Difference between revisions of "Ontologies"

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The Phenoscape Project uses community anatomy, quality, spatial, and taxonomic ontologies for the annotation of phenotypes from the comparative biology literature. The development of these ontologies follows OBO Foundry principles as much as possible, including reuse of ontology terms as the preferred mechanism for using shared terms. These ontologies can be  downloaded, searched, and visualized at [http://www.ontobee.org/ Ontobee] or [http://bioportal.bioontology.org/ NCBO BioPortal]. The ontologies are also available for download from [http://www.obofoundry.org/ OBO Foundry] and can also be viewed using the OBO-Edit or [https://protege.stanford.edu/ Protégé] desktop software.
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The Phenoscape Project uses community anatomy, quality, spatial, and taxonomic ontologies for the annotation of phenotypes from the comparative biology literature. The development of these ontologies follows OBO Foundry principles as much as possible, including reuse of ontology terms as the preferred mechanism for using shared terms. These ontologies can be  downloaded, searched, and visualized at [http://www.ontobee.org/ Ontobee], [http://bioportal.bioontology.org/ NCBO BioPortal], or downloaded from [http://www.obofoundry.org/ OBO Foundry]. Ontologies can also be edited and viewed using the [https://protege.stanford.edu/ Protégé] desktop software.
  
 
= Anatomy Ontologies =
 
= Anatomy Ontologies =
  
== Previous work on ontology coordination ==
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== Uberon Anatomy Ontology ==
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We use and contribute to the Uberon Anatomy Ontology, into which the Teleost Anatomy Ontology, Amphibian Anatomy Ontology,  and Vertebrate Skeletal Anatomy Ontology were merged. More information about the development of Uberon can be found in [https://doi.org/10.1186/gb-2012-13-1-r5 Mungall et al. (2012)] and [http://dx.doi.org/10.1186/2041-1480-5-21 Haendel et al. (2014)].
  
In the past we held regular project [[Anatomy_Ontology_Conf_calls| anatomy ontology conference calls]] to discuss ontology development with the curators of the various anatomy ontologies (ZFA, .... The limb/fin branch was the primary focus of ontology development in Phenoscape II. We also coordinated our development calls with the [http://phenotypercn.org Phenotype RCN] vertebrate working group.
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Uberon is separated into a core file and an "extension" file (phenoscape-ext) which allows for separate editing by Phenoscape curators and the core Uberon developers. New terms required by Phensocape for annotation of vertebrate phenotypes are added to phenoscape-ext, which also contains the terms sourced from the TAO, AAO, and VSAO. We use the [https://protege.stanford.edu/ Protégé] desktop software to edit phenoscape-ext. The release version of Uberon contains both core and ext terms in a single file.
  
== Phenoscape-ext ==
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* Ontology update requests can be made on the Uberon term request tracker: [https://github.com/obophenotype/uberon/issues]
Phenoscape-ext contains the TAO, AAO, and VSAO combined with Uberon. This adds an additional 2500+ classes to the core Uberon, all contributed by the Phenoscape project. Phenoscape-ext is our first foray into working directly in OWL.
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* Source edit file available here: [https://github.com/obophenotype/uberon-phenoscape-ext]
  
* Ontology update requests can be made on the Uberon term request tracker: [https://github.com/cmungall/uberon/issues]
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phenoscape-ext.owl is the editors version. The release uberon/ext.owl retains the import chains and is pre-reasoned. uberon/ext.obo merges the import chain into one ontology because obo does not have good support for imports. Many of the other uberon derived artifacts such as composite-metazoan do not use ext but this may be changed in the future. See [http://uberon.org; uberon.org] for details of all the various cuts.
* Source edit file available here: [https://phenoscape.svn.sourceforge.net/svnroot/phenoscape/trunk/vocab/edit/phenoscape-ext.owl]
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* Release files are available here:
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[http://purl.obolibrary.org/obo/uberon/ext.obo http://purl.obolibrary.org/obo/uberon/ext.obo]
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==Anatomy ontologies merged with Uberon and no longer under development ==
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===Vertebrate Skeletal Anatomy Ontology (VSAO) ===
  
