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

Chen, Yian chenyian at nibiohn.go.jp
Mon Aug 3 09:09:15 BST 2015


I think you need to configure the "kegg_config.properties" in the 
resources folder.
Your taxon ID could not be found in the kegg_config.properties.

On 2015/08/03 16:55, Pengcheng Yang wrote:
> 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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