Difference between revisions of "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. 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 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.
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The 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 create equivalent terms from other ontologies and keep links to them using a cross-referencing strategy to external ontology identifiers.
 
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We hold 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 is the focus of ontology development in year 1 across the various ontologies described below.
 
  
 
= Anatomy Ontologies =
 
= Anatomy Ontologies =
  
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==Vertebrate Musculoskeletal Anatomy Ontology (VAO) ==
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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)].
  
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VAO contains terms representing structures in the musculoskeletal 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). VAO can be downloaded at the [http://obofoundry.org/cgi-bin/detail.cgi?id=vertebrate_anatomy OBO Foundry] and browsed at [http://bioportal.bioontology.org/ontologies/45737?p=terms BioPortal].
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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.
  
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Ontology update requests can be made on the Vertebrate Anatomy term request tracker. Requests are forwarded to the vertebrate anatomy mailing list.
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* Ontology update requests can be made on the Uberon term request tracker: [https://github.com/obophenotype/uberon/issues]
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* Source edit file available here: [https://github.com/obophenotype/uberon-phenoscape-ext]
  
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* Submit term requests to the [http://sourceforge.net/tracker/?group_id=76834&atid=2257941 vertebrate anatomy request tracker]
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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.
  
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* Subscribe to the [http://lists.sourceforge.net/lists/listinfo/obo-vertebrate-anatomy vertebrate anatomy mailing list] for notification of term requests
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==Anatomy ontologies merged with Uberon and no longer under development ==
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===Vertebrate Skeletal Anatomy Ontology (VSAO) ===
  
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* Source edit directory available here: [https://phenoscape.svn.sourceforge.net/svnroot/phenoscape/trunk/vocab/skeletal/obo/]
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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)].
  
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====Development====
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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.
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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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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]
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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]].
  
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== Amniote Anatomy Ontology (AMAO) ==
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=== Amphibian Anatomy Ontology (AAO) ===
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AMAO is a new anatomy ontology being developed for amniotes. It will import the VAO and MIREOT non-skeletal terms from the Uber Anatomy Ontology [http://obofoundry.org/cgi-bin/detail.cgi?id=uberon (Uberon)].
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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.
  
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To Do
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==Model organism anatomy ontologies ==
  
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* Source edit directory available here:
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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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=== 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)].
  
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* Submit term requests to
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* 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].
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* Term requests can be submitted on the [http://sourceforge.net/tracker/?group_id=76834&atid=1205376 mouse anatomy tracker]
  
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* Subscribe to the X list for notification of term requests
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=== Xenopus Anatomy Ontology (XAO) ===
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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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=== Amphibian Anatomy Ontology (AAO) ===
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* 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].
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AAO is a multispecies ontology for amphibian anatomy. It will be used to annotate characters from the amphibian systematics literature. 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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* Term tracker is available here: [https://sourceforge.net/tracker/?atid=1127722&group_id=76834]
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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]
  
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To Do
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=== Zebrafish Anatomical Ontology (ZFA) ===
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* Source edit directory available here:
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ZFA is used by [http://zfin.org ZFIN] to annotate mutant phenotypes for the model organsim zebrafish (''Danio rerio'').
  
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* Submit term requests to
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* 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].
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* Term requests can be submitted to the [http://sourceforge.net/tracker/?group_id=76834&atid=994726 ZFA tracker].
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* 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]
  
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* Subscribe to the X list for notification of term requests
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ZFA terms are cross referenced to TAO terms, and these cross references will be maintained and updated as needed.
  
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====Development====
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== Previous work on ontology coordination ==
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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. 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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=== Mouse Adult Gross Anatomy (MA) ===
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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.
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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. 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]
 
  
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See the [http://phenoscape.org/wiki/Anatomy_Ontology_Development_Plan#Mouse_Adult_Gross_Anatomy_.28MA.29 MA development plan] for more details on its release schedule and development.
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= Taxonomy Ontologies =
  
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=== Teleost Anatomy Ontology (TAO) ===
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== Vertebrate Taxonomy Ontology (VTO) ==
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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)]. 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].  Term requests can be submitted to the [http://sourceforge.net/tracker/?group_id=76834&atid=994764 TAO tracker].
 
  
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See the [http://phenoscape.org/wiki/Anatomy_Ontology_Development_Plan#Teleost_Anatomy_Ontology_.28TAO.29 TAO development plan] for more details on its release schedule and development.
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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.
  
