Re: data integration

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Re: data integration

Julie Sullivan
Hi Aditi,

Your config looks correct to me!

According to BioGRID, they have only one bee interaction:

        http://wiki.thebiogrid.org/doku.php/statistics

And I don't see a GeneID in the XML, so you might not even see that one
interaction.

Here are the InterMine docs for BioGRID

http://intermine.readthedocs.org/en/latest/database/data-sources/library/interactions/biogrid/

Julie

On 27/10/14 20:08, Tayal, Aditi wrote:

> Hey Julie,
>
> For displaying in cytoscape with the biogrid information, I did the following:
>
>
> webconfig-model.xml
>
> <reportdisplayer javaClass="org.intermine.bio.web.displayer.CytoscapeNetworkDisplayer"
>          jspName="model/cytoscapeNetworkDisplayer.jsp"
>          replacesFields="interactions"
>          placement="Interactions"
>          types="Gene,Protein"/>
>
> struts-config
> <action path="/cytoscapeNetworkExport" type="org.intermine.bio.web.struts.CytoscapeNetworkExportAction"/>
> <action path="/cytoscapeNetworkAjax" type="org.intermine.bio.web.struts.CytoscapeNetworkAjaxAction"/>
>
> aspects.xml
>
> <aspect name="Interactions">
>    <subtitle>IntAct</subtitle>
>    <icon-image>model/images/interaction.gif</icon-image>
>    <large-image>model/images/interaction.gif</large-image>
>    <tile-name></tile-name>
>    <intro-text>
>      Protein-protein interactions from IntAct (PSI-MI format), genetic interactions from the BioGRID and miRNA target predictions from miRBase.
>    </intro-text>
>    <tile-name>model/interactions.jsp</tile-name>
>    <aspect-source name="BioGRID" url="http://www.thebiogrid.org/"/>
> </aspect>
>
>
> gff_keys.properties
> DataSet.key = name
> DataSource.key = name
> SOTerm.key = name, ontology
> Organism.key = taxonId
> Ontology.key = name
> Publication.key = pubMedId
> Gene.key_primaryIdentifier = primaryIdentifier
> Gene.key_primaryidentifier=primaryIdentifier
> Gene.key_secondaryidentifier=secondaryIdentifier
> Gene.key_symbol=symbol, organism
> Gene.key_biogrid=name, symbol
>
>
> biogrid_keys.properties
>
>   DataSet.key_title=name
> DataSource.key_name=name
> Gene.key_primaryidentifier=primaryIdentifier
> Gene.key_symbol_org=symbol, organism
> InteractionExperiment.key_name_pub=name, publication
> Interaction.key_interaction=gene1, gene2
> InteractionTerm.key_name=name
> Ontology.key_title=name
> OntologyTerm.key_identifier=identifier
> OntologyTerm.key_name_ontology=name, ontology
> Organism.key_taxonid=taxonId
> Publication.key_pubmed=pubMedId
> Gene.key_symbol=symbol
> Gene.key_biogrid= symbol, name
>
>
>
> biogrid.config.prop
>
> # amel
> 7460.symbol = shortLabel
> 7460.xref.primaryIdentifier = GeneID
>
>
>
>
> Am I missing something? my interaction table is still empty. Sorry for the long email.
>
> Thank you,
> Aditi
>
>
> ________________________________________
> From: Julie Sullivan [[hidden email]]
> Sent: Friday, October 24, 2014 10:54 AM
> To: Tayal, Aditi
> Subject: Re: [InterMine Dev] data integration
>
> 1. Can you query for interactions? Are you sure the data loaded
> correctly? Here's an example:
>
> http://www.flymine.org/release-40.0/template.do?name=Gene_Interactions
>
> Can you run a similar query?
>
> 2. GBrowse can reference another server:
>
> http://intermine.readthedocs.org/en/latest/webapp/report-page/report-displayers-examples/#gbrowse
>
> On 24/10/14 15:56, Tayal, Aditi wrote:
>> Hello Julie,
>>
>> Thank you for your quick response. I have a couple of questions.
>> 1) I am trying to show gff and biogrid data in cytoscape.  I understand it pulls information from the interaction table. But my interaction table is empty!! Is there special settings for it? I did exactly what was mentioned in the manual about cytoscape.
>>
>> 2) for gbrowse is it required to have a local instance of it on the server where you are trying to set up intermine? I have been trying to use one installed on a different server and it's not working.
>>
>> Thank you,
>> Aditi
>>
>> ________________________________________
>> From: Julie Sullivan [[hidden email]]
>> Sent: Thursday, October 23, 2014 4:58 AM
>> To: Tayal, Aditi
>> Cc: [hidden email]
>> Subject: Re: [InterMine Dev] data integration
>>
>> Hi Aditi
>>
>> Here are the docs for the GFF source:
>>
>> http://intermine.readthedocs.org/en/latest/database/data-sources/library/gff/
>>
>> So you can use the `gff_config.properties` configuration file to set
>> values for your genes. e.g. something like:
>>
>> 511145.attributes.locus_tag=secondaryIdentifier
>>
>> This would set the locus_tag in the GFF to be Gene.secondaryIdentifier
>> in your database and webapp.
>>
>> As for chromosome location, take a look at these:
>>
>> http://intermine.readthedocs.org/en/latest/database/database-building/post-processing/
>>
>> `create-chromosome-locations-and-lengths` is probably what you need.
>>
>> Try that and let us know?
>>
>> Cheers
>> Julie
>>
>> On 22/10/14 22:17, Tayal, Aditi wrote:
>>> Hello Sir/Madam,
>>>
>>> I am developing an intermine for bees. I am having trouble integrating
>>> data.
>>>
>>> I connected biogrid with gff file through the gff_keys.properties file
>>> and biogid_keys.properties file. However, When i release the webapp I am
>>> only able to see the symbol information that connects the gff and
>>> biogrid. I want to display other information like the chromosome
>>> location, secondary identifier, length on the Biogrid information page.
>>> How do we extract more information from the gff to display on the
>>> biogrid page?
>>>
>>> Any pointers will be appreciated
>>>
>>> Thank you,
>>> Aditi
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>>>
>>
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: Orthodb configuration

