Difference between revisions of "Ontology Annotator"
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* PostgreSQL database backend (could probably be modified to other SQL databases). | * PostgreSQL database backend (could probably be modified to other SQL databases). | ||
* Apache webserver. | * Apache webserver. | ||
− | * Documentation for main CGI, javascript, and modules | + | * Documentation for main CGI, javascript, and modules:[http://www.its.caltech.edu/~wormbase/oa/docs|OA docs] |
The above description can also be found here: [http://www.caltech.edu/~wormbase/oa/docs/main.html| Web-page for OA] | The above description can also be found here: [http://www.caltech.edu/~wormbase/oa/docs/main.html| Web-page for OA] |
Revision as of 19:06, 29 February 2012
Description
The Ontology Annotator (OA) is a curation tool developed by WormBase for a variety of curation purposes including the curation of phenotypes, attaching GO terms to genes, genetic interactions, transgenes, free-text descriptions of genes, and several other data-types. The OA uses CGI, javascript and a postgreSQL database and is web-based, eliminating issues that may arise due to operating system differences and the need for an user to install other dependent software. The OA in many ways is similar to [Phenote] (phenote.org). The OA mainly consists of an Editor, where new data is entered or where pre-existing data can be queried and edited, a Data-Table for data review and a Term-Information panel where information about a term like IDs, synonyms etc., is displayed. The OA includes features like term autocomplete from pre-loaded ontologies, a fast AJAX loading of terms, ability to save/query to/from a postgreSQL database, duplicating data, editing several lines of data at once, and filtering the data. The display to some extent can be custom-organized as columns in the Data-Table can be sorted by dragging and the width of each data-column adjusted. For complex data-types with several fields, the OA allows a tabbed organization.
List of WormBase OA configurations:
- Antibody
- Concise description
- Gene class
- Gene ontology
- Gene regulation
- Interaction
- Molecule
- Phenotype
- Picture
- Process
- Transgene
The OA uses :
- Perl CGI.
- Yahoo!'s YUI library and a local javascript file.
- PostgreSQL database backend (could probably be modified to other SQL databases).
- Apache webserver.
- Documentation for main CGI, javascript, and modules:docs
The above description can also be found here: Web-page for OA
Wish List
- Include dependencies wherever possible. For example, if making an IMP annotation for a given gene, have a gene-specific drop down menu of alleles or RNAi experiments for the WITH column. Or, if making an IGI annotation for the paper, have a drop down list of all genes mentioned in the paepr. Similarly, when entering a GO term, have the ontology (P, F, or C) get entered automatically. (From Curation Interface Meeting)
- Term information window - information should reflect where cursor is placed in the editor window, e.g. Paper should reflect paper info
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