Ontology Annotator
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
- Disease
- Expression pattern
- Gene class
- Gene ontology
- Gene regulation
- Interaction
- Molecule
- Movie
- Phenotype
- Picture
- Process Term
- RNAi
- Topic
- 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:OA 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
Batch upload to OA from tab-delimited file
[New as of November 2013] A script has been written that will allow curators to upload data in bulk to the OA through the submission of a properly formatted tab-delimited (TSV) file. The script is located on Mangolassi/Tazendra at:
/home/postgres/public_html/cgi-bin/oa/scripts/populate_oa_tab_file/populate_oa_tab_file.pl
Usage:
Enter (cd) the directory with the script and run by entering:
./populate_oa_tab_file.pl mangolassi #### testfile
to enter into the Sandbox OA (on Mangolassi) where '####' is the curator's WBPerson ID
./populate_oa_tab_file.pl tazendra #### realfile
to enter into the Live OA (on Tazendra) where '####' is the curator's WBPerson ID
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