MouseBIRN.MAGEentries (r1.1 vs. r1.28)
Diffs

 <<O>>  Difference Topic MAGEentries (r1.28 - 06 Jun 2007 - QueenieNg)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 338 to 338
META FILEATTACHMENT Illumina33TissuesTab2MBEC1_v2.xls attr="" comment="Rob Williams' Illumina33Tissues data in Tab2MAGE format" date="1178925669" path="C:\Documents and Settings\qng\My Documents\BIRN\uad\Illumina33TissuesTab2M#BEC1_v2.xls" size="66048" user="qng" version="1.1"
META FILEATTACHMENT concept_review.xls attr="" comment="Concept Terms for BIRN MAGE entries" date="1179440012" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\Ontology\concept_review.xls" size="61440" user="qng" version="1.2"
META FILEATTACHMENT MPTP_ML.xml attr="" comment="Daniel's MPTP data in MAGE-ML Format" date="1179334395" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\MAGE\MAGE-TAB\Tab2MAGE-20070424\output\MPTP_ML.xml" size="90755" user="qng" version="1.1"
Changed:
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META FILEATTACHMENT illumina33.xml attr="" comment="Rob Williams' Illumina33Tissues data in MAGE-ML format" date="1181078807" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\MAGE\MAGE-TAB\Tab2MAGE-20070424\output\illumina33.xml" size="524177" user="qng" version="1.1"
>
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META FILEATTACHMENT illumina33.xml attr="" comment="Rob Williams' Illumina33Tissues data in MAGE-ML format" date="1181148527" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\MAGE\MAGE-TAB\Tab2MAGE-20070424\output\illumina33.xml" size="508951" user="qng" version="1.2"

 <<O>>  Difference Topic MAGEentries (r1.27 - 05 Jun 2007 - QueenieNg)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 335 to 335

META FILEATTACHMENT GEO_metada.xls attr="h" comment="Daniel's GEO SOFTmatrix file and the mapping between SOFTmatrix and MAGE-TAB" date="1178571963" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metada.xls" size="29696" user="qng" version="1.2"
META FILEATTACHMENT GEO_metadata.xls attr="" comment="Daniel's MPTP data in GEOArchive format" date="1179440250" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\Sample\GEO_metadata.xls" size="41984" user="qng" version="1.2"
Changed:
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META FILEATTACHMENT Illumina33TissuesTab2MBEC1_v2.xls attr="" comment="Rob Williams' Illumina33Tissues Tab2MAGE format" date="1178925669" path="C:\Documents and Settings\qng\My Documents\BIRN\uad\Illumina33TissuesTab2M#BEC1_v2.xls" size="66048" user="qng" version="1.1"
>
>
META FILEATTACHMENT Illumina33TissuesTab2MBEC1_v2.xls attr="" comment="Rob Williams' Illumina33Tissues data in Tab2MAGE format" date="1178925669" path="C:\Documents and Settings\qng\My Documents\BIRN\uad\Illumina33TissuesTab2M#BEC1_v2.xls" size="66048" user="qng" version="1.1"

META FILEATTACHMENT concept_review.xls attr="" comment="Concept Terms for BIRN MAGE entries" date="1179440012" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\Ontology\concept_review.xls" size="61440" user="qng" version="1.2"
META FILEATTACHMENT MPTP_ML.xml attr="" comment="Daniel's MPTP data in MAGE-ML Format" date="1179334395" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\MAGE\MAGE-TAB\Tab2MAGE-20070424\output\MPTP_ML.xml" size="90755" user="qng" version="1.1"
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META FILEATTACHMENT illumina33.xml attr="" comment="Rob Williams' Illumina33Tissues data in MAGE-ML format" date="1181078807" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\MAGE\MAGE-TAB\Tab2MAGE-20070424\output\illumina33.xml" size="524177" user="qng" version="1.1"

 <<O>>  Difference Topic MAGEentries (r1.26 - 17 May 2007 - QueenieNg)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 334 to 334

