Difference between revisions of "Ontologies"

From phenoscape
Jump to: navigation, search
(fixed link to Fish Collection Codes Vocabulary)
 
(41 intermediate revisions by 7 users not shown)
Line 1: Line 1:
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. These ontologies are publicly available and being used and extended by the community [[Contributors|(view the list)]]. Where possible, we are also reusing external ontologies (e.g., PATO) from the broader biological community for the greatest interoperability across data types. The development of these ontologies follows OBO Foundry principles as much as possible, including reuse of ontology terms (by import or MIREOT) as the preferred mechanism for using shared terms. These anatomy ontologies are available from the OBO CVS-based version-control system, from which they are regularly loaded into the NCBO [http://bioportal.bioontology.org/ BioPortal] where they can be readily browsed, searched, and visualized. The ontologies are also available for download as .obo files from [http://www.obofoundry.org/ OBO Foundry] and can also be viewed using the [http://oboedit.org/ OBO-Edit] desktop or [http://protege.stanford.edu/| Protege] software.
+
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. These ontologies are publicly available and being used and extended by the community [[Contributors|(view the list)]]. Where possible, we are also reusing external ontologies (e.g., PATO) from the broader biological community for the greatest interoperability across data types. The development of these ontologies follows OBO Foundry principles as much as possible, including reuse of ontology terms (by import or MIREOT) as the preferred mechanism for using shared terms. These anatomy ontologies are available from the OBO CVS-based version-control system, from which they are regularly loaded into the NCBO [http://bioportal.bioontology.org/ BioPortal] where they can be readily browsed, searched, and visualized. The ontologies are also available for download as .obo files from [http://www.obofoundry.org/ OBO Foundry] and can also be viewed using the [http://oboedit.org/ OBO-Edit] or [http://protege.stanford.edu/| Protege] desktop software.
 
+
 
+
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 link to external terms using a cross-referencing strategy to external ontology identifiers (see [[http://www.obofoundry.org/wiki/index.php/Inter-ontology_Links| Interontology links]])
+
  
 +
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 link to external terms using a cross-referencing strategy to external ontology identifiers (see [http://www.obofoundry.org/wiki/index.php/Inter-ontology_Links Interontology links])
  
 
= Anatomy Ontologies =
 
= Anatomy Ontologies =
  
ONTOLOGY COORDINATION
+
== Ontology coordination ==
  
New personnel training topics for building and using ontologies are posted [[Annotator tutorial topics| here.]]
+
* [[Annotator tutorial topics| New personnel training topics for building and using ontologies]]
 +
* [[Ontology_workflow| Ontology editing workflow]]
 +
* See also the [http://code.google.com/p/nescent-anatomy-course/source/browse/#svn%2Ftrunk%2Fmaterial_for_course| course materials for the anatomy ontology course] held at NESCent in August of 2012
  
See also the course materials for the anatomy ontology course held at NESCent in August of 2012: [[http://code.google.com/p/nescent-anatomy-course/source/browse/#svn%2Ftrunk%2Fmaterial_for_course| NESCent Anatomy Ontology Course]]
+
In the past we have held regular project [[Anatomy_Ontology_Conf_calls| anatomy ontology conference calls]] to discuss development with the curators of the various anatomy ontologies listed below. The limb/fin branch was the focus of ontology development in year 1. Currently, we coordinate our development calls with the [http://phenotypercn.org Phenotype RCN] vertebrate working group monthly calls. Information about these calls is sent to the obo-anatomy, phenotype-rcn vertebrate google groups, and the phenoscape project listservs. These calls are open to everyone and call in info and notes from them is available at the [http://wiki.phenotypercn.org/wiki/Vertebrates Vertebrate Working Group Wiki Page].
  
Ontology editing workflow is here: [[Ontology_workflow| Ontology Workflow]]
+
In addition, the Phenoscape curators have been meeting weekly to have joint ontology editing sessions. Please let us know if you would like to join us, Melissa Haendel has been coordinating these sessions (haendel@ohsu.edu).
  
