Resources for Data Contributors
Viewing ontologies
On the web
Many ontologies are available for browsing at the NCBO BioPortal. For example:
Click the "Visualize" button on the ontology's homepage to browse it graphically.
Other ontologies:
The teleost taxonomy and anatomy ontologies is now available:
It is generated, with some modifications, from: Catalog of Fishes.
On your desktop
You can download the ontologies as OBO files from the above web sites. You can download and install OBO-Edit to view in a desktop application.
Annotating phenotypes
Genus-differentia definitions
Term definitions in the teleost anatomy ontology (TAO) take the form of genus-differentia definitions:
B is an A that has X.
The term (B) is defined by its membership in higher category (A) and distinguished by characteristics (X). The following are examples of genus-differentia definitions in the TAO:
1. The antorbital is a dermal bone that is located on the anterior margin of the infraorbital series, dorsal to the first infraorbital and lateral to the nasal bone.
2. The dentary is a dermal bone that forms the anterolateral part of the lower jaw.
In example 1, the definition mentions the parent dermal bone of the term antorbital followed by the characteristics that differentiate antorbital from all other dermal bones.
Logical definitions (also known as cross-products) are constructed as the intersection between terms and are genus-differentia definitions.
Phenote
Phenote is used by ZFIN and FlyBase for mutant phenotype annotation. We are developing enhancements to the Phenote EQ Editor for PhenoScape data curation. Some of the PhenoScape-specific enhancements include:
- A specimen list window allowing repeated annotation of the specimens within one publication.
- A phylogeny view allowing application of an EQ annotation to all specimens from a clade at once.
Installation and start up
- You need Java 1.5 or newer to run Phenote. For the Mac this requires Mac OS X 10.4 or newer.
- Launch Phenote using the webstart link. Alternatively, you can try the in-progress builds with the latest features, packaged for Mac OS X or Windows.
- Choose the "phenomap" configuration before beginning (this will soon be replaced by a "phenoscape" config).
- So far most curators are using the Excel-compatible tab-delimited format for saving files.
Usage
The following table describes the entry fields in the PhenoScape configuration. Phenote does not force you to fill in them all, but see the table for when to use each field.
| Field | Usage |
|---|---|
| Publication | the publication describing the character state CrossRef has a free-text query form for looking up DOIs |
| Taxon | Genus & species |
| Catalog Number | museum lot ID |
| Specimen Count | number of specimens from lot examined |
| Preparation | type of specimen preparation (skeleton, cleared & stained, etc.) |
| Entity | term from anatomy ontology (currently using zebrafish) |
| Quality | term from PATO - should be "value" term, unless you are filling in an absolute measurement (e.g. "length") |
| Additional Entity | term from anatomy ontology - only use if the Quality term descends from "relational quality of continuant" |
| Measurement | absolute measurement - useful as value for terms such as "length" |
| Unit | unit of measurement, if Numerical Value is filled in |
| Compare To | a taxon to which this phenotype is in comparison to (optional) |
| Textual Description | textual description of character state in publication |
| Image URI | web link to an image, if available |
Please report any issues you come across by using the Phenote tracker.
Term post-composition and pre-coordination
Terms can be post-composed at annotation time rather than pre-composed (pre-coordinated) within the ontology. Post-composed terms are created in Phenote and follow genus-differentia definitions and, unlike pre-composed terms, do not have an ID.
Post-composition
Example 1: ‘branched dorsal fin ray’
E= TAO: dorsal fin lepidotrichium^has_quality(PATO:branched)
Example 2: ‘supraorbital ventral projection’
bony projection^part_of [(ventral region)^part_of (supraorbital bone)] Ea= TAO: bony projection Eb= BSPO: ventral region part_of TAO: supraorbital bone
Note that Entity E1b is created within the post-composition (it is not an ‘additional entity’)
Post-composition in Phenote is enabled using the ‘comp’ button next to the Entity field. In example 1, the genus term is ‘dorsal fin lepidotrichium’ and the differentia term is ‘branched.’ The term in example 2 requires nesting because term Eb is a post-composed term (it is not an ‘additional entity’).
Pre-composition
The above term would be pre-coordinated using OBO-edit as: TAO: supraorbital ventral projection intersection of TAO: bony projection intersection of TAO: ventral region of suprorbital
TAO: ventral region of suprorbital intersection of BSPO: ventral region intersection of TAO: suprorbital
Known Issues:
Nesting of post-composed terms is not yet enabled in Phenote but has been requested. The post-compose feature in Phenote allows addition of multiple differentia that apply to the intial genus term. In the meantime, we will create these post-composed terms that require nesting with a reminder in the 'curator notes' field that these terms will need proper updating once nesting is enabled.
Ontology change requests
Here are links to ontology term trackers:
