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{{FAQ
release=2.4.0 |
entrydate=April 20, 2011 |
topic=Installation and Upgrade |
Qtext=A step-by-step guide to Create MAGE-TAB template specific to RPLA Project |
Atext= |
Create RPLA providers in the contact table as for other array providers:
insert into contact (discriminator, provider, name) values ('O', 1,'Zeptosens'); |
After the insert, use statement below to find the ID for the contact just created:
Select ID from contact where name ='Zeptosens'; |
Create a new RPLA assay type in the database in the assay_type table:
insert into assay_type (name) values ('RPLA'); |
Since a new technical term: reverse_phase_protein_array_features would be inserted into term_source table under the source of caArray, it is necessary to check if the source of *caArray*has already added in term_source table. During the normal caArray installation, caArray should have been added to the term_source table with a default ID =4. To verify, apply the select statement below:
select * from term_source where name='caArray' |
If caArray is not a valid source in the term_source table, it should be added with the insert statement below:
insert into term_source (name, version, url) values ('caArray','2.0','https://array.nci.nih.gov') |
After source caArray added, use the SELECT statement above to find the ID for the source caArray just created in the term_source table. The id will be used in the insert statement below to add the new terminology reverse_phase_protein_array_features to the term table:
insert into term (value, source) values('reverse_phase_protein_array_features', <id of term_source inserted above>); |
Use the SELECT statement below to find the ID for the term just created:
SELECT ID from term where value = 'reverse_phase_protein_array_features'; |
Use this ID in the INSERT statement below:
insert into term_categories (term_id, category_id) values (<id of term inserted above>, 224); |
Create MAGE-TAB ADF dummy array design files (.ADF files) for the array provider Zeptosens, created in Step 1. The dummy file can be a empty file with a simple header.
Upload new array designs for each ADF using the caArray web application (For more details, please refer to Using caArray: Uploading Array Design File ). The new file will have the final status of "Imported no Parsed".
After uploading dummy array designs into caArray, update their array_design table entries in the database to lsid_authority to be Zeptosens.com, lsid_namespace to be PhysicalArrayDesign. This SQL statement will work only after the array design file is added to caArray.
update array_design set lsid_authority = 'Zeptosens.com', |
Next step is to create new file types for the RPLA data file formats you have. This modification is not at the database level, but file level. The file is:
caarray_src_2_3_1_1/caarray.war/src/main/java/ApplicationResources.properties |
Following is an example the RPLA data file in text format:
experiment.files.filetype.Zeptosens_TXT = Zeptosens TXT |
After the properties is edited, caArray must be rebuilt and redeployed.
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