General specifications

General specifications for Textpresso-based CCC Curation

Input

location of files on Textpresso for retrieving paper titles and abstracts

Arabidopsis: /data2/data-processing/data/arabidopsis/Data/processedfiles/title/ /data2/data-processing/data/arabidopsis /Data/processedfiles/abstract/

dictyBase:

FlyBase:

source files for curatable sentences - supplied by Textpresso team, stored on tazendra

Arabidopsis: /home/acedb/kimberly/ccc_tair/tair_ccc_datafiles/

dictyBase:

FlyBase:

gene name to gene identifier mapping file - update schedule?

Arabidopsis: /home/acedb/kimberly/ccc_tair/tair_ccc_datafiles

dictyBase:

FlyBase:

Curation

web-based curation form

Arabidopsis: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/tair/tair_ccc.cg

postgres table for storing curation

Arabidopsis: ccc_tair_gene_comp_go

dictyBase: ccc_dicty_gene_comp_go

FlyBase: ccc_flybase_gene_comp_go

postgres table for storing comments (changed 11/2011 to make implementation-specific tables, add directory/source file column)

Arabidopsis: ccc_tair_comment

dictyBase: ccc_dicty_comment

FlyBase: ccc_flybase_comment

Output - three-column or GAF

gene name to gene identifier mapping file

Arabidopsis: /home/acedb/kimberly/ccc_tair/tair_ccc_datafiles

GO term - GO ID mappings

All implementations: http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo

paper identifier mapping file

Arabidopsis: /data2/data-processing/data/arabidopsis/Data/processedfiles/accession/

NCBI taxon ID

Arabidopsis: 3702

dictyBase: 44689

FlyBase: 7227