Resources for Data Contributors

Viewing ontologies

On the web

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

• Teleost Anatomy Ontology (TAO)

• Teleost Taxonomy Ontology (TTO) (generated, with some modifications, from the Catalog of Fishes)

• Phenotype and Trait Ontology (PATO)

Click on the "Visualization" tab to browse the ontologies graphically.

Other ontologies:

• Evidence Code Ontology

• OBO-relations

• Spatial Ontology

On your desktop

Ontologies can be downloaded as OBO files from the above web sites, and viewed on your desktop using the OBO-Edit desktop software.

Annotating phenotypes

Phenex

Phenex is used by PhenoScape for annotation of comparative phenotypes. Phenex can be downloaded at:

https://sourceforge.net/project/showfiles.php?group_id=76834&package_id=295042

For Mac, click on the link "phenex-1.0-beta12-mac.zip"

For Windows, click on the link "phenex-1.0-beta12-win.zip"

Installation and start up

You need Java 1.5 or newer to run Phenex. For the Mac this requires Mac OS X 10.4 or newer. How to check your java version:

• Windows:

Go to http://www.java.com. Click on "Do I have Java?". On the following page don't worry if it says "Oops! You don't have the recommended Java installed." Look at the next line where it might say "Your Java version is Version 6 update 5". It should be Version 5 or higher. If you don't have Java at all or have an older version, please click on the Download Java Now link and install it.

• Mac:

If you have a Mac, you should be fine if you have Mac OS X 10.4 or higher (Java comes with the system). Click on the Apple menu at the left of your menubar, and choose "About This Mac". Under "Mac OS X" it should have the Mac OS version number.

Usage

The following table describes the entry fields in the PhenoScape configuration. Phenex 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")
Related 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.

Curatorial Best Practices

Taxon Lists

• Creating Taxon Lists
• Updating Taxon Lists (for taxonomic experts)

Character Annotation

• Creating Character Lists
• Guide to Character Annotation

Ontology change requests

• Term Request Instructions
• Links to ontology term trackers
  • Teleost anatomy tracker
  • Teleost taxonomy ontology tracker
  • PATO tracker