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 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=Zebrafish%20anatomy%20and%20development Zebrafish anatomy and development]
 
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* [http://www.bioontology.org/ncbo/faces/pages/ontology_details.xhtml?ontology_display_name=PATO PATO]
 
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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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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.obofoundry.org/ro/ OBO-relations]
 
  
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The [[taxonomy 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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==2. Access Project Files==
  
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===On your desktop===
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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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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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==3. Access PDFs for Curation ==
  
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==Annotating phenotypes==
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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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===Genus-differentia definitions===
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==4. Use Ontologies to Annotate Characters ==
  
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Term definitions in the teleost anatomy ontology (TAO) take the form of genus-differentia definitions:
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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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B is an A that has X.
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==5. Update Taxon Lists==
  
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The term (B) is defined by its membership in higher category (A) and distinguished by characteristics (X). The following are examples of genus-differentia definitions in the TAO:
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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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1. The antorbital is a dermal bone that is located on the anterior margin of the infraorbital series, dorsal to the first infraorbital and lateral to the nasal bone.  
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==6. Request New Terms for Ontologies==
  
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2. The dentary is a dermal bone that forms the anterolateral part of the lower jaw.
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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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In example 1, the definition mentions the parent dermal bone of the term antorbital followed by the characteristics that differentiate antorbital from all other dermal bones.
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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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[http://wiki.geneontology.org/index.php/Logical_Definitions Logical definitions] (also known as cross-products) are constructed as the intersection between terms and are genus-differentia definitions.
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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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===Phenote===
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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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[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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[[Category:Curation]]
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[[Category:Help]]
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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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====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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* Launch Phenote using the [http://www.phenote.org/phenote/latest/phenote.jnlp webstart link].  Alternatively, you can try the in-progress builds with the latest features, packaged for [https://www.nescent.org/wg/phenoscape/images/4/40/Phenote-MacOSX.zip Mac OS X] or [https://www.nescent.org/wg/phenoscape/images/d/db/Phenote-Windows.zip Windows].
 
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* Choose the "phenomap" configuration before beginning (this will soon be replaced by a "phenoscape" config).
 
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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
 
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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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==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/?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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