Ontologies included with Phenote

Phenote comes pre-packaged with several ontologies, including:

File name Description
Anatomy & Development The ontologies in this category are specific to individual organisms.  Since the typical Phenote user will only be documenting one organism type, they should only need one organismal ontology.  Occasionally, developmental timing/staging is included in separate ontologies, that may need to be used separately.
fly_anatomy.obo   Fly Anatomy
fma_obo.obo Foundational Model of Anatomy:  Adult Human Anatomy Ontology.  This ontology has been converted from its native OWL format.
human-dev-anat-abstract.obo  Human Developmental Anatomy - Abstract:  Use this ontology when recording human anatomical entities that are not from adults
worm_anatomy.obo C. elegans Anatomy
worm_development.obo C. elegans Stage ontology
zebrafish_anatomy.obo Zebrafish anatomy and staging ontologies
Other Biological
cell.obo Ontology of Cell Types, such as neuron, gonadal, skin, etc.
chebi.obo Ontology of Chemicals
context.obo Genetic Context Ontology
evidence_code.obo  Ontology of Evidence Codes.  These are the codes attributed the annotations made by the Gene Ontology Consortium.  Imbeded in these codes is experimental information, and may not be ideal for every group.
gene_ontology.obo  The Gene Ontology.  This single file includes the three ontologies from the Gene Ontology Consortium:  Biological Process, Cellular Component, and Molecular Function.
so.obo The Sequence Ontology.  This ontology includes the definitions of sequence features often used to describe genetic abberations.
Phenotypes & Qualities Ontologies in this category include both pre-composed phenotypic qualities, as well as the more abstract ontology of qualities and measurements.
c_elegans_phenotype_ontology.obo A precomposed ontology of qualities used for
mammalian_phenotype.obo A precomposed ontology of qualities used for mouse phenotype descriptions.
quality.obo A general ontology of qualities.  Formerly known at the Phenotype and Trait ontology, PATO still goes by this name.
relationship.obo

The general relationships used between entity terms.  These are standard relationship terms that should have equivalent meanings between ontologies.  These relationship terms have specific applications, where some can be applied between continuants, some between occurants, and others between continuants and occurants.  For more information on relationship types, please read further information on the Relationship.obo site:

http://www.obofoundry.org/ro/

spatial.obo A general ontology of qualities as entities can be related to each other spatially.  (for example, a cell is proximal to another cell; an organ is anterior of another organ, etc).  The concepts contained in this ontology are being incorporated into PATO.
unit.obo A general ontology of units that can be applied to any entity containing a measurable quality.

If your favorite ontology is not included in this list, don't worry!  You can use any ontology for your annotations, provided it is in OBO format.  You can use your own ontology, or download them from the repository of your choice, such as

Open Biological Ontologies site at http://obo.sourceforge.net/ or the

NCBO BioPortal http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml

If your ontology is in OWL format, you could convert it using the OWL2OBO conversion tool, described at:

http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page