[Feedback] Site Feedback: annotation curation needs to be fixed

[feedback at gramene.org]

URL         : http://gramene.org/ftp-download

Subject     : Site Feedback: annotation curation needs to be fixed

Name        : Sunita Kumari

Email       : kumari at cshl.edu

Organization: CSHL

Comments    : 

Please see an example below. PO and GO annotations need to be corrected in db_xref. 

GO duplications:
                     /db_xref="GO:0005783"
                     /db_xref="GO:0005783"
                    /db_xref="GO:0006665"
                     /db_xref="GO:0006665"
                     /db_xref="GO:0016125"
                     /db_xref="GO:0016125"

PO errors: 
                     /db_xref="PO:PO:0004505"
                     /db_xref="PO:PO:0007131"
                     /db_xref="PO:PO:0025281"



Here is an Ensembl example:
     gene            complement(5928..8737)
                     /gene=AT1G01020
                     /locus_tag="ARV1"
                     /note="Arv1-like protein [Source:TAIR;Acc:AT1G01020]"
     mRNA            join(complement(8571..8737),complement(8417..8464),
                     complement(8236..8325),complement(7942..7987),
                     complement(7762..7835),complement(7564..7649),
                     complement(7384..7450),complement(7157..7232),
                     complement(6437..7069),complement(5928..6263))
                     /gene="AT1G01020"
                     /note="transcript_id=AT1G01020.1"
     CDS             join(complement(8571..8666),complement(8417..8464),
                     complement(8236..8325),complement(7942..7987),
                     complement(7762..7835),complement(7564..7649),
                     complement(7384..7450),complement(7157..7232),
                     complement(6915..7069))
                     /gene="AT1G01020"
                     /protein_id="AT1G01020.1"
                     /note="transcript_id=AT1G01020.1"
                     /db_xref="RefSeq_peptide:NP_171610"
                     /db_xref="RefSeq_mRNA:NM_099984"
                     /db_xref="Uniprot/SPTREMBL:Q5MK24"
                     /db_xref="TAIR_LOCUS_MODEL:AT1G01020.1"
                     /db_xref="EMBL:AK228414"
                     /db_xref="EMBL:AY758070"
                     /db_xref="EMBL:CP002684"
                     /db_xref="GO:0005783"
                     /db_xref="GO:0005783"
                     /db_xref="GO:0005794"
                     /db_xref="GO:0006665"
                     /db_xref="GO:0006665"
                     /db_xref="GO:0016125"
                     /db_xref="GO:0016125"
                     /db_xref="GO:0032366"
                     /db_xref="GO:0032541"
                     /db_xref="GO:0097036"
                     /db_xref="protein_id:AAV92715"
                     /db_xref="protein_id:AEE27217"
                     /db_xref="protein_id:BAF00348"
                     /db_xref="TAIR_TRANSLATION:AT1G01020"
                     /db_xref="PO:PO:0004505"
                     /db_xref="PO:PO:0007131"
                     /db_xref="PO:PO:0025281"
                     /db_xref="UniParc:UPI000049B80B"
                     /translation="MAASEHRCVGCGFRVKSLFIQYSPGNIRLMKCGNCKEVADEYIE
                     CERMIIFIDLILHRPKVYRHVLYNAINPATVNIQHLLWKLVFAYLLLDCYRSLLLRKS
                     DEESSFSDSPVLLSIKVLIGVLSANAAFIISFAIATKGLLNEVSRRREIMLGIFISSY
                     FKIFLLAMLVWEFPMSVIFFVDILLLTSNSMALKVMTESTMTRCIAVCLIAHLIRFLV
                     GQIFEPTIFLIQIGSLLQYMSYFFRIV"
     mRNA            join(complement(8571..8737),complement(8417..8464),
                     complement(8236..8325),complement(7942..7987),
                     complement(7762..7835),complement(7564..7649),
                     complement(7157..7450),complement(6790..7069))
                     /gene="AT1G01020"
                     /note="transcript_id=AT1G01020.2"
     CDS             join(complement(8571..8666),complement(8417..8464),
                     complement(8236..8325),complement(7942..7987),
                     complement(7762..7835),complement(7564..7649),
                     complement(7315..7450))
                     /gene="AT1G01020"
                     /protein_id="AT1G01020.2"
                     /note="transcript_id=AT1G01020.2"
                     /db_xref="RefSeq_peptide:NP_001030923"
                     /db_xref="RefSeq_mRNA:NM_001035846"
                     /db_xref="Uniprot/SPTREMBL:F4HQG4"
                     /db_xref="TAIR_LOCUS_MODEL:AT1G01020.2"
                     /db_xref="EMBL:CP002684"
                     /db_xref="protein_id:AEE27218"
                     /db_xref="TAIR_TRANSLATION:AT1G01020"
                     /db_xref="PO:PO:0004505"
                     /db_xref="PO:PO:0007131"
                     /db_xref="PO:PO:0025281"
                     /db_xref="UniParc:UPI00005DBF0C"
                     /translation="MAASEHRCVGCGFRVKSLFIQYSPGNIRLMKCGNCKEVADEYIE
                     CERMIIFIDLILHRPKVYRHVLYNAINPATVNIQHLLWKLVFAYLLLDCYRSLLLRKS
                     DEESSFSDSPVLLSIKVLIGVLSANAAFIISFAIATKGLLNEVSRRREIMLGIFISSY
                     FKIFLLAMLVCCSFTSHLIPNIEVPNFLSIP"


Sunita


http://www.warelab.org/bugs/view.php?id=5306