Difference between revisions of "Resources for Data Contributors"

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(Character Annotation)
 
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==Annotating phenotypes==
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The following instructions outline the resources used by Phenoscape curators for the annotation of evolutionary phenotypes.  If you are a student intern, please refer to the [http://phenoscape.org/wiki/Student_Instructions Student Instructions] page for more information and links.
  
===Download Most Recent Version of Phenex===
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Data uploaded to the Phenoscape Knowledgebase are made available under a Creative Commons Attribution 3.0 Unported license (see [[Phenoscape data policy]])
  
Phenex was developed by Phenoscape for annotation of evolutionary phenotypes.  Phenex can be downloaded at:
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==1. Download Most Recent Version of Phenex==
  
https://sourceforge.net/project/showfiles.php?group_id=76834&package_id=295042
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Phenex was developed by Phenoscape for annotation of evolutionary phenotypes. You can find instructions for downloading and installing Phenex at the [[Phenex|'''Phenex homepage''']].
  
For Mac, click on the link "phenex-1.0-beta12-mac.zip"
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==2. Access Project Files==
  
For Windows, click on the link "phenex-1.0-beta12-win.zip"
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Phenoscape project files are XML files (more specifically, they are in [http://nexml.org NeXML] format) created using Phenex and available on GitHub at https://github.com/phenoscape/phenoscape-data.
  
====Installation and start up====
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==3. Access PDFs for Curation ==
  
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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Phenoscape maintains a collection of PDFs for curation. Please ask project personnel (Wasila or Paula) for access to the collection.
  
* Windows:
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==4. Use Ontologies to Annotate Characters ==
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:
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The primary activity of a curator is to annotate the free-text characters from systematic studies using ontologiesInstructions for this activity can be found in the [[Guide to Character Annotation | '''Phenoscape Guide to Character Annotation''']].
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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==5. Update Taxon Lists==
  
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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 [[Creating Taxon Lists| '''creating taxon lists''']] in Phenex or instructions for [[Update Taxon Lists| '''updating taxon lists''']] with valid taxon names.
  
==Curatorial Best Practices==
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==6. Request New Terms for Ontologies==
  
===[[Data Repository Access Instructions]]===
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Curation drives ontology development and many new terms and relationships need to be added. Submit requests for updates to the ontologies used in Phenoscape to the following term trackers:
  
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* [https://github.com/cmungall/uberon/issues Uber Anatomy Ontology (Uberon) term tracker]
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* [http://sourceforge.net/tracker/?group_id=76834&atid=595654 Phenotype and Trait Ontology (PATO) term tracker]
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* [http://sourceforge.net/tracker/?group_id=224046&atid=2519810 Vertebrate Taxonomy Ontology (VTO) term tracker]
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* [http://phenoscape.org/wiki/Ontologies#Fish_Collection_Codes_Vocabulary Collection Codes Vocabulary]
  
===Taxon Lists===
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==7. Edit the Anatomy Ontology ==
*'''[[Creating Taxon Lists]]'''
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* [http://phenoscape.org/wiki/Ontology_workflow Ontology Editing Guidelines]
*'''[[Update Taxon Lists|Updating Taxon Lists (for taxonomic experts)]]'''
 
===Character Annotation===
 
*'''[[Guide to Character Annotation]]'''
 
  
===Ontology change requests===
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==8. Subscribe to Curator and Ontology Request Mailing Lists ==
*'''[[Term_Requests | Term Request Instructions]]'''
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* Discussion of ontology development and Open Biomedical Ontologies community issues  ''[https://groups.google.com/forum/#!forum/obo-discuss obo-discuss]
*'''Links to ontology term trackers'''
 
** [http://sourceforge.net/tracker/?group_id=76834&atid=994764 Teleost anatomy tracker]
 
** [http://sourceforge.net/tracker/?atid=1046550&group_id=76834 Teleost taxonomy ontology tracker]
 
** [http://sourceforge.net/tracker/?group_id=76834&atid=595654 PATO tracker]
 
  
 
[[Category:Curation]]
 
[[Category:Curation]]
 
[[Category:Help]]
 
[[Category:Help]]

Latest revision as of 01:17, 26 March 2019

The following instructions outline the resources used by Phenoscape curators for the annotation of evolutionary phenotypes. If you are a student intern, please refer to the Student Instructions page for more information and links.

Data uploaded to the Phenoscape Knowledgebase are made available under a Creative Commons Attribution 3.0 Unported license (see Phenoscape data policy)

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 available on GitHub at https://github.com/phenoscape/phenoscape-data.

3. Access PDFs for Curation

Phenoscape maintains a collection of PDFs for curation. Please ask project personnel (Wasila or Paula) for access to the collection.

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 creating taxon lists in Phenex or instructions for updating taxon lists with valid taxon names.

6. Request New Terms for Ontologies

Curation drives ontology development and many new terms and relationships need to be added. Submit requests for updates to the ontologies used in Phenoscape to the following term trackers:

7. Edit the Anatomy Ontology

8. Subscribe to Curator and Ontology Request Mailing Lists

  • Discussion of ontology development and Open Biomedical Ontologies community issues obo-discuss