Difference between revisions of "iRefIndex/PBR Notes"

From irefindex
(New page: Importing MITAB output from the iRefIndex 5.1 build and a build done using the BIND PSI-XML data, then comparing the interaction details for BIND, the following distribution is observed: ...)
 
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Preliminary BIND PSI-XML parsing results.
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== Results ==
 +
 
Importing MITAB output from the iRefIndex 5.1 build and a build done using the BIND PSI-XML data, then comparing the interaction details for BIND, the following distribution is observed:
 
Importing MITAB output from the iRefIndex 5.1 build and a build done using the BIND PSI-XML data, then comparing the interaction details for BIND, the following distribution is observed:
  
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* Interactions only in BIND PSI-XML: 2923
 
* Interactions only in BIND PSI-XML: 2923
  
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== Queries ==
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Common interactions:
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select count(distinct mitab_sources.rigid)
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from i5_mitab_sources
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inner join mitab_sources
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  on i5_mitab_sources.rigid = mitab_sources.rigid
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  and i5_mitab_sources.name = mitab_sources.name
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where mitab_sources.name = 'bind';
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Interactions only in iRefIndex 5.1:
 +
 
 +
select count(distinct rigid)
 +
from i5_mitab_sources
 +
where i5_mitab_sources.name = 'bind'
 +
  and rigid not in (select rigid from mitab_sources where mitab_sources.name = 'bind');
 +
 
 +
Interactions only in BIND PSI-XML:
 +
 
 +
select count(distinct rigid)
 +
from mitab_sources
 +
where mitab_sources.name = 'bind'
 +
  and rigid not in (select rigid from i5_mitab_sources where i5_mitab_sources.name = 'bind');
 +
 
 +
== Other Stuff ==
  
 
This is what I did for the unnecessary "new BIND vs. other sources" experiment...
 
This is what I did for the unnecessary "new BIND vs. other sources" experiment...

Revision as of 11:02, 21 September 2009

Preliminary BIND PSI-XML parsing results.

Results

Importing MITAB output from the iRefIndex 5.1 build and a build done using the BIND PSI-XML data, then comparing the interaction details for BIND, the following distribution is observed:

iRefIndex 5.1
(Total) (9811)
3818
PSI-XML (8916) 2923 5993

To summarise:

  • Common interactions: 5993
  • Interactions only in iRefIndex 5.1: 3818
  • Interactions only in BIND PSI-XML: 2923

Queries

Common interactions:

select count(distinct mitab_sources.rigid)
from i5_mitab_sources
inner join mitab_sources
  on i5_mitab_sources.rigid = mitab_sources.rigid
  and i5_mitab_sources.name = mitab_sources.name
where mitab_sources.name = 'bind';

Interactions only in iRefIndex 5.1:

select count(distinct rigid)
from i5_mitab_sources
where i5_mitab_sources.name = 'bind'
  and rigid not in (select rigid from mitab_sources where mitab_sources.name = 'bind');

Interactions only in BIND PSI-XML:

select count(distinct rigid)
from mitab_sources
where mitab_sources.name = 'bind'
  and rigid not in (select rigid from i5_mitab_sources where i5_mitab_sources.name = 'bind');

Other Stuff

This is what I did for the unnecessary "new BIND vs. other sources" experiment...

Downloaded the following:

  • BioGrid
  • CORUM
  • DIP
  • HPRD
  • Intact
  • MINT
  • MIPS (MPPI)
  • OPHID

Modified the following:

  • BioGrid - removed all but human data

Parsed all sources mentioned above.

Removed all non-9606 records.

Did ROG assignment and so on.

Made the reports.