In the past we have held regular project [https://www.phenoscape.org/wiki/Anatomy_Ontology_Conf_calls anatomy ontology conference calls] to discuss development with the curators of these ontologies. The limb/fin branch was the focus of ontology development in year 1 across the various ontologies described below. Currently, we coordinate our development calls with the phenotype RCN vertebrate working group monthly calls. Information about these calls is sent to the obo-anatomy, phenotype-rcn vertebrate google group, and the phenoscape project listserves. These calls are open to everyone and call in info and notes from these calls is available here: [http://wiki.phenotypercn.org/wiki/Vertebrates| Vertebrate Working Group Wiki Page]
+
== Phenoscape-ext ==
 +
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.
  
In addition, the phenoscape curators have been meeting twice weekly to have joint ontology editing sessions. Please let us know if you would like to join us, Melissa Haendel has been coordinating these sessions (haendel@ohsu.edu).
+
* Ontology update requests can be made on the Uberon term request tracker: [https://github.com/cmungall/uberon/issues]
 +
* Source edit file available here: [https://phenoscape.svn.sourceforge.net/svnroot/phenoscape/trunk/vocab/edit/phenoscape-ext.owl]
 +
* Release files are available here:
  
 +
[http://purl.obolibrary.org/obo/uberon/ext.obo http://purl.obolibrary.org/obo/uberon/ext.obo]
  
 +
[http://purl.obolibrary.org/obo/uberon/ext.owl  http://purl.obolibrary.org/obo/uberon/ext.owl]
  
==Phenoscape-ext ==
+
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.
Phenoscape-ext contains the TAO, AAO, and VSAO combined with Uberon. We are currently in the process of reconciling the issues that arose during this merge, so you may see some messiness for a bit.  This ontology will be used by phenoscape for annotation of evolutionary characters. Phenoscape-ext is our first foray into working directly in OWL.
+
  
Ontology update requests can be made on the Uberon term request tracker:
+
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.
[https://github.com/cmungall/uberon/issues]
+
  
* Source edit file available here: [https://phenoscape.svn.sourceforge.net/svnroot/phenoscape/trunk/vocab/edit/phenoscape-ext.owl]
+
* [http://www.obofoundry.org/wiki/index.php/UBERON:Main_Page#Phenoscape-ext_.28new.29 Further information about Uberon and the Phenoscape-ext merge]
* PURL: http://purl.obolibrary.org/obo/uberon/phenoscape-ext.owl
+
 
+
Further information about Uberon and the Phenoscape-ext merge is available here:
+
[http://www.obofoundry.org/wiki/index.php/UBERON:Main_Page#Phenoscape-ext_.28new.29]
+
  
 
==Vertebrate Skeletal Anatomy Ontology (VSAO) ==
 
==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 [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].
+
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)]
  
* Release version available here: [http://phenoscape.svn.sourceforge.net/svnroot/phenoscape/tags/vocab-releases/VSAO/vsao.obo]
+
* Release version available here: [http://purl.obolibrary.org/obo/vsao.obo]
  
Note that VSAO as released represents the outcome of the skeletal anatomy workshop held at NESCent [https://phenoscape.org/wiki/Skeletal_Anatomy_Jamboree] and corresponding paper due out in PlosOne.
+
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.
NOTE: VSAO development moving forward has been merged into the above Phenoscape-ext ontology described above.
+
  
VSAO will be expanded to include terms in the skeletal system 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 phenoscape-ext. Shared terms that already exist in multispecies ontologies will be obsoleted, given a "replaced_by" relationship to the relevant phenoscape-ext 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 or phenoscape-ext ID for radio-ulna.
+
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.
 
