Resources for Data Contributors

Viewing ontologies

On the web

Many ontologies are available for browsing at the NCBO BioPortal. For example:

• Zebrafish anatomy and development
• PATO

Click the "Visualize" button on the ontology's homepage to browse it graphically.

Other ontologies:

• OBO-relations

The teleost taxonomy and anatomy ontologies is now available:

• Teleost taxonomy
• Teleost Anatomy Ontology (TAO)

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

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.
• 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 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

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.

Proper syntax for relative length

For the characters that relate the length of one bone to another, ratios are used in Phenote. For example: Length of infraorbital 2: (0) over twice as long as infraorbital 1; (1) less than twice as long as infraorbital 1. This would be indicated in Phenote as follows:

E1: Infraorbital 2, Q: increased length, , E2 : Infraorbital 1, Measurement: >2, Unit: ratio

E1: Infraorbital 2, Q: decreased length, , E2 : Infraorbital 1, Measurement: <2, Unit: ratio

Ontology change requests

Here are links to ontology term trackers:

• Teleost anatomy tracker
• Zebrafish anatomy tracker
• Teleost taxonomy ontology tracker
• PATO tracker