Difference between revisions of "Ontology Annotator"
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− | == | + | ==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 can be found here. | ||
+ | ==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) | #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 | #Term information window - information should reflect where cursor is placed in the editor window, e.g. Paper should reflect paper info |
Revision as of 18:42, 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 can be found here.
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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