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=== Xenopus Anatomy Ontology (XAO) ===
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*[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.
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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].
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*[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.
  
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See the [http://phenoscape.org/wiki/Anatomy_Ontology_Development_Plan#Xenopus_Anatomy_Ontology_.28XAO.29 XAO development plan] for more details on its release schedule and development.
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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.
  
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=== Zebrafish Anatomical Ontology (ZFA) ===
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*[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.
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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].  Term requests can be submitted to the [http://sourceforge.net/tracker/?group_id=76834&atid=994726 ZFA tracker].
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*[http://gni.globalnames.org/ Global Names Index (GNI)] - Extensive list of names.
  
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See the [http://phenoscape.org/wiki/Anatomy_Ontology_Development_Plan#Zebrafish_Anatomical_Ontology_.28ZFA.29 ZFA development plan] for more details on its release schedule and development.
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== Teleost Taxonomy Ontology (TTO) ==
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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.
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* The TTO in OWL format is [http://purl.obolibrary.org/obo/tto.owl available here].
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* Browse TTO [http://bioportal.bioontology.org/ontologies/38703 at BioPortal]
  
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== Taxonomy Ontologies ==
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== Taxonomic Rank Vocabulary (TAXRANK) ==
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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.
  
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=== Teleost Taxonomy Ontology (TTO) ===
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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.
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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]].
 
  
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=== Amphibian Taxonomy Ontology (ATO) ===
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* The TAXRANK vocabulary is available in OWL format [http://purl.obolibrary.org/obo/taxrank.owl here].
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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].
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* The vocabulary can be browsed at [http://bioportal.bioontology.org/ontologies/1419 Bioportal].
  
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=== Vertebrate Taxonomy Ontology (VTO) ===
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== Fish Collection Codes Vocabulary ==
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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.
 
  
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=== Other Taxonomic Resources ===
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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].
  
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==== Amniotes ====
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The current release, as used in Phenex is
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*Birds The [http://www.worldbirdnames.org/index.html IOC checklist] provides a current taxonomy and common names, but no taxonomic synonyms.
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[https://sourceforge.net/p/obo/svn/HEAD/tree/phenote/trunk/obo-files/fish_collection_abbreviation.obo Fish Collection Abbreviations]
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*Mammals Wilson and Reader (1993) is the standard, but the available electronic version of their taxonomy is IP encumbered.
 
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====Fossil Taxa====
 
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*[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.
 
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==== Taxonomic (hierarchy) Resources ====
 
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*[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.
 
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*[http://www.itis.gov/ ITIS] Has some vetting by area experts, but coverage is not complete (nor uncontroversial).
 
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*[http://www.catalogueoflife.org/ Catalogue of Life] Claimed to incorporate all of ITIS plus Species2000.  Updated quarterly.
 
  
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==== Nomenclature Resources ====
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== Amphibian Taxonomy Ontology (ATO) ==
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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.
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The ATO has been deprecated in favor of generating the Amphibian component of the VTO directly from [http://amphibiaweb.org/amphib_names.txt Amphibiaweb].
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* [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.
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* [http://bioportal.bioontology.org/ontologies/40791?p=terms The version available at BioPortal] is very old and neither used in VTO nor recommended.
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* [http://gni.globalnames.org/ Global Names Index (GNI)] - Extensive list of names but no hierarchy.
 
  
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=== Additional documentation ===
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== Additional documentation ==
 
* [[Documenting taxon concepts used in a publication]]
 
* [[Documenting taxon concepts used in a publication]]
 
* [[Taxonomy ontology: ranks, unknown/unnamed species, & related issues]]
 
* [[Taxonomy ontology: ranks, unknown/unnamed species, & related issues]]
 
* [[Hypodigm|Ambiguous specimen information: annotating phenotypes for specimens or species]] (also called the Hypodigm problem)
 
* [[Hypodigm|Ambiguous specimen information: annotating phenotypes for specimens or species]] (also called the Hypodigm problem)
  
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=== Taxonomic Rank Vocabulary ===
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= Shared Ontologies =
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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.
 
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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].
 
−
 
 
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* Browse [http://bioportal.bioontology.org/ontologies/38703 TTO at BioPortal]
 
−
* 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).
 
−
 
 
−
=== Fish Collection Codes Ontology ===
 
−
 
 
−
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].
 
−
 
 
−
The current release, as used in Phenex is
 
−
[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 17:42, 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.

Retrieved from "https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Ontologies&oldid=12030"