Difference between revisions of "Resources for Data Contributors"
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===On the web=== | ===On the web=== | ||
| − | Many [[Ontologies|ontologies]] are available for browsing at the [http://www.bioontology.org/ncbo/faces/index.xhtml NCBO BioPortal]. | + | Many [[Ontologies|ontologies]] are available for browsing at the [http://www.bioontology.org/ncbo/faces/index.xhtml NCBO BioPortal]. For example: |
* [http://bioportal.bioontology.org/visualize/38362 Teleost Anatomy Ontology (TAO)] | * [http://bioportal.bioontology.org/visualize/38362 Teleost Anatomy Ontology (TAO)] | ||
| Line 10: | Line 10: | ||
* [http://bioportal.bioontology.org/visualize/38339 Phenotype and Trait Ontology (PATO)] | * [http://bioportal.bioontology.org/visualize/38339 Phenotype and Trait Ontology (PATO)] | ||
| − | Click the " | + | Click on the "Visualization" tab to browse the ontologies graphically. |
Other ontologies: | Other ontologies: | ||
Revision as of 16:07, 13 October 2008
Viewing ontologies
On the web
Many ontologies are available for browsing at the NCBO BioPortal. For example:
- Teleost Taxonomy Ontology (TTO) (generated, with some modifications, from the Catalog of Fishes)
Click on the "Visualization" tab to browse the ontologies graphically.
Other ontologies:
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.
- Though you can launch Phenote using the 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.
- Choose the "phenoscape" configuration before beginning.
- 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") |
| Related 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.
Curatorial Best Practices
Data Repository Access Instructions
Merging files in Phenex
Taxon Lists
Character Annotation
Ontology change requests
- Term Request Instructions
- Links to ontology term trackers
