Data Model version 2.1.2
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Class: Target


    The information on the target.
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link targetStore to class TargetStore
Main key: serial
Mandatory Attributes: commonName, whyChosen, protein
Known Subclasses: None
Children:
link targetStatus to class TargetStatus
Constructor: newObj = Target( targetStore,commonName=value, whyChosen=value, protein=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
biochemicalFunction Text 0..1 The biochemical function within the biological pathway of the target. e.g. 'Cytosine deaminase'.  
biologicalProcess Text 0..1 The biological process where the target is involved. e.g. 'Unknown'.  
catalyticActivity Text 0..1 The official statement of catalytic activity. e.g. 'CYTOSINE + H(2)O = URACIL + NH(3)'.  
cellLocation Line 0..1 The typical location of the target within a cell. e.g. 'cytoplasmic'.  
commonName Line 1..1 The common name of the target is the name used to identify the target e.g. 'Endonuclease IV'.  
details String 0..1 Detail field for comments.  
functionDescription String 0..1 The function description is an human-readable description of the biochemical function. e.g. 'Converts cytosine to uracil or 5-methylcytosine to thymine by deaminating carbon number 4'.  
geneName Line 0..1 The official name of the gene for this target. e.g. 'fcy1'.  
localName Line 0..1 Local name is what the target is known as in the lab e.g. 'A6'.  
orf Line 0..1 Open Reading Frame name.  
pathway Text 0..1 The description of the biological processes this target is related to. e.g. 'Pyrimidine salvage pathway'.  
proteinName Line 0..1 The official name of the protein for this target. By default: 'theoretical protein'. e.g. 'Cytosine deaminase'.  
seqString String 1..1 Derived. This is usually the amino acid sequence derived from Molecule.Polymer.  
serial Int 1..1 Unique identifier.  
similarityDetails String 0..1 Information relating this target to other organisms/genes/proteins. e.g. 'Belongs to the cytidine and deoxycytidylate deaminases family.'  
systematicName Line 0..1 The systematic name of the target is the 'proper' scientific name e.g. 'Endodeoxyribonuclease IV'.  
topology Text 0..1 The topology of the target is a general description of its topology or if it is a membrane protein, the topology could refer to the membrane one predicted by the TMHMM program or obtained by experimental observation.  
whyChosen String 1..1 Details of the basis for the selection of this target.  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
annotations ccp.api.general.Annotation.Annotation 0..* Targets annotated by Annotation.  
blueprintComponents ccp.api.lims.ExpBlueprint.BlueprintComponent 0..* BlueprintComponents linked to a single Target, representing the fact that different fragments of the same target may be studied in various contexts.  
citations ccp.api.general.Citation.Citation 0..* Citations describing target.  
creator ccp.api.general.Affiliation.Person 0..1 The person who is in charge for this target or who created this target.  
dbRefs ccp.api.general.DbRef.Entry 0..*  
nucleicAcids ccp.api.lims.RefSampleComponent.MolComponent 0..* The nucleic acid MolComponent used to describe the Target  
parent TargetStore 1..1 link to parent object - synonym for targetStore  
projects Project 0..* The list of project to wich this target belongs.  
protein ccp.api.lims.RefSampleComponent.MolComponent 1..1 The MolComponent used to describe the Target protein  
species ccp.api.general.Taxonomy.NaturalSource 0..1 Specie of target.  
targetGroups TargetGroup 0..* The list of target groups to wich this target belongs.  
targetStatus TargetStatus 0..* (Child link). child link to class TargetStatus  
targetStore TargetStore 1..1 (Parent link). parent link  

Inherited Attributes (not in package): accessactiveAccessroottopObject

Attribute Methods (in package)

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Attribute Method Return Parameters Comment
biochemicalFunction
getBiochemicalFunction Text -
setBiochemicalFunction - Text
biologicalProcess
getBiologicalProcess Text -
setBiologicalProcess - Text
catalyticActivity
getCatalyticActivity Text -
setCatalyticActivity - Text
cellLocation
getCellLocation Line -
setCellLocation - Line
commonName
getCommonName Line -
setCommonName - Line
details
getDetails String -
setDetails - String
functionDescription
getFunctionDescription String -
setFunctionDescription - String
geneName
getGeneName Line -
setGeneName - Line
localName
getLocalName Line -
setLocalName - Line
orf
getOrf Line -
setOrf - Line
pathway
getPathway Text -
setPathway - Text
proteinName
getProteinName Line -
setProteinName - Line
seqString
getSeqString String - non-std.
serial
getSerial Int -
setSerial - Int
similarityDetails
getSimilarityDetails String -
setSimilarityDetails - String
systematicName
getSystematicName Line -
setSystematicName - Line
topology
getTopology Text -
setTopology - Text
whyChosen
getWhyChosen String -
setWhyChosen - String

