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

Julie Sullivan julie at flymine.org
Mon Aug 3 10:10:37 BST 2015


Can you send me the configuration you added to the file?

This is the list of KEGG organisms and associated abbreviations:

	http://www.genome.jp/kegg/catalog/org_list.html


On 03/08/15 10:06, Pengcheng Yang wrote:
>
> Hi Chen Yian and Julie Sullivan,
>
> Thank you for your reply and the information.
>
> I have tried both the following two methods, the talbe "genespathways"
> remains empty.
> 1) Adding the org.taxonId=1111 to the
> bio/sources/kegg-pathway/resources/kegg-pathway_keys.properties file.
> Here the taxonId and organism name were coined for confidential reason.
> 2) remove the "kegg.organisms" property from project.xml file.
>
> I have checked the related information maybe useful:
> 1) "select  * from pathway" return expected information.
> 2) I compared the kegg-pathway.log1 file from mymine and malariamine and
> found the following that specific to mymine, not existed in
> malariamine's kegg-pathway.log1
>
> <     [javac] org/intermine/model/bio/ProteinDomainRegion.java added as
> org/intermine/model/bio/ProteinDomainRegion.class is outdated.
> <     [javac] org/intermine/model/bio/ProteinDomainRegionShadow.java
> added as org/intermine/model/bio/ProteinDomainRegionShadow.class is
> outdated.
> 3172,3173d3169
> <     [javac] org/intermine/model/bio/ProteinRegion.java added as
> org/intermine/model/bio/ProteinRegion.class is outdated.
> <     [javac] org/intermine/model/bio/ProteinRegionShadow.java added as
> org/intermine/model/bio/ProteinRegionShadow.class is outdated.
> 3217c3213
> <     [javac]
> /home/pengchy/Soft/05.SystemBiology/intermine/mymine/dbmodel/build/gen/src/org/intermine/model/bio/ProteinDomainRegion.java
>
> <     [javac]
> /home/pengchy/Soft/05.SystemBiology/intermine/mymine/dbmodel/build/gen/src/org/intermine/model/bio/ProteinDomainRegionShadow.java
>
> 3352,3353d3345
> <     [javac]
> /home/pengchy/Soft/05.SystemBiology/intermine/mymine/dbmodel/build/gen/src/org/intermine/model/bio/ProteinRegion.java
>
> <     [javac]
> /home/pengchy/Soft/05.SystemBiology/intermine/mymine/dbmodel/build/gen/src/org/intermine/model/bio/ProteinRegionShadow.java
>
> 3540,3541d3531
> <   [lib:jar] org/intermine/model/bio/ProteinDomainRegion.class added as
> org/intermine/model/bio/ProteinDomainRegion.class is outdated.
> <   [lib:jar] org/intermine/model/bio/ProteinDomainRegionShadow.class
> added as org/intermine/model/bio/ProteinDomainRegionShadow.class is
> outdated.
> 3543,3544d3532
> <   [lib:jar] org/intermine/model/bio/ProteinRegion.class added as
> org/intermine/model/bio/ProteinRegion.class is outdated.
> <   [lib:jar] org/intermine/model/bio/ProteinRegionShadow.class added as
> org/intermine/model/bio/ProteinRegionShadow.class is outdated.
> <   [lib:jar] adding entry
> org/intermine/model/bio/ProteinDomainRegion.class
> <   [lib:jar] adding entry
> org/intermine/model/bio/ProteinDomainRegionShadow.class
> 3720,3721d3705
> <   [lib:jar] adding entry org/intermine/model/bio/ProteinRegion.class
> <   [lib:jar] adding entry
> org/intermine/model/bio/ProteinRegionShadow.class
> <     [javac] org/intermine/model/bio/ProteinDomainRegion.java added as
> org/intermine/model/bio/ProteinDomainRegion.class is outdated.
> <     [javac] org/intermine/model/bio/ProteinDomainRegionShadow.java
> added as org/intermine/model/bio/ProteinDomainRegionShadow.class is
> outdated.
> 7230,7231d7211
> <     [javac] org/intermine/model/bio/ProteinRegion.java added as
> org/intermine/model/bio/ProteinRegion.class is outdated.
> <     [javac] org/intermine/model/bio/ProteinRegionShadow.java added as
> org/intermine/model/bio/ProteinRegionShadow.class is outdated.
> 7275c7255
>
> Thanks a lot!
>
> Best,
> Pengcheng Yang
>
>
>
> On 2015/8/3 16:14, Julie Sullivan wrote:
>> Here are the docs on the kegg source:
>>
>> http://intermine.readthedocs.org/en/latest/database/data-sources/library/pathways/kegg/
>>
>>
>> KEGG uses its own prefix, which InterMine does not know. You have to
>> configure this in the config file.
>>
>> e.g. KEGG uses "dme" for Drosophila melanogaster and the data file is
>> named "dme_gene_map.tab".
>>
>> The reason why malaria worked is that is already configured:
>>
>> https://github.com/intermine/intermine/blob/master/bio/sources/kegg-pathway/main/resources/kegg_config.properties#L37
>>
>>
>> You have two options:
>>
>> 1. remove the taxon ID from your project XML file, all genes will be
>> loaded
>>
>> 2. configure the taxon ID in the kegg_config.properties
>>
>>
>>
>> On 03/08/15 08:55, 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)
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> dev mailing list
>>>>> dev at intermine.org
>>>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>>>
>>>>
>>>
>>>
>>>
>>
>
>
>



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