(r1.1 vs. r1.9) MAGEWorkingPage < MouseBIRN

MouseBIRN.MAGEWorkingPage (r1.1 vs. r1.9)

Diffs

<<O>> Difference Topic MAGEWorkingPage (r1.9 - 20 Sep 2007 - QueenieNg)

META TOPICPARENT	GeneExpressionDM

20 Apr 2007

Line: 40 to 40

- CHADO data schema
- See specifically the Expression module.
Adopting Gemma database from UBiC(UBC Bioinformatics Center)

Added:

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- HTML Version of the model

Developer work based on our “official” first draft of BIRN MAGE

<<O>> Difference Topic MAGEWorkingPage (r1.8 - 20 Sep 2007 - QueenieNg)

META TOPICPARENT	GeneExpressionDM

20 Apr 2007

Line: 20 to 20

Compare and differentiate the information between MAGE and XCEDE.
Compare and differentiate the information between MAGE and BioWarehouse framework.
- We may need to write our own MAGE loader to cover those packages that are not supported by the existing MAGE loader created by BioWarehouse.

Added:

>
>

Compare and differentiate the information between BioWarehouse framework, CHADO Model, and Gemma database.

Link to the MAGE Entries Working page

Line: 38 to 39

The Generic Model Organism Database consortium
- CHADO data schema
- See specifically the Expression module.

Added:

>
>

Adopting Gemma database from UBiC(UBC Bioinformatics Center)

Developer work based on our “official” first draft of BIRN MAGE

<<O>> Difference Topic MAGEWorkingPage (r1.7 - 25 Apr 2007 - JylBoline)

META TOPICPARENT	GeneExpressionDM

20 Apr 2007

Line: 45 to 45

Import the MAGE files to BioWarehouse.
Create webservices to export the data from BioWarehouse to MAGE or other XML format that the client application supports.
Create XSLT to transforma MAGE to XCEDE and vice versa.

Added:

>
>

Minutes and Plans

MAGE_04_25_07.doc: 04/25/07: minutes from first MAGE meeting, overview and plan

Added:

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META FILEATTACHMENT	MAGE_04_25_07.doc	attr="" comment="04/25/07: minutes from first MAGE meeting, overview and plan" date="1177542832" path="MAGE_04_25_07.doc" size="34304" user="jboline" version="1.1"

<<O>> Difference Topic MAGEWorkingPage (r1.6 - 25 Apr 2007 - WilliamBug)

META TOPICPARENT	GeneExpressionDM

20 Apr 2007

Line: 26 to 26

References or links of interest

Affymetrix and EPI sites do provide very detailed explanation and examples of their usage of MAGE.

Changed:

<
<

The MAGE Good Practice section. http://www.ebi.ac.uk/~ele/ext/submitter.html
The Excel spreadsheet for mapping the MAGE-OM to data within Stanford Microarray database. http://www.mged.org/Workgroups/MAGE/mage.html

>
>

The MAGE Good Practice section at EBI
MAGE at the The MGED Site
- The Excel spreadsheet for mapping the MAGE-OM to data within Stanford Microarray database
- Model views:
  - Graphic display of MAGE OM
  - an HTML view
BioWarehouse
- BioWarehouse BMC Bioinformatics article - March 2006
- the BioWarehouse MAGE Loader page
The Generic Model Organism Database consortium
- CHADO data schema
- See specifically the Expression module.

Developer work based on our “official” first draft of BIRN MAGE

<<O>> Difference Topic MAGEWorkingPage (r1.5 - 25 Apr 2007 - JylBoline)

META TOPICPARENT	GeneExpressionDM

20 Apr 2007

Line: 6 to 6

For the past couple months, we have been trying to adopt MAGE as our standard, and make our existing BIRN Micro-array database to be MAGE compliant. Since BioWarehouse has the API and database framework that supports MAGE, we have decided to migrate our existing database to BioWarehouse.

Primary goal: Create MouseBIRN or BIRN group instance of MAGE by itemizing those packages in MAGE that are applicable to most MouseBIRN or BIRN group, and mapping our existing data model to MAGE-OM.