[http://purl.obolibrary.org/obo/uberon/ext.owl  http://purl.obolibrary.org/obo/uberon/ext.owl]
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VSAO contains terms representing structures in the skeletal system of vertebrates. It references terms from the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO) Biological Process, Cell Ontology (CL), and the Phenotype and Trait Ontology (PATO). VSAO can be downloaded at the [http://obofoundry.org/cgi-bin/detail.cgi?id=vertebrate_skeletal_anatomy OBO Foundry] and browsed at [http://bioportal.bioontology.org/ontologies/45737?p=terms BioPortal]. Development of the VSAO is described in [http://dx.plos.org/10.1371/journal.pone.0051070 Dahdul et al. (2012)].
  
phenoscape-ext.owl will remain the editors version. The release uberon/ext.owl retains the import chains and is pre-reasoned. uberon/ext.obo merges the import chain into one ontology because obo does not have good support for imports. Mant of the other uberon derived artefacts such as composite-metazoan do not use ext but this may be changed in the future. See [http://uberon.org; uberon.org] for details of all the various cuts.
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The VSAO as released represents the outcome of the [[Skeletal_Anatomy_Jamboree| skeletal anatomy workshop held at NESCent]] and [http://dx.plos.org/10.1371/journal.pone.0051070 corresponding paper in PLOS ONE]. New skeletal terms for the limb/fin and cranial skeleton have and will continue to be added to the Phenoscape-ext ontology based on work done at the Phenotype RCN Vertebrate Working Group meeting in Boulder, CO (June 1-3, 2011) and from ongoing work.
  
We will continue to reconcile the issues that arose during this merge (started in August, 2012, first release on Feb 22, 2013), so you may continue to see some issues.  This ontology will be used by Phenoscape for annotation of evolutionary characters.
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=== Teleost Anatomy Ontology (TAO) ===
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TAO is a multi-species ontology for teleost fishes that was initialized with terms from the Zebrafish Anatomical Ontology (ZFA). The development of the TAO focused on the skeletal system because it varies significantly across fishes, is well-preserved in fossil specimens, and it is often the focus of morphologically-based evolutionary studies in ichthyology. The development of the TAO is described in [http://sysbio.oxfordjournals.org/content/59/4/369.full Dahdul et al. (2010)]. TAO can be downloaded from the [http://obofoundry.org/cgi-bin/detail.cgi?id=teleost_anatomy OBO Foundry]  and browse at [http://bioportal.bioontology.org/visualize/38362 BioPortal]. Further documentation [[Teleost_Anatomy_Ontology| about TAO is described here]].
  
* [http://www.obofoundry.org/wiki/index.php/UBERON:Main_Page#Phenoscape-ext_.28new.29 Further information about Uberon and the Phenoscape-ext merge]
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=== Amphibian Anatomy Ontology (AAO) ===
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AAO is a multispecies ontology for amphibian anatomy. Development of AAO is described in [https://doi.org/10.1142/9789812772435_0035 Maglia et al. (2007)]. View AAO at the [http://bioportal.bioontology.org/ontologies/AAO BioPortal]. The last updated version (April 2012) includes terms merged from the Xenopus Anatomy Ontology and updates from David Blackburn and Wasila Dahdul.
  
