Difference between revisions of "Resources for Data Contributors"

From phenoscape
(Phenex)
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==Annotating phenotypes==
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===Download Most Recent Version of Phenex===
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Phenex is used by PhenoScape for annotation of comparative phenotypes.  Phenex can be downloaded at:
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https://sourceforge.net/project/showfiles.php?group_id=76834&package_id=295042
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For Mac, click on the link "phenex-1.0-beta12-mac.zip"
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For Windows, click on the link "phenex-1.0-beta12-win.zip"
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====Installation and start up====
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 +
You need Java 1.5 or newer to run Phenex.  For the Mac this requires Mac OS X 10.4 or newer. How to check your java version:
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 +
* Windows:
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Go to http://www.java.com.  Click on "Do I have Java?".  On the following page don't worry if it says "Oops!  You don't have the recommended Java installed."  Look at the next line where it might say "Your Java version is Version 6 update 5".  It should be Version 5 or higher.  If you don't have Java at all or have an older version, please click on the Download Java Now link and install it.
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 +
* Mac:
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If you have a Mac, you should be fine if you have Mac OS X 10.4 or higher (Java comes with the system).  Click on the Apple menu at the left of your menubar, and choose "About This Mac".  Under "Mac OS X" it should have the Mac OS version number.
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==Viewing ontologies==
 
==Viewing ontologies==
  
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Ontologies can be downloaded as OBO files from the above web sites, and viewed on your desktop using the [http://oboedit.org/ OBO-Edit] desktop software.
 
Ontologies can be downloaded as OBO files from the above web sites, and viewed on your desktop using the [http://oboedit.org/ OBO-Edit] desktop software.
  
==Annotating phenotypes==
 
 
 
 
===Phenex===
 
 
Phenex is used by PhenoScape for annotation of comparative phenotypes.  Phenex can be downloaded at:
 
 
https://sourceforge.net/project/showfiles.php?group_id=76834&package_id=295042
 
 
For Mac, click on the link "phenex-1.0-beta12-mac.zip"
 
 
For Windows, click on the link "phenex-1.0-beta12-win.zip"
 
 
====Installation and start up====
 
 
You need Java 1.5 or newer to run Phenex.  For the Mac this requires Mac OS X 10.4 or newer. How to check your java version:
 
 
* Windows:
 
Go to http://www.java.com.  Click on "Do I have Java?".  On the following page don't worry if it says "Oops!  You don't have the recommended Java installed."  Look at the next line where it might say "Your Java version is Version 6 update 5".  It should be Version 5 or higher.  If you don't have Java at all or have an older version, please click on the Download Java Now link and install it.
 
 
* Mac:
 
If you have a Mac, you should be fine if you have Mac OS X 10.4 or higher (Java comes with the system).  Click on the Apple menu at the left of your menubar, and choose "About This Mac".  Under "Mac OS X" it should have the Mac OS version number.
 
  
 
====Usage====
 
====Usage====

Revision as of 15:15, 22 October 2008

Annotating phenotypes

Download Most Recent Version of Phenex

Phenex is used by PhenoScape for annotation of comparative phenotypes. Phenex can be downloaded at:

https://sourceforge.net/project/showfiles.php?group_id=76834&package_id=295042

For Mac, click on the link "phenex-1.0-beta12-mac.zip"

For Windows, click on the link "phenex-1.0-beta12-win.zip"

Installation and start up

You need Java 1.5 or newer to run Phenex. For the Mac this requires Mac OS X 10.4 or newer. How to check your java version:

  • Windows:

Go to http://www.java.com. Click on "Do I have Java?". On the following page don't worry if it says "Oops! You don't have the recommended Java installed." Look at the next line where it might say "Your Java version is Version 6 update 5". It should be Version 5 or higher. If you don't have Java at all or have an older version, please click on the Download Java Now link and install it.

  • Mac:

If you have a Mac, you should be fine if you have Mac OS X 10.4 or higher (Java comes with the system). Click on the Apple menu at the left of your menubar, and choose "About This Mac". Under "Mac OS X" it should have the Mac OS version number.


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

Ontologies can be downloaded as OBO files from the above web sites, and viewed on your desktop using the OBO-Edit desktop software.


Usage

The following table describes the entry fields in the PhenoScape configuration. Phenex 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