[BioPython] UniGene parser

[Sagar Damle]

Hi cayte,
  the unigeneparser looks simple in design and works just right.  I have a couple of suggestions, though they're not all that interesting and are probably more my personal preference.

  - make a list out of the cDNA sources (['heart', 'lung', 'placenta'])
  - under table 'selected model' separate column 2 & 3 values into a list (in the printout, I can't tell if you're already doing this)
    In general, I guess, make rows with more than 1 value column, a list of values in the tabledictionary.
  - change 'see also' tablename to something more intuitive ('links'?)
 
sagar



On Tue, 16 Jul 2002 18:53:17 -0700
"Cayte" <katel@worldpath.net> wrote:

>   I just did some experiments with LocusLink files and when I strip out the
> html tags very little information is left.
> For this reason I think I should use the same approach as UniGene.  Have you
> checked out Record in
> Unigene? Is this what you want?
> 
>                                                        Cayte
> 

key EST SEQUENCES
        key is AA101851
            cDNA clone IMAGE:489768 Uterus 5' read 2.0 kb
        key is AA102060
            cDNA clone IMAGE:489768 Uterus 3' read 2.0 kb
        key is AA938640
            cDNA clone IMAGE:1574076 Kidney 3' read 1.8 kb
        key is R82654
            cDNA clone IMAGE:149308 Placenta 3' read 2.4 kb
        key is R82703
            cDNA clone IMAGE:149308 Placenta 5' read 2.4 kb
key EXPRESSION INFORMATION
        key is SAGE
            Gene to Tag mapping
        key is cDNA sources
            Brain, CNS, Colon, Germ Cell, Heart, Kidney, Lung, Muscle, Ovary, Pancreas, Parathyroid, Placenta, Pooled, Prostate, Stomach, Testis, Tonsil, Uterus, Whole embryo, cervix, colon, head_neck, lung, muscle, nervous_normal, ovary, pancreas, uterus
key MAPPING INFORMATION
        key is Chromosome
            3
        key is Cytogenetic Position
            3q13.3
        key is UniSTS entries
                1765
                A004F36
                stSG42984
key SEE ALSO
        key is HomoloGene
            Hs.13225
        key is LocusLink
            8702
        key is OMIM
            604015
key SELECTED MODEL
        key is C. elegans
            PID:g3880435- similar to n-acetyllactosamine synthase39 % / 217 aa
        key is D. melanogaster
            PID:g4972702- unknown41 % / 277 aa
        key is H. sapiens
            PID:g3132900- beta-1,4-galactosyltransferase100 % / 343 aa
        key is M. musculus
            PID:g3869131- beta-1,4-galactosyltransferase II51 % / 262 aa
        key is R. norvegicus
            PID:g3258653- UDP-Gal:glucosylceramide beta-1,4-galactosyltransferase43 % / 262 aa
key UniGene Cluster
        Hs.13225
key mRNA/GENE SEQUENCES
        key is AB024436
            Homo sapiens mRNA for beta-1,4-galactosyltransferase IV, complete cds
        key is AF022367
            Homo sapiens beta-1,4-galactosyltransferase mRNA, complete cds
        key is AF038662
            Homo sapiens chromosome 3q13 beta-1,4-galactosyltransferase mRNA, complete cds
        key is AK001006
            Homo sapiens cDNA FLJ10144 fis, clone HEMBA1003286, highly similar to Homo sapiens mRNA for beta-1,4-galactosyltransferase IV