iRefIndex/PBR Notes

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 distributions are observed:

Interactions

			iRefIndex 5.1
	(Total)		(7122)
			1324
PSI-XML	(8706)	2908	5798

To summarise:

• Common interactions: 5798
• Interactions only in iRefIndex 5.1: 1324
• Interactions only in BIND PSI-XML: 2908

Interactors

			iRefIndex 5.1
	(Total)		(5669)
			1450
PSI-XML	(5152)	933	4219

To summarise:

• Common interactors: 4219
• Interactors only in iRefIndex 5.1: 1450
• Interactors only in BIND PSI-XML: 933

Queries

Common interactions:

select count(distinct mitab_sources.rigid)
from i5_mitab_sources
inner join i5_mitab_interactions
  on i5_mitab_sources.uidA = i5_mitab_interactions.uidA
  and i5_mitab_sources.uidB = i5_mitab_interactions.uidB
  and i5_mitab_sources.rigid = i5_mitab_interactions.rigid
  and i5_mitab_interactions.taxA = 9606
  and i5_mitab_interactions.taxB = 9606
inner join mitab_sources
  on i5_mitab_sources.rigid = mitab_sources.rigid
  and i5_mitab_sources.name = mitab_sources.name
inner join mitab_interactions
  on mitab_sources.uidA = mitab_interactions.uidA
  and mitab_sources.uidB = mitab_interactions.uidB
  and mitab_sources.rigid = mitab_interactions.rigid
  and mitab_interactions.taxA = 9606
  and mitab_interactions.taxB = 9606
where mitab_sources.name = 'bind';

Interactions only in iRefIndex 5.1:

select count(distinct i5_mitab_sources.rigid)
from i5_mitab_sources
inner join i5_mitab_interactions
  on i5_mitab_sources.uidA = i5_mitab_interactions.uidA
  and i5_mitab_sources.uidB = i5_mitab_interactions.uidB
  and i5_mitab_sources.rigid = i5_mitab_interactions.rigid
  and i5_mitab_interactions.taxA = 9606
  and i5_mitab_interactions.taxB = 9606
where i5_mitab_sources.name = 'bind'
  and i5_mitab_sources.rigid not in (
    select distinct mitab_sources.rigid
    from mitab_sources
    inner join mitab_interactions
      on mitab_sources.uidA = mitab_interactions.uidA
      and mitab_sources.uidB = mitab_interactions.uidB
      and mitab_sources.rigid = mitab_interactions.rigid
      and mitab_interactions.taxA = 9606
      and mitab_interactions.taxB = 9606
    where mitab_sources.name = 'bind'
    );

Interactions only in BIND PSI-XML:

select count(distinct mitab_sources.rigid)
from mitab_sources
inner join mitab_interactions
  on mitab_sources.uidA = mitab_interactions.uidA
  and mitab_sources.uidB = mitab_interactions.uidB
  and mitab_sources.rigid = mitab_interactions.rigid
  and mitab_interactions.taxA = 9606
  and mitab_interactions.taxB = 9606
where mitab_sources.name = 'bind'
  and mitab_sources.rigid not in (
    select distinct i5_mitab_sources.rigid
    from i5_mitab_sources
    inner join i5_mitab_interactions
      on i5_mitab_sources.uidA = i5_mitab_interactions.uidA
      and i5_mitab_sources.uidB = i5_mitab_interactions.uidB
      and i5_mitab_sources.rigid = i5_mitab_interactions.rigid
      and i5_mitab_interactions.taxA = 9606
      and i5_mitab_interactions.taxB = 9606
    where i5_mitab_sources.name = 'bind'
    );

Common interactors:

select count(distinct X.uid)
from (
  select i5_mitab_sources.uidA as uid
  from i5_mitab_sources
  inner join i5_mitab_interactions
    on i5_mitab_sources.uidA = i5_mitab_interactions.uidA
  where name = 'bind' and taxA = 9606
  union
  select i5_mitab_sources.uidB as uid
  from i5_mitab_sources
  inner join i5_mitab_interactions
    on i5_mitab_sources.uidB = i5_mitab_interactions.uidB
  where name = 'bind' and taxB = 9606
  ) as X
inner join (
  select mitab_sources.uidA as uid
  from mitab_sources
  inner join mitab_interactions
    on mitab_sources.uidA = mitab_interactions.uidA
  where name = 'bind' and taxA = 9606
  union
  select mitab_sources.uidB as uid
  from mitab_sources
  inner join mitab_interactions
    on mitab_sources.uidB = mitab_interactions.uidB
  where name = 'bind' and taxB = 9606
  ) as Y
  on X.uid = Y.uid;

Interactors only in iRefIndex 5.1:

select count(distinct X.uid)
from (
  select i5_mitab_sources.uidA as uid
  from i5_mitab_sources
  inner join i5_mitab_interactions
    on i5_mitab_sources.uidA = i5_mitab_interactions.uidA
  where name = 'bind' and taxA = 9606
  union
  select i5_mitab_sources.uidB as uid
  from i5_mitab_sources
  inner join i5_mitab_interactions
    on i5_mitab_sources.uidB = i5_mitab_interactions.uidB
  where name = 'bind' and taxB = 9606
  ) as X
where X.uid not in (
  select mitab_sources.uidA as uid
  from mitab_sources
  inner join mitab_interactions
    on mitab_sources.uidA = mitab_interactions.uidA
  where name = 'bind' and taxA = 9606
  union
  select mitab_sources.uidB as uid
  from mitab_sources
  inner join mitab_interactions
    on mitab_sources.uidB = mitab_interactions.uidB
  where name = 'bind' and taxB = 9606
  );

Interactors only in BIND PSI-XML:

select count(distinct X.uid)
from (
  select mitab_sources.uidA as uid
  from mitab_sources
  inner join mitab_interactions
    on mitab_sources.uidA = mitab_interactions.uidA
  where name = 'bind' and taxA = 9606
  union
  select mitab_sources.uidB as uid
  from mitab_sources
  inner join mitab_interactions
    on mitab_sources.uidB = mitab_interactions.uidB
  where name = 'bind' and taxB = 9606
  ) as X
where X.uid not in (
  select i5_mitab_sources.uidA as uid
  from i5_mitab_sources
  inner join i5_mitab_interactions
    on i5_mitab_sources.uidA = i5_mitab_interactions.uidA
  where name = 'bind' and taxA = 9606
  union
  select i5_mitab_sources.uidB as uid
  from i5_mitab_sources
  inner join i5_mitab_interactions
    on i5_mitab_sources.uidB = i5_mitab_interactions.uidB
  where name = 'bind' and taxB = 9606
  );

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.