==Vertebrate Skeletal Anatomy Ontology (VSAO) ==
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==Model organism anatomy ontologies ==
  
VSAO contains terms representing structures in the skeletal system of vertebrates. It references terms from the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO) Biological Process, Cell Ontology (CL), and the Phenotype and Trait Ontology (PATO). VSAO can be downloaded at the [http://obofoundry.org/cgi-bin/detail.cgi?id=vertebrate_skeletal_anatomy OBO Foundry] and browsed at [http://bioportal.bioontology.org/ontologies/45737?p=terms BioPortal]. Development of the VSAO is described in [http://dx.plos.org/10.1371/journal.pone.0051070 Dahdul et al. (2012)]
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Phenotype data for model organisms are imported into the Phenoscape KB for mouse (MGI), human (HPO), zebrafish (ZFIN), and frog (Xenbase). Uberon maintains cross-references to terms from the corresponding model organism anatomy ontologies.
 
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* Release version available here: [http://purl.obolibrary.org/obo/vsao.obo]
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=== Mouse Adult Gross Anatomy (MA) ===
 
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Note that VSAO as released represents the outcome of the [[Skeletal_Anatomy_Jamboree| skeletal anatomy workshop held at NESCent]] and  [http://dx.plos.org/10.1371/journal.pone.0051070 corresponding paper in PLOS ONE]. Note also that VSAO development moving forward has been merged into the Phenoscape-ext ontology described above.
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New skeletal terms for the limb/fin and cranial skeleton have and will continue to be added to the Phenoscape-ext ontology based on work done at the Phenotype RCN Vertebrate Working Group meeting in Boulder, CO (June 1-3, 2011) and from ongoing work.
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== Amphibian Anatomy Ontology (AAO) ==
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AAO is a multispecies ontology for amphibian anatomy.
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* Download AAO from the [http://obofoundry.org/cgi-bin/detail.cgi?id=amphibian_anatomy OBO Foundry] and browse at [http://bioportal.bioontology.org/ontologies/45269?p=terms BioPortal]
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* Source edit directory available [http://phenoscape.svn.sourceforge.net/viewvc/phenoscape/trunk/vocab/AAO_v2.1.obo here].  The current version (April 2012) includes terms merged from the Xenopus Anatomy Ontology and updates from David Blackburn and Wasila Dahdul.
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NOTE: as per above case with VSAO, AAO has been merged into phenoscape-ext and is no longer under development.
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== Teleost Anatomy Ontology (TAO) ==
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TAO is a multi-species ontology for teleost fishes that was initialized with terms from the Zebrafish Anatomical Ontology (ZFA). The development of the TAO currently focuses on the skeletal system because it varies significantly across fishes, is well-preserved in fossil specimens, and it is often the focus of morphologically-based evolutionary studies in ichthyology. The development of the TAO is described in [http://sysbio.oxfordjournals.org/content/59/4/369.full Dahdul et al. (2010)].
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* Download TAO from the [http://obofoundry.org/cgi-bin/detail.cgi?id=teleost_anatomy OBO Foundry]  and browse at [http://bioportal.bioontology.org/visualize/38362 BioPortal].
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* [[Teleost_Anatomy_Ontology| Further documentation about TAO]]
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NOTE: as per above case with VSAO, the TAO has been merged into phenoscape-ext and is no longer under development.
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== Mouse Adult Gross Anatomy (MA) ==
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The Adult Mouse Anatomy (MA) ontology contains terms that represent structures in the postnatal mouse (''Mus'') and is used to annotate gene expression and phenotypes for the mouse at [http://www.informatics.jax.org/ Mouse Genome Informatics (MGI)] and other resources. Development of the MA is described in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088948/ Hayamizu et al. (2005)].  
 
The Adult Mouse Anatomy (MA) ontology contains terms that represent structures in the postnatal mouse (''Mus'') and is used to annotate gene expression and phenotypes for the mouse at [http://www.informatics.jax.org/ Mouse Genome Informatics (MGI)] and other resources. Development of the MA is described in [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1088948/ Hayamizu et al. (2005)].  
  
