SlipGURU Dipartimento di Informatica e Scienze dell'Informazione Università Degli Studi di Genova

PKCID Package

PKCID Package

Provides concrete implementation of PKCIDMap builders.

GPL Module

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.

kdvs.fw.impl.map.PKCID.GPL.GOTERM2EM_TMPL = <kdvs.fw.DBTable.DBTemplate object at 0x67cbed0>

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.

class kdvs.fw.impl.map.PKCID.GPL.PKCIDMapGOGPL

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:

    1. domain–unaware one that does not group individual terms according to domains,
    1. domain–aware one that groups individual terms according to domains

The domain–aware mapping is stored in public attribute domains_map.

getMapForDomain(domain)

Return part of PKCIDMap referring to specific GO domain.

Parameters :

domain : string

GO domain name, one of: ‘BP’, ‘MF’, ‘CC’

Returns :

domain_part_map : SetBDMap

part of PKCIDMap the refers to specific GO domain

Raises :

Error :

if domain name is incorrectly specified

build(anno_dsv, map_db_key)

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

valid instance of DSV that contains Affymetrix annotations data

map_db_key : string

ID of the database that will hold mapping table

Raises :

Error :

if DSV containing Affymetrix annotation data is incorrectly specified, is not created, or is empty

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