iRefIndex/PBR Notes

From irefindex
Revision as of 13:51, 21 September 2009 by PaulBoddie (talk | contribs) (→‎Results: Restricted to 9606 interactors.)

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 (8916) 3118 5798

To summarise:

  • Common interactions: 5798
  • Interactions only in iRefIndex 5.1: 1324
  • Interactions only in BIND PSI-XML: 3118

Interactors

iRefIndex 5.1
(Total) (5669)
1450
PSI-XML (5324) 1105 4219

To summarise:

  • Common interactors: 4219
  • Interactors only in iRefIndex 5.1: 1450
  • Interactors only in BIND PSI-XML: 1105

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
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
where mitab_sources.name = 'bind'
  and taxA = 9606
  and taxB = 9606;

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
where i5_mitab_sources.name = 'bind'
  and taxA = 9606
  and taxB = 9606
  and i5_mitab_sources.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 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
  where i5_mitab_sources.name = 'bind'
    and taxA = 9606
    and taxB = 9606
  );

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 uidA as uid
  from mitab_sources
  where name = 'bind'
  union
  select uidB as uid
  from mitab_sources
  where name = 'bind'
  ) 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 uidA as uid from mitab_sources where name = 'bind' union select uidB as uid from mitab_sources where name = 'bind');

Interactors only in BIND PSI-XML:

select count(distinct X.uid)
from (select uidA as uid from mitab_sources where name = 'bind' union select uidB as uid from mitab_sources where name = 'bind') 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.