+
New skeletal terms for the limb/fin and cranial skeleton have and will continue to be added based on work done at the Phenotype RCN Vertebrate Working Group meeting in Boulder, CO (June 1-3, 2011) and from ongoing work here: [https://docs.google.com/spreadsheet/ccc?key=0Aj8NJdyb-leqdFdTaEJjNkMyUXR1SE1PSUNJc0gwcmc#gid=0]
+
  
 
== Amphibian Anatomy Ontology (AAO) ==
 
== Amphibian Anatomy Ontology (AAO) ==
AAO is a multispecies ontology for amphibian anatomy. 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]
+
AAO is a multispecies ontology for amphibian anatomy.
  
 +
* 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]
 
* 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.
 
* 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.
  
Line 54: Line 51:
  
 
== Teleost Anatomy Ontology (TAO) ==
 
== 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 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)]. 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].
+
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)].
  
Further documentation about TAO is located here: [[Teleost_Anatomy_Ontology|Teleost_Anatomy_Ontology]]
+
* 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].
 +
* [[Teleost_Anatomy_Ontology| Further documentation about TAO]]
  
NOTE: as per above case with VSAO, AAO has been merged into phenoscape-ext and is no longer under development.
+
NOTE: as per above case with VSAO, the TAO has been merged into phenoscape-ext and is no longer under development.
  
 
== Mouse Adult Gross Anatomy (MA) ==
 
== 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 [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 MA is available for download at the [http://obofoundry.org/cgi-bin/detail.cgi?id=adult_mouse_anatomy OBO Foundry] and can be browsed using the [http://www.informatics.jax.org/searches/AMA_form.shtml Mouse Anatomy Browser].
+
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 MA is available for download at the [http://obofoundry.org/cgi-bin/detail.cgi?id=adult_mouse_anatomy OBO Foundry] and can be browsed using the [http://www.informatics.jax.org/searches/AMA_form.shtml Mouse Anatomy Browser].
 
* 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) ==
 
== 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 can be downloaded at the [http://obofoundry.org/cgi-bin/detail.cgi?id=xenopus_anatomy OBO Foundry] and browsed at the [http://bioportal.bioontology.org/ontologies/45264?p=terms BioPortal].
+
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.
  
* Term tracker is available here:
+
* XAO can be downloaded at the [http://obofoundry.org/cgi-bin/detail.cgi?id=xenopus_anatomy OBO Foundry] and browsed at the [http://bioportal.bioontology.org/ontologies/45264?p=terms BioPortal].
* Source directory is available here:
+
* Term tracker is available here: [https://sourceforge.net/tracker/?atid=1127722&group_id=76834]
 +
* 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) ==
 
== Zebrafish Anatomical Ontology (ZFA) ==
ZFA is used by [http://zfin.org ZFIN] to annotate mutant phenotypes for the model organsim zebrafish (''Danio rerio''). ZFA can be downloaded from the [http://obofoundry.org/cgi-bin/detail.cgi?id=zebrafish_anatomy OBO Foundry] and browsed at the [http://bioportal.bioontology.org/ontologies/1051 BioPortal].
+
ZFA is used by [http://zfin.org ZFIN] to annotate mutant phenotypes for the model organsim zebrafish (''Danio rerio'').  
  
 +
* Download from the [http://obofoundry.org/cgi-bin/detail.cgi?id=zebrafish_anatomy OBO Foundry] or browse at the [http://bioportal.bioontology.org/ontologies/1051 BioPortal].
 
* Term requests can be submitted to the [http://sourceforge.net/tracker/?group_id=76834&atid=994726 ZFA tracker].
 
* Term requests can be submitted to the [http://sourceforge.net/tracker/?group_id=76834&atid=994726 ZFA tracker].
 
* Edit version is kept internally at ZFIN, but a prerelease edit version is available at [http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/preversion.zfish.obo]
 
* Edit version is kept internally at ZFIN, but a prerelease edit version is available at [http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/anatomy/gross_anatomy/animal_gross_anatomy/fish/preversion.zfish.obo]
  
====Development====
 
 
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.
  
