Lab Resources Bulk Load

  • add something here

Fields

AttachScores

This adds new scores to the ORFs.

  1. Make the Lab Bulk Load window active in the Board.
  2. On the Bulk Load menu click Attach Scores.
  3. In the folder list, locate and open the folder that contains the file.
  4. Click the file, and then click Load Scores File.

Note

  • The currently attached scores will be replaced with the new ones.
  • TODO: file format and an example

Attach DB References

This adds DB references to ORFs.

  1. Make the Lab Bulk Load window active in the Board.
  2. On the Bulk Load menu click Attach DB References.
  3. In the folder list, locate and open the folder that contains the file.
  4. Click the file, and then click Load DB References File.

Note

  • A Sesame Administrator needs to be contacted to remove or correct a DB reference already attached to an ORF.
  • No DB reference will be attached more than once to an ORF.
  • The CSV file containing the DB refrences consists of the header row followed by rows that contain comma separated data.
  • Example File
  • The header, and the column order must be exactly as in the Example File.
  • There should be no empty rows between the header and the data rows, nor among the data rows.
  • Column headers and definitions
    orf_id This is the unique Sesame ORF Id of the ORF record to which the DB references will be attached.
    The ORF Id is the catenation of the 'GO.' prefix and the unique ORF No, e.g. 'GO.13'.
    dbreferences External Database reference strings.
    If there is more than one, separate them by commas, and doublequote.
    Every dbreference must be of the form:
    db_name:db_id
    or
    db_name:db_id:db_date
    Predefined db_name strings:
    BMRB, CAS, CCRIS, CHEBI, EINECS, FEMA, GenBank, HSDB, KEGG, MAtDB, MMCD, NSC, OMIM, PDB, PIR, PUBCHEM CID, PUBCHEM SID, SWISS-PROT, TIGR, TrEMBL
    Example for a field consisting of 3 external database references:
    "GenBank:xxx,OMIM:nnn,SWISS-PROT:zzz:2008-04-01"
    Each and every db_name is up to 16 characters.
    Each and every db_id is up to 24 characters.
    If present, db_date must be of the form yyyy-mm-dd.
  • For a DB Reference to be shown in a browser, the db_name has to be defined in System Resources URL Base.
  • The Attach DB References menu item is enabled for the Lab Master and for Lab Members with a Can Do privilege.
  • The Can Do Resource value is LAB_RSC_ATTACHDBREFERENCES.

Verify DB References

This checks if the format of the file and the columns is correct.

  1. Make the Lab Bulk Load window active in the Board.
  2. On the Bulk Load menu click Verify DB References.
  3. In the folder list, locate and open the folder that contains the file.
  4. Click the file, and then click Verify DB References File.

Note

  • For the DB References file format and column definitions see the notes in Attach DB References.
  • The Verify DB References menu item is enabled for every Lab Member.
  • The DB References will be not added to the ORFs.

Attach ORF Modifications

This adds ORF modification descriptions to ORFs.

  1. Make the Lab Bulk Load window active in the Board.
  2. On the Bulk Load menu click Attach ORF Modifications.
  3. In the folder list, locate and open the folder that contains the file.
  4. Click the file, and then click Load ORF Modifications File.

Note

  • A Sesame Administrator needs to be contacted to remove or correct an ORF modification already attached to an ORF.
  • No ORF modification will be attached more than once to an ORF.
  • The CSV file containing the ORF modifications consists of the header row followed by rows that contain comma separated data.
  • Example File
  • The header, and the column order must be exactly as in the Example File.
  • There should be no empty rows between the header and the data rows, nor among the data rows.
  • Column headers and definitions
    orf_id This is the unique Sesame ORF Id of the ORF record to which the DB references will be attached.
    The ORF Id is the catenation of the 'GO.' prefix and the unique ORF No, e.g. 'GO.13'.
    orfmodifications ORF modification descriptions from ORF Modification Lab Resource.
    If there is more than one, separate them by commas, and doublequote.
    Example for a field consisting of 2 ORF Modification strings:
    "orf modification 1,orf modification 2"
    Each and every ORF Modification string can be up to 100 characters.
  • The Attach ORF Modifications menu item is enabled for the Lab Master and for Lab Members with a Can Do privilege.
  • The Can Do Resource value is LAB_RSC_ATTACHORFMODIFICATIONS.

