WormBase Model:Clone

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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

I have been working on importing the AddGene data that Chris was given quite some time ago. This has become more pressing since caltech literature curators are starting to utilise these vectors in their curation. I have also picked up additional Fire vector kit vectors from various kit releases during the 90s.

I have made test data available here: FTP_file_link

To accommodate this data I propose the following tag additions to the ?Clone model.


?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
#        Resistance_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

New tags: To capture the PI name associated with the AddGene submission.

Produced_by Person ?Person

Author ?Author // Will be auto-populated


Mutation ?Text // This is an AddGene field


Primer1 ?Text // If primers are available the name of the primer is captured


Primer2 ?Text // If primers are available the name of the primer is captured


Resistance_marker ?Text //AddGene field for Resistance genes being carried


Length Insert UNIQUE Int // capture length/size of Insert

Backbone UNIQUE Int // capture length/size of Vector Backbone


Vector_type ?Text // The majority of the AddGene vectors are classified by a Type field


Ligation ?Text // This is commonly used and sometimes used as a primary reference


Add the XREF + new tag:

Derived_from ?Clone XREF Parent_of // This allows a simple hierarchy

Parent_of ?Clone XREF Derived_from