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* Term requests can be submitted on the [http://sourceforge.net/tracker/?group_id=76834&atid=1205376 mouse anatomy tracker]
 
* Term requests can be submitted on the [http://sourceforge.net/tracker/?group_id=76834&atid=1205376 mouse anatomy tracker]
  
== Xenopus Anatomy Ontology (XAO) ==
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=== Xenopus Anatomy Ontology (XAO) ===
 
XAO contains terms that represent anatomical structures for the model organism ''Xenopus laevis'' (African clawed frog). [http://www.xenbase.org Xenbase] uses XAO to annotate Xenopus gene expression and phenotypes.
 
XAO contains terms that represent anatomical structures for the model organism ''Xenopus laevis'' (African clawed frog). [http://www.xenbase.org Xenbase] uses XAO to annotate Xenopus gene expression and phenotypes.
  
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* Source directory is available here: [http://phenoscape.svn.sourceforge.net/viewvc/phenoscape/trunk/vocab/xenopus_anatomy_2.0.8_eriks3.obo]
 
* Source directory is available here: [http://phenoscape.svn.sourceforge.net/viewvc/phenoscape/trunk/vocab/xenopus_anatomy_2.0.8_eriks3.obo]
  
== Zebrafish Anatomical Ontology (ZFA) ==
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=== Zebrafish Anatomical Ontology (ZFA) ===
 
ZFA is used by [http://zfin.org ZFIN] to annotate mutant phenotypes for the model organsim zebrafish (''Danio rerio'').  
 
ZFA is used by [http://zfin.org ZFIN] to annotate mutant phenotypes for the model organsim zebrafish (''Danio rerio'').  
  
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ZFA terms are cross referenced to TAO terms, and these cross references will be maintained and updated as needed.
 
ZFA terms are cross referenced to TAO terms, and these cross references will be maintained and updated as needed.
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== Previous work on ontology coordination ==
 +
 +
Previously, Phenoscape coordinated the development and integration of vertebrate skeletal terms across anatomy ontologies for vertebrates, with taxonomic focus on teleosts, zebrafish, amphibians, Xenopus, amniotes, and mouse. The limb/fin branch was the primary focus of ontology development in Phenoscape II. We held regular project [[Anatomy_Ontology_Conf_calls| anatomy ontology conference calls]] to discuss ontology development with the curators of the various anatomy ontologies (ZFA, XAO, MA). We also coordinated our development calls with the [http://phenotypercn.org Phenotype RCN] vertebrate working group. Currently, we use and contribute new terms to the Uberon anatomy ontology (metazoans) into which the Teleost Anatomy Ontology,  Amphibian Anatomy Ontology,  and Vertebrate Skeletal Anatomy Ontology were merged.
  
 
= Taxonomy Ontologies =
 
= Taxonomy Ontologies =

Latest revision as of 17:42, 17 July 2018

The Phenoscape Project uses community anatomy, quality, spatial, and taxonomic ontologies for the annotation of phenotypes from the comparative biology literature. The development of these ontologies follows OBO Foundry principles as much as possible, including reuse of ontology terms as the preferred mechanism for using shared terms. These ontologies can be downloaded, searched, and visualized at Ontobee, NCBO BioPortal, or downloaded from OBO Foundry. Ontologies can also be edited and viewed using the Protégé desktop software.

Anatomy Ontologies

Uberon Anatomy Ontology

We use and contribute to the Uberon Anatomy Ontology, into which the Teleost Anatomy Ontology, Amphibian Anatomy Ontology, and Vertebrate Skeletal Anatomy Ontology were merged. More information about the development of Uberon can be found in Mungall et al. (2012) and Haendel et al. (2014).

Uberon is separated into a core file and an "extension" file (phenoscape-ext) which allows for separate editing by Phenoscape curators and the core Uberon developers. New terms required by Phensocape for annotation of vertebrate phenotypes are added to phenoscape-ext, which also contains the terms sourced from the TAO, AAO, and VSAO. We use the Protégé desktop software to edit phenoscape-ext. The release version of Uberon contains both core and ext terms in a single file.

