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 teleost [[taxonomy ontology|taxonomy]] and anatomy ontologies is now available:
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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=Teleost%20taxonomy Teleost taxonomy]
 
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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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It is generated, with some modifications, from: [http://www.calacademy.org/RESEARCH/ichthyology/catalog/fishcatsearch.html Catalog of Fishes].
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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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===On your desktop===
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==3. Access PDFs for Curation ==
  
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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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Phenoscape maintains a collection of PDFs for curation. Please ask project personnel (Wasila or Paula) for access to the collection.
  
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==Annotating phenotypes==
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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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===Phenote===
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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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[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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==6. Request New Terms for Ontologies==
  
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* [[Phenote:Specimen List|A specimen list window]] allowing repeated annotation of the specimens within one publication.
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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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* [[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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* [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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====Installation and start up====
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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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* 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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==8. Subscribe to Curator and Ontology Request Mailing Lists ==
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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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* Discussion of ontology development and Open Biomedical Ontologies community issues ''[https://groups.google.com/forum/#!forum/obo-discuss obo-discuss]
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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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[[Category:Curation]]
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[[Category:Help]]
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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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Eb= BSPO: ventral region part_of TAO: supraorbital bone
 
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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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=====Pre-composition=====
 
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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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intersection of TAO: bony projection
 
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intersection of TAO: ventral region of suprorbital
 
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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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===Genus-differentia definitions===
 
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Term definitions in the teleost anatomy ontology (TAO) take the form of genus-differentia definitions:
 
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B is an A that has X.
 
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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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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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2. The dentary is a dermal bone that forms the anterolateral part of the lower jaw.
 
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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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[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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===Proper syntax for relative length===
 
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For the characters that relate the length of one bone to another, ratios are used in Phenote.  For example: Length of infraorbital 2: (0) over twice as long as infraorbital 1; (1) less than twice as long as infraorbital 1. This would be indicated in Phenote as follows:
 
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E1: Infraorbital 2, Q: increased length, , E2 : Infraorbital 1, Measurement:  >2, Unit: ratio
 
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E1: Infraorbital 2, Q: decreased length, , E2 : Infraorbital 1, Measurement:  <2, Unit: ratio
 
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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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