Issue 5532: Recommend adding StandardQuantitationType, 'Failed' of type boolean (gene-expression-ftf)
Source: Rosetta Biosoftware Business Unit (Mr. Michael D Miller, nobody)
Nature: Uncategorized Issue
Severity: 
Summary: Recommend adding StandardQuantitationType, 'Failed' of type boolean, 
to represent overall failure


Resolution of the issue would change:
MAGE-OM and the generated MAGE.xmi
MAGE-ML.dtd
3.1.17, "QuantitationType" of the documentation

Resolution: see below
Revised Text: 2.1.17, "QuantitationType" of the documentation

Figure 2-20 will be updated (see QuantitationType.png)

Add documentation section for Failed after documentation for Ratio

Currently: does not exist

Becomes:

" Failed

Values associated with this QuantitationType indicate a failure of some kind for a particular DesignElement for a BioAssay. Of type boolean.

Derived from StandardQuantitationType"
 
 
 MAGE-OM and the generated MAGE.xmi are updated to add the new class named Failed
 
 
  MAGE-ML.dtd

Currently:

"<!ENTITY % QuantitationType_classes "SpecializedQuantitationType |

DerivedSignal |

MeasuredSignal |

Error |

PValue |

ExpectedValue |

Ratio |

PresentAbsent" >

<!ENTITY % QuantitationType_ref "QuantitationType_ref |

SpecializedQuantitationType_ref |

DerivedSignal_ref |

MeasuredSignal_ref |

Error_ref |

PValue_ref |

ExpectedValue_ref |

Ratio_ref |

PresentAbsent_ref" >"

Becomes:

"<!ENTITY % QuantitationType_classes "SpecializedQuantitationType |

DerivedSignal |

MeasuredSignal |

Error |

PValue |

ExpectedValue |

Ratio |

PresentAbsent |

Failed" >

<!ENTITY % QuantitationType_ref "QuantitationType_ref |

SpecializedQuantitationType_ref |

DerivedSignal_ref |

MeasuredSignal_ref |

Error_ref |

PValue_ref |

ExpectedValue_ref |

Ratio_ref |

PresentAbsent_ref |

Failed_ref" >"

Currently:

Declaration for Failed doesn't exist

Becomes:

"<!--

Element and Attlist declarations for Failed

Values associated with this QuantitationType indicate a failure of 

some kind for a particular DesignElement for a BioAssay. Of type 

boolean.

Associations

Inherites associations from base class StandardQuantitationType.

Attributes

Inherites attributes from base class StandardQuantitationType.

-->

<!ELEMENT Failed_ref EMPTY >

<!ATTLIST Failed_ref identifier CDATA #REQUIRED 

name CDATA #IMPLIED >

<!ELEMENT Failed ((%StandardQuantitationType_content;)) >

<!ATTLIST Failed %StandardQuantitationType_attrs; >"
 

Actions taken:
July 20, 2002: received issue
December 11, 2002: closed issue
Discussion: 
This will allow a standard way to mark a feature has having failed to be extracted successfully by feature extraction
End of Annotations:=====
Recommend adding StandardQuantitationType, 'Failed' of type boolean, 
to represent overall failure


Resolution of the issue would change:
MAGE-OM and the generated MAGE.xmi
MAGE-ML.dtd
3.1.17, "QuantitationType" of the documentation


(MAGE ISSUE 117)