Difference between revisions of "General specifications"
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'''Input''' | '''Input''' | ||
+ | |||
location of files on Textpresso for retrieving paper titles and abstracts | location of files on Textpresso for retrieving paper titles and abstracts | ||
− | source files for curatable sentences | + | ''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/ | ||
− | gene name to gene identifier mapping file | + | ''dictyBase'': |
+ | |||
+ | ''FlyBase'': | ||
+ | |||
+ | |||
+ | gene name to gene identifier mapping file - update schedule? | ||
+ | |||
+ | ''Arabidopsis'': /home/acedb/kimberly/ccc_tair/tair_ccc_datafiles | ||
+ | |||
+ | ''dictyBase'': | ||
+ | |||
+ | ''FlyBase'': | ||
'''Curation''' | '''Curation''' | ||
+ | |||
web-based curation form | web-based curation form | ||
+ | |||
+ | ''Arabidopsis'': http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/tair/tair_ccc.cg | ||
+ | |||
postgres table for storing curation | 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''' | '''Output - three-column or GAF''' | ||
+ | |||
gene name to gene identifier mapping file | gene name to gene identifier mapping file | ||
− | taxon ID | + | ''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 |
Latest revision as of 19:18, 17 November 2011
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