  • Ontology update requests can be made on the Uberon term request tracker: [1]
  • Source edit file available here: [2]

phenoscape-ext.owl is the editors version. The release uberon/ext.owl retains the import chains and is pre-reasoned. uberon/ext.obo merges the import chain into one ontology because obo does not have good support for imports. Many of the other uberon derived artifacts such as composite-metazoan do not use ext but this may be changed in the future. See uberon.org for details of all the various cuts.

Anatomy ontologies merged with Uberon and no longer under development

Vertebrate Skeletal Anatomy Ontology (VSAO)

VSAO contains terms representing structures in the skeletal system of vertebrates. It references terms from the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO) Biological Process, Cell Ontology (CL), and the Phenotype and Trait Ontology (PATO). VSAO can be downloaded at the OBO Foundry and browsed at BioPortal. Development of the VSAO is described in Dahdul et al. (2012).

The VSAO as released represents the outcome of the skeletal anatomy workshop held at NESCent and corresponding paper in PLOS ONE. New skeletal terms for the limb/fin and cranial skeleton have and will continue to be added to the Phenoscape-ext ontology based on work done at the Phenotype RCN Vertebrate Working Group meeting in Boulder, CO (June 1-3, 2011) and from ongoing work.

Teleost Anatomy Ontology (TAO)

TAO is a multi-species ontology for teleost fishes that was initialized with terms from the Zebrafish Anatomical Ontology (ZFA). The development of the TAO focused on the skeletal system because it varies significantly across fishes, is well-preserved in fossil specimens, and it is often the focus of morphologically-based evolutionary studies in ichthyology. The development of the TAO is described in Dahdul et al. (2010). TAO can be downloaded from the OBO Foundry and browse at BioPortal. Further documentation about TAO is described here.

Amphibian Anatomy Ontology (AAO)

AAO is a multispecies ontology for amphibian anatomy. Development of AAO is described in Maglia et al. (2007). View AAO at the BioPortal. The last updated version (April 2012) includes terms merged from the Xenopus Anatomy Ontology and updates from David Blackburn and Wasila Dahdul.

Model organism anatomy ontologies

Phenotype data for model organisms are imported into the Phenoscape KB for mouse (MGI), human (HPO), zebrafish (ZFIN), and frog (Xenbase). Uberon maintains cross-references to terms from the corresponding model organism anatomy ontologies.

Mouse Adult Gross Anatomy (MA)

The Adult Mouse Anatomy (MA) ontology contains terms that represent structures in the postnatal mouse (Mus) and is used to annotate gene expression and phenotypes for the mouse at Mouse Genome Informatics (MGI) and other resources. Development of the MA is described in Hayamizu et al. (2005).

Xenopus Anatomy Ontology (XAO)

XAO contains terms that represent anatomical structures for the model organism Xenopus laevis (African clawed frog). Xenbase uses XAO to annotate Xenopus gene expression and phenotypes.

  • XAO can be downloaded at the OBO Foundry and browsed at the BioPortal.
  • Term tracker is available here: [3]
  • Source directory is available here: [4]

Zebrafish Anatomical Ontology (ZFA)

ZFA is used by ZFIN to annotate mutant phenotypes for the model organsim zebrafish (Danio rerio).

  • Download from the OBO Foundry or browse at the BioPortal.
  • Term requests can be submitted to the ZFA tracker.
  • Edit version is kept internally at ZFIN, but a prerelease edit version is available at [5]

ZFA terms are cross referenced to TAO terms, and these cross references will be maintained and updated as needed.

Previous work on ontology coordination

Previously, Phenoscape coordinated the development and integration of vertebrate skeletal terms across anatomy ontologies for vertebrates, with taxonomic focus on teleosts, zebrafish, amphibians, Xenopus, amniotes, and mouse. The limb/fin branch was the primary focus of ontology development in Phenoscape II. We held regular project anatomy ontology conference calls to discuss ontology development with the curators of the various anatomy ontologies (ZFA, XAO, MA). We also coordinated our development calls with the Phenotype RCN vertebrate working group. Currently, we use and contribute new terms to the Uberon anatomy ontology (metazoans) into which the Teleost Anatomy Ontology, Amphibian Anatomy Ontology, and Vertebrate Skeletal Anatomy Ontology were merged.

