TAIR

Gene Ontology Curation at TAIR

Specifications for Curation Pipeline

Summary

This document is an outline of the Arabidopsis Textpresso for CCC pipeline. The initial trial run will be for all papers in the Textpresso for Arabidopsis corpus published in 2008. Results will be split into two files: results from papers already curated for GO Cellular Component and results from papers not curated for GO Cellular Component. Curation made using on on-line curation form will be output to a Gene Association file format for incorporation into the main TAIR file submitted to GO.

Pipeline

Paper Acquisition

• TAIR curator sends PDFs of Arabidopsis or other relevant papers to Textpresso (Michael) approximately every six months.

• Other relevant papers without a PDF are downloaded by Textpresso team, if possible.

Textpresso Search for Cellular Component Annotations

• Search Arabidopsis corpus using four categories:

1) CCC assay terms

2) CCC cellular component

3) CCC verbs

4) genes (arabidopsis)

• Filters

1) 2008

• Running this search on the Textpresso for Arabidopsis site gives 55814 matches in 1421 documents, with total paper scores ranging from 660 to 7.

Curation - Sentence Input and Annotation

• The output of the searches will be sentences sorted into two separate files. The criterion for sorting is whether any Cellular Component Annotations exist for that paper in TAIR's Gene Association file.

• Each file will be available in the curation form for curators to assess search results.

• Results of searches will be presented in the curation form, in a three-column format: 1) gene or protein name, 2) cellular component category term, 3) if available, a suggested GO term from the existing category term-GO term relationship index.

Curation - Output to Gene Association File

Curation will be output to in the form of a Gene Association file that can be picked up by the TAIR curators and added to the main Gene Association file that they submit to GO.

Output will need to reference the Arabidopsis gene mapping file here:

ftp://ftp.arabidopsis.org/home/tair/Genes/gene_aliases.20101027

There are three columns:

1. locus name (can be a symbol, if this a genetic locus, or an AGI identifier, if it is cloned)

2. symbol

3. full name (not always available)

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