 
= Taxonomy Ontologies =
 
= Taxonomy Ontologies =
  
=== Teleost Taxonomy Ontology (TTO) ===
+
== Vertebrate Taxonomy Ontology (VTO) ==
Phenotypes are associated with species using a taxonomy ontology, the [[Teleost Taxonomy Ontology]] (TTO) derived from the [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes] (see also the [http://bioportal.bioontology.org/visualize/38363 representation on BioPortal], which can be navigated on-line). The TTO is updated in concert with Catalog of Fishes updates.  Changes to the TTO relative to the latest version generated from a dump from the Catalog of Fishes are documented [[TTO_Changes]].
+
  
=== Amphibian Taxonomy Ontology (ATO) ===
+
The Vertebrate Taxonomy Ontology [http://dx.doi.org/10.1186/2041-1480-4-34 (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 http://purl.obolibrary.org], and there is a repository at [https://code.google.com/p/vertebrate-taxonomy-ontology/ 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 [http://amphibiaweb.org/amphib_names.txt 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.
The ATO is derived from the [http://amphibiaweb.org/ AmphibiaWeb] list, which provides both taxonomy and some synonyms from ITIS and the [http://www.iucnredlist.org/initiatives/amphibians IUCN redlist].
+
  
=== Vertebrate Taxonomy Ontology (VTO) ===
+
*[http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ 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.
The Vertebrate Taxonomy Ontology includes the TTO, ATO, as well as a new Amniote Taxonomy Ontology.  An [http://phenoscape.svn.sourceforge.net/viewvc/phenoscape/trunk/vocab/vertebrate_taxonomy.obo initial release], including TTO and ATO, but using pan-vertebrate resources (see below) rather than a separate AmTO was made in May 2011.  This taxonomy covers vertebrates and was built by starting with the NCBI taxonomy for vertebrates and splicing in TTO (except hagfish), ATO, and the IOC taxonomy of living birds. Synonyms from ITIS and Catalog of Life were attached if the primary name matched a name in the existing taxonomy. Subspecies names were added to their parent species as synonyms (not subclasses).  The taxonomy is currently in the OBO format used for TTO and ATO, which includes the use of the Taxonomic Rank Vocabulary to tag taxa with specified rank.
+
*[http://paleodb.org/ 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.
  
=== Other Taxonomic Resources ===
+
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.
  
==== Amniotes ====
+
*[http://www.fishbase.org/ 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.
*Birds The [http://www.worldbirdnames.org/index.html IOC checklist] provides a current taxonomy and common names, but no taxonomic synonyms.
+
*[http://gni.globalnames.org/ Global Names Index (GNI)] - Extensive list of names.
*Mammals Wilson and Reader (1993) is the standard, but the available electronic version of their taxonomy is IP encumbered.
+
  
====Fossil Taxa====
+
== Teleost Taxonomy Ontology (TTO) ==
*[http://paleodb.org/ 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.
+
The [[Teleost Taxonomy Ontology]] (TTO) is derived from the [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes] (see also the [http://bioportal.bioontology.org/visualize/38363 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.
 +
* The TTO in OWL format is [http://purl.obolibrary.org/obo/tto.owl available here].
 +
* Browse TTO [http://bioportal.bioontology.org/ontologies/38703 at BioPortal]
  
==== Taxonomic (hierarchy) Resources ====
+
== Taxonomic Rank Vocabulary (TAXRANK) ==
*[http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ NCBI] This was used to fill in the gaps (non-avian amniotes) in the current proposed 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.
+
During 2010, we released a separate [[Taxonomic Rank Vocabulary]], and removed all rank terms (e.g., family, genus, etc.) from the taxa within the TTOTaxa 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.
*[http://www.itis.gov/ ITIS] Has some vetting by area experts, but coverage is not complete (nor uncontroversial).
+
*[http://www.catalogueoflife.org/ Catalogue of Life] Claimed to incorporate all of ITIS plus Species2000.  Updated quarterly.
+
  
==== Nomenclature Resources ====
+
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 ontologiesDeveloping 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.
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 websiteTaxonomic resources (above) can be used as sources of names as well.
+
* [http://www.fishbase.org/ Fishbase] - their taxonomy is close to TTO (both based on Catalog of Fishes), but TTO uses it strictly as a name resource.
+
* [http://gni.globalnames.org/ Global Names Index (GNI)] - Extensive list of names but no hierarchy.
+
  
