Difference between revisions of "WormBase Model:Clone"
From WormBaseWiki
Jump to navigationJump to search| (5 intermediate revisions by one other user not shown) | |||
| Line 157: | Line 157: | ||
== AddGene vector model extensions == | == 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://ftp.sanger.ac.uk/pub/wormbase/STAFF/pad/AddGene/New_clone_data.ace FTP_file_link] | ||
| + | |||
| + | To accommodate this data I propose the following tag additions to the ?Clone model. | ||
| + | |||
<pre> | <pre> | ||
| Line 162: | Line 171: | ||
Species UNIQUE ?Species | Species UNIQUE ?Species | ||
Reference ?Paper XREF Clone | Reference ?Paper XREF Clone | ||
| − | + | # Produced_by Person ?Person | |
| − | + | # Author ?Author | |
Sequence ?Sequence XREF Clone | Sequence ?Sequence XREF Clone | ||
Remark General_remark ?Text | Remark General_remark ?Text | ||
| Line 187: | Line 196: | ||
Does_not_hybridize_to ?Clone XREF Negative_probe ?Grid | Does_not_hybridize_to ?Clone XREF Negative_probe ?Grid | ||
In_strain ?Strain XREF Clone | In_strain ?Strain XREF Clone | ||
| − | + | # Mutation ?Text | |
PCR_product ?PCR_product XREF Clone | PCR_product ?PCR_product XREF Clone | ||
| − | + | # Primer1 ?Text | |
| − | + | # Primer2 ?Text | |
| − | + | # Resistance_marker ?Text | |
Length Seq_length UNIQUE Int // bp | Length Seq_length UNIQUE Int // bp | ||
Gel_length UNIQUE Float // Kb | Gel_length UNIQUE Float // Kb | ||
| − | + | # Insert UNIQUE Int | |
| − | + | # Backbone UNIQUE Int | |
Location ?Laboratory #Lab_Location | Location ?Laboratory #Lab_Location | ||
URL Text // to link to MRC_geneservice website ar2 | URL Text // to link to MRC_geneservice website ar2 | ||
| Line 231: | Line 240: | ||
Other Text // added to catch all clones 011017 dl | Other Text // added to catch all clones 011017 dl | ||
Transgene ?Transgene XREF Clone | Transgene ?Transgene XREF Clone | ||
| − | + | # Vector_type ?Text | |
| − | + | # Derived_from ?Clone XREF Parent_of | |
| − | + | # Parent_of ?Clone XREF Derived_from | |
| − | + | # Ligation ?Text | |
</pre> | </pre> | ||
| + | |||
| + | 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 | ||
Latest revision as of 22:24, 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
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
