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Difference between revisions of "Chado Library Module"
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+ | ===A dsRNA library=== | ||
+ | |||
+ | June 1, 2006 written by Kathleen Falls. The original Wiki page is here: http://cedar.bio.indiana.edu/mediawiki/index.php/RNAi_primer_and_amplicon_implementation. | ||
+ | |||
+ | |||
+ | ====Background==== | ||
+ | |||
+ | The aim is to stored information about a dsRNA library and its bulk-loaded amplicons and primers in Chado. There are sites performing RNAi screens for which there are link-outs in chado (DRSC, FLIGHT, Heidelberg RNAi) by genes hit by the screens. Initially the plan is to store the dsRNA primers and amplicons with there chromosomal locations mapped to the current release. The goal is to link the libraries, dsRNA amplicons with genes and phenotypes. | ||
+ | |||
+ | * dsRNA library: contains collections of dsRNA amplicons, primarily from the screening centers. Currently it holds the DRSC collection. | ||
+ | * dsRNA amplicon: sequence of 100-500 bp selected from genomic DNA designed to amplify an exonic region or selected from cDNA | ||
+ | * dsRNA primers: PCR primers pairs of 15-25 bp designed to amplify dsRNA amplicon | ||
+ | |||
+ | ====Implementation==== | ||
+ | |||
+ | * The dsRNA library uniquename and name is typically name or initials of the screening center e.g. ''DRSC'' for Drosophila RNAi Screening Center. | ||
+ | * The dsRNA library is stored in ''library'' table, type "dsRNA library". | ||
+ | * The ''libraryprop'' table stores a general description for each library as type ''comment'' and for the DRSC library the DNA amplified from as type ''strain'' value ''Oregon R''. | ||
+ | * The ''library_pub'' is reference to uniquename FBrf0188751 (personal communication to FlyBase). | ||
+ | |||
+ | Each dsRNA amplicon is stored in the ''feature'' table. The uniquename is FBrinnnnnnn generated by script and tracked in a log file, the type is ''pcr_product'' and no residues are stored. Each has a ''featureloc'' entry relating back to chromosome_arm. Strand was determined by extracting residues from fmin+1 to fmax for an amplicon then for each each primer pair testing for an exact match by length and orientation. | ||
+ | |||
+ | The dsRNA primers are a feature with uniquename FBrinnnnnnn_R and _S, type oligonucleotide and the residues are stored. They are linked to their dsRNA amplicon in ''feature_relationship'', as type ''primer_progenitor_of'' with each primer as subject and the dsRNA amplicon as object. | ||
+ | |||
+ | The ''feature_pub'' for dsRNA amplicons and primers is a reference to FBrf0188751 (personal communication to FlyBase). | ||
+ | |||
+ | The ''featureloc_pub'' for dsRNA amplicons remapped to rel5 is FBrf0188751 (personal communication to FlyBase) while the ''featureloc_pub'' for dsRNA amplicons mapped by BLAST of the primers to rel5 is FBrf0104946 (FlyBase inference by analysis). | ||
+ | |||
+ | Each dsRNA amplicon feature record is linked to ''library'' in the ''library_feature'' table. | ||
+ | |||
+ | ====Relationship graph==== | ||
+ | |||
+ | |||
+ | ---------------------------------------------------------------------- chromosomal arm | ||
+ | ^ ^ | ||
+ | | | | ||
+ | | floc | | ||
+ | | | | ||
+ | -------------------------------------- dsRNA | ||
+ | ^ ^ / \ ^ ^ | ||
+ | | fr | | | | fr | | ||
+ | | | | | | | | ||
+ | pcr primer R ------------ | | ---------- pcr primer S | ||
+ | --partof | | | ||
+ | --------------------------------------- dsRNA library-->library_feature | ||
==Tables== | ==Tables== |
Revision as of 14:07, 13 April 2007
Contents
Introduction
The library module is designed to store detailed information about molecular libraries. The library module uses the sequence module, thus the library in question could be any collection of sequences that the sequence module can describe. It is expected that most of the description of a given library would come through the use of ontology terms.
