[BioSQL-l] bioentries in a sequence cluster

[Peter Müller]

Dear list,

I have a few questions, but maybe with a working example, I can derive the rest.

With perl-db I can fetch a Bio::Cluster Object wit this query:
(I found no documentation about c::subject and p::object ...)

$query->datacollections(
          ["Bio::PrimarySeqI c::subject",
          "Bio::PrimarySeqI p::object",
         "Bio::PrimarySeqI<=>Bio::ClusterI<=>Bio::Ontology::TermI"]);

$query->where(["p.accession_number = 'NM_000015'"]);

my $adp = $db->get_object_adaptor('Bio::Cluster');
my $qres = $adp->find_by_query($query);


That's great - but here I ask for a sequence accession-number.

Is it possible to aks for the Clone (IMAGE:4722596) or for an STS accession-number where the result is also a cluster object?
"give me the cluster(s) where in the sequence-line is a clone-entry with this number 'IMAGE:4722596' ....
"give me the cluster(s) where in the STS-line is an accession-number with this value 'PMC310725P3'...
PROTID and NID would be also interesting.

UniGene-snippet:
STS         ACC=PMC310725P3 UNISTS=272646
PROTSIM     ORG=10090; PROTGI=6754794; PROTID=NP_035004.1; PCT=76.55; ALN=288
SEQUENCE    ACC=BG569293.1; NID=g13576946; CLONE=IMAGE:4722596; END=5'; LID=6989; SEQTYPE=EST; TRACE=44157214

regards
pan




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