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

[Thomas O. <ot...@fi...>]

Trish-

I thought another time over the stuff below.

Like I wrote before, I do not know how to enter the datasets, if there 
are involved more than two compounds in the reaction.

Apart of this, I think the classification-table (class) I send last week 
fit good with his schema. It will provide more information about the 
reaction, the compounds and the enzyme derived from kegg.

So just tell me how to solve the problem above, and I try to write a 
parse with the ga.

Cheers,
Thomas

Trish Whetzel wrote:

>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
>>    
>>
> 
>
>
>
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