Using the Library module
The following are examples showing how to use this module to describe a library.
A FlyBase cDNA library
Written by Haiyan Zhang, April 14, 2006, the original Wiki page is here: http://cedar.bio.indiana.edu/mediawiki/index.php/Library_module_implementation.
Background
The cDNA library contains complementary DNA molecules synthesized from mRNA molecules in a cell. One cDNA library has only one cloning vector.
- cDNA_clone: Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host.
- cDNA: DNA synthesized by reverse transcriptase using RNA as a template.
- EST: Expressed Sequence Tag: The sequence of a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long.
Implementation
- Library name and uniquenames are generally from the first 2 letters of the the cDNA_clones, or the first 2 letters and vector name e.g. AT library, HL_pOT2 libary
- Library stored in library table, type as cDNA library.
- libraryprop table stores the general description for each library as type comment and the vector for each library as type element.
- Library synonyms are linked in library_synonym table.
- Library's references are linked in library_pub table.
- Each cDNA_clone, cDNA, EST, vector is a feature with the corresponding type.
- cDNA_clone has no residues information.
- library_feature connects library and its cDNA_clones.
- cDNA, EST and vector are connected with cDNA_clone in feature_relationship table, as type partof. cDNA_clone is the object_id, cDNA/EST/vector is the subject_id.
Relationship graph
pOTB7 __________ vector/plasmid || --partof \/ AT13713 library -->library_feature ==> ------------------------- cDNA_clone ^ /\ --partof ^ | || AY113251 | partof-- | _________________ | cDNA | | | | | |--partof BF499196 ________ | ___________ EST AT13713.contig1 | | CK130673 | | | AT13713.contig2 | | | ---------------------------------------- genomic contig
Naming conventions
Rules for chado clones and clone features:
- cDNA_clone: uniquename = FBclxxxxxxx, name = clone id number e.g. LD12345
- cDNA: uniquename = accession number (if possible), name = clone id number e.g. LD12345
- EST: uniquename = accession number (if possible), name = clone id number.5prime,3prime,:contig etc e.g. LD12345.5prime
A dsRNA library
June 1, 2006 written by Kathleen Falls. The original Wiki page is here: http://cedar.bio.indiana.edu/mediawiki/index.php/RNAi_primer_and_amplicon_implementation.
Background
The aim is to stored information about a dsRNA library and its bulk-loaded amplicons and primers in Chado. There are sites performing RNAi screens for which there are link-outs in chado (DRSC, FLIGHT, Heidelberg RNAi) by genes hit by the screens. Initially the plan is to store the dsRNA primers and amplicons with there chromosomal locations mapped to the current release. The goal is to link the libraries, dsRNA amplicons with genes and phenotypes.
- dsRNA library: contains collections of dsRNA amplicons, primarily from the screening centers. Currently it holds the DRSC collection.
- dsRNA amplicon: sequence of 100-500 bp selected from genomic DNA designed to amplify an exonic region or selected from cDNA
- dsRNA primers: PCR primers pairs of 15-25 bp designed to amplify dsRNA amplicon
Implementation
- The dsRNA library uniquename and name is typically name or initials of the screening center e.g. DRSC for Drosophila RNAi Screening Center.
- The dsRNA library is stored in library table, type "dsRNA library".
- The libraryprop table stores a general description for each library as type comment and for the DRSC library the DNA amplified from as type strain value Oregon R.
- The library_pub is reference to uniquename FBrf0188751 (personal communication to FlyBase).
Each dsRNA amplicon is stored in the feature table. The uniquename is FBrinnnnnnn generated by script and tracked in a log file, the type is pcr_product and no residues are stored. Each has a featureloc entry relating back to chromosome_arm. Strand was determined by extracting residues from fmin+1 to fmax for an amplicon then for each each primer pair testing for an exact match by length and orientation.