Taxonomy Ontologies

Vertebrate Taxonomy Ontology (VTO)

The Vertebrate Taxonomy Ontology (Midford, Dececchi, et al. 2013) includes the TTO, ATO, and uses the NCBI taxonomy as a source covering amniotes and basal chordates outside the scope of the TTO. The ontology has an assigned OBO purl http://purl.obolibrary.org, and there is a repository at https://code.google.com/p/vertebrate-taxonomy-ontology/. The current release covers vertebrates and was built by starting with the NCBI taxonomy for vertebrates and splicing in TTO (except hagfish), and the downloadable amphibiaweb taxonomy.  Subspecies names were added to their parent species as synonyms (not subclasses). The taxonomy is currently in the available in OWL format, as generated by the OBO release tool. It also uses the Taxonomic Rank Vocabulary to tag taxa with specified rank.

  • NCBI This taxonomy provides the amniote portions of the current VTO. This provides taxonomy for GenBank submissions (including fossil taxa), but does not claim to be an authoritative source (and generally doesn't cover taxa that have not been submitted). It does provide some taxonomic synonyms as well.
  • Paleobiology Database This covers all groups represented in the fossil record - we have implemented a way to incorporate bulk taxonomy downloads in the VTO. We are still somewhat uncertain about how hierarchies are (dynamically) built in this resource.

These can provide links to additional synonyms and resources (e.g., TTO uses fishbase to provide common names and links to their pages). Taxonomic synonyms are particularly useful as aids to data curation, but common names can assist users in browsing the website. Taxonomic resources (above) can be used as sources of names as well.

  • Fishbase - their taxonomy is close to TTO (both based on Catalog of Fishes). TTO (hence VTO) uses it as a source of common names and includes links to Fishbase's species pages.
  • Global Names Index (GNI) - Extensive list of names.

Teleost Taxonomy Ontology (TTO)

The Teleost Taxonomy Ontology (TTO) is derived from the Catalog of Fishes (see also the representation on BioPortal, which can be navigated on-line). The TTO was developed from the Phenoscape I project and provides coverage of fish in the VTO. The TTO is updated in concert with Catalog of Fishes updates.

Taxonomic Rank Vocabulary (TAXRANK)

During 2010, we released a separate Taxonomic Rank Vocabulary, and removed all rank terms (e.g., family, genus, etc.) from the taxa within the TTO. Taxa in the TTO specify their ranks as property values via the metadata relation has_rank, but the object of the has_rank links is contained in the TAXRANK vocabulary.

Developing TAXRANK as a vocabulary, rather than an ontology (e.g., by defining an ordering relation between ranks) should facilitate its reuse in other taxonomic ontologies. Developing a cross-authority (e.g., ICZN, ICBN, etc.) ontology of ranks may be possible, but there does not appear to be a compelling need for such an ontology.

  • The TAXRANK vocabulary is available in OWL format here.
  • The vocabulary can be browsed at Bioportal.

Fish Collection Codes Vocabulary

There is a flat vocabulary of fish collections, based on a list used in Catalog of Fishes, though with a few additions listed on the Fish Collection Updates page. The master list, from which the OBO-format ontology is generated is available as a google docs spreadsheet. It has been augmented with links to entries in the Biodiversity Collections Index.

The current release, as used in Phenex is Fish Collection Abbreviations

Amphibian Taxonomy Ontology (ATO)

The ATO has been deprecated in favor of generating the Amphibian component of the VTO directly from Amphibiaweb.

Additional documentation

Shared Ontologies

These ontologies listed below were initiated by the model organism communities. Phenoscape is actively involved in extending these ontologies.