Difference between revisions of "Resources for Data Contributors"

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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.
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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])
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==1. Download Most Recent Version of Phenex==
 
==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|Phenex homepage]].
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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''']].
  
 
==2. Access Project Files==
 
==2. Access Project Files==
  
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 Instructions|Instructions for accessing the data repository]] if you are interested in perusing or adding to them.
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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 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.
  
==3. Download PDFs and Ontology Posters as Needed on Phenoscape Fileshare ==
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==3. Access PDFs for Curation ==
You can download publication PDFs and powerpoint posters of the TAO and PATO ontologies by connecting to the Phenoscape file share.
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Connecting in MAC OS X
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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.
# In finder > Go > Connect to Server
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# Type in https://ftp.nescent.org/[sharename] .   For example, https://ftp.nescent.org/phenoscape-data
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# Accept security warning about certificate
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# enter username and password (ask a Phenoscaper)
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Connecting in Windows XP
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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.
# Go to "My Network Places"
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# Add a Network Place (pulls up wizard)
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# Click Next twice
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# In internet or Network address box, type in  https://ftp.nescent.org/phenoscape-data/
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**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.
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# Accept certificate warning, if given.
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# Give the share a meaningful name. Default is usually fine.
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# Finish
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==4. Use Ontologies to Annotate Characters ==
 
==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 [[Guide to Character Annotation | Phenoscape Guide to Character Annotation]].
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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''']].
  
 
==5. Update Taxon Lists==
 
==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 [[Update Taxon Lists| updating 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.
  
 
==6. Request New Terms for Ontologies==
 
==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]].
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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]
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==7. Edit the Anatomy Ontology ==
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* [http://phenoscape.org/wiki/Ontology_workflow Ontology Editing Guidelines]
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==8. Subscribe to Curator and Ontology Request Mailing Lists ==
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* 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]
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* Discussion of EQ formalism, phenotype description, PATO terms:  ''[https://lists.sourceforge.net/mailman/listinfo/obo-phenotype obo-phenotype]
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* Discussion of anatomy ontology issues ''[https://lists.sourceforge.net/lists/listinfo/obo-anatomy obo-anatomy]
  
 
[[Category:Curation]]
 
[[Category:Curation]]
 
[[Category:Help]]
 
[[Category:Help]]

Latest 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