Difference between revisions of "Resources for Data Contributors"

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(3. Download PDFs and Ontology Posters as Needed on Phenoscape Fileshare)
(2. Access Project Files)
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==2. Access Project Files==
 
==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 [[Data Repository Access Instructions | here ]].
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Phenoscape project files are XML files (more specifically, they are in [http://nexml.org NeXML] format) created using Phenex and housed in a subversion-controlled data repository.  Please read the [[Data Repository Access InstructionsiInstructions for accessing the data repository]] if you are interested in perusing or adding to them.
  
 
==3. Download PDFs and Ontology Posters as Needed on Phenoscape Fileshare ==
 
==3. Download PDFs and Ontology Posters as Needed on Phenoscape Fileshare ==

Revision as of 03:26, 14 January 2009

1. Download Most Recent Version of Phenex

Phenex was developed by Phenoscape for annotation of evolutionary phenotypes. You can find instructions for downloading and installing Phenex at the Phenex homepage.

2. Access Project Files

Phenoscape project files are XML files (more specifically, they are in NeXML format) created using Phenex and housed in a subversion-controlled data repository. Please read the Data Repository Access InstructionsiInstructions for accessing the data repository if you are interested in perusing or adding to them.

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://ftp.nescent.org/[sharename] . For example, https://ftp.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.