Re: [base] Reporter file Upload (Agilent Chip)

Mon, 24 Apr 2006 02:31:06 -0700 

Hi David,
If you are able to map all the data that you want to insert from the Agilent chip file to a DB column, you don't need the doc describing how to add custom clmns in your DB. 


When specifying a file format in BASE, you have to specify 2 patterns in 
addition to do the mapping. One pattern for recognising the text file as 
belonging to this format, and one pattern for recognizing the line 
specifying the column headers in your tab-delimited file. BASE provides 
drop-down menus for you to select a line to be recognised, and BASE will 
generate a pattern for you to recognise the selected line.


You need to do this before a "test with file" can be successful.


Also check that the number of columns limits are correct, if they are 
wrong, no data lines with the correct number of items will be found.


Hope this helps,
Kjell

Zhao, David wrote:


-----Original Message-----

From: Zhao, David 
Sent: Friday, April 21, 2006 10:32 AM

To: 'basedb-users@lists.sourceforge.net'
Subject: RE: [base] Reporter file Upload (Agilent Chip)

Thanks, Kjell. I found Paul's thread on "Customizing RawBioAssayData and 
Reporter" (http://sourceforge.net/mailarchive/message.php?msg_id=9861016), but 
couldn't see the attached doc file.
What I've done with aglient chip data uploade was:
1. import the tab-delimited chip data with header, data looks like this:
ProbeID PrimaryAccession        RefSeqAccession GenbankAccession        
UniGeneID       EntrezGeneID    GeneSymbol      GeneName        EnsemblID       
TIGRID  GO      Description     GenomicCoordinates      Cytoband
A_51_P401471    AK011951                AK011951        Mm.379129       67160   
                ENSMUST00000003784      TC1477950               Mus musculus 10 
days embryo whole body cDNA, RIKEN full-length enriched library, 
clone:2610301D06 product:ELONGATION FACTOR-LIKE PROTEIN, full insert sequence 
[AK011951]       chr19:8174931-8174990   mm|19qA
A_51_P315841    NM_178444       NM_178444       NM_178444       Mm.268933       
353156                  ENSMUST00000078614      NP360173        
GO:0001525(angiogenesis)|GO:0005509(calcium ion 
binding)|GO:0005615(extracellular space)|GO:0030336(negative regulation of cell 
migration)      Mus musculus EGF-like domain 7 (Egfl7), transcript variant a, 
mRNA [NM_178444]  chr2:26524781-26524840  mm|2qA3
....

2. specify "Reporter file format", find corresponding columns for the existing 
database columns:
Reporter ID     \1\

Species		 
UniGene cluster ID	\5\

Gene name       \8\

Gene symbol	\7\		 
Length		 
Sequence		 
Vector		 
Tissue		 
Library		 
Accession	\2\		 
NID		 
Chrom.	\13\	 
Cytoband	\14\	 
Markers		 
Antibiotics		 
LocusLink	\3\		 
OMIM		 
Start pos.		 
End pos.


But when "test with file", I got " Warning: The file does not match this format: 
Data not yet found after 0 lines", and when I try to update, no row was updated.
Please help!

David   
-----Original Message-----
From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Kjell Petersen
Sent: Friday, April 21, 2006 1:37 AM
To: basedb-users@lists.sourceforge.net
Subject: Re: [base] Reporter file Upload (Agilent Chip)


The upload limits are set in the php.ini file, the BASE intsallation 
documentation (in the tar ball) pin-points the exact parameters in the 
PHP section.



After editing php.ini, apache must be restarted for the php module in 
apache to read the changes.


Cheers,
Kjell

Zhao, David wrote:


 


Hi there,

I'm trying to upload Agilent chip data into BASE, is there a How-to on this 
subject (couldn't find it in the BASE documentation), can I add custom more 
columns? How can I bypass 2MB file upload limit? Thanks very much in advance!


David 






   




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Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
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