=== Additional documentation ===
+
* The TAXRANK vocabulary is available in OWL format [http://purl.obolibrary.org/obo/taxrank.owl here].
* [[Documenting taxon concepts used in a publication]]
+
* The vocabulary can be browsed at [http://bioportal.bioontology.org/ontologies/1419 Bioportal].
* [[Taxonomy ontology: ranks, unknown/unnamed species, & related issues]]
+
* [[Hypodigm|Ambiguous specimen information: annotating phenotypes for specimens or species]] (also called the Hypodigm problem)
+
  
=== Taxonomic Rank Vocabulary ===
+
== Fish Collection Codes Vocabulary ==
During 2010, we released a separate [[Taxonomic Rank Vocabulary]] (TAXRANK), 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 can be browsed at  [http://bioportal.bioontology.org/ontologies/1419 Bioportal].
+
There is a flat vocabulary of fish collections, based on [http://research.calacademy.org/research/ichthyology/catalog/abtabr.html 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 [https://docs.google.com/spreadsheet/ccc?key=0AmUeHhtnDeCZcDZpa1YwVG82Zlhwcmc4OTk4elJhTlE google docs spreadsheet]. It has been augmented with links to entries in the [http://biodiversitycollectionsindex.org/ Biodiversity Collections Index].
  
* Browse [http://bioportal.bioontology.org/ontologies/38703 TTO at BioPortal]
+
The current release, as used in Phenex is
* Download TTO from [http://bioportal.bioontology.org/visualize/38703 Bioportal] or [http://www.obofoundry.org/ OBO Foundry] (use [http://oboedit.org/ OBO Edit] desktop software to open and view .obo file).
+
[https://sourceforge.net/p/obo/svn/HEAD/tree/phenote/trunk/obo-files/fish_collection_abbreviation.obo Fish Collection Abbreviations]
  
=== Fish Collection Codes Ontology ===
+
== Amphibian Taxonomy Ontology (ATO) ==
 +
The ATO has been deprecated in favor of generating the Amphibian component of the VTO directly from [http://amphibiaweb.org/amphib_names.txt Amphibiaweb].
 +
* [http://bioportal.bioontology.org/ontologies/40791?p=terms The version available at BioPortal] is very old and neither used in VTO nor recommended.
  
There is a vocabulary of fish collections, based on [http://research.calacademy.org/research/ichthyology/catalog/abtabr.html 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 ontology is generated is available as a [https://docs.google.com/spreadsheet/ccc?key=0AmUeHhtnDeCZcDZpa1YwVG82Zlhwcmc4OTk4elJhTlE google docs spreadsheet]. It has been augmented with links to entries in the [http://biodiversitycollectionsindex.org/static/index.html Biodiversity Collections Index].
+
== Additional documentation ==
 +
* [[Documenting taxon concepts used in a publication]]
 +
* [[Taxonomy ontology: ranks, unknown/unnamed species, & related issues]]
 +
* [[Hypodigm|Ambiguous specimen information: annotating phenotypes for specimens or species]] (also called the Hypodigm problem)
  
The current release, as used in Phenex is
+
= Shared Ontologies =
[https://obo.svn.sourceforge.net/viewvc/obo/phenote/trunk/obo-files/fish_collection_abbreviation.obo?view=markup Fish Collection Abbreviations]
+
 
+
== Shared Ontologies ==
+
  
 
These ontologies listed below were initiated by the model organism communities. Phenoscape is actively involved in extending these ontologies.
 
These ontologies listed below were initiated by the model organism communities. Phenoscape is actively involved in extending these ontologies.
 
