Difference between revisions of "Resources for Data Contributors"
(→Annotating phenotypes) |
(→Curatorial Best Practices) |
||
| Line 118: | Line 118: | ||
==Curatorial Best Practices== | ==Curatorial Best Practices== | ||
| + | There is an in-progress [[Guide to Character Annotation]] which will eventually replace the following information. | ||
===Genus-differentia definitions=== | ===Genus-differentia definitions=== | ||
Revision as of 15:20, 17 April 2008
Contents
Viewing ontologies
On the web
Many ontologies are available for browsing at the NCBO BioPortal. For example:
Click the "Visualize" button on the ontology's homepage to browse it graphically.
Other ontologies:
The teleost taxonomy and anatomy ontologies is now available:
It is generated, with some modifications, from: Catalog of Fishes.
On your desktop
You can download the ontologies as OBO files from the above web sites. You can download and install OBO-Edit to view in a desktop application.
Annotating phenotypes
Phenote
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:
- A specimen list window allowing repeated annotation of the specimens within one publication.
- A phylogeny view allowing application of an EQ annotation to all specimens from a clade at once.
For more information please see the Phenote User Guide.
Installation and start up
- You need Java 1.5 or newer to run Phenote. For the Mac this requires Mac OS X 10.4 or newer.
- Launch Phenote using the webstart link. Alternatively, you can try the in-progress builds with the latest features, packaged for Mac OS X or Windows.
- Choose the "phenomap" configuration before beginning (this will soon be replaced by a "phenoscape" config).
- So far most curators are using the Excel-compatible tab-delimited format for saving files.
Usage
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.
| Field | Usage |
|---|---|
| Publication | the publication describing the character state CrossRef has a free-text query form for looking up DOIs |
| Taxon | Genus & species |
| Catalog Number | museum lot ID |
| Specimen Count | number of specimens from lot examined |
| Preparation | type of specimen preparation (skeleton, cleared & stained, etc.) |
| Entity | term from anatomy ontology (currently using zebrafish) |
| Quality | term from PATO - should be "value" term, unless you are filling in an absolute measurement (e.g. "length") |
| Additional Entity | term from anatomy ontology - only use if the Quality term descends from "relational quality of continuant" |
| Measurement | absolute measurement - useful as value for terms such as "length" |
| Unit | unit of measurement, if Numerical Value is filled in |
| Compare To | a taxon to which this phenotype is in comparison to (optional) |
| Textual Description | textual description of character state in publication |
| Image URI | web link to an image, if available |
Please report any issues you come across by using the Phenote tracker.
Term post-composition and pre-coordination
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.
Post-composition
Example 1: ‘branched dorsal fin ray’
E= TAO: dorsal fin lepidotrichium^has_quality(PATO:branched)
Example 2: ‘supraorbital ventral projection’
bony projection^part_of [(ventral region)^part_of (supraorbital bone)]
Ea= TAO: bony projection
Eb= BSPO: ventral region part_of TAO: supraorbital bone
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’).
Pre-composition
The above term would be pre-coordinated using OBO-edit as:
TAO: supraorbital ventral projection
intersection of TAO: bony projection
intersection of TAO: ventral region of suprorbital
TAO: ventral region of suprorbital
intersection of BSPO: ventral region
intersection of TAO: suprorbital
Known Issues:
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.
Curatorial Best Practices
There is an in-progress Guide to Character Annotation which will eventually replace the following information.
Genus-differentia definitions
Term definitions in the teleost anatomy ontology (TAO) take the form of genus-differentia definitions:
B is an A that has X.
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:
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.
2. The dentary is a dermal bone that forms the anterolateral part of the lower jaw.
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.
Logical definitions (also known as cross-products) are constructed as the intersection between terms and are genus-differentia definitions.
Proper syntax for relative length
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:
E1: Infraorbital 2, Q: increased length, , E2 : Infraorbital 1, Measurement: >2, Unit: ratio
E1: Infraorbital 2, Q: decreased length, , E2 : Infraorbital 1, Measurement: <2, Unit: ratio
Ontology change requests
Here are links to ontology term trackers:
