[Biojava-l] RefSeq bioJava parser problem
Cox, Greg
gcox@netgenics.com
Tue, 14 May 2002 15:34:15 -0400
Unfortunately, not. This is probably the weakest point in BioJava's parsing
right now.
As you may have noticed, there's a more serious problem with the reference
information. If a reference doesn't contain a field that others do, nothing
is added under that key, causing them to get out of sync. For example:
REFERENCE
TITLE foo
TITLE bar
AUTHOR wanner
When this gets turned into a biojava sequence, TITLE has [foo, bar] and
AUTHOR has [wanner] but there's no way to tell which one wanner goes with.
Good luck
Greg
> -----Original Message-----
> From: wanner.de@pg.com [mailto:wanner.de@pg.com]
> Sent: Tuesday, May 14, 2002 11:41 AM
> To: biojava-l@biojava.org
> Subject: [Biojava-l] RefSeq bioJava parser problem
>
>
> Hi,
>
> Appreciate the responses to the refSeq question. We've been
> able to put togther
> a reliable parser using the example in TestRefSeqPrt.
>
> Have an additional question now. Are there any utility
> methods within bioJava
> that can be used to handle parsed values that are returned by
> bioJava in list
> form.
>
> For example the following value was returned from bioJava for
> a sequence
> annotation with key MEDLINE:
>
> [98127055, 99357812]
>
>
> Another example is the value that was returned from bioJava
> for a feature annotation with key db_xref:
>
> [LocusID:946, MIM:604405]
>
> bioJava does good work in accumulating the information
> together and placing it under a specific annotation, does
> anyone know if there are method to extract listMembers or
> parameter/value pairs already available in bioJava?
>
> thx,
> Dave
>
> > > LOCUS NP_000221 167 aa
> > linear PRI 29-JAN-2002
> > > DEFINITION leptin precursor; leptin (murine obesity
> > homolog); obesity; obesity
> > > (murine homolog, leptin) [Homo sapiens].
> > > ACCESSION NP_000221
> > > PID g4557715
> > > VERSION NP_000221.1 GI:4557715
> > > DBSOURCE REFSEQ: accession NM_000230.1
> > > KEYWORDS .
> > > SOURCE human.
> > > ORGANISM Homo sapiens
> > > Eukaryota; Metazoa; Chordata; Craniata;
> > Vertebrata; Euteleostomi;
> > > Mammalia; Eutheria; Primates; Catarrhini;
> > Hominidae; Homo.
> > > REFERENCE 1 (residues 1 to 167)
> > > AUTHORS Friedman JM, Leibel RL, Siegel DS, Walsh J
> and Bahary N.
> > > TITLE Molecular mapping of the mouse ob mutation
> > > JOURNAL Genomics 11 (4), 1054-1062 (1991)
> > > MEDLINE 92147101
> > > PUBMED 1686014
> > > REFERENCE 2 (residues 1 to 167)
> > > AUTHORS Zhang Y, Proenca R, Maffei M, Barone M, Leopold
> > L and Friedman JM.
> > > TITLE Positional cloning of the mouse obese gene and
> > its human homologue
> > > JOURNAL Nature 372 (6505), 425-432 (1994)
> > > MEDLINE 95075453
> > > PUBMED 7984236
> > > REMARK Erratum:[[published erratum appears in Nature 1995 Mar
> > > 30;374(6521):479]]
> > > REFERENCE 3 (residues 1 to 167)
> > > AUTHORS Masuzaki H, Ogawa Y, Isse N, Satoh N, Okazaki
> > T, Shigemoto M, Mori
> > > K, Tamura N, Hosoda K, Yoshimasa Y et al.
> > > TITLE Human obese gene expression. Adipocyte-specific
> > expression and
> > > regional differences in the adipose tissue
> > > JOURNAL Diabetes 44 (7), 855-858 (1995)
> > > MEDLINE 95309556
> > > PUBMED 7789654
> > > REFERENCE 4 (residues 1 to 167)
> > > AUTHORS Green ED, Maffei M, Braden VV, Proenca R,
> > DeSilva U, Zhang Y, Chua
> > > SC Jr, Leibel RL, Weissenbach J and Friedman JM.
> > > TITLE The human obese (OB) gene: RNA expression
> > pattern and mapping on
> > > the physical, cytogenetic, and genetic maps of
> > chromosome 7
> > > JOURNAL Genome Res. 5 (1), 5-12 (1995)
> > > MEDLINE 96352898
> > > PUBMED 8717050
> > > REFERENCE 5 (residues 1 to 167)
> > > AUTHORS Isse N, Ogawa Y, Tamura N, Masuzaki H, Mori K,
> > Okazaki T, Satoh N,
> > > Shigemoto M, Yoshimasa Y, Nishi S et al.