Verify ORF Modifications

This checks if the format of the file and the columns is correct, and checks if the ORF Modifications are from the ORF Modification Lab Resource.

  1. Make the Lab Bulk Load window active in the Board.
  2. On the Bulk Load menu click Verify ORF Modifications.
  3. In the folder list, locate and open the folder that contains the file.
  4. Click the file, and then click Verify ORF Modifications File.

Note

  • For the ORF Modifications file format and column definitions see the notes in Attach ORF Modifications.
  • The Verify ORF Modifications menu item is enabled for every Lab Member.
  • The ORF Modifications will be not added to the ORFs.

Load ORFs From CSV File

This adds ORFs to Sesame.

  1. Make the Lab Bulk Load window active in the Board.
  2. On the Bulk Load menu click Load ORFs from CSV File.
  3. In the folder list, locate and open the folder that contains the file.
  4. Click the file, and then click Load CSV File.

Note

  • The CSV file consists of the header row followed by rows that contain comma separated data.
  • Example File
  • The header, and the column order must be exactly as in the Example File.
  • Commas in the field values are allowed only in quoted fields, i.e. "this,that"
  • There should be no empty rows between the header and the data rows, nor among the data rows.
  • Column headers and definitions
    src_no The Src No Field from the System Resources Source Organism or Lab Resources Source Organism. If a particular Source Organism is not in the resource table, contact a Sesame Administrator to add it first.
    lab_id Lab specific Id.
    Up to 30 characters.
    chromosome Chromosome.
    Up to 8 characters.
    main_id This is the 'Main Id', but not the unique Sesame Id. The Unique Sesame Id is autogenerated during the upload.
    Up to 30 characters.
    gene_locus Gene Locus.
    Up to 16 characters.
    gene_locator Gene Locator.
    Up to 8 characters.
    prot_name Protein Name.
    Up to 300 characters.
    prot_category Protein Category.
    Choices:
    H - Hypothetical
    K - Known
    P - Putative
    U - Unknown
    1 character.
    pred_strclass Predicted Structure Class.
    Choices:
    A - All-Alpha
    B - All-Beta
    C - Alpha-Beta
    I - Irregular
    U - Unclassified
    D - Membrane All-Alpha
    E - Membrane All-Beta
    F - Membrane Alpha-Beta
    G - Membrane Irregular
    M - Membrane Unclassified
    1 character.
    struct_known Structure Known.
    Choices:
    Y - Yes
    Empty field if the structure is not known.
    Up to 1 character.
    paralogue_id Paralogue Id.
    Up to 100 characters.
    residuelength Amino Acid Sequence Length.
    The known value, or -1.
    It will be recalculated during the upload.
    gcodelength Nucleotide Sequence Length.
    The known value, or -1.
    It will be recalculated during the upload.
    aacode Amino Acid Sequence.
    If there is a gcode, it will be recalculated from it during the upload.
    Up to 8000 characters.
    nofintrons Number of Introns.
    The known value, or -1 if not known.
    sigpeplength Signal Peptide Length.
    The known value, or -1 if not known.
    molweight Molecular Weight. The known value, or -1.
    It will be recalculated during the upload.
    e280nm Molar Absorption Coefficient, or Molar Extinction Coefficient.
    The known value, or -1.
    It will be recalculated during the upload.
    pi Isoelectric Point.
    The known value, or -1.
    It will be recalculated during the upload.
    parent_no Parent Number.
    The unique Sesame ORF No or Database No of the parent ORF already in Sesame.
    0 if there is no parent.
    orf_type ORF Type.
    Choices:
    0 - Original ORF
    1 - Chunk
    2 - Splice
    3 - Mutant
    4 - Extension
    5 - RNA
    6 - DNA
    7 - Amino Acid Sequence Only
    8 - Fusion
    For up to date values, see System Resources ORF Type at the Sesame instance used.
    sourcedb_name Source Database Name.
    Up to 20 characters.
    sourcedb_version Source Database Version.
    Up to 20 characters.
    sourcedb_date Source Database Date.
    Date in format yyyy-mm-dd, or empty field.