Changed:

<
<

>
>

Background

So far, we have our initial MouseBIRN MAGE instance created based on MPTP data. This is a very preliminary form, and still open for suggestion. After our meeting with Stanley Nelson’s group, we found that they are also revolutionizing their existing MAGE instance, and we may not share similar data structures. However, they provide valuable input, and based on those and our research, here are some issues hopefully we can get it ironed out ASAP so that we can move forward.

Changed:

<
<

>
>

Tasks

Standardize some of the entries format across Mouse BIRN or BIRN test beds like
- the identifier prefix

Line: 21 to 21

Compare and differentiate the information between MAGE and BioWarehouse framework.
- We may need to write our own MAGE loader to cover those packages that are not supported by the existing MAGE loader created by BioWarehouse.

Added:

>
>

Link to the MAGE Entries Working page

References or links of interest

Affymetrix and EPI sites do provide very detailed explanation and examples of their usage of MAGE.

The MAGE Good Practice section. http://www.ebi.ac.uk/~ele/ext/submitter.html
The Excel spreadsheet for mapping the MAGE-OM to data within Stanford Microarray database. http://www.mged.org/Workgroups/MAGE/mage.html

Changed:

<
<

>
>

Developer work based on our “official” first draft of BIRN MAGE

Create XSLT to transform BIRN Microarray data or GeneNetwork data to MAGE format.

<<O>> Difference Topic MAGEWorkingPage (r1.4 - 24 Apr 2007 - JylBoline)

META TOPICPARENT	GeneExpressionDM

20 Apr 2007

Line: 11 to 11

Tasks

Changed:

<
<

Standardize some of the entries format across Mouse BIRN or BIRN test beds like

>
>

Standardize some of the entries format across Mouse BIRN or BIRN test beds like

- the identifier prefix
- database reference code
- ontology entries

<<O>> Difference Topic MAGEWorkingPage (r1.3 - 23 Apr 2007 - QueenieNg)

  META TOPICPARENT  GeneExpressionDM 

20 Apr 2007

  Introduction of the issue 
For the past couple months, we have been trying to adopt MAGE as our standard, and make our existing BIRN Micro-array database to be MAGE compliant. Since BioWarehouse has the API and database framework that supports MAGE, we have decided to migrate our existing database to BioWarehouse.
-<
<
+Primary goal:  Create MouseBIRN or BIRN group instance of MAGE by itemizing those packages in MAGE that are applicable to most MouseBIRN or BIRN group.
->
>
+Primary goal:  Create MouseBIRN or BIRN group instance of MAGE by itemizing those packages in MAGE that are applicable to most MouseBIRN or BIRN group, and mapping our existing data model to MAGE-OM.
   Background 
So far, we have our initial MouseBIRN MAGE instance created based on MPTP data. This is a very preliminary form, and still open for suggestion. After our meeting with Stanley Nelson’s group, we found that they are also revolutionizing their existing MAGE instance, and we may not share similar data structures. However, they provide valuable input, and based on those and our research, here are some issues hopefully we can get it ironed out ASAP so that we can move forward.

  Tasks
-<
<
+Standardize some of the entries format across Mouse BIRN or BIRN test beds like
->
>
+ Standardize some of the entries format across Mouse BIRN or BIRN test beds like
  the identifier prefix

 database reference code 

 ontology entries 

 acceptable data file format 

 log entries information
-<
<
+Click on MAGEentries to go to the page to work on these entries.

Compare and differentiate the information between MAGE and XCEDE. 
Compare and differentiate the information between MAGE and BioWarehouse framework.
->
>
+ Compare and differentiate the information between MAGE and XCEDE. 

 Compare and differentiate the information between MAGE and BioWarehouse framework.
  We may need to write our own MAGE loader to cover those packages that are not supported by the existing MAGE loader created by BioWarehouse.

<<O>> Difference Topic MAGEWorkingPage (r1.2 - 20 Apr 2007 - QueenieNg)

META TOPICPARENT	GeneExpressionDM

20 Apr 2007

Introduction of the issue

Changed:

<
<

For the past couple months, we have been trying to adopt MAGE as our standard, and make our existing BIRN Micro-array database to be MAGE compliant. Since BioWarehouse^? has the API and database framework that supports MAGE, we have decided to migrate our existing database to BioWarehouse^?.

>
>

Changed:

<
<

Primary goal: Create MouseBIRN^? or BIRN group instance of MAGE by itemizing those packages in MAGE that are applicable to most MouseBIRN^? or BIRN group.

