proof of concept

Ok, say I want the target(s) involved with compound 5555. You can follow
along at home by getting the files compounds.n3 activities.n3
assay2target.n3 target_dictionary.n3 from pele:/tmp/masak-can-haz-n3-files/.
Keep in mind that activities.n3 isn't complete.

$ grep -B4 MOLREGNO activities.n3 | grep -B4 'MOLREGNO         "5555"'
<star:activities/207697> a staro:ACTIVITIES;
    staro:ACTIVITY_ID      "1038792";
    staro:ASSAY_ID         "207697";
    staro:DOC_ID           "15844";
    staro:MOLREGNO         "5555";
--
<star:activities/204029> a staro:ACTIVITIES;
    staro:ACTIVITY_ID      "1038786";
    staro:ASSAY_ID         "204029";
    staro:DOC_ID           "15844";
    staro:MOLREGNO         "5555";

$ grep -A1 'staro:ASSAY_ID          "207697";' assay2target.n3 

$ grep -A1 'staro:ASSAY_ID          "204029";' assay2target.n3 
    staro:ASSAY_ID          "204029";
    staro:TID               "50185";

$ grep -B1 -A13 'staro:TID               "50185";' target_dictionary.n3
<star:target_dictionary/50185> a staro:TARGET_DICTIONARY;
    staro:TID               "50185";
    staro:TARGET_TYPE       "ORGANISM";
    staro:DB_SOURCE         "";
    staro:DESCRIPTION       "";
    staro:GENE_NAMES        "";
    staro:PREF_NAME         "Staphylococcus aureus";
    staro:SYNONYMS          "";
    staro:KEYWORDS          "";
    staro:PROTEIN_MD5SUM    "";
    staro:TAX_ID            "1280";
    staro:IN_DRUGSTORE      "0";
    staro:IN_STARLITE       "1";
    staro:PROTEIN_ACCESSION "";
    staro:PROTEIN_SEQUENCE  "".

I'll now turn this into a Perl script that does all this automatically.

Update: And here's that script:

$ ./find-targets 5555
<star:target_dictionary/50185> a staro:TARGET_DICTIONARY;
    staro:TID               "50185";
    staro:TARGET_TYPE       "ORGANISM";
    staro:DB_SOURCE         "";
    staro:DESCRIPTION       "";
    staro:GENE_NAMES        "";
    staro:PREF_NAME         "Staphylococcus aureus";
    staro:SYNONYMS          "";
    staro:KEYWORDS          "";
    staro:PROTEIN_MD5SUM    "";
    staro:TAX_ID            "1280";
    staro:IN_DRUGSTORE      "0";
    staro:IN_STARLITE       "1";
    staro:PROTEIN_ACCESSION "";
    staro:PROTEIN_SEQUENCE  "".
$ cat find-targets 
#!/usr/bin/perl -w
use strict;

die "Usage: find-targets <target-num>\n"
    if @ARGV != 1;

my $molregno = shift @ARGV;

my $activities = `grep -B4 MOLREGNO activities.n3 | grep -B4 'MOLREGNO         "$molregno"'`;

my @assay_ids;
while ($activities =~ /ASSAY_ID\s+"(\d+)"/g) {
    push @assay_ids, $1;
}

my @targets;
for my $assay_id (@assay_ids) {
    my $targets = `grep -A1 'ASSAY_ID          "$assay_id"' assay2target.n3`;
    while ($targets =~ /TID\s+"(\d+)"/g) {
        push @targets, $1;
    }
}

for my $target (@targets) {
    system("grep -B1 -A13 'staro:TID               \"$target\";' target_dictionary.n3");
}

---

My work here is done. Hope it can be of some use. Checking out for the day.