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Class: NaturalSource


    Natural source of molecule.
Attributes
Link Attributes
Attribute Methods
Link Attribute Methods
Class Methods
Factory Methods
Other Methods
Appendix

Inheritance:


Details:

Parent: link taxonomy to class Taxonomy
Main key: serial
Mandatory Attributes: organismName
Known Subclasses: None
Children: None
Constructor: newObj = NaturalSource( taxonomy,organismName=value, ... )

Attributes (in package)

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Attribute Type Multiplicity Description
atccNumber Line 0..1 ATCC number of cell line. Should be removed?  
cellLine Line 0..1 Source cell line.  
cellLocation String 0..1 The source cell location.  
cellType Line 0..1 Source cell type.  
details String 0..1 Details, comments, notes about natural source.  
fraction Text 0..1 Is this the same as tissueFraction (which would then be a better name)?  
geneMnemonic Text 0..1 Gene Mnemonic.  
genus Line 0..1 Organism genus.  
ictvCode Text 0..1 The code for the International Comitee on Taxonomy of Viruses.  
kingdom Line 0..1 kingdom to which organism belongs (in theory derivable from genus and species).  
ncbiTaxonomyId Text 0..1 The ID for the NCBI taxonomy node.  
organ Line 0..1 Source Organ.  
organelle Text 0..1 Organelle from which molecule is derived.  
organismAcronym Text 0..1 The organism acronym.  
organismName Text 1..1 Common name of organism.  
plasmid Text 0..1 Plasmid name, if molecule is (part of) a plasmid.  
plasmidDetails String 0..1 N/A  
scientificName Line 0..1 The NCBI scientific name. (= genius + species). This should really be a derived attribute!  
secretion String 0..1 Secretion from which molecule is derived.  
serial Int 1..1 The serial number is the key for class NaturalSource and together with the parent object serves as a unique identifier for the NaturalSource. Serial numbers are generated by the API. Serial numbers of deleted objects are not reused.  
species Line 0..1 Organism species.  
strain Line 0..1 Organism strain.  
subVariant Text 0..1 Organism sub-variant.  
superKingdom Line 0..1 super-kingdom to which organism belongs (in theory derivable from genus and species).  
tissue Line 0..1 Source tissue.  
variant Line 0..1 Organism variant.  

Inherited Attributes (not in package): applicationDataclassNamefieldNamesinConstructorisDeletedmetaclasspackageNamepackageShortNamequalifiedName

Link Attributes (in package)

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Attribute Type Multiplicity Description
entryMolecules ccp.api.nmr.NmrEntry.EntryMolecule 0..* Connection to Nmr Entries where this is used as experimental source of a molecule  
molSeqFragments ccp.api.molecule.Molecule.MolSeqFragment 0..* MOlecule fragments arising from NaturalSource  
molecules ccp.api.molecule.Molecule.Molecule 0..* Molecules from natural source.  
parent Taxonomy 1..1 link to parent object - synonym for taxonomy  
targets ccp.api.lims.Target.Target 0..* Targets corresponding to this natural source.  
taxonomy Taxonomy 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
atccNumber
getAtccNumber Line -
setAtccNumber - Line
cellLine
getCellLine Line -
setCellLine - Line
cellLocation
getCellLocation String -
setCellLocation - String
cellType
getCellType Line -
setCellType - Line
details
getDetails String -
setDetails - String
fraction
getFraction Text -
setFraction - Text
geneMnemonic
getGeneMnemonic Text -
setGeneMnemonic - Text
genus
getGenus Line -
setGenus - Line
ictvCode
getIctvCode Text -
setIctvCode - Text
kingdom
getKingdom Line -
setKingdom - Line
ncbiTaxonomyId
getNcbiTaxonomyId Text -
setNcbiTaxonomyId - Text
organ
getOrgan Line -
setOrgan - Line
organelle
getOrganelle Text -
setOrganelle - Text
organismAcronym
getOrganismAcronym Text -
setOrganismAcronym - Text
organismName
getOrganismName Text -
setOrganismName - Text
plasmid
getPlasmid Text -
setPlasmid - Text
plasmidDetails
getPlasmidDetails String -
setPlasmidDetails - String
scientificName
getScientificName Line -
setScientificName - Line
secretion
getSecretion String -
setSecretion - String
serial
getSerial Int -
setSerial - Int
species
getSpecies Line -
setSpecies - Line
strain
getStrain Line -
setStrain - Line
subVariant
getSubVariant Text -
setSubVariant - Text
superKingdom
getSuperKingdom Line -
setSuperKingdom - Line
tissue
getTissue Line -
setTissue - Line
variant
getVariant Line -
setVariant - Line

