Difference between revisions of "Resources for Data Contributors"

From phenoscape
(Usage)
(Usage)
Line 56: Line 56:
 
| Quality || term from PATO - should be "value" term, unless you are filling in an absolute measurement (e.g. "length")
 
| Quality || term from PATO - should be "value" term, unless you are filling in an absolute measurement (e.g. "length")
 
|-
 
|-
| Additionall Entity || term from anatomy ontology - only use if the Quality term descends from "relational quality of continuant"
+
| 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"
 
| Measurement || absolute measurement - useful as value for terms such as "length"

Revision as of 17:53, 14 August 2007

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 taxonomy ontology is not yet available, but it will be generated from the 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 PhenoMap data curation. Some of the PhenoMap-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.
  • You can download a customized Phenote configuration file which is suited to our data. See the instructions on how to use a custom configuration.
  • If you are using a Mac, it can be tricky to access the Phenote configuration folder using the Finder - it begins with a "." and as a result is invisible. To get to it while using the Finder, in the menubar select Go > Go to Folder..., then type "~/.phenote", and press the Go button. You should then see the folder.
  • Save your files using the PhenoSyntax file format (or perhaps the Excel-compatible tab-delimited format - not tested yet).

Usage

The following table describes the entry fields in the PhenoMap 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
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

Ontology change requests

Here are links to ontology term trackers:

  • PATO tracker
  • Zebrafish anatomy - does anyone know if there is a term tracker?