META FILEATTACHMENT GEO_metada.xls attr="h" comment="Daniel's GEO SOFTmatrix file and the mapping between SOFTmatrix and MAGE-TAB" date="1178571963" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metada.xls" size="29696" user="qng" version="1.2"
Changed:
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META FILEATTACHMENT GEO_metadata.xls attr="" comment="Daniel's MPTP data in GEOArchive format" date="1178921247" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metadata.xls" size="29696" user="qng" version="1.1"
>
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META FILEATTACHMENT GEO_metadata.xls attr="" comment="Daniel's MPTP data in GEOArchive format" date="1179440250" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\Sample\GEO_metadata.xls" size="41984" user="qng" version="1.2"

META FILEATTACHMENT Illumina33TissuesTab2MBEC1_v2.xls attr="" comment="Rob Williams' Illumina33Tissues Tab2MAGE format" date="1178925669" path="C:\Documents and Settings\qng\My Documents\BIRN\uad\Illumina33TissuesTab2M#BEC1_v2.xls" size="66048" user="qng" version="1.1"
Changed:
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META FILEATTACHMENT concept_review.xls attr="" comment="Concept Terms for BIRN MAGE entries" date="1178925737" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\Ontology\concept_review.xls" size="38400" user="qng" version="1.1"
>
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META FILEATTACHMENT concept_review.xls attr="" comment="Concept Terms for BIRN MAGE entries" date="1179440012" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\Ontology\concept_review.xls" size="61440" user="qng" version="1.2"

META FILEATTACHMENT MPTP_ML.xml attr="" comment="Daniel's MPTP data in MAGE-ML Format" date="1179334395" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\MAGE\MAGE-TAB\Tab2MAGE-20070424\output\MPTP_ML.xml" size="90755" user="qng" version="1.1"

 <<O>>  Difference Topic MAGEentries (r1.25 - 16 May 2007 - QueenieNg)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 334 to 334

META FILEATTACHMENT GEO_metada.xls attr="h" comment="Daniel's GEO SOFTmatrix file and the mapping between SOFTmatrix and MAGE-TAB" date="1178571963" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metada.xls" size="29696" user="qng" version="1.2"
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META FILEATTACHMENT GEO_metadata.xls attr="" comment="" date="1178921247" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metadata.xls" size="29696" user="qng" version="1.1"
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META FILEATTACHMENT GEO_metadata.xls attr="" comment="Daniel's MPTP data in GEOArchive format" date="1178921247" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metadata.xls" size="29696" user="qng" version="1.1"

META FILEATTACHMENT Illumina33TissuesTab2MBEC1_v2.xls attr="" comment="Rob Williams' Illumina33Tissues Tab2MAGE format" date="1178925669" path="C:\Documents and Settings\qng\My Documents\BIRN\uad\Illumina33TissuesTab2M#BEC1_v2.xls" size="66048" user="qng" version="1.1"
META FILEATTACHMENT concept_review.xls attr="" comment="Concept Terms for BIRN MAGE entries" date="1178925737" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\Ontology\concept_review.xls" size="38400" user="qng" version="1.1"
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META FILEATTACHMENT MPTP_ML.xml attr="" comment="Daniel's MPTP data in MAGE-ML Format" date="1179334395" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\MAGE\MAGE-TAB\Tab2MAGE-20070424\output\MPTP_ML.xml" size="90755" user="qng" version="1.1"

 <<O>>  Difference Topic MAGEentries (r1.24 - 15 May 2007 - QueenieNg)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 17 to 17
    • Recommendations: We need input on what other types of information should be kept in this area

Ontology Entries

Changed:
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<		 Click here?for entries need to be mapped to BIRNLex.
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>		 Click herefor entries need to be mapped to BIRNLex.