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
annotations
getAnnotations ccp.api.general.Annotation.Annotation Set -
setAnnotations - ccp.api.general.Annotation.Annotation Set
sortedAnnotations ccp.api.general.Annotation.Annotation List -
addAnnotation - ccp.api.general.Annotation.Annotation
removeAnnotation - ccp.api.general.Annotation.Annotation
findFirstAnnotation ccp.api.general.Annotation.Annotation keyword=value pairs
findAllAnnotations ccp.api.general.Annotation.Annotation Set keyword=value pairs
blueprintComponents
getBlueprintComponents ccp.api.lims.ExpBlueprint.BlueprintComponent Set -
setBlueprintComponents - ccp.api.lims.ExpBlueprint.BlueprintComponent Set
sortedBlueprintComponents ccp.api.lims.ExpBlueprint.BlueprintComponent List -
addBlueprintComponent - ccp.api.lims.ExpBlueprint.BlueprintComponent
removeBlueprintComponent - ccp.api.lims.ExpBlueprint.BlueprintComponent
findFirstBlueprintComponent ccp.api.lims.ExpBlueprint.BlueprintComponent keyword=value pairs
findAllBlueprintComponents ccp.api.lims.ExpBlueprint.BlueprintComponent Set keyword=value pairs
citations
getCitations ccp.api.general.Citation.Citation Set -
setCitations - ccp.api.general.Citation.Citation Set
sortedCitations ccp.api.general.Citation.Citation List -
addCitation - ccp.api.general.Citation.Citation
removeCitation - ccp.api.general.Citation.Citation
findFirstCitation ccp.api.general.Citation.Citation keyword=value pairs
findAllCitations ccp.api.general.Citation.Citation Set keyword=value pairs
creator
getCreator ccp.api.general.Affiliation.Person -
setCreator - ccp.api.general.Affiliation.Person
dbRefs
getDbRefs ccp.api.general.DbRef.Entry Set -
setDbRefs - ccp.api.general.DbRef.Entry Set
sortedDbRefs ccp.api.general.DbRef.Entry List -
addDbRef - ccp.api.general.DbRef.Entry
removeDbRef - ccp.api.general.DbRef.Entry
findFirstDbRef ccp.api.general.DbRef.Entry keyword=value pairs
findAllDbRefs ccp.api.general.DbRef.Entry Set keyword=value pairs
nucleicAcids
getNucleicAcids ccp.api.lims.RefSampleComponent.MolComponent Set -
setNucleicAcids - ccp.api.lims.RefSampleComponent.MolComponent Set
sortedNucleicAcids ccp.api.lims.RefSampleComponent.MolComponent List -
addNucleicAcid - ccp.api.lims.RefSampleComponent.MolComponent
removeNucleicAcid - ccp.api.lims.RefSampleComponent.MolComponent
findFirstNucleicAcid ccp.api.lims.RefSampleComponent.MolComponent keyword=value pairs
findAllNucleicAcids ccp.api.lims.RefSampleComponent.MolComponent Set keyword=value pairs
parent
getParent TargetStore -
projects
getProjects Project Set -
setProjects - Project Set
sortedProjects Project List -
findFirstProject Project keyword=value pairs
findAllProjects Project Set keyword=value pairs
protein
getProtein ccp.api.lims.RefSampleComponent.MolComponent -
setProtein - ccp.api.lims.RefSampleComponent.MolComponent
species
getSpecies ccp.api.general.Taxonomy.NaturalSource -
setSpecies - ccp.api.general.Taxonomy.NaturalSource
targetGroups
getTargetGroups TargetGroup Set -
setTargetGroups - TargetGroup Set
sortedTargetGroups TargetGroup List -
addTargetGroup - TargetGroup
removeTargetGroup - TargetGroup
findFirstTargetGroup TargetGroup keyword=value pairs
findAllTargetGroups TargetGroup Set keyword=value pairs
targetStatus
getTargetStatus TargetStatus Set -
sortedTargetStatus TargetStatus List -
findFirstTargetStatus TargetStatus keyword=value pairs
findAllTargetStatus TargetStatus Set keyword=value pairs
targetStore
getTargetStore TargetStore -

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey Target memops.api.Implementation.MemopsObject, Any List static
getFullKey Any List Boolean
getLocalKey Any -
get Any String
set - String, Any

Factory Methods (in package)

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Method Return Parameters
newTargetStatus TargetStatus date, code, ...

Other Methods (in package)

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Method Return Parameters Comment
None

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2006-08-16-14:22:51_00035

isImplicit:

False

Tag

Value
repositoryId $Id: $

Tag

Value
repositoryTag $Name: $

Special constructor code:

None

Special destructor code:

None

Special postDestructor code:

None

Constraints:

None
Known inward one-way links: None
  Data Model Version 2.1.2
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Fri Mar 28 11:18:18 2014    from data model package  ccp.api.lims.Target.Target   revision ?  
  Work done by the CCPN team.
www.ccpn.ac.uk