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.
  
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===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]])
  
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Many [[Ontologies|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==
  
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* [http://bioportal.bioontology.org/visualize/38362 Teleost Anatomy Ontology (TAO)]
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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''']].
  
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* [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])
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==2. Access Project Files==
  
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* [http://bioportal.bioontology.org/visualize/38339 Phenotype and Trait Ontology (PATO)]
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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.
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Click on the "Visualization" tab to browse the ontologies graphically.
 
  
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Other ontologies:
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==3. Access PDFs for Curation ==
  
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*[http://bioportal.bioontology.org/visualize/36625 Evidence Code Ontology]
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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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* [http://www.obofoundry.org/ro/ OBO-relations]
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==4. Use Ontologies to Annotate Characters ==
  
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*[http://bioportal.bioontology.org/visualize/29952 Spatial Ontology]
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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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===On your desktop===
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==5. Update Taxon Lists==
  
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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.
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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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==Annotating phenotypes==
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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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===Phenex===
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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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Phenex is used by PhenoScape for annotation of comparative phenotypes.  Phenex can be downloaded at:
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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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https://sourceforge.net/project/showfiles.php?group_id=224046&package_id=287165&release_id=628849
 
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For Mac, click on the link "phenex-1.0-beta10-mac.zip"
 
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For Windows, click on the link "phenex-1.0-beta10-win.zip"
 
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====Installation and start up====
 
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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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* Windows:
 
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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. 
 
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* Mac:
 
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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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====Usage====
 
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The following table describes the entry fields in the PhenoScape configuration. Phenex does not force you to fill in them all, but see the table for when to use each field.
 
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{| border="1" cellspacing="0" cellpadding="3"
 
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! Field
 
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! Usage
 
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|-
 
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| Publication || the publication describing the character state<br/>CrossRef has a [http://www.crossref.org/SimpleTextQuery/ free-text query form] for looking up DOIs
 
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|-
 
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| Taxon || Genus & species
 
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|-
 
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| Catalog Number || museum lot ID
 
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|-
 
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| Specimen Count || number of specimens from lot examined
 
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|-
 
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| Preparation || type of specimen preparation (skeleton, cleared & stained, etc.)
 
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|-
 
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| Entity || term from anatomy ontology (currently using zebrafish)
 
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|-
 
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| Quality || term from PATO - should be "value" term, unless you are filling in an absolute measurement (e.g. "length")
 
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|-
 
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| Related Entity || term from anatomy ontology - only use if the Quality term descends from "relational quality of continuant"
 
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|-
 
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| Measurement || absolute measurement - useful as value for terms such as "length"
 
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|-
 
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| Unit || unit of measurement, if Numerical Value is filled in
 
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|-
 
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| Compare To || a taxon to which this phenotype is in comparison to (optional)
 
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|-
 
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| Textual Description || textual description of character state in publication
 
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|-
 
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| Image URI || web link to an image, if available
 
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|}
 
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Please report any issues you come across by using the [https://sourceforge.net/tracker/?group_id=76834&atid=887913 Phenote tracker].
 
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==Curatorial Best Practices==
 
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===[[Data Repository Access Instructions]]===
 
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===[[Phenex|Merging files in Phenex]]===
 
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===Taxon Lists===
 
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*'''[[Creating Taxon Lists]]'''
 
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*'''[[Update Taxon Lists|Updating Taxon Lists (for taxonomic experts)]]'''
 
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===Character Annotation===
 
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*'''[[Creating and Editing Character Lists|Creating Character Lists]]'''
 
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*'''[[Guide to Character Annotation]]'''
 
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===Ontology change requests===
 
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*'''[[Term_Requests | Term Request Instructions]]'''
 
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*'''Links to ontology term trackers'''
 
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** [http://sourceforge.net/tracker/?group_id=76834&atid=994764 Teleost anatomy tracker]
 
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** [http://sourceforge.net/tracker/?atid=1046550&group_id=76834 Teleost taxonomy ontology tracker]
 
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** [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
Retrieved from "https://wiki.phenoscape.org/wg/phenoscape/index.php?title=Resources_for_Data_Contributors&oldid=12058"