>
>

Primary goal: Create MouseBIRN or BIRN group instance of MAGE by itemizing those packages in MAGE that are applicable to most MouseBIRN or BIRN group.

Background

Changed:

<
<

So far, we have our initial Mouse BIRN MAGE instance created based on MPTP data. This is a very preliminary form, and still open for suggestion. After our meeting with Stanley Nelson’s group, we found that they are also revolutionizing their existing MAGE instance, and we may not share similar data structures. However, they provide valuable input, and based on those and our research, here are some issues hopefully we can get it ironed out ASAP so that we can move forward.

>
>

Tasks

Standardize some of the entries format across Mouse BIRN or BIRN test beds like

Line: 20 to 20

Click on MAGEentries to go to the page to work on these entries.

Compare and differentiate the information between MAGE and XCEDE.

Changed:

<
<

Compare and differentiate the information between MAGE and BioWarehouse^? framework.

We may need to write our own MAGE loader to cover those packages that are not supported by the existing MAGE loader created by BioWarehouse^?.

>
>

Compare and differentiate the information between MAGE and BioWarehouse framework.

We may need to write our own MAGE loader to cover those packages that are not supported by the existing MAGE loader created by BioWarehouse.

References or links of interest

Line: 31 to 31

Developer work based on our “official” first draft of BIRN MAGE

Changed:

<
<

Create XSLT to transform BIRN Microarray data or GeneNetwork^? data to MAGE format.
Import the MAGE files to BioWarehouse^?.
Create webservices to export the data from BioWarehouse^? to MAGE or other XML format that the client application supports.

>
>

Create XSLT to transform BIRN Microarray data or GeneNetwork data to MAGE format.
Import the MAGE files to BioWarehouse.
Create webservices to export the data from BioWarehouse to MAGE or other XML format that the client application supports.

Create XSLT to transforma MAGE to XCEDE and vice versa.

<<O>> Difference Topic MAGEWorkingPage (r1.1 - 20 Apr 2007 - JylBoline)

Line: 1 to 1

Added:

>
>

META TOPICPARENT	GeneExpressionDM

20 Apr 2007

Introduction of the issue

Primary goal: Create MouseBIRN^? or BIRN group instance of MAGE by itemizing those packages in MAGE that are applicable to most MouseBIRN^? or BIRN group.

Background

So far, we have our initial Mouse BIRN MAGE instance created based on MPTP data. This is a very preliminary form, and still open for suggestion. After our meeting with Stanley Nelson’s group, we found that they are also revolutionizing their existing MAGE instance, and we may not share similar data structures. However, they provide valuable input, and based on those and our research, here are some issues hopefully we can get it ironed out ASAP so that we can move forward.

Tasks

Standardize some of the entries format across Mouse BIRN or BIRN test beds like

the identifier prefix
database reference code
ontology entries
acceptable data file format
log entries information

Click on MAGEentries to go to the page to work on these entries.

Compare and differentiate the information between MAGE and XCEDE. Compare and differentiate the information between MAGE and BioWarehouse^? framework.

We may need to write our own MAGE loader to cover those packages that are not supported by the existing MAGE loader created by BioWarehouse^?.

References or links of interest

Affymetrix and EPI sites do provide very detailed explanation and examples of their usage of MAGE.

The MAGE Good Practice section. http://www.ebi.ac.uk/~ele/ext/submitter.html
The Excel spreadsheet for mapping the MAGE-OM to data within Stanford Microarray database. http://www.mged.org/Workgroups/MAGE/mage.html

Developer work based on our “official” first draft of BIRN MAGE

Create XSLT to transform BIRN Microarray data or GeneNetwork^? data to MAGE format.
Import the MAGE files to BioWarehouse^?.
Create webservices to export the data from BioWarehouse^? to MAGE or other XML format that the client application supports.
Create XSLT to transforma MAGE to XCEDE and vice versa.

Topic: MAGEWorkingPage . { View | Diffs | r1.9 | > | r1.8 | > | r1.7 | More }

Revision r1.1 - 20 Apr 2007 - 20:57 - JylBoline
Revision r1.9 - 20 Sep 2007 - 18:58 - QueenieNg