Last Updated: February 5, 2002

This directory includes files containing domain-GO Function
associations (rules). 

The following files are provided:

     ProDom_NO_IEA_rules.tab
     ProDom_ALL_rules.tab

     CDD_NO_IEA_rules.tab
     CDD_ALL_rules.tab

For a detailed description of how these rules were 
generated, please see www.cbil.upenn.edu/GO.

File Format
===========

These files are tab delimited and include the following
fields:

 
   Field	      	Description
----------------------------------------------------------------------------
1. AlgInv        This is an internal identifier that simply allows us to track
                 the process used to populate our database.

2. Rule Set ID   This in an internal identifier that groups all GO terms  
                 associated with a given domain.  Each domain with a rule
                 will have a single unique rule set id for each generation
                 of the rules.

3. Rule ID       This is an internal identifier that is assigned to a 
                 specific rule (domain-GO term association).  Each GO
                 term associated with a domain will have a unique rule id
                 for each generation of the rules.

4. External DB Name 
                 This field lists the name of the domain database used

5. Source ID     This field contains the source identifier from the 
                 domain database.

6. GO ID         The GO id for the term associated with this domain

7. Rule Type     Rule type.  See www.cbil.upenn.edu/GO for more details

8. Num Proteins  Number of GOAPs used to generate this rule

9. Pvalue Threshold
                 Theshold p-value that can be used when applying this rule
                 This is the p-value representing the highest p-value that
                 explains this rule

10.Confidence    Either a computationally generated or manually assigned 
                 confidence in the rule.  Will be one of (low, med, high, 
                 low_complx, repeat). low_complx and repeat refer to the 
                 domain and have only been assigned manually; these may
                 be filtered out during application of the rule. 

11. manually reviewed
                 Whether this rule has been manually reviewed.  0 => no,
                 1=> yes. 
 





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