Resources for Data Contributors

From phenoscape
Revision as of 21:41, 3 April 2008 by Wasila (talk | contribs) (Known Issues:)

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:

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

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:

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 required during annotation, we will note in the 'curator notes' field that these terms will need proper updating once nesting is possible.

Ontology change requests

Here are links to ontology term trackers: