[Gusdev-gusdev] Re: KEGG data (fwd)

[Trish W. <wh...@pc...>]

Forwarding some mail regarding KEGG data that did not make it to the list.

Trish

---------- Forwarded message ----------
Hi Thomas,

Attached is the basic flow of data entry in order to represent the 
reaction below. Let me know if/what questions you may have on this. 

Sincerely,
Trish

========
Attachment

Mapping KEGG Data into GUS

Case Study:
Map the pathway C00103 <=> C00668 (alpha-D-glucose 1-phosphate =
alpha-D-glucose 6-phosphate) which involves the enzyme 5.4.2.2
(phosphoglucomutase)

Information Needed:
-GenBank Accession for the Enzymes in the Pathway of interest
In order to be able to point to a row in DoTs.ExternalAASequence, the 
following
tables need to be loaded DoTS.ExternalNASequence <-na_sequence_id->
DoTS.RNAFeature <-na_feature_id-> DoTS.TranslatedAAFeature, this can then 
be
joined to DoTS.ExternalAASequence using aa_sequence_id

-Table that holds information on small molecules

Tables Involved:
Dots::Pathway
DoTS::PathwayInteraction
DoTS::Interaction
DoTS::InteractionType
DoTS::EffectorActionType
DoTS::RowSet
DoTS::RowSetMember
SRes::ReviewStatus

Flow of Data Entry:
NOTE:  this pathway will need to be represented as 2 interactions
NOTE:  Need to find/create tables to store compounds, look in EcoCyc 
and/or
BioComp, Adam Arkin, cheminformatics info

-insert into dots.pathway (name, description) values ('RN00010' , 
'Glycolysis /
Gluconeogenesis');
RESULT: $pathway_id

-insert into dots.interactiontype (name, description) values ('term from
controlled vocabulary' , 'definition of term');
RESULT: $interaction_id

-insert into dots.effectoractiontype (name, description,
external_database_release_id, source_id) values ('phosphorylation' , 
'residue
modification' , 'ADD ext_db_rel_id for PSI Ontology' , 'MI:0170');
RESULT: $effector_action_type_id

For Interaction 1 and 2
-insert into dots.rowset ();
RESULT: $row_set_id1
-insert into dots.rowsetmember (row_set_id, table_id, row_id) values
('$row_set_id1', 'table_id of DoTS.ExternalAASequence' , 'PK of row of
interest'); --> this represents the enzyme (effector)

For Interaction 1
-insert into dots.rowset ();
RESULT: $row_set_id2
-insert into dots.rowsetmember (row_set_id, table_id, row_id) values
('$row_set_id2',  'table_id for table with small molecules/compounds' ,
'Primary key of row of interest in the table with small 
molecules/compounds');
--> this represents the molecule (target)

For interaction 2
-insert into dots.rowset ();
RESULT: $row_set_id3
-insert into dots.rowsetmember (row_set_id, table_id, row_id) values
('$row_set_id' , 'table_id for table with small molecules/compounds' , 
'Primary
key of row of interest in the table with small molecules/compounds'); --> 
this
represents the molecule (target)

-insert into dots.interaction (interaction_type_id, 
effector_action_type_id,
effector_row_set_id, target_row_set_id, has_direction, direction_is_known)
values ($interaction_type_id, $effector_action_type_id, $row_set_id1,
$row_set_id2, 'integer to represent direction', '1');
RESULT: $interaction_id

-insert into dots.pathwayinteraction (pathway_id, interaction_id) values
($pathway_id, $interaction_id);
========

> To understand the talbe, maybe it would be easier to do an example:
> So how would you save in the table this reaction, of Pathway Map0010 
> (http://www.genome.ad.jp/dbget-bin/get_pathway?org_name=rn&mapno=00010):
> 
> D-Glucose 1-phosphate (C00103) <--- reaction alpha-D-Glucose 1-phosphate 1,6-phosphomutase (envolving enzyme 5.4.2.2 <http://www.genome.ad.jp/dbget-bin/www_bget?enzyme+5.4.2.2>         5.4.2.5 <http://www.genome.ad.jp/dbget-bin/www_bget?enzyme+5.4.2.5>
> 
> ) --->  C00668 
> <http://www.genome.ad.jp/dbget-bin/get_linkdb?compound+C00668>  
> alpha-D-Glucose 6-phosphate
> 
> Maybe this helps me to understand the table.
> 
> Thanks,
> Thomas