Difference between revisions of "WormBase Model:Clone"

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Data to be removed:
 
Data to be removed:
 
  17 Created via Positive_gene (All cloned genes, so can probably go)
 
  17 Created via Positive_gene (All cloned genes, so can probably go)
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 +
== AddGene vector model extensions ==
 +
 +
<pre>
 +
?Clone  Evidence #Evidence
 +
        Species UNIQUE ?Species
 +
        Reference ?Paper XREF Clone
 +
        Produced_by Person ?Person
 +
                    Author ?Author
 +
        Sequence    ?Sequence XREF Clone
 +
        Remark  General_remark ?Text
 +
                Y_remark ?Text
 +
                PCR_remark ?Text
 +
        Position  Map ?Map XREF Clone #Map_position
 +
                  pMap UNIQUE  ?Contig XREF Clone  UNIQUE Int UNIQUE Int
 +
                                                // pMap units are bands
 +
                  Clone_left_end ?Sequence      // filled by XREF
 +
                  Clone_right_end ?Sequence    // filled by XREF
 +
                  Pos_neg_data ?Pos_neg_data
 +
        Positive Positive_gene  ?Gene XREF Positive_clone
 +
                Positive_variation  ?Variation XREF Positive_clone ?Author
 +
                Inside_rearr    ?Rearrangement XREF Clone_inside ?Author
 +
                Hybridizes_to  ?Clone XREF Positive_probe ?Grid
 +
                Hybridizes_weak ?Clone XREF Pos_probe_weak ?Grid
 +
                Positive_probe  ?Clone XREF Hybridizes_to ?Grid
 +
                Pos_probe_weak  ?Clone XREF Hybridizes_weak ?Grid
 +
        Negative Negative_gene  ?Gene XREF Negative_clone
 +
                Negative_locus  ?Locus XREF Negative_clone ?Author
 +
                Outside_rearr  ?Rearrangement XREF Clone_outside ?Author
 +
                Negative_probe  ?Clone XREF Does_not_hybridize_to ?Grid
 +
                Does_not_hybridize_to ?Clone XREF Negative_probe ?Grid
 +
        In_strain ?Strain XREF Clone
 +
        Mutation ?Text
 +
        PCR_product ?PCR_product XREF Clone
 +
        Primer1 ?Text
 +
        Primer2 ?Text
 +
        Resistence_marker ?Text
 +
        Length  Seq_length UNIQUE Int                  // bp
 +
                Gel_length UNIQUE Float                // Kb
 +
                Insert UNIQUE Int
 +
                Backbone UNIQUE Int
 +
        Location ?Laboratory #Lab_Location
 +
        URL Text                          // to link to MRC_geneservice website ar2
 +
        Gridded ?Grid
 +
        Grid_data ?Grid_data
 +
        FingerPrint    Gel_Number UNIQUE Int
 +
                        Approximate_Match_to UNIQUE ?Clone XREF Canonical_for
 +
                        Exact_Match_to UNIQUE ?Clone XREF Canonical_for
 +
                        Funny_Match_to UNIQUE ?Clone XREF Canonical_for
 +
                        Canonical_for ?Clone UNIQUE Int UNIQUE Int
 +
                                // start and stop offsets from self start
 +
                        Bands  UNIQUE Int UNIQUE Int
 +
                        Gel ?Motif  #Lane              // Magic tag2 construct
 +
        Contig9 Chromosome UNIQUE ?Map
 +
                Vaxmap UNIQUE Float
 +
                In_Situ  UNIQUE Int UNIQUE Int // percent of physical chromosome
 +
                Cosmid_grid
 +
                Canon_for_cosmid
 +
                Flag    UNIQUE Int
 +
                Autopos
 +
        Expression_construct    Pattern ?Text  // archaic
 +
        cDNA_group Contains ?Clone XREF Contains Text
 +
                  Contained_in ?Clone XREF Contained_in
 +
                  Best_match UNIQUE ?Text
 +
        Expr_pattern ?Expr_pattern XREF Clone
 +
        Sequence_status Shotgun UNIQUE DateType
 +
                        Finished UNIQUE DateType
 +
                        Accession_number UNIQUE ?Text
 +
        DB_info  Database ?Database ?Database_field ?Accession_number XREF Clone // added [031120 krb]
 +
        Type UNIQUE Cosmid            // 000824 Lincoln's additions to segregate clones
 +
                    Fosmid            // added 06/12/01 by krb for dl
 +
                    YAC
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                    cDNA
 +
                    Plasmid
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                    Other Text        // added to catch all clones 011017 dl
 +
        Transgene ?Transgene XREF Clone
 +
        Vector_type ?Text
 +
        Derived_from ?Clone XREF Parent_of
 +
        Parent_of ?Clone XREF  Derived_from
 +
        Ligation ?Text
 +
</pre>

