenoscape project is coordinating the development and integration of multispecies and single species anatomy ontologies for vertebrates, with taxonomic focus on teleosts, zebrafish, amphibians, Xenopus, amniotes, and mouse. The limb/fin branch is the focus of ontology development in year 1.

The development of these ontologies follows OBO Foundry principles. Reusing ontology terms (by import or MIREOT) is the preferred mechanism for using shared terms and VAO will be imported into TAO, AAO, and AMAO. However, the existing model organism databases are largely hardcoded to reference identifiers for their own ontologies (e.g., MGI database reads MA term identifiers). In the long term, we will be exploring how to import terms into these ontologies. In the interim, the existing MOD vertebrate ontologies will continue to duplicate equivalent terms from other ontologies, with cross-references to the external ontology identifiers.

Year 1 Development Plan

Vertebrate Musculoskeletal Anatomy Ontology (VAO)

VAO will be expanded to include terms in the muscular and skeletal systems that are shared by two or more multispecies vertebrate ontologies. These shared terms will be imported into the multispecies ontologies. For example, ‘femur’, a term applicable to AAO and AMAO, will be added to VAO and imported into AMAO (Year 1) and AAO (Year 2). Shared terms that already exist in multispecies ontologies will be obsoleted, given a "replaced_by" relationship to the relevant VAO term, and the shared term subsequently imported into the ontology. Terms shared by a multispecies ontology and its corresponding single-species ontology (e.g., AAO and XAO) would also ideally be imported from the multispecies ontology into the single species ontology (or rather, a single ontology for that taxonomic group could be used). However, because MODs currently cannot import terms, shared terms will instead be duplicated in single species ontologies and cross-referenced to the term in the external ontology. For example, because XAO and AAO both contain ‘radio-ulna’, the term XAO term will cross-reference the AAO ID for radio-ulna.

Next target release date: Late August 2011

Features:

  • New skeletal terms for the limb/fin and cranial skeleton will be added based on work done at the Phenotype RCN Vertebrate Working Group meeting in Boulder, CO (June 1-3, 2011)
  • Relationships to terms from external ontologies (GO, PATO, CL) will be included

Teleost Anatomy Ontology (TAO)

Next target release date: Late August 2011

Features:

  • VAO musculo-skeletal terms will be imported, and existing TAO terms applicable outside of Teleostei will be obsoleted and added to VAO for subsequent import

Amphibian Anatomy Ontology (AAO)

Next target release date: Late August 2011

Features:

  • children of "unclassified anatomical entity" will be given appropriate is_a parents
  • add VAO xrefs

As a long term goal, AAO and XAO will be aligned, XAO terms will cross reference their AAO parents, and these ontologies will be regularly synchronized. However, because AAO development is not scheduled for the first year (whereas XAO will be adding many new non-skeletal terms), an initial synchronization at the beginning of year 1 will take place, followed by cloning AAO from XAO at the beginning of year 2. Specifically, AAO terms applicable to Xenopus will be added to XAO and given an AAO xref. If AAO xrefs VAO, then the VAO ID should be used preferentially over the AAO ID. Relationships for xrefed terms will be the same as those in AAO. AAO terms not applicable to Xenopus won't be added or cross-referenced in XAO. In Year 1, XAO will continue to add new terms whereas AAO development will be frozen.

In Year 2, AAO will be cloned out from XAO, with AAO xrefs converted into primary AAO IDs and new AAO identifiers created for terms added to XAO in year 1. The non-Xenopus AAO terms that weren't added to XAO will then be added to the newly cloned AAO. XAO will retain xrefs to AAO terms.

Amniote Anatomy Ontology (AMAO)

Next target release date:

Features:

  • In the initial release, musculo-skeletal terms from VAO and non-skeletal terms from the amniote subset of the Uber Anatomy Ontology (Uberon) will be imported into AMAO

Zebrafish Anatomical Ontology (ZFA)

ZFA terms are cross referenced to TAO terms, and these cross references will be maintained and updated as needed. In addition, cross references to VAO musculo-skeletal terms will be added.

Next target release date:

Features:

Xenopus Anatomy Ontology (XAO)

(see desciption of XAO/AAO merge above)

Next target release date:

Features:

  • Cross references to AAO and VAO musculo-skeletal terms will be added

Mouse Adult Gross Anatomy (MA)

Next target release date:

Features:

  • Cross references to VAO musculo-skeletal terms will be added
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