> > > TITLE Structural organization and chromosomal
> > assignment of the human
> > > obese gene
> > > JOURNAL J. Biol. Chem. 270 (46), 27728-27733 (1995)
> > > MEDLINE 96070903
> > > PUBMED 7499240
> > > REFERENCE 6 (residues 1 to 167)
> > > AUTHORS Gong,D.W., Bi,S., Pratley,R.E. and Weintraub,B.D.
> > > TITLE Genomic structure and promoter analysis of the
> > human obese gene
> > > JOURNAL J. Biol. Chem. 271 (8), 3971-3974 (1996)
> > > MEDLINE 96223958
> > > REFERENCE 7 (residues 1 to 167)
> > > AUTHORS Niki T, Mori H, Tamori Y, Kishimoto-Hashirmoto
> > M, Ueno H, Araki S,
> > > Masugi J, Sawant N, Majithia HR, Rais N et al.
> > > TITLE Human obese gene: molecular screening in
> > Japanese and Asian Indian
> > > NIDDM patients associated with obesity
> > > JOURNAL Diabetes 45 (5), 675-678 (1996)
> > > MEDLINE 96198511
> > > PUBMED 8621021
> > > REFERENCE 8 (residues 1 to 167)
> > > AUTHORS Comuzzie,A.G., Hixson,J.E., Almasy,L.,
> > Mitchell,B.D., Mahaney,M.C.,
> > > Dyer,T.D., Stern,M.P., MacCluer,J.W. and Blangero,J.
> > > TITLE A major quantitative trait locus determining
> > serum leptin levels
> > > and fat mass is located on human chromosome 2
> > > JOURNAL Nat. Genet. 15 (3), 273-276 (1997)
> > > MEDLINE 97207647
> > > PUBMED 9054940
> > > REFERENCE 9 (residues 1 to 167)
> > > AUTHORS Clement,K., Vaisse,C., Lahlou,N., Cabrol,S.,
> Pelloux,V.,
> > > Cassuto,D., Gourmelen,M., Dina,C., Chambaz,J.,
> > Lacorte,J.M.,
> > > Basdevant,A., Bougneres,P., Lebouc,Y.,
> > Froguel,P. and Guy-Grand,B.
> > > TITLE A mutation in the human leptin receptor gene
> > causes obesity and
> > > pituitary dysfunction
> > > JOURNAL Nature 392 (6674), 398-401 (1998)
> > > MEDLINE 98196670
> > > PUBMED 9537324
> > > REFERENCE 10 (residues 1 to 167)
> > > AUTHORS Friedman,J.M. and Halaas,J.L.
> > > TITLE Leptin and the regulation of body weight in mammals
> > > JOURNAL Nature 395 (6704), 763-770 (1998)
> > > MEDLINE 99010835
> > > COMMENT REVIEWED REFSEQ: This record has been curated
> > by NCBI staff. The
> > > reference sequence was derived from U43653.1.
> > > Summary: This gene is similar to the mouse
> > obesity gene (ob). The
> > > protein encoded by this gene is secreted by
> > white adipocytes. In
> > > the mouse study, mutations in this gene are
> > linked to severe and
> > > morbid obesity.
> > > FEATURES Location/Qualifiers
> > > source 1..167
> > > /organism="Homo sapiens"
> > > /db_xref="taxon:9606"
> > > /chromosome="7"
> > > /map="7q31.3"
> > > Protein 1..167
> > > /product="leptin precursor"
> > > /note="leptin (murine obesity
> > homolog); obesity (murine
> > > homolog, leptin)"
> > > sig_peptide 1..21
> > > Region 22..167
> > > /region_name="Leptin"
> > > /note="Leptin"
> > > /db_xref="CDD:pfam02024"
> > > mat_peptide 22..167
> > > /product="leptin"
> > > CDS 1..167
> > > /gene="LEP"
> > > /coded_by="NM_000230.1:57..560"
> > > /db_xref="LocusID:3952"
> > > /db_xref="MIM:164160"
> > > ORIGIN
> > > 1 mhwgtlcgfl wlwpylfyvq avpiqkvqdd tktliktivt
> > rindishtqs vsskqkvtgl
> > > 61 dfipglhpil tlskmdqtla vyqqiltsmp srnviqisnd
> > lenlrdllhv lafskschlp
> > > 121 wasgletlds lggvleasgy stevvalsrl qgslqdmlwq ldlspgc
> > > //
> > >
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> > > http://biojava.org/mailman/listinfo/biojava-l
> > >
> >
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