Difference between revisions of "Resources for Data Contributors"

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==Viewing ontologies==
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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.
  
===On the web===
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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]])
  
Many ontologies are available for browsing at the [http://www.bioontology.org/ncbo/faces/index.xhtml NCBO BioPortal].  For example:
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==1. Download Most Recent Version of Phenex==
* [http://www.bioontology.org/ncbo/faces/pages/ontology_details.xhtml?ontology_display_name=Zebrafish%20anatomy%20and%20development Zebrafish anatomy and development]
 
* [http://www.bioontology.org/ncbo/faces/pages/ontology_details.xhtml?ontology_display_name=PATO PATO]
 
Click the "Visualize" button on the ontology's homepage to browse it graphically.
 
  
The taxonomic ontology is not yet available, but it will be generated from the [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes].
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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''']].
  
===On your desktop===
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==2. Access Project Files==
  
You can download the ontologies as OBO files from the above web sites.  You can download and install [http://oboedit.org/ OBO-Edit] to view in a desktop application.
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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.
  
==Annotating phenotypes==
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==3. Access PDFs for Curation ==
  
We are working on a specialized [[EQ Editor]] for data curation. Until it is ready for use, EQ annotations can be created using [http://www.phenote.org/ Phenote]. You can download a customized [[Media:phenomap.cfg.zip|Phenote configuration file]] which is suited to our data. See the [http://www.phenote.org/content/howtos/customize.shtml instructions] on how to use a custom configuration.
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Phenoscape maintains a collection of PDFs for curation. Please ask project personnel (Wasila or Paula) for access to the collection.
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==4. Use Ontologies to Annotate Characters ==
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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''']].
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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.
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==6. Request New Terms for Ontologies==
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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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* Discussion of ontology development and Open Biomedical Ontologies community issues ''[https://groups.google.com/forum/#!forum/obo-discuss obo-discuss]
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[[Category:Curation]]
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[[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