    If empty field, the current date will be inserted durint the upload.
    noftd Number of Predicted Transmembrane Segments.
    -1 if not known.
    closesthomologue Closest Homologue.
    Up to 400 characters.
    coiledcoil Coiled Coil.
    Percentage, a decimal number between 0.0 and 100.0
    -1 if not known.
    gccontent G + C Content.
    Percentage, a decimal number between 0.0 and 100.0
    -1 if not known.
    lowcomplexity Low Complexity.
    Percentage, a decimal number between 0.0 and 100.0
    -1 if not known.
    position Position.
    Describes the start end end of the segmentsin the genome.
    Up to 2000 characters.
    manuallyedited Manually Edited.
    Choices:
    Y - Yes
    N - No
    1 character.
    gcode Nucleotide Sequence.
    Up to 24000 characters.
    pref Nucleotide Sequence Prefix.
    Up to 4000 characters.
    suf Nucleotide Sequence Suffix.
    Up to 4000 characters.
    targetscore Target Score.
    Up to 30 characters.
    pred_cleavsite Predicted Cleavage Site.
    Up to 30 characters.
    cluster_seed Cluster Seed.
    Up to 100 characters.
    pfamdomains PFAM Domains.
    Empty field if not known.
    If there is more than one, separate them by commas, and doublequote.
    Example for a field consisting of 2 PFAM strings:
    "PF02170 PAZ domain 8.4e-50,PF00270 DEAD/DEAH box helicase 2.3e-06"
    Each and every PFAM string can be up to 300 characters.
    dbreferences External Database reference strings.
    Empty field if none.
    If there is more than one, separate them by commas, and doublequote.
    Every dbreference must be of the form:
    db_name:db_id
    or
    db_name:db_id:db_date
    Predefined db_name strings:
    BMRB, CAS, CCRIS, CHEBI, EINECS, FEMA, GenBank, HSDB, KEGG, MAtDB, MMCD, NSC, OMIM, PDB, PIR, PUBCHEM CID, PUBCHEM SID, SWISS-PROT, TIGR, TrEMBL
    Example for a field consisting of 3 external database references:
    "GenBank:xxx,OMIM:nnn,SWISS-PROT:zzz:2008-04-01"
    Each and every db_name is up to 16 characters.
    Each and every db_id is up to 24 characters.
    If present, db_date must be of the form yyyy-mm-dd.
    orfmodifications ORF modification descriptions from ORF Modifications Lab Resource.
    Empty field if none.
    If there is more than one, separate them by commas, and doublequote.
    Example for a field consisting of 2 ORF Modification strings:
    "orf modification 1,orf modification 2"
    Each and every ORF Modification string can be up to 100 characters.
  • The Lab Bulk Load window will show the line number of the lines that have been loaded. Note, that Line 1 is the header line.
  • The Load ORFs From CSV File menu item is enabled for Sesame users with a Can Do privilege.
  • To give the Can Do privilege to user JoeSmith from lab QsLab, execute the following SQL statement:
    insert into candothis values ('JoeSmith', 'LAB_RSC_ORFLOAD', 'QsLab', 'labMember');
  • To revoke the Can Do privilege for this resource from user JoeSmith, execute the following SQL statement:
    delete from candothis where user_name='JoeSmith' and what='LAB_RSC_ORFLOAD' and ass_name='QsLab' and ass_type='labMember';

Verify ORFs From CSV File

This checks if the format of the file and the columns is correct.

  1. Make the Lab Bulk Load window active in the Board.
  2. On the Bulk Load menu click Verify ORFs from CSV File.
  3. In the folder list, locate and open the folder that contains the file.
  4. Click the file, and then click Load CSV File.

Note

  • For the ORF CSV file format and column definitions see the notes in Load ORFs From CSV File.
  • The Verify ORFs From CSV File menu item is enabled for every Lab Member.
  • The ORFs will be not uploaded..

Load SDF Data

This...

  1. Make the Lab Bulk Load window active in the Board.
  2. On the Bulk Load menu click Load SDF Data.

Note

CrystalFarm

This...

  1. Make the Lab Bulk Load window active in the Board.
  2. On the Bulk Load menu click CrystalFarm.

Note

General Comments

  • To open the Lab Bulk Load window in the Board, on the Options menu select Lab Resources then click Bulk Load.

See also

Copyright © 1999-2009 Zsolt Zolnai, and the University of Wisconsin - Madison