Difference between revisions of "Resources for Data Contributors"

From phenoscape
Jump to: navigation, search
(3. Download Publication PDFs and Curation Posters)
(47 intermediate revisions by 5 users not shown)
Line 1: Line 1:
==1. Download Most Recent Version of Phenex==
+
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.
  
Phenex was developed by Phenoscape for annotation of evolutionary phenotypes. Phenex can be downloaded at:
+
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])
  
https://sourceforge.net/project/showfiles.php?group_id=76834&package_id=295042
+
==1. Download Most Recent Version of Phenex==
  
For Mac, click on the link "phenex-1.0-beta12-mac.zip"
+
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 Windows, click on the link "phenex-1.0-beta12-win.zip"
+
==2. Access Project Files==
  
====Installation and start up====
+
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.
  
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:
+
==3. Access PDFs for Curation ==
  
* Windows:
+
Phenoscape uses [http://www.mendeley.com/ Mendeley] to maintain the collection of PDFs for curation. Please ask project personnel (Wasila or Paula) for an invitation to join the group.
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:
+
Phenoscape also maintains a collection of PDFs for teleost publications on the Phenoscape file share (webdav).  Please ask a Phenoscaper for directions and the username and password.
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==
+
==4. Use Ontologies to Annotate Characters ==
  
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 ]].
+
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 [[Guide to Character Annotation | '''Phenoscape Guide to Character Annotation''']].
  
==3. Download Publication PDFs and Curation Posters ==
+
==5. Update Taxon Lists==
  
Connecting in MAC OS X
+
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.
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
+
  
Connecting in Windows XP
+
==6. Request New Terms for Ontologies==
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://webdav.nescent.org/[sharename]/#
+
* For example, https://webdav.nescent.org/phenoscape-data/#
+
* (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.
+
5. Accept certificate warning, if given.
+
6. Give the share a meaningful name. Default is usually fine.
+
7. Finish
+
  
==4. Update Taxon Lists==
+
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:
  
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 [[Update Taxon Lists| updating taxon lists]].
+
* [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]
  
==5. Use Ontologies to Annotate Characters ==
+
==7. Edit the Anatomy Ontology ==
 
+
* [http://phenoscape.org/wiki/Ontology_workflow Ontology Editing Guidelines]
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 [[Guide to Character Annotation | Phenoscape Guide to Character Annotation]].
+
 
+
==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_Requests | Term Request Instructions]].
+
==8. Subscribe to Curator and Ontology Request Mailing Lists ==
 +
* Phenoscape Curators mailing list (for discussion and communication of data curation issues, solutions, and progress):  [http://lists.sourceforge.net/lists/listinfo/phenoscape-curators phenoscape-curators]
 +
* Discussion of EQ formalism, phenotype description, PATO terms:  ''[https://lists.sourceforge.net/mailman/listinfo/obo-phenotype obo-phenotype]
 +
* Discussion of anatomy ontology issues ''[https://lists.sourceforge.net/lists/listinfo/obo-anatomy obo-anatomy]
  
 
[[Category:Curation]]
 
[[Category:Curation]]
 
[[Category:Help]]
 
[[Category:Help]]

Revision as of 21:18, 3 June 2016

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 uses Mendeley to maintain the collection of PDFs for curation. Please ask project personnel (Wasila or Paula) for an invitation to join the group.

Phenoscape also maintains a collection of PDFs for teleost publications on the Phenoscape file share (webdav). Please ask a Phenoscaper for directions and the username and password.

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

  • Phenoscape Curators mailing list (for discussion and communication of data curation issues, solutions, and progress): phenoscape-curators
  • Discussion of EQ formalism, phenotype description, PATO terms: obo-phenotype
  • Discussion of anatomy ontology issues obo-anatomy