Provides concrete implementation for all abstract entities regarding handling annotations. Also, provides annotation source–specific functionalities.
Provides specific functionality for handling HUGO Gene Nomenclature Committee (HGNC) annotation data (http://www.genenames.org/). KDVS uses HGNC annotation data to resolve gene naming problems that may arise from using old microarray annotations. HGNC data refer to gene names as ‘symbols’. The data contain all history of approval of individual symbols; some symbols are withdrawn according to the current knowledge of the genes. HGNC data are downloaded in the form of DSV file; see README in ‘data’ directory for more details. Typically, HGNC data are loaded into KDVS DB and wrapped in DSV instance; ‘experimert’ application does it automatically.
Column in HGNC data that contains approved symbol(s).
Column in HGNC data that contains status of specific gene symbol.
Column in HGNC data that contains type of genetic locus that the symbol describes; it could be valid protein products, tRNA gene, etc.
Column in HGNC data that contains previously approved symbols.
Column in HGNC data that contains valid synonyms for specific symbol; some synonyms, although not official, are still widely used in different research environments and must be accounted for when resolving any gene name.
Column in HGNC data that contains Entrez Gene ID for specific symbol; although it is regularly updated, the user should pay attention for its accuracy.
Column in HGNC data that contains Ensembl Gene ID for specific symbol; although it is regularly updated, the user should pay attention for its accuracy.
Column in HGNC data that contains (possibly many) RefSeq IDs for specific symbol; although it is regularly updated, the user should pay attention for its accuracy.
Default DSV separator for the HGNC data file.
Value in ‘Status’ column referring to the fact that the specific symbol has approved status (i.e. is considered official at this moment).
Values in ‘Status’ column referring to the fact that the specific symbol has been withdrawn (i.e. is no longer considered valid); however, it may still be encountered among very old data.
Suffix that is appended to each withdrawn symbol; KDVS removes it to fasten the querying.
Refers to empty value in any column of HGNC data.
Database template used by KDVS to create fast query table for resolving synonyms. It defines the name ‘hgnc_synonyms’ and columns ‘synonym’, ‘approved’. The ID column is ‘synonym’. All columns are indexed. With it, user obtains approved symbol given the synonym.
Database template used by KDVS to create fast query table for resolving previous symbols. It defines the name ‘hgnc_previous’ and columns ‘previous’, ‘approved’. The ID column is ‘previous’. All columns are indexed. With it, user obtains approved symbol given the previous symbol.
Manually correct HGNC data after loading into DB and wrapping into DSV instance. It removes suffix (defined in HGNC_WITHDRAWN_GS_PART) from withdrawn symbols in order to fasten further querying. This call must be used in the application that uses HGNC data, and must be made after HGNC data has been loaded and wrapped into DSV instance.
Parameters : | hgnc_dsv : DSV
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Create helper table that eases resolving of previous gene symbols with HGNC data. The helper table may be created in different subordinated database than original HGNC data. The table is specified via template.
Parameters : | hgnc_dsv : DSV
map_db_key : string
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Returns : | previousDT : DBTable
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See also
Create helper table that eases resolving of synonymic gene symbols with HGNC data. The helper table may be created in different subordinated database than original HGNC data. The table is specified via template.
Parameters : | hgnc_dsv : DSV
map_db_key : string
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Returns : | synonymsDT : DBTable
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See also