Revision as of 16:51, 18 March 2014

WormBase Models

Curator Comments/Description

Model

////////////////////////////////////////////////////////////////////////////////
// ?Clone class
////////////////////////////////////////////////////////////////////////////////

?Clone  Evidence #Evidence
        Remark  General_remark ?Text 
                Y_remark ?Text
                PCR_remark ?Text
        Position  Map ?Map XREF Clone #Map_position
                  pMap UNIQUE  ?Contig XREF Clone  UNIQUE Int UNIQUE Int 
                                                // pMap units are bands
                  Clone_left_end ?Sequence      // filled by XREF
                  Clone_right_end ?Sequence     // filled by XREF
                  Pos_neg_data ?Pos_neg_data
        Positive Positive_gene   ?Gene XREF Positive_clone
                 Positive_variation  ?Variation XREF Positive_clone ?Author
                 Inside_rearr    ?Rearrangement XREF Clone_inside ?Author
                 Hybridizes_to   ?Clone XREF Positive_probe ?Grid
                 Hybridizes_weak ?Clone XREF Pos_probe_weak ?Grid
                 Positive_probe  ?Clone XREF Hybridizes_to ?Grid
                 Pos_probe_weak  ?Clone XREF Hybridizes_weak ?Grid
        Negative Negative_gene   ?Gene XREF Negative_clone
                 Negative_locus  ?Locus XREF Negative_clone ?Author
                 Outside_rearr   ?Rearrangement XREF Clone_outside ?Author
                 Negative_probe  ?Clone XREF Does_not_hybridize_to ?Grid
                 Does_not_hybridize_to ?Clone XREF Negative_probe ?Grid
        In_strain ?Strain XREF Clone
        Sequence    ?Sequence XREF Clone
        PCR_product ?PCR_product XREF Clone
        Length  Seq_length UNIQUE Int                   // bp
                Gel_length UNIQUE Float                 // Kb
        Location ?Laboratory #Lab_Location
        URL Text                          // to link to MRC_geneservice website ar2
        Gridded ?Grid
        Grid_data ?Grid_data 
        FingerPrint     Gel_Number UNIQUE Int
                        Approximate_Match_to UNIQUE ?Clone XREF Canonical_for
                        Exact_Match_to UNIQUE ?Clone XREF Canonical_for 
                        Funny_Match_to UNIQUE ?Clone XREF Canonical_for 
                        Canonical_for ?Clone UNIQUE Int UNIQUE Int 
                                // start and stop offsets from self start
                        Bands   UNIQUE Int UNIQUE Int
                        Gel ?Motif  #Lane               // Magic tag2 construct
        Contig9 Chromosome UNIQUE ?Map 
                Vaxmap UNIQUE Float
                In_Situ  UNIQUE Int UNIQUE Int // percent of physical chromosome
                Cosmid_grid
                Canon_for_cosmid
                Flag    UNIQUE Int
                Autopos
        Expression_construct    Pattern ?Text   // archaic
        Reference ?Paper XREF Clone
        cDNA_group Contains ?Clone XREF Contains Text
                   Contained_in ?Clone XREF Contained_in
                   Best_match UNIQUE ?Text
        Expr_pattern ?Expr_pattern XREF Clone
        Sequence_status Shotgun UNIQUE DateType
                        Finished UNIQUE DateType
                        Accession_number UNIQUE Text
        DB_info  Database ?Database ?Database_field UNIQUE ?Accession_number XREF Clone // added [031120 krb]
        Type UNIQUE Cosmid            // 000824 Lincoln's additions to segregate clones
                    Fosmid            // added 06/12/01 by krb for dl
                    YAC
                    cDNA
                    Plasmid
                    Other Text        // added to catch all clones 011017 dl
        Transgene ?Transgene XREF Clone
        Derived_from    ?Clone

Proposed Changes

unused tags

Evidence

Negative_locus

Negative_probe

Does_not_hybridize_to

Seq_length

URL

Grid_data

Gel

Expression_construct

Pattern

Contained_in

Class contents WS242

215788 Objects/Object references. (removed a few of these while creating report)

Fosmids:

15355 Don Moerman
1738 C. elegans genomic

Cosmids:

17887 Cosmids ->  Cosmid Tag
5548  Other elegans cosmids
7 Other clones C. elegans?
2 BACs clones C. elegans?

cDNA

142175 Yugi Kohara EST clone objects.
2590 Stratagene ESTs CEE* CEM*
1380 OST
1645 Chris Martin C. elegans EST project cm*
40 UofArizona WASHU C. elegans EST project ca*
326 Unknown EST project CES*
48 Cadmium Response gene ESTs DDRT* VL*