  1. Information about who is providing the data and where they are from
    • Role (Submitter/Experimenter)
    • Primary Investigator
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    • Institute
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    • Institute name, url

    • Funder and Grant #
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    • Contact Information
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    • Contact Information (phone, email)

    • Other?
  1. File information
    • File name
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    • File location on other DB
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    • File location on other DB (url, uri, or urn)

    • File format
    • Date file generated (need this?)
    • Other?
  1. Experiment Information
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    • Experiment name
    • Experiment description

    • Array Chip Type
    • Annotation or Reference to an external annotation database
    • Normalization or Summarization
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    • Public accessible?
    • Publication Status (published, unpublished, submitted, in press, confidential)

  1. Experiment details
    • IRB information or human subject information
    • Group of Interest (normal, control, diseased, pre-diseased)
Line: 43 to 47
    • Treatment chemical/compound
    • Tissue or structures information
  1. Subject(s) information
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    • Species
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    • Species (preferred name and scientific name)

    • Strains
    • Developmental Stage (embryonic stages and adult stages)
    • Age/Age Unit
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    • Gender (male, female, hemphrodites, other)
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    • Sex(male, female, hemphrodites, other)

Ontology references:
Line: 92 to 96
Date of Experiment yyyy-mm-dd
Public Release Date yyyy-mm-dd
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PubMedID?  
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PubMedID  

Publication Author List  
Publication Status  
Experment Description  
Line: 123 to 127

 This is a software package supported by ArrayExpress curators, which is able to generate MAGE-ML from Tab2MAGE spreadsheet document.The spreadsheet consists of three sections, separated by one or more blank lines: Experiment, Protocol and Hybridization.

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Line: 323 to 327

Case Reference

* Daniel Sforza: Microarray data Workflow Presentation
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<		 * Rob William: Illumina33Tissues Tab2MAGE format?
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Working Page to look at the Minimum Amount of Metadata a Microarray Data Submitter should provide

 <<O>>  Difference Topic MAGEentries (r1.23 - 14 May 2007 - QueenieNg)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 17 to 17
    • Recommendations: We need input on what other types of information should be kept in this area

Ontology Entries

Added:
>
>		 Click here?for entries need to be mapped to BIRNLex.

  1. Information about who is providing the data and where they are from
    • Role (Submitter/Experimenter)
Line: 322 to 323

Case Reference

* Daniel Sforza: Microarray data Workflow Presentation
Changed:
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<		 * Rob William: Illumina33Tissues Tab2MAGE format?
>
>		 * Rob William: Illumina33Tissues Tab2MAGE format?

Working Page to look at the Minimum Amount of Metadata a Microarray Data Submitter should provide

 <<O>>  Difference Topic MAGEentries (r1.22 - 11 May 2007 - QueenieNg)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 322 to 322

Case Reference

* Daniel Sforza: Microarray data Workflow Presentation
Added:
>
>		 * Rob William: Illumina33Tissues Tab2MAGE format?

Working Page to look at the Minimum Amount of Metadata a Microarray Data Submitter should provide
Line: 329 to 330

META FILEATTACHMENT GEO_metada.xls attr="h" comment="Daniel's GEO SOFTmatrix file and the mapping between SOFTmatrix and MAGE-TAB" date="1178571963" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metada.xls" size="29696" user="qng" version="1.2"
META FILEATTACHMENT GEO_metadata.xls attr="" comment="" date="1178921247" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metadata.xls" size="29696" user="qng" version="1.1"
Added:
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META FILEATTACHMENT Illumina33TissuesTab2MBEC1_v2.xls attr="" comment="Rob Williams' Illumina33Tissues Tab2MAGE format" date="1178925669" path="C:\Documents and Settings\qng\My Documents\BIRN\uad\Illumina33TissuesTab2M#BEC1_v2.xls" size="66048" user="qng" version="1.1"
META FILEATTACHMENT concept_review.xls attr="" comment="Concept Terms for BIRN MAGE entries" date="1178925737" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\Ontology\concept_review.xls" size="38400" user="qng" version="1.1"