=== Phenotype and Trait Ontology ===
 
  
 
* [http://bioportal.bioontology.org/visualize/38339 Phenotype and Trait Ontology (PATO)]
 
* [http://bioportal.bioontology.org/visualize/38339 Phenotype and Trait Ontology (PATO)]
 
+
* [http://bioportal.bioontology.org/visualize/36625 Evidence Code Ontology]
=== Evidence Code Ontology ===
+
 
+
*[http://bioportal.bioontology.org/visualize/36625 Evidence Code Ontology]
+
 
+
=== Relations Ontology ===
+
 
* [http://www.obofoundry.org/ro/ OBO-relations]
 
* [http://www.obofoundry.org/ro/ OBO-relations]
 
+
* [http://bioportal.bioontology.org/visualize/29952 Spatial Ontology]
=== Spatial Ontology ===
+
* [http://www.evolutionaryontology.org/ Comparative Data Analysis Ontology (CDAO)], developed by the [http://www.nescent.org/wg_evoinfo/Main_Page EvoInfo working group] at NESCent, and used within the Phenoscape OBD data repository.
*[http://bioportal.bioontology.org/visualize/29952 Spatial Ontology]
+
 
+
=== Comparative Data Analysis Ontology ===
+
CDAO is developed by the [http://www.nescent.org/wg_evoinfo/Main_Page EvoInfo working group] at NESCent, and is being used within the Phenoscape OBD data repository.
+
* [http://www.evolutionaryontology.org/ CDAO]
+
  
 
[[Category:Ontology]]
 
[[Category:Ontology]]

Latest revision as of 17:36, 29 June 2016

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. These ontologies are publicly available and being used and extended by the community (view the list). Where possible, we are also reusing external ontologies (e.g., PATO) from the broader biological community for the greatest interoperability across data types. The development of these ontologies follows OBO Foundry principles as much as possible, including reuse of ontology terms (by import or MIREOT) as the preferred mechanism for using shared terms. These anatomy ontologies are available from the OBO CVS-based version-control system, from which they are regularly loaded into the NCBO BioPortal where they can be readily browsed, searched, and visualized. The ontologies are also available for download as .obo files from OBO Foundry and can also be viewed using the OBO-Edit or Protege desktop software.

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 link to external terms using a cross-referencing strategy to external ontology identifiers (see Interontology links)

Anatomy Ontologies

Ontology coordination

In the past we have held regular project anatomy ontology conference calls to discuss development with the curators of the various anatomy ontologies listed below. The limb/fin branch was the focus of ontology development in year 1. Currently, we coordinate our development calls with the Phenotype RCN vertebrate working group monthly calls. Information about these calls is sent to the obo-anatomy, phenotype-rcn vertebrate google groups, and the phenoscape project listservs. These calls are open to everyone and call in info and notes from them is available at the Vertebrate Working Group Wiki Page.

In addition, the Phenoscape curators have been meeting weekly to have joint ontology editing sessions. Please let us know if you would like to join us, Melissa Haendel has been coordinating these sessions (haendel@ohsu.edu).

Phenoscape-ext

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.

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

http://purl.obolibrary.org/obo/uberon/ext.obo

http://purl.obolibrary.org/obo/uberon/ext.owl

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 uberon.org for details of all the various cuts.

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.

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)

  • Release version available here: [3]

Note that VSAO as released represents the outcome of the skeletal anatomy workshop held at NESCent and corresponding paper in PLOS ONE. Note also that VSAO development moving forward has been merged into the Phenoscape-ext ontology described above.

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.

Amphibian Anatomy Ontology (AAO)

AAO is a multispecies ontology for amphibian anatomy.

  • Download AAO from the OBO Foundry and browse at BioPortal
  • Source edit directory available here. The current version (April 2012) includes terms merged from the Xenopus Anatomy Ontology and updates from David Blackburn and Wasila Dahdul.

NOTE: as per above case with VSAO, AAO has been merged into phenoscape-ext and is no longer under development.

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 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 Dahdul et al. (2010).

NOTE: as per above case with VSAO, the TAO has been merged into phenoscape-ext and is no longer under development.

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: [4]
  • Source directory is available here: [5]

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 [6]

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

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.