Plasmids:

20256 sjj PCR product clone
2152 Other plasmids
   289 from Expression_patterns
   1774 C. elegans genomic?
   99 Variety of sources Fire Vector Kit etc.
   33 Not specified via plasmid but created via XREF from Positive_gene

YACs:

8850 C. elegans YACs


Other

934 Potential C. elegans Fingerprinted cosmids/fosmids/YACs no type specified.
1 C. elegans BAC clone
1 C. elegans genomic clone of unknown origin
1 Clone for the MTCE genome
114 YAC_BRIDGE clones??
119 fUL# clones created by Expr_pattern XREF
24 Odd pieces of cibble


Data to be removed:

17 Created via Positive_gene (All cloned genes, so can probably go)

AddGene vector model extensions

?Clone  Evidence #Evidence
        Species UNIQUE ?Species
        Reference ?Paper XREF Clone
        Produced_by Person ?Person
                    Author ?Author
        Sequence    ?Sequence XREF Clone
        Remark  General_remark ?Text 
                Y_remark ?Text
                PCR_remark ?Text
        Position  Map ?Map XREF Clone #Map_position
                  pMap UNIQUE  ?Contig XREF Clone  UNIQUE Int UNIQUE Int 
                                                // pMap units are bands
                  Clone_left_end ?Sequence      // filled by XREF
                  Clone_right_end ?Sequence     // filled by XREF
                  Pos_neg_data ?Pos_neg_data
        Positive Positive_gene   ?Gene XREF Positive_clone
                 Positive_variation  ?Variation XREF Positive_clone ?Author
                 Inside_rearr    ?Rearrangement XREF Clone_inside ?Author
                 Hybridizes_to   ?Clone XREF Positive_probe ?Grid
                 Hybridizes_weak ?Clone XREF Pos_probe_weak ?Grid
                 Positive_probe  ?Clone XREF Hybridizes_to ?Grid
                 Pos_probe_weak  ?Clone XREF Hybridizes_weak ?Grid
        Negative Negative_gene   ?Gene XREF Negative_clone
                 Negative_locus  ?Locus XREF Negative_clone ?Author
                 Outside_rearr   ?Rearrangement XREF Clone_outside ?Author
                 Negative_probe  ?Clone XREF Does_not_hybridize_to ?Grid
                 Does_not_hybridize_to ?Clone XREF Negative_probe ?Grid
        In_strain ?Strain XREF Clone
        Mutation ?Text
        PCR_product ?PCR_product XREF Clone
        Primer1 ?Text
        Primer2 ?Text
        Resistence_marker ?Text
        Length  Seq_length UNIQUE Int                   // bp
                Gel_length UNIQUE Float                 // Kb
                Insert UNIQUE Int
                Backbone UNIQUE Int
        Location ?Laboratory #Lab_Location
        URL Text                          // to link to MRC_geneservice website ar2
        Gridded ?Grid
        Grid_data ?Grid_data 
        FingerPrint     Gel_Number UNIQUE Int
                        Approximate_Match_to UNIQUE ?Clone XREF Canonical_for
                        Exact_Match_to UNIQUE ?Clone XREF Canonical_for 
                        Funny_Match_to UNIQUE ?Clone XREF Canonical_for 
                        Canonical_for ?Clone UNIQUE Int UNIQUE Int 
                                // start and stop offsets from self start
                        Bands   UNIQUE Int UNIQUE Int
                        Gel ?Motif  #Lane               // Magic tag2 construct
        Contig9 Chromosome UNIQUE ?Map 
                Vaxmap UNIQUE Float
                In_Situ  UNIQUE Int UNIQUE Int // percent of physical chromosome
                Cosmid_grid
                Canon_for_cosmid
                Flag    UNIQUE Int
                Autopos
        Expression_construct    Pattern ?Text   // archaic
        cDNA_group Contains ?Clone XREF Contains Text
                   Contained_in ?Clone XREF Contained_in
                   Best_match UNIQUE ?Text
        Expr_pattern ?Expr_pattern XREF Clone
        Sequence_status Shotgun UNIQUE DateType
                        Finished UNIQUE DateType
                        Accession_number UNIQUE ?Text
        DB_info  Database ?Database ?Database_field ?Accession_number XREF Clone // added [031120 krb]
        Type UNIQUE Cosmid            // 000824 Lincoln's additions to segregate clones
                    Fosmid            // added 06/12/01 by krb for dl
                    YAC
                    cDNA
                    Plasmid
                    Other Text        // added to catch all clones 011017 dl
        Transgene ?Transgene XREF Clone
        Vector_type ?Text
        Derived_from ?Clone XREF Parent_of
        Parent_of ?Clone XREF  Derived_from
        Ligation ?Text