General
How do I get started?
Please visit the Downloads page to download and install Phenote.
What version of Java do I need to run Phenote?
The Phenote installer requires Java 1.5+. You can download the latest Java (1.6, aka Java SE 6) here. (If you have an older Mac, you may not be able to install Java 1.6, but you can run Phenote with Java 1.5.)
Where can I ask my burning questions?
There are several discussion groups that are relevant to Phenote users. You'll find a list on our Contact page.
I found a bug in Phenote. How do I report errors?
We want to know about any problems you have with Phenote. Please use our Bug Report tracker.
There's a function/feature I wish Phenote had. Can you add it?
You can request new features through our Feature Request tracker. Please be sure to select "new feature" as the Group.
Ontologies
What kinds of ontologies can I use to annotate in Phenote?
You can use any kind of domain specific ontologies. While Phenote is a tool being developed for annotation of biological phenotypes, it can certainly be adapted to any domain whose knowledge is captured with ontologies.
Can I use OBO and/or OWL format ontologies?
Yes! However, there's a little catch. You will need to convert your OWL ontology to OBO format first. In the future, we plan to include a feature to convert on-the-fly.
How can I convert my OWL ontology to OBO format?
There's an online tool to help with this conversion: OWL-OBO converter
Can I use my own ontologies?
Yes you can! You don't have to use ontologies that are in public repositories if you don't want to. Please consult the User Guide for more detailed instructions...
Can I use my own pre-coordinated phenotype ontology?
Yes! Phenote is a generic tool that allows you to use any kind of ontology. Its simplicity allows the user to mix and match different kinds of annotations from different kinds of ontologies. So, you might use your pre-coordinated phenotype ontology for one kind of statement, and then combine a different entity+quality ontology for another statement.
What's the difference between using a pre-coordinated phenotype ontology, and E+Q statements?
Is there one place I can go to browse through all the available ontologies?
Yep! There are several online resources that can help you learn more. Some of these include:
Using Phenote
Is there some online documentation?
You bet! Check out our User's Guide (which is also included inside the Phenote application).
When I'm annotating, I can't seem to find the right terms.
Sometimes a term you are looking for is really just a synonym of another term. Make sure you have "synonyms" selected under the "Settings" menu.
If you still can't find it, it might be that the ontology is really missing a term. Ontologies, while extensive, are never complete, and are under active development. There are usually online term request resources for each ontology. You will need to contact each ontology resource separately.
Can I output my data in RDF-OWL?
Not yet, but that feature is coming soon.
When I launch Phenote, it hangs.
The most likely cause of this is that the configuration you chose includes a lot of large ontologies, and your computer doesn't have enough memory to load all of them. Ontologies keep getting bigger, and some configurations include a dozen or more ontologies, all of which have to be loaded by Phenote. The best workaround is to edit your configuration file and remove any unneeded ontologies, or use "slim" ontologies (smaller versions of the ontologies, with unneeded terms or fields left out).