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://www.bioontology.org/ncbo/faces/pages/ontology_details.xhtml?ontology_display_name=Teleost%20anatomy%20and%20development%20(TAO) 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://www.bioontology.org/ncbo/faces/pages/ontology_details.xhtml?ontology_display_name=Teleost%20taxonomy 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://www.bioontology.org/ncbo/faces/pages/ontology_details.xhtml?ontology_display_name=PATO 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 the "Visualize" button on the ontology's homepage to browse it graphically.
 
  
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Other ontologies:
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==3. Access PDFs for Curation ==
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* [http://www.obofoundry.org/ro/ OBO-relations]
 
  
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*[http://www.bioontology.org/ncbo/faces/pages/ontology_details.xhtml?ontology_display_name=Spatial%20Ontology Spatial 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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[[Category:Curation]]
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==4. Use Ontologies to Annotate Characters ==
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[[Category:Help]]
 
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===On your desktop===
 
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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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==Annotating phenotypes==
 
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===Phenote===
 
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[http://www.phenote.org/ Phenote] is used by ZFIN and FlyBase for mutant phenotype annotation.  We are developing enhancements to the Phenote [[EQ Editor]] for PhenoScape data curation.  Some of the PhenoScape-specific enhancements include:
 
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* [[Phenote:Specimen List|A specimen list window]] allowing repeated annotation of the specimens within one publication.
 
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* [[Phenote:Phylogeny Chooser|A phylogeny view]] allowing application of an EQ annotation to all specimens from a clade at once.
 
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For more information please see the [[Phenote User Guide]].
 
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====Installation and start up====
 
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* You need Java 1.5 or newer to run Phenote.  For the Mac this requires Mac OS X 10.4 or newer.
 
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* Though you can launch Phenote using the [http://www.phenote.org/phenote/latest/phenote.jnlp webstart link], we recommend installing the latest in-progress build, packaged for Mac OS X or Windows. These builds will have the latest features. Please see the [[Phenote User Guide]] for details.
 
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* Choose the "phenoscape" configuration before beginning.
 
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* So far most curators are using the Excel-compatible tab-delimited format for saving files.
 
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====Usage====
 
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The following table describes the entry fields in the PhenoScape configuration.  Phenote 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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| Additional 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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===Term post-composition and pre-coordination===
 
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Terms can be post-composed at the time of annotation rather than pre-composed (also known as pre-coordinated) within the ontology. Post-composed terms are created in Phenote and follow genus-differentia definitions. Unlike pre-composed terms, do not have an ID.
 
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=====Post-composition=====
 
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''Example 1'': ‘branched dorsal fin ray’
 
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E= TAO: dorsal fin lepidotrichium^has_quality(PATO:branched)
 
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''Example 2'': ‘supraorbital ventral projection’
 
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bony projection^part_of [(ventral region)^part_of (supraorbital bone)]
 
  
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Ea= TAO: bony projection
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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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Eb= BSPO: ventral region part_of TAO: supraorbital bone
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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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Post-composition in Phenote is enabled using the ‘comp’ button next to the Entity field.  In example 1, the genus term is ‘dorsal fin lepidotrichium’ and the differentia term is ‘branched.’  The term in example 2 requires nesting because term Eb is a post-composed term (it is not an ‘additional entity’).
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==6. Request New Terms for Ontologies==
  
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=====Pre-composition=====
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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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The above term would be pre-coordinated using OBO-edit as:
 
  
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TAO: supraorbital ventral projection
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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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intersection of TAO: bony projection
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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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intersection of TAO: ventral region of suprorbital
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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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TAO: ventral region of suprorbital
 
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intersection of BSPO: ventral region
 
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intersection of TAO: suprorbital
 
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====Known Issues:====
 
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The post-compose feature in Phenote allows addition of multiple differentia that apply to the initial genus term but nesting of terms is not yet enabled. In the meantime, when post-composed terms that require nesting are needed for annotation, we will note in the 'curator notes' field that these terms will need proper updating once nesting is possible.
 
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==Curatorial Best Practices==
 
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====[[Creating Taxon Lists]]====
 
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====[[Creating and Editing Character Lists|Creating Character Lists]]====
 
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====[[Update Taxon Lists|Updating Taxon Lists (for taxonomic experts)]]====
 
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====[[Term Requests|How to Submit Term Requests]]====
 
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====[[Guide to Character Annotation]]====
 
  
 
[[Category:Curation]]
 
[[Category:Curation]]
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[[Category:Help]]
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==Ontology change requests==
 
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Here are 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/?group_id=76834&atid=994726 Zebrafish 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]
 

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
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