 <<O>>  Difference Topic MAGEentries (r1.21 - 11 May 2007 - QueenieNg)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 327 to 327

 Working Page to look at the Minimum Amount of Metadata a Microarray Data Submitter should provide
Changed:
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META FILEATTACHMENT GEO_metada.xls attr="" comment="Daniel's GEO SOFTmatrix file and the mapping between SOFTmatrix and MAGE-TAB" date="1178571963" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metada.xls" size="29696" user="qng" version="1.2"
>
>
META FILEATTACHMENT GEO_metada.xls attr="h" comment="Daniel's GEO SOFTmatrix file and the mapping between SOFTmatrix and MAGE-TAB" date="1178571963" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metada.xls" size="29696" user="qng" version="1.2"
META FILEATTACHMENT GEO_metadata.xls attr="" comment="" date="1178921247" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metadata.xls" size="29696" user="qng" version="1.1"

 <<O>>  Difference Topic MAGEentries (r1.20 - 11 May 2007 - JylBoline)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 323 to 323

Case Reference

* Daniel Sforza: Microarray data Workflow Presentation
Added:
>
>
Working Page to look at the Minimum Amount of Metadata a Microarray Data Submitter should provide

META FILEATTACHMENT GEO_metada.xls attr="" comment="Daniel's GEO SOFTmatrix file and the mapping between SOFTmatrix and MAGE-TAB" date="1178571963" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metada.xls" size="29696" user="qng" version="1.2"

 <<O>>  Difference Topic MAGEentries (r1.19 - 11 May 2007 - JylBoline)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 135 to 135

 Daniel has submitted a microarray dataset to GEO using the SOFTmatrix and GEOarchive metadata format, and found it much clearer with example and annotations for large Affymetrix datasets. Their format may be easier for researchers to organize their information easily, and easily integrate with the database entries.

Example
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  • Click here for Daniel's submittied file, which also includes the mapping between GEOarchive meta data and MAGE-TAB metadata.
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  • Click here for Daniel's submittied file, which also includes the mapping between GEOarchive meta data and MAGE-TAB metadata.


 <<O>>  Difference Topic MAGEentries (r1.18 - 07 May 2007 - QueenieNg)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 323 to 323

Case Reference

* Daniel Sforza: Microarray data Workflow Presentation
Changed:
<
<
META FILEATTACHMENT GEO_metada.xls attr="" comment="Daniel's GEO SOFTmatrix file and the mapping between SOFTmatrix and MAGE-TAB" date="1178557843" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metada.xls" size="29696" user="qng" version="1.1"
>
>
META FILEATTACHMENT GEO_metada.xls attr="" comment="Daniel's GEO SOFTmatrix file and the mapping between SOFTmatrix and MAGE-TAB" date="1178571963" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metada.xls" size="29696" user="qng" version="1.2"

 <<O>>  Difference Topic MAGEentries (r1.17 - 07 May 2007 - QueenieNg)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 127 to 127
Added:
>
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GEO SOFTmatrix and GEOarchive

Daniel has submitted a microarray dataset to GEO using the SOFTmatrix and GEOarchive metadata format, and found it much clearer with example and annotations for large Affymetrix datasets. Their format may be easier for researchers to organize their information easily, and easily integrate with the database entries.

