Resources for Data Contributors
Contents
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:
- Teleost taxonomy (generated, with some modifications, from the Catalog of Fishes)
- Teleost Anatomy Ontology (TAO)
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
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.
For more information please see the Phenote User Guide.
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.
- Though you can launch Phenote using the webstart link, we recommend installing the latest in-progress build, packaged for Mac OS X or Windows. These builds will have the latest features. Please see the Phenote User Guide for details.
- Choose the "phenoscape" configuration before beginning.
- 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 the time of annotation rather than pre-composed (also known as pre-coordinated) within the ontology. Post-composed terms are created in Phenote and follow genus-differentia definitions. 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
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:
The post-compose feature in Phenote allows addition of multiple differentia that apply to the initial genus term but nesting of terms is not yet enabled. In the meantime, when post-composed terms that require nesting are needed for annotation, we will note in the 'curator notes' field that these terms will need proper updating once nesting is possible.
Curatorial Best Practices
Ontology change requests
Here are links to ontology term trackers:
