Difference between revisions of "Resources for Data Contributors"

From phenoscape
(Download Most Recent Version of Phenex)
(8. Subscribe to Curator and Ontology Request Mailing Lists)
(75 intermediate revisions by 5 users not shown)
Line 1: Line 1:
==Annotating phenotypes==
+
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===
+
Data uploaded to the Phenoscape Knowledgebase are made available under a Creative Commons Attribution 3.0 Unported license (see [http://phenoscape.org/wiki/Phenoscape_data_policy Phenoscape data policy])
  
Phenex was developed by Phenoscape for annotation of evolutionary phenotypes.  Phenex can be downloaded at:
+
==1. Download Most Recent Version of Phenex==
  
https://sourceforge.net/project/showfiles.php?group_id=76834&package_id=295042
+
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"
+
==2. Access Project Files==
  
For Windows, click on the link "phenex-1.0-beta12-win.zip"
+
Phenoscape project files are XML files (more specifically, they are in [http://nexml.org NeXML] format) created using Phenex and housed in a shared [http://www.dropbox.com DropBox] folder (named 'Phenoscape-data'). Please contact Wasila or Paula if you are interested in perusing or adding to them.
  
====Installation and start up====
+
==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:
+
Phenoscape maintains a collection of PDFs for curation. Please ask project personnel (Wasila or Paula) for access to the collection.
  
* Windows:
+
==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:
+
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.
 
  
==Viewing ontologies==
+
==5. Update Taxon Lists==
  
===On the web===
+
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.
  
Many [[Ontologies|ontologies]] are available for browsing at the [http://www.bioontology.org/ncbo/faces/index.xhtml NCBO BioPortal]. For example:
+
==6. Request New Terms for Ontologies==
  
* [http://bioportal.bioontology.org/visualize/38362 Teleost Anatomy Ontology (TAO)]
+
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:
  
* [http://bioportal.bioontology.org/visualize/38363 Teleost Taxonomy Ontology (TTO)] (generated, with some modifications, from the [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes])
+
* [https://github.com/cmungall/uberon/issues Uber Anatomy Ontology (Uberon) term tracker]
 +
* [http://sourceforge.net/tracker/?group_id=76834&atid=595654 Phenotype and Trait Ontology (PATO) term tracker]
 +
* [http://sourceforge.net/tracker/?group_id=224046&atid=2519810 Vertebrate Taxonomy Ontology (VTO) term tracker]
 +
* [http://phenoscape.org/wiki/Ontologies#Fish_Collection_Codes_Vocabulary Collection Codes Vocabulary]
  
* [http://bioportal.bioontology.org/visualize/38339 Phenotype and Trait Ontology (PATO)]
+
==7. Edit the Anatomy Ontology ==
Click on the "Visualization" tab to browse the ontologies graphically.
+
* [http://phenoscape.org/wiki/Ontology_workflow Ontology Editing Guidelines]
  
Other ontologies:
+
==8. Subscribe to Curator and Ontology Request Mailing Lists ==
 
+
* Discussion of ontology development and Open Biomedical Ontologies community issues  ''[https://groups.google.com/forum/#!forum/obo-discuss obo-discuss]
*[http://bioportal.bioontology.org/visualize/36625 Evidence Code Ontology]
 
 
 
* [http://www.obofoundry.org/ro/ OBO-relations]
 
 
 
*[http://bioportal.bioontology.org/visualize/29952 Spatial Ontology]
 
 
 
===On your desktop===
 
 
 
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.
 
 
 
 
 
 
 
 
 
==Curatorial Best Practices==
 
 
 
===[[Data Repository Access Instructions]]===
 
 
 
===[[Phenex|Merging files in Phenex]]===
 
 
 
 
 
===Taxon Lists===
 
*'''[[Creating Taxon Lists]]'''
 
*'''[[Update Taxon Lists|Updating Taxon Lists (for taxonomic experts)]]'''
 
===Character Annotation===
 
*'''[[Creating and Editing Character Lists|Creating Character Lists]]'''
 
*'''[[Guide to Character Annotation]]'''
 
===Ontology change requests===
 
*'''[[Term_Requests | Term Request Instructions]]'''
 
*'''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]]

Revision as of 17:51, 17 July 2018

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 housed in a shared DropBox folder (named 'Phenoscape-data'). Please contact Wasila or Paula if you are interested in perusing or adding to them.

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