Example
  • Click here for Daniel's submittied file, which also includes the mapping between GEOarchive meta data and MAGE-TAB metadata.
  • Link to GEO site
  • Metadata mapping between GEOarchive and MAGE-TAB.
    GEOarchive MAGE-TAB
    SERIES IDF
    title Investigation Title
    summary Experiment Description
    overall design Experimental Design
    type N/A
    contributor[] Person Last Name
    Person First Name
    Person Mid Initial
    PLATFORM  
    title Investigation Title
    technology Protocol Contact
    distribution N/A
    organism Characteristics[] in SDRF section
    manufacturer Term Source
    manufacture protocol Term Source File
    SAMPLES SDRF
    Sample name Sample Name
    title Hybridization Name
    CEL file [Affymetrix submissions only] Array Data File
    EXP file [Affymetrix submissions only] Array Data File
    source name Source Name, Material Type
    organism Characteristics[organism]
    characteristics[] Characteristics[] (e.g Characteristics[Strain], Characteristics[Gender], Characteristics[Age])
    molecule Extract Name, Material Type
    label Label
    description Description
    platform reference to Term Source Name in IDF file
    PROTOCOLS  
    growth protocol Protocol Name, Protocol Type, Protocol Description
    treatment protocol Investigation Title
    extract protocol Same as Above
    EXP file [Affymetrix submissions only] Same as Above
    label protocol Same as Above
    hyb protocol Same as Above
    scan protocol Same as Above
    data processing Normalization Name
    value definition N/A


MAGE-ML

Line: 272 to 323

Case Reference

* Daniel Sforza: Microarray data Workflow Presentation
Added:
>
>
META FILEATTACHMENT GEO_metada.xls attr="" comment="Daniel's GEO SOFTmatrix file and the mapping between SOFTmatrix and MAGE-TAB" date="1178557843" path="C:\Documents and Settings\qng\My Documents\BIRN\Gene Expression\GEO_metada.xls" size="29696" user="qng" version="1.1"

 <<O>>  Difference Topic MAGEentries (r1.16 - 03 May 2007 - QueenieNg)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 56 to 56

Changed:
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MAGE-TAB Examples and Use Cases

MAGE-TAB is a simplied version of MAGE-ML, and is proposed to be part of MAGEv2. It consists four different types of files: Investigation Description Format(IDF), Array Design Format(ADF), Sample and Data Relationship Format(SDRF), Raw and processed data files.
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MAGE-TAB

MAGE-TAB is a simplied version of MAGE-ML, and is proposed to be part of MAGEv2. The data is arranged in tabular format instead of XML like MAGE-ML. It consists four different types of files: Investigation Description Format(IDF), Array Design Format(ADF), Sample and Data Relationship Format(SDRF), Raw and processed data files.

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Examples and Use Cases

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Investigation Description Format (IDF) Example:
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Investigation Description Format (IDF) Example:

Investigation Title Chronic Mouse Model of Parkinson's Disease
Experimental Design Parkinson_Disease_Design
Line: 103 to 107
Term Source File http://fireball.drexelmed.edu/birnlex/
Term Source Version 1.2

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Sample and Data Relationship Format(SDRF) Example
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Sample and Data Relationship Format(SDRF) Example

Sourc Name Hybridization Name Array Design REF TERM SOURCE REF Array Data File Derived Array Data File
Sample 1 Experiment 1 A-AFFY-MOE430 AFFYMETRIX_TERM Data1.CEL AFFY_data1.CHP
Line: 112 to 116
M6_FCX Mouse Brain Frontal Cortex Adult   MPTP M6_FCX_Ext M6_FCX_lab_biotin Biotin M6_CTx_hyb
C6_FCX Mouse Brain Frontal Cortex Adult   Saline C6_FCX_Ext C6_FCX_lab_biotin Biotin C6_CTX_hyb
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Tab2MAGE

This is a software package supported by ArrayExpress curators, which is able to generate MAGE-ML from Tab2MAGE spreadsheet document.The spreadsheet consists of three sections, separated by one or more blank lines: Experiment, Protocol and Hybridization.


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Example XML broken down by MAGE-ML package

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MAGE-ML

Example XML broken down by MAGE-ML package

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Audit and Security
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Audit and Security

Audit and Security package contains classes that describe an individaul contact information, or an oragnization information, as wells as the the security group they belong, and the role they play.

Classes Item Detail Example
Line: 138 to 154
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Description
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Description

Description package contains classes that describe the external databases or annotations being referenced to.

