Re: [Gusdev-gusdev] unique sequence designator for DoTS.NASequence

[Bindu G. <bi...@sa...>]

Terry -

At 23:17 -0500 7/20/03, Terry Clark wrote:
>Hi Bindu and others, 
>You might have seen that I made a few minor
>changes to
>    GUS::Common::Plugin::LoadGeneFeaturesFromXML::makeChromosome()
>to get the TIGR Arabidopsis genome uploaded into GUS working
>because the sequence identification mapping is not yet worked out.
>I have some questions and comments about this.
>
>In the plugin at makeChromosome() there is a query performed
>to determine whether the submitted sequence is in the db.
>The approach that is in place uses a query selecting entries
>based on attributes values for:
>    i) taxonomy, ii) external_release_id, and iii) source_id
>There is some code commented out here, since the plugin
>is under construction.

You are right about the fact that
(taxon_id, external_database_release_id, source_id) is being used
to attempt retrieval of the sequence.

   # NOTE: for falciparum XML, map_asmbl_id_to_source_id method was used to set
   #       the source_id appropriately.
   $enaSeq{source_id} = $self->map_asmbl_id_to_source_id($T);

... i.e. picking source_id from TIGR XML


Code commented out in the plugin, before attempting retrieval
of the externalNASequence, is :

   # NOTE: for P_yoelii, source_id is of the form: chrPyl_(\d\d\d\d\d)
   #       so, source_id needs to be cushioned with 0s (zeroes)
   #my $tmpStr = $T->{ASSEMBLY}->{ASMBL_ID}->{content};
   #while (length ($tmpStr) < 5) { $tmpStr = '0'.$tmpStr; }
   #$enaSeq{source_id} = 'chrPyl_' . $tmpStr;

The comment is *not* because plugin is still being worked on. It
exists as the source_id is being constructed from such a line in
the P_yoelii XML file:

<ASMBL_ID CLONE_NAME = "MALPY00111">111</ASMBL_ID>

source_id here is chrPyl_00111 in GUS, and so needed the different
(than the P falciparum XML files) mechanism for the source_id


>It's not clear to me that the intent of source_id is
>to uniquely identify the sequence. Is that so?

yes, that is so, along with taxon_id and external_database_release_id.

>Presently, source_id is constructed from with the hardwiring
>in the mapping         vvvv that we're working on.
>       source_id = ASMBL_ID_2_stringMap + ASMBL_ID
>The source_id above is a unique name by virtue of ASMBL_ID.
>
>On the other hand, NAME is an attractive self-documenting GUS
>attribute that tempts me to use it for the query checking for novelty.
>In the plugin, NAME was/is set to CLONE_NAME, which seems fine,
>although with the caveat for TIGR, this is labeled as for their
>internal use.
>
>In the TIGR XML, the CLONE_NAME and ASMBL_ID are two alternative candidates
>for uniquely naming a sequence. TIGR documents CLONE_NAME for internal
>use and ASMBL_ID for external use in uniquely identifying a sequence.
>
>I punted for now by adding the condition to the query
>    $ena_gus->setName($T->{ASSEMBLY}->{HEADER}->{CLONE_NAME})
>i.e., the attributes
>    i) taxonomy, ii) external_release_id, and iii) CLONE_NAME
>
>What do you think?

Perhaps this will work well. I have only looked at XML files of
falciparum and yoelii so far, and that too, only 1 revision of
these. So, not much experience with all this.

Else, we should think of a strategy (a method within the plugin)
to modify source_id after collecting field contents of some XML
tag/attribute, and having specified some choice parameters. INHO
this doesn't sound like a good way to go for various reasons.


Bindu



>Terry
>
>
>
>
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