Re: [GUSDEV] how to handle relationships between external database identifiers and ec numbers

[Steve F. <sfi...@pc...>]

Jian-

this seems reasonable to me.

steve

Jian Lu wrote:

> Hi Folks,
>
> We have such a situation that when running our annotation pipeline, we 
> need to know the relationships between external database identifiers 
> and EC numbers. Here is an example of TIGRAFAM info data: TIGR02496.INFO
> ID  NrdJ
> AC  TIGR02496
> DE  ribonucleoside diphosphate reductase, B12-dependent
> AU  Selengut J
> TC  855.00 855.00
> NC  120.00 120.00
> AL  clustalw
> IT  equivalog
> EN  ribonucleoside diphosphate reductase, B12-dependent
> GS  nrdJ
> EC  1.17.4.1
> TP  TIGRFAMs
>
> We have EC numbers loaded into SRes.EnzymeClass and TIGRFAM ids into 
> SRes.ExternalDatabaseEntry, but we couldn't find a place within GUS 
> schema to store the relationship of them. There is a table 
> DoTS.AASequenceEnzymeClass that could be linked to EC numbers, but it 
> requires aa_sequence_id which is not what we need. So we created a 
> table called DoTS.ECAssociation to store any id with relation to EC 
> numbers. This is very similar to gene ontology association 
> DoTS.GOAssociation. Any comment?
>
> create table DoTS.ECAssociation (
>    ec_association_id        number(10) not null,
>    table_id                number(10) not null,
>    row_id                    number(10) not null,
>    enzyme_class_id            number(12) not null,
>    review_status_id        number(12),
>    ec_association_date        date,
>    modification_date    date        not null,
>    user_read        number(1)    not null,
>    user_write        number(1)    not null,
>    group_read        number(1)    not null,
>    group_write        number(1)    not null,
>    other_read        number(1)    not null,
>    other_write        number(1)    not null,
>    row_user_id        number(12)    not null,
>    row_group_id        number(4)    not null,
>    row_project_id        number(4)    not null,
>    row_alg_invocation_id    number(12)    not null
> );
>
>
>
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