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Package: RefSampleComponent


    DRAFT - backward compatibility of future versions not guaranteed.
    Sample composition and description of the individual components. Includes information specific for certain biochemical techniques.
Classes
Data Types
Data Obj Types

Imported Packages:

Classification,   ccp.api.general.Affiliation,   ccp.api.general.DbRef,   ccp.api.general.Taxonomy,   ccp.api.molecule.LabeledMolecule,   ccp.api.molecule.Molecule,   memops.api.AccessControl,   memops.api.Implementation

Packages Importing ccp.api.lims.RefSampleComponent:

ExpBlueprint,   Sample,   Target

Classes:

Class Description
AbstractComponent The abstract component is used to define the details which characterise all components, these are name, any synonyms and a CAS number. There are 4 subclasses of abstract component: Molecular component (MolComponent), Cell, Substance and Composite.
Cell Cell is a subclass of AbstractComponent. The information on the cell component.
ComponentDbRef The link between a database reference (DbRef) and a component.
Composite Composite is a subclass of AbstractComponent. It is a non-covalent complex of any kind. E.g. A DNA duplex, a micelle, possibly containing other molecules. A protein with an inhibitor bound. A cell containing plasmids.
CompositeElement One element of the composite.
CompositeInteraction The interaction between two composite elements.
Construct This is a subtype of MolComponent. It is used to summarise information about a construct such as an expression vector plasmid.
IsotopeLabel Isotope label or labeling pattern. Refers to elements of a type given by elementSymbol. If self.molResidues is set the substitution is limited to these residues. If self.atomNames is set the substitution is limited to atoms with these names.
Label Label (isotopic, fluorophore, X-ray anomalous scatterer, or other) attached to AbstractComponent. Isotope labeling given in SpecificLabelGroup and IsotopeLabel must be consistent with labeling given in the Label class, as both are valid together.
MolCompFeature The MolCompFeature is used to assign information to each part of the MolComponent sequence, as defined by a series of MolResidues with consecutive serials.
MolComponent One type of component. A Molecular component (MolComponent) represents a pure component of known melecular structure. This includes most chemicals, proteins, DNA, RNA, DNA/RNA and also enzymes, constructs and primers. Restriction enzymes, primers and constructs are subtypes of MolCOmponent with additional features recorded. NaCl is a MolComponent, so is lysozyme.
Primer This is a subtype of MolComponent. A specific oligonucleotide or primer such as a PCR-primer used to amplify nucleic acid fragments.
RefSampleComponentStore TopObject for RefSampleComponent package
RestrictionEnzyme This is a subtype of MolComponent. Restriction enzymes are known to cleave nucleic acide sequences at certain positions.
SpecificLabelGroup Group of specific isotope labels that apply together to an individual molecule. Molecules that are mixtures of isotopomers may have several SpecificLabelGroups. Isotope labeling given in SpecificLabelGroup and IsotopeLabel must be consistent with labeling given in the Label class, as both are valid together.
Substance A Substance should be limited to cases that cannot be put under any of the others. Typically: bovine calf serum, light petroleum, wheat germ extract, algal hydrolysate.

Data Obj Types:

Type Description
None

Data Types:

Type Description
ConstructStatus This is an open enumeration of the construct status for the Construct: 'empty', 'with target', ...
FeatureType This is an open enumeration of the feature type for the MolCompFeature: 'tag', 'cleavage site', 'promoter', 'resistance', 'marker', 'product', ...
LabelName Label name. NB TBD The eumeration needs to be expanded to cover standard label names.
LabelType Type of label. NB TBD The eumeration needs to be expanded to cover standard label types.
StatusType This is an open enumeration of the status type for the MolCompFeature: 'cutted', 'uncutted', ...

Package guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:22:52_00056
  Data Model Version 2.0.5
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Mon Mar 26 16:58:19 2012    from data model package  ccp.api.lims.RefSampleComponent   revision 1.47  
  Work done by the CCPN team.
www.ccpn.ac.uk