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
  );

Retrieving BIND Identifiers

The following queries determine the appropriate set of interactions and then derive the BIND identifiers from them.

Find all BIND identifiers in iRefIndex 5.1:

create table export_all_i5_bind as
select distinct i5_mitab_interaction_identifiers.uid
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 i5_mitab_interaction_identifiers
  on i5_mitab_sources.uidA = i5_mitab_interaction_identifiers.uidA
  and i5_mitab_sources.uidB = i5_mitab_interaction_identifiers.uidB
  and i5_mitab_sources.rigid = i5_mitab_interaction_identifiers.rigid
where name = 'bind' and uid like 'bind:%';

Find all BIND identifiers in BIND PSI-XML:

create table export_all_xml_bind as
select distinct mitab_interaction_identifiers.uid
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
inner join mitab_interaction_identifiers
  on mitab_sources.uidA = mitab_interaction_identifiers.uidA
  and mitab_sources.uidB = mitab_interaction_identifiers.uidB
  and mitab_sources.rigid = mitab_interaction_identifiers.rigid
where name = 'bind' and uid like 'bind:%';

Find BIND identifiers for common interactions where those interactions are known by the same identifier:

create table export_common_bind as
select distinct i5_mitab_interaction_identifiers.uid
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 i5_mitab_interaction_identifiers
  on i5_mitab_sources.uidA = i5_mitab_interaction_identifiers.uidA
  and i5_mitab_sources.uidB = i5_mitab_interaction_identifiers.uidB
  and i5_mitab_sources.rigid = i5_mitab_interaction_identifiers.rigid
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
inner join mitab_interaction_identifiers
  on mitab_sources.uidA = mitab_interaction_identifiers.uidA
  and mitab_sources.uidB = mitab_interaction_identifiers.uidB
  and mitab_sources.rigid = mitab_interaction_identifiers.rigid
  and i5_mitab_interaction_identifiers.uid = mitab_interaction_identifiers.uid
where mitab_sources.name = 'bind'
  and i5_mitab_interaction_identifiers.uid like 'bind:%';

Find BIND identifiers for interactions only in iRefIndex 5.1:

create table export_i5_bind as
select distinct i5_mitab_interaction_identifiers.uid
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 i5_mitab_interaction_identifiers
  on i5_mitab_sources.uidA = i5_mitab_interaction_identifiers.uidA
  and i5_mitab_sources.uidB = i5_mitab_interaction_identifiers.uidB
  and i5_mitab_sources.rigid = i5_mitab_interaction_identifiers.rigid
where i5_mitab_sources.name = 'bind'
  and i5_mitab_interaction_identifiers.uid like '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
    inner join mitab_interaction_identifiers
      on mitab_sources.uidA = mitab_interaction_identifiers.uidA
      and mitab_sources.uidB = mitab_interaction_identifiers.uidB
      and mitab_sources.rigid = mitab_interaction_identifiers.rigid
    where mitab_sources.name = 'bind'
    );

Find BIND identifiers for interactions only in BIND PSI-XML:

create table export_xml_bind as
select distinct mitab_interaction_identifiers.uid
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
inner join mitab_interaction_identifiers
  on mitab_sources.uidA = mitab_interaction_identifiers.uidA
  and mitab_sources.uidB = mitab_interaction_identifiers.uidB
  and mitab_sources.rigid = mitab_interaction_identifiers.rigid
where mitab_sources.name = 'bind'
  and mitab_interaction_identifiers.uid like '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
    inner join i5_mitab_interaction_identifiers
      on i5_mitab_sources.uidA = i5_mitab_interaction_identifiers.uidA
      and i5_mitab_sources.uidB = i5_mitab_interaction_identifiers.uidB
      and i5_mitab_sources.rigid = i5_mitab_interaction_identifiers.rigid
    where i5_mitab_sources.name = 'bind'
    );

Observations

There are 183614 BIND identifiers in the iRefIndex 5.1 release, 188690 in the BIND PSI-XML dataset.

The following distribution of BIND identifiers for interactions was observed (with each cell representing an intersection of the listed sets):

	Common	iRefIndex 5.1 only	BIND PSI-XML only
Common	(8639)
iRefIndex 5.1 only	76	(1613)
BIND PSI-XML only	0	1088	(3248)

In other words:

• There are 8639 common BIND identifiers in total.
• There are 1613 BIND identifiers appearing for interactions only in iRefIndex 5.1.
• There are 3248 BIND identifiers appearing for interactions only in the BIND PSI-XML dataset.
• Although the intersection between "iRefIndex 5.1 only" and "BIND PSI-XML only" should yield zero interactions, since by definition an interaction in one of these sets should not appear in another, 1088 BIND identifiers appear in both.
• Of the interactions that should only be referenced by iRefIndex 5.1, 76 BIND identifiers also refer to interactions in both iRefIndex 5.1 and the BIND PSI-XML dataset.
• Of the interactions that should only be referenced by the BIND PSI-XML dataset, 0 BIND identifiers also refer to interactions in both iRefIndex 5.1 and the BIND PSI-XML dataset. This is as expected.

In fact, some BIND identifiers appear to refer to more than one RIG identifier. For example:

• BIND identifier 100771 refers to 5TlbBV7VB0MFa/R1cmyeByxSFjw in only the iRefIndex 5.1 release, but also to pXZtvCDYsluwWrmdXf5FJmQ0y54 in that release and in the BIND PSI-XML dataset.
• BIND identifier 100321 refers to VwWuNAmhR/FDx6FtF6FacwAmzr0 in only the iRefIndex 5.1 release, but to Dr5ri7vTj02leEUMKr35jj1fP/c in only the BIND PSI-XML dataset.

See bug #133 for further details and discussion.

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.