Difference between revisions of "Resources for Data Contributors"

From phenoscape
(Ontology change requests)
(On the web)
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===On the web===
 
===On the web===
  
Many [[Ontologies|ontologies]] are available for browsing at the [http://www.bioontology.org/ncbo/faces/index.xhtml NCBO BioPortal]. For example:
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Many [[Ontologies|ontologies]] are available for browsing at the [http://www.bioontology.org/ncbo/faces/index.xhtml NCBO BioPortal]. For example:
  
 
* [http://bioportal.bioontology.org/visualize/38362 Teleost Anatomy Ontology (TAO)]
 
* [http://bioportal.bioontology.org/visualize/38362 Teleost Anatomy Ontology (TAO)]
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* [http://bioportal.bioontology.org/visualize/38339 Phenotype and Trait Ontology (PATO)]
 
* [http://bioportal.bioontology.org/visualize/38339 Phenotype and Trait Ontology (PATO)]
Click the "Visualize" button on the ontology's homepage to browse it graphically.
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Click on the "Visualization" tab to browse the ontologies graphically.
  
 
Other ontologies:
 
Other ontologies:

Revision as of 16:07, 13 October 2008

Viewing ontologies

On the web

Many ontologies are available for browsing at the NCBO BioPortal. For example:

Click on the "Visualization" tab to browse the ontologies graphically.

Other ontologies:

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 PhenoScape data curation. Some of the PhenoScape-specific enhancements include:


For more information please see the Phenote User Guide.

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.
  • Though you can launch Phenote using the webstart link, we recommend installing the latest in-progress build, packaged for Mac OS X or Windows. These builds will have the latest features. Please see the Phenote User Guide for details.
  • Choose the "phenoscape" configuration before beginning.
  • So far most curators are using the Excel-compatible tab-delimited format for saving files.

Usage

The following table describes the entry fields in the PhenoScape 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
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