Difference between revisions of "WormBase Model:Clone"
From WormBaseWiki
Jump to navigationJump to searchLine 155: | Line 155: | ||
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) | ||
+ | |||
+ | == 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 | ||
+ | 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 | ||
+ | </pre> |
Revision as of 16:51, 18 March 2014
Contents
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