[InterMine Dev] kegg-pathway load: genespathways table is empty

Pengcheng Yang yangpc at biols.ac.cn
Mon Aug 3 08:55:33 BST 2015


Hi Julie Sullivan,

Thank you for your reply.

I listed the kegg-pathway part of the project.xml file for the two mine. 
It seems they have no difference except the path and organisms.

[1] The project.xml of my mine:
----------------------
<source name="kegg-pathway" type="kegg-pathway">
        <property name="kegg.organisms" value="1111"/>
       <property name="src.data.dir" location="/path/to/mymine/kegg/"/>
     </source>

[2] The project.xml of malariamine
     <source name="kegg-pathway" type="kegg-pathway">
       <property name="kegg.organisms" value="36329"/>
       <property name="src.data.dir" location="/path/to/malaria/kegg/"/>
     </source>

I have checked the file org_gene_map.tab file, its format indeed is: 
GeneID<tb>mapid<space>mapid<space>mapid

Best,
Pengcheng Yang

On 2015/8/3 15:32, Julie Sullivan wrote:
> Sorry you are having problems with the kegg source!
>
> Can you clarify what is different about the two project XML files?
>
> On 02/08/15 10:01, Pengcheng Yang wrote:
>> Hi InterMiner developers,
>>
>> Thank you all who answered my questions. Here is another question that
>> blocked my way to deploy my InterMine.
>>
>> To load kegg-pathway data, I set the project.xml as that in malariamine
>> and prepared the two files map_title.tab and org_gene_map.tab. When I
>> load the data using "ant -Dsource=kegg-pathway -v 1> kegg-pathway.log1
>> 2> kegg-pathway.log2", the kegg-pathway.log1 said at the end [1].
>> However, when I query in the postgres database using SQL language:
>> "select * from genespathways", nothing returned.
>>
>> But when I do the same thing for malariamine after loading kegg-pathway
>> data, I got the pathways to genes information as [2] listed. So I
>> compared the log information between my mine and malariamine, and found
>> my mine hasn't build several the indexes as [3] listed.
>>
>> Because I have used the same sources kegg-pathway as malariamine, so
>> what the problem here?
>>
>> Any suggestions and comments are welcom! Thanks a lot!
>>
>> Best,
>> Pengcheng Yang
>>
>>
>> ---------------------------------
>> [1] build successful log information from my mine after load 
>> kegg-pathway
>> /BUILD SUCCESSFUL//
>> //Total time: 21 seconds//
>> //[Thread-16] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
>> db.common-tgt-items is being shutdown.//
>> //[Thread-8] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
>> db.common-tgt-items is being shutdown.//
>> //[Thread-16] INFO com.zaxxer.hikari.pool.HikariPool - HikariCP pool
>> db.production is being shutdown./
>>
>> [2] genespathways table from malariamine database.
>>
>>   pathways |  genes
>> ----------+---------
>>    2000002 | 1002796
>>    2000002 | 1003874
>>    2000002 | 1004075
>>
>> [3] the log information not appeared in my mine but in malariamine.
>>   [integrate] Creating index: CREATE INDEX Gene__key_secondaryidentifier
>> ON Gene (secondaryIdentifier, organismid)
>>   [integrate] Creating index: CREATE INDEX Gene__key_symbol_org ON Gene
>> (symbol, organismid)
>>   [integrate] Creating index: CREATE INDEX Gene__key_primaryidentifier
>> ON Gene (primaryIdentifier)
>>   [integrate] Creating index: CREATE INDEX Organism__key_taxonid ON
>> Organism (taxonId)
>>   [integrate] Creating index: CREATE INDEX SOTerm__key ON SOTerm (name,
>> ontologyid)
>>
>>
>> _______________________________________________
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>> dev at intermine.org
>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>
>





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