Link Attribute Methods (in package)

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Attribute Method Return Parameters Comment
entryMolecules
getEntryMolecules ccp.api.nmr.NmrEntry.EntryMolecule Set -
setEntryMolecules - ccp.api.nmr.NmrEntry.EntryMolecule Set
sortedEntryMolecules ccp.api.nmr.NmrEntry.EntryMolecule List -
addEntryMolecule - ccp.api.nmr.NmrEntry.EntryMolecule
removeEntryMolecule - ccp.api.nmr.NmrEntry.EntryMolecule
findFirstEntryMolecule ccp.api.nmr.NmrEntry.EntryMolecule keyword=value pairs
findAllEntryMolecules ccp.api.nmr.NmrEntry.EntryMolecule Set keyword=value pairs
molSeqFragments
getMolSeqFragments ccp.api.molecule.Molecule.MolSeqFragment Set -
setMolSeqFragments - ccp.api.molecule.Molecule.MolSeqFragment Set
sortedMolSeqFragments ccp.api.molecule.Molecule.MolSeqFragment List -
addMolSeqFragment - ccp.api.molecule.Molecule.MolSeqFragment
removeMolSeqFragment - ccp.api.molecule.Molecule.MolSeqFragment
findFirstMolSeqFragment ccp.api.molecule.Molecule.MolSeqFragment keyword=value pairs
findAllMolSeqFragments ccp.api.molecule.Molecule.MolSeqFragment Set keyword=value pairs
molecules
getMolecules ccp.api.molecule.Molecule.Molecule Set -
setMolecules - ccp.api.molecule.Molecule.Molecule Set
sortedMolecules ccp.api.molecule.Molecule.Molecule List -
addMolecule - ccp.api.molecule.Molecule.Molecule
removeMolecule - ccp.api.molecule.Molecule.Molecule
findFirstMolecule ccp.api.molecule.Molecule.Molecule keyword=value pairs
findAllMolecules ccp.api.molecule.Molecule.Molecule Set keyword=value pairs
parent
getParent Taxonomy -
targets
getTargets ccp.api.lims.Target.Target Set -
setTargets - ccp.api.lims.Target.Target Set
sortedTargets ccp.api.lims.Target.Target List -
addTarget - ccp.api.lims.Target.Target
removeTarget - ccp.api.lims.Target.Target
findFirstTarget ccp.api.lims.Target.Target keyword=value pairs
findAllTargets ccp.api.lims.Target.Target Set keyword=value pairs
taxonomy
getTaxonomy Taxonomy -

Class Methods (in package)

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Method Return Parameters Comment
checkValid - Boolean
checkAllValid - Boolean
getByKey NaturalSource 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
None

Other Methods (in package)

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Method Return Parameters Comment
None

Appendix

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guid:

www.ccpn.ac.uk_Fogh_2006-08-16-18:19:50_00003

isImplicit:

False

Tag

Value
repositoryId $Id: NaturalSource.xml,v 1.47 2011-01-13 14:40:32 rhfogh Exp $

Tag

Value
repositoryTag $Name: not supported by cvs2svn $

Special constructor code:

None

Special destructor code:

None

Constraints:

None
Known inward one-way links: ccp.api.lims.RefSampleComponent.AbstractComponent.naturalSource
  Data Model Version 2.0.6
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  Autogenerated by  PyApiDocGen  revision 1.3   on  Wed Aug 7 15:06:19 2013    from data model package  ccp.api.general.Taxonomy.NaturalSource   revision 1.47  
  Work done by the CCPN team.
www.ccpn.ac.uk