Resources for Data Contributors
Viewing ontologies
On the web
Many ontologies are available for browsing at the NCBO BioPortal. For example:
- Teleost Taxonomy Ontology (TTO) (generated, with some modifications, from the Catalog of Fishes)
Click on the "Visualization" tab to browse the ontologies graphically.
Other ontologies:
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-beta10-mac.zip"
For Windows, click on the link "phenex-1.0-beta10-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
Data Repository Access Instructions
Merging files in Phenex
Taxon Lists
Character Annotation
Ontology change requests
- Term Request Instructions
- Links to ontology term trackers