The dsRNA primers are a feature with uniquename FBrinnnnnnn_R and _S, type oligonucleotide and the residues are stored. They are linked to their dsRNA amplicon in feature_relationship, as type primer_progenitor_of with each primer as subject and the dsRNA amplicon as object.
The feature_pub for dsRNA amplicons and primers is a reference to FBrf0188751 (personal communication to FlyBase).
The featureloc_pub for dsRNA amplicons remapped to rel5 is FBrf0188751 (personal communication to FlyBase) while the featureloc_pub for dsRNA amplicons mapped by BLAST of the primers to rel5 is FBrf0104946 (FlyBase inference by analysis).
Each dsRNA amplicon feature record is linked to library in the library_feature table.
Relationship graph
---------------------------------------------------------------------- chromosomal arm ^ ^ | | | floc | | | -------------------------------------- dsRNA ^ ^ / \ ^ ^ | fr | | | | fr | | | | | | | pcr primer R ------------ | | ---------- pcr primer S --partof | | --------------------------------------- dsRNA library-->library_feature
Tables
Table: library
F-Key | Name | Type | Description |
---|---|---|---|
library_id | serial | PRIMARY KEY | |
organism_id | integer | UNIQUE#1 NOT NULL | |
name | character varying(255) | ||
uniquename | text | UNIQUE#1 NOT NULL | |
type_id | integer | UNIQUE#1 NOT NULL The type_id foreign key links to a controlled vocabulary of library types. Examples of this would be: "cDNA_library" or "genomic_library" |
Tables referencing this one via Foreign Key Constraints:
Table: library_cvterm
The table library_cvterm links a library to controlled vocabularies which describe the library. For instance, there might be a link to the anatomy cv for "head" or "testes" for a head or testes library.
F-Key | Name | Type | Description |
---|---|---|---|
library_cvterm_id | serial | PRIMARY KEY | |
library_id | integer | UNIQUE#1 NOT NULL | |
cvterm_id | integer | UNIQUE#1 NOT NULL | |
pub_id | integer | UNIQUE#1 NOT NULL |
Table: library_feature
library_feature links a library to the clones which are contained in the library. Examples of such linked features might be "cDNA_clone" or "genomic_clone".
F-Key | Name | Type | Description |
---|---|---|---|
library_feature_id | serial | PRIMARY KEY | |
library_id | integer | UNIQUE#1 NOT NULL | |
feature_id | integer | UNIQUE#1 NOT NULL |
Table: library_pub
F-Key | Name | Type | Description |
---|---|---|---|
library_pub_id | serial | PRIMARY KEY | |
library_id | integer | UNIQUE#1 NOT NULL | |
pub_id | integer | UNIQUE#1 NOT NULL |
Table: library_synonym
F-Key | Name | Type | Description |
---|---|---|---|
library_synonym_id | serial | PRIMARY KEY | |
synonym_id | integer | UNIQUE#1 NOT NULL | |
library_id | integer | UNIQUE#1 NOT NULL | |
pub_id | integer | UNIQUE#1 NOT NULL The pub_id link is for relating the usage of a given synonym to the publication in which it was used. | |
is_current | boolean | NOT NULL DEFAULT true The is_current bit indicates whether the linked synonym is the current -official- symbol for the linked library. | |
is_internal | boolean | NOT NULL DEFAULT false Typically a synonym exists so that somebody querying the database with an obsolete name can find the object they are looking for under its current name. If the synonym has been used publicly and deliberately (e.g. in a paper), it my also be listed in reports as a synonym. If the synonym was not used deliberately (e.g., there was a typo which went public), then the is_internal bit may be set to "true" so that it is known that the synonym is "internal" and should be queryable but should not be listed in reports as a valid synonym. |
Table: libraryprop
F-Key | Name | Type | Description |
---|---|---|---|
libraryprop_id | serial | PRIMARY KEY | |
library_id | integer | UNIQUE#1 NOT NULL | |
type_id | integer | UNIQUE#1 NOT NULL | |
value | text | ||
rank | integer | UNIQUE#1 NOT NULL |