Classes Item Detail Example
Line: 148 to 164
  Ontology Entries    
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Array
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Array

Array package contains classes that describe individual arrays, including detailed information on relevant manufacturing proccesses. It also contains references to the LIMS data that might contain BioMaterial information being used.

Classes Item Detail Example
Line: 160 to 176
    other array properties should be automatically loaded based on the array chip model
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ArrayDesign
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ArrayDesign

ArrayDesign package contains classes that describe a microarray design. PhysicalArrayDesign describes the design that is being used to manufacture physical array.

Classes Item Detail Remarks and Example
Line: 171 to 187
    Species ontology term
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DesignElement
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DesignElement

DesignElement contains classes that describes the purpose of each Array. The Feature describe the intended location on the Array. It can be specified as reporters or CompositeSequence for the arrays.
Line: 181 to 197
  Control Type    
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Experiment
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Experiment

Experiment package contains a collection of BioAssays that are related to the ExperimentalDesign. ExperimentalDesign is the description and collection of ExperimentalFactors and the BioAssays information.

Classes Item Detail Example
Line: 192 to 208
ExperimentDesign
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BioSequence
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BioSequence

BioSequence is a representation of DNA, RNA, protein sequence. It can be represented as Clone, Gene or a sequence.

Classes Item Detail Example
BioSequence      
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BioMaterial
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BioMaterial

BioMaterial package describes the biological material being used, and the description of the creation through BioSource, BioSample, LabelExtract classes. BioMaterial can be related to other BioMaterial through DAG(directed acyclic graph). BioSample are products of treatments that are of interest. It can be used as the sources of other BioSamples. BioSource is the raw material information. LabelExtracts are special BioSamples? that have Compounds that are detectable.

Classes Item Detail Example
Line: 211 to 227
  LabelExtract    
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BioAssay
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BioAssay

BioAssay represents both physical and computational groupings of arrays and biomaterials. PhysicalBioAssay is a bioAssay created by the BioAssayCreation event. A measured bioAssay is the direct processing of information in a physical bioAssay by the featureExtraction event. DerivedBioAssay is created by the Transformation BioEvent? from one or more MeasuredBioAssays or DerivedBioAssays.

Classes Item Detail Example
Line: 227 to 243
  Channel    
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BioAssayData
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BioAssayData

BioAssayData describes gene expression data. BioDataValues contain the actual values.

Classes Item Detail Example
Line: 238 to 254
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Protocol
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Protocol

Classes Item Detail Example
Protocol      
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QuantitationType
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QuantitationType

QuantitationType describes the data that are communicated in microarray experiments. It can be Standard or Specialized types. The standard types can be MeasuredSignal, DerivedSignal, Ratio or PresentAbsent, or PValue, Error and ExpectedValue. Specialized types are user defined.

Classes Item Detail Example

 <<O>>  Difference Topic MAGEentries (r1.15 - 02 May 2007 - QueenieNg)

META TOPICPARENT MAGEWorkingPage
- 20 Apr 2007

Working Page to standardize some of the MAGE entries across Mouse BIRN or BIRN test beds

Line: 108 to 108
Sample 1 Experiment 1 A-AFFY-MOE430 AFFYMETRIX_TERM Data1.CEL AFFY_data1.CHP
Changed:
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Sample Name Characteristics
[Organism] 		Characteristics
[Organism Part] 		Characteristics
[Developmental Stage] 		Protocol REF Parameter Value
[Compound] 		Extract Name Labeled Extract Name Label Hybridization Name
M6_FCX Brain Frontal Cortex Adult   MPTP M6_FCX_Ext M6_FCX_lab_biotin Biotin M6_CTx_hyb
C6_FCX Brain Frontal Cortex Adult   Saline C6_FCX_Ext C6_FCX_lab_biotin Biotin C6_CTX_hyb
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Sample Name Characteristics [Organism] Characteristics [Organism Part] Characteristics [Organism Part] Characteristics
[Developmental Stage] 		Protocol REF Parameter Value
[Compound] 		Extract Name Labeled Extract Name Label Hybridization Name
M6_FCX Mouse Brain Frontal Cortex Adult   MPTP M6_FCX_Ext M6_FCX_lab_biotin Biotin M6_CTx_hyb
C6_FCX Mouse Brain Frontal Cortex Adult   Saline C6_FCX_Ext C6_FCX_lab_biotin Biotin C6_CTX_hyb


