Provides concrete implementation of PKCIDMap builder that uses Gene Ontology as prior knowledge source for data subsets generation. It uses Affymetrix annotations shipped with specified microarray; those annotations shall contain mapping between the individual probe(set)s and Gene Ontology terms (i.e. prior knowledge concepts). The currently implemented builder is tailored for processing of Affymetrix annotations. See Affymetrix annotations for more details. The mapping is based solely on the annotations, i.e. it utilizes GO terms present at the time when annotations were constructed. KDVS provides concrete manager (GOManager) that offers more control over Gene Ontology content.
Custom database template that hold querying data used in fast construction of GO–based PKCIDMap. It defines the name ‘goterm2em’ and columns ‘term_id’, ‘em_id’, ‘term_evc’, ‘term_name’, ‘term_domain’. The ID column ‘term_id’ is indexed. The application ‘experiment’ utilizes this table. See PKC2EM_TMPL for detailed discussion.
Bases: kdvs.fw.Map.PKCIDMap
PKCIDMap builder that uses Affymetrix annotations available at Gene Expression Omnibus. Annotations must already be loaded “as–is” into KDVS DB and wrapped into DSV instance. The mapping table follows custom template GOTERM2EM_TMPL. This builder constructs two mappings:
- domain–unaware one that does not group individual terms according to domains,
- domain–aware one that groups individual terms according to domains
The domain–aware mapping is stored in public attribute domains_map.
Return part of PKCIDMap referring to specific GO domain.
Parameters : | domain : string
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Returns : | domain_part_map : SetBDMap
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Raises : | Error :
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Construct the mapping using resources already present in KDVS DB (via DBManager) and wrapped in DSV instances. The mapping is built as database table and wrapped into DBTable instance; it is stored in public attribute dbt of this instance. After the build is finished, the public attribute built is set to True. This builder requires Affymetrix annotations data already loaded in KDVS DB and wrapped in DSV instance.
Parameters : | anno_dsv : DSV
map_db_key : string
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Raises : | Error :
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