Difference between revisions of "Resources for Data Contributors"
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* Launch Phenote using the [http://www.phenote.org/phenote/latest/phenote.jnlp webstart link]. | * Launch Phenote using the [http://www.phenote.org/phenote/latest/phenote.jnlp webstart link]. | ||
| − | * You can download a customized [[Media:phenomap.cfg.zip|Phenote configuration file]] which is suited to our data. See the [http://www.phenote.org/content/howtos/customize.shtml instructions] on how to use a custom configuration. | + | * You can download a customized [[Media:phenomap.cfg.zip|Phenote configuration file]] which is suited to our data. See the [http://www.phenote.org/content/howtos/customize.shtml 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 Finder, in the menubar select Go > Go to Folder..., then type "~/.phenote", and press Go. 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). | * Save your files using the PhenoSyntax file format (or perhaps the Excel-compatible tab-delimited format - not tested yet). | ||
Revision as of 21:04, 13 June 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 taxonomic 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
PhenoMaP EQ Editor
We are working on a specialized EQ Editor for data curation. Until it is ready for use, EQ annotations can be created using Phenote.
Phenote
Phenote is used by ZFIN and FlyBase for mutant phenotype annotation.
Installation and start up
- 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 Finder, in the menubar select Go > Go to Folder..., then type "~/.phenote", and press Go. 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 |
| Specimen | museum lot ID |
| 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") |
| Add'l Entity | term from anatomy ontology - only use if the Quality term descends from "relational quality of continuant" |
| Numerical Value | absolute measurement - useful as value for terms such as "length" |
| Unit | unit of measurement, if Numerical Value is filled in |
| Original 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?
