General specifications

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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