 <<O>>  Difference Topic MAGEentries (r1.14 - 30 Apr 2007 - QueenieNg)

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Sample Name Characteristics
[Organism] 		Characteristics
[Organism Part] 		Characteristics
[Developmental Stage] 		Protocol REF Parameter Value
[Compound] 		Extract Name Labeled Extract Name Label Hybridization Name
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Sample_1_Exp Brain Frontal Cortex Adult   MPTP MPTP Ext M6 FCX MPTP M6 Exp Pt 2
Sample_1_Ctrl Brain Frontal Cortex Adult   Saline Saline Ext C6 FCX Saline C6 Ctrl Pt 2
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M6_FCX Brain Frontal Cortex Adult   MPTP M6_FCX_Ext M6_FCX_lab_biotin Biotin M6_CTx_hyb
C6_FCX Brain Frontal Cortex Adult   Saline C6_FCX_Ext C6_FCX_lab_biotin Biotin C6_CTX_hyb


 <<O>>  Difference Topic MAGEentries (r1.13 - 26 Apr 2007 - QueenieNg)

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    • Age/Age Unit
    • Gender (male, female, hemphrodites, other)

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Ontology references:

MAGE-TAB Examples and Use Cases


 <<O>>  Difference Topic MAGEentries (r1.12 - 25 Apr 2007 - QueenieNg)

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- 20 Apr 2007

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MAGE-TAB Examples and Use Cases

MAGE-TAB is a simplied version of MAGE-ML, and is proposed to be part of MAGEv2. It consists four different types of files: Investigation Description Format(IDF), Array Design Format(ADF), Sample and Data Relationship Format(SDRF), Raw and processed data files.
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<		 Click tab2MAGE Home Page or MAGE Group for MAGE-TAB v1.0 specification and further info.
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Investigation Description Format (IDF) Example:
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<		 TermDefinition
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Investigation Description Format (IDF) Example:

Investigation Title Chronic Mouse Model of Parkinson's Disease
Experimental Design Parkinson_Disease_Design

 <<O>>  Difference Topic MAGEentries (r1.11 - 25 Apr 2007 - QueenieNg)

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- 20 Apr 2007

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 Click tab2MAGE Home Page or MAGE Group for MAGE-TAB v1.0 specification and further info.

Investigation Description Format (IDF) Example:
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TermDefinition


Investigation Title Chronic Mouse Model of Parkinson's Disease
Experimental Design Parkinson_Disease_Design
Experimental Factor Name genetic_modification_design

 <<O>>  Difference Topic MAGEentries (r1.10 - 25 Apr 2007 - QueenieNg)

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- 20 Apr 2007

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Changed:
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MAGE-TAB Exmples and Use Cases

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MAGE-TAB Examples and Use Cases


MAGE-TAB is a simplied version of MAGE-ML, and is proposed to be part of MAGEv2. It consists four different types of files: Investigation Description Format(IDF), Array Design Format(ADF), Sample and Data Relationship Format(SDRF), Raw and processed data files.

Click tab2MAGE Home Page or MAGE Group for MAGE-TAB v1.0 specification and further info.

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Term Source File http://fireball.drexelmed.edu/birnlex/
Term Source Version 1.2

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Sample and Data Relationship Format(SDRF) Exmple
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Sample and Data Relationship Format(SDRF) Example

Sourc Name Hybridization Name Array Design REF TERM SOURCE REF Array Data File Derived Array Data File
Sample 1 Experiment 1 A-AFFY-MOE430 AFFYMETRIX_TERM Data1.CEL AFFY_data1.CHP