Resources for Data Contributors

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Revision as of 14:52, 25 October 2008 by Wasila (Talk | contribs) (3. Download Publication PDFs and Ontology Posters)

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1. Download Most Recent Version of Phenex

Phenex was developed by Phenoscape for annotation of evolutionary 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.

2. Access Project Files

Phenoscape project files are .xml files created using Phenex and housed a data repository. Instructions for accessing the data repository can be found here .

3. Download PDFs and Ontology Posters as Needed on Phenoscape Fileshare

You can download publication PDFs and powerpoint posters of the TAO and PATO ontologies by connecting to the Phenoscape file share.

Connecting in MAC OS X

  1. In finder > Go > Connect to Server
  2. Type in https://webdav.nescent.org/[sharename] . For example, https://webdav.nescent.org/phenoscape-data
  3. Accept security warning about certificate
  4. enter username and password (ask a Phenoscaper)

Connecting in Windows XP

  1. Go to "My Network Places"
  2. Add a Network Place (pulls up wizard)
  3. Click Next twice
  4. In internet or Network address box, type in https://ftp.nescent.org/phenoscape-data/
    • Note: (there is a bug in MS implementation of webdav client. In fact, Internet explorer and this method use two different means of connecting to webdav. go figure. Therefore, you must suffix the URL with the pound sign as a workaround to the bug.
  1. Accept certificate warning, if given.
  2. Give the share a meaningful name. Default is usually fine.
  3. Finish

4. Use Ontologies to Annotate Characters

The primary activity of a curator is to annotate the free-text characters from systematic studies using ontologies. Instructions for this activity can be found in the Phenoscape Guide to Character Annotation.

5. Update Taxon Lists

Most project files require a taxonomic expert to review the taxonomy used in a publication and update to reflect current taxonomy. Please see instructions for updating taxon lists.

6. Request New Terms for Ontologies

Curation drives ontology development and many new terms and relationships need to be added. For instructions on how to make these changes, please and see the Term Request Instructions.