Difference between revisions of "General specifications"
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location of files on Textpresso for retrieving paper titles and abstracts | 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/ | + | ''Arabidopsis'': /data2/data-processing/data/arabidopsis/Data/processedfiles/title/ /data2/data-processing/data/arabidopsis |
| + | /Data/processedfiles/abstract/ | ||
| + | ''dictyBase'': | ||
| − | + | ''FlyBase'': | |
| − | gene name to gene identifier mapping file | + | 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 | ''Arabidopsis'': /home/acedb/kimberly/ccc_tair/tair_ccc_datafiles | ||
| + | |||
| + | ''dictyBase'': | ||
| + | |||
| + | ''FlyBase'': | ||
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''Arabidopsis'': ccc_tair_gene_comp_go | ''Arabidopsis'': ccc_tair_gene_comp_go | ||
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| + | ''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 | ||
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''Arabidopsis'': /home/acedb/kimberly/ccc_tair/tair_ccc_datafiles | ''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/ | ||
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
