Difference between revisions of "Resources for Data Contributors"
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| 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") | ||
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| − | | | + | | Additional Entity || term from anatomy ontology - only use if the Quality term descends from "relational quality of continuant" |
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| 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
Contents
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:
- A specimen list window allowing repeated annotation of the specimens within one publication.
- A phylogeny view allowing application of an EQ annotation to all specimens from a clade at once.
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?