Julie Sullivan
Hi Aditi

Again, that worked for me. I added those lines of config and
successfully created 15464 genes (and associated homologues).

Maybe do what you did for the harvester ant, run "ant clean" and try again?

Julie

On 20/11/14 21:45, Tayal, Aditi wrote:

> Hi Julie,
>
> I have been trying to configure orthodb for the following species and my
> database is empty. I did the same thing you advised me for Pogonomyrmex
> barbatus. Please refer to the email below.
>
>
> taxon.610380.genus= Harpegnathos
> taxon.610380.species= saltator
> Thank you
>
>
>
>
>
>
> On Nov 18, 2014, at 11:01 AM, [hidden email]
> <mailto:[hidden email]> wrote:
>
>> That worked for me. I added those lines, and successfully created genes.
>>
>> Maybe run ant clean first? e.g. you are still using the old compiled
>> files.
>>
>>> Hi Julie,
>>>
>>> I added the code you suggested. My database is till empty for
>>> Pogonomyrmex
>>> barbatus. Are there any other modifications I might have to make?
>>>
>>> Thank you
>>>
>>>
>>> On Nov 18, 2014, at 3:54 AM, Julie Sullivan <[hidden email]
>>> <mailto:[hidden email]>> wrote:
>>>
>>>>
>>>>
>>>>> /Does the parser for orthodb data automatically updates its lookup
>>>> table
>>>>> depending on the organism?
>>>>
>>>> No, we use a file we generated to look up organism names. If you add
>>>> your organism to it, it should work fine. Here is what worked for me:
>>>>
>>>> https://github.com/intermine/intermine/commit/330309caac713ceb950f5e6efa6a4fdd53ced1ac
>>>>
>>>> I've made a ticket to do this automatically:
>>>>
>>>> https://github.com/intermine/intermine/issues/814
>>>>
>>>>
>>>> On 17/11/14 20:04, Tayal, Aditi wrote:
>>>>> Hi Julie,
>>>>> I am trying to load orthodb data for "Pogonomyrmex barbatus/"
>>>>> //Taxonomy
>>>>> ID: /144034/ in intermine. The gene id for this organism is present in
>>>>> the gff. However, the data is from the orthodb file is not loading  and
>>>>> the database is empty. I tried doing this with and without the ID
>>>>> resolver. /
>>>>> /Does the parser for orthodb data automatically updates its lookup
>>>>> table
>>>>> depending on the organism? Or is there some modifications we have to do
>>>>> to the parser / gene info table.?/
>>>>> /
>>>>> /
>>>>> /
>>>>> /
>>>>> / Following is a snip of the orthodb and the gff /
>>>>> /
>>>>> /
>>>>> /
>>>>> /
>>>>> /orthodb file(/OrthoDB7_ALL_METAZOA_tabtext)
>>>>> /
>>>>> /
>>>>> 286EOG72K577PB22745-PA*PB22745*Pogonomyrmex
>>>>> barbatus9HYMENULLNULLIPR000608 IPR016135
>>>>> /
>>>>> /
>>>>> gff file
>>>>>
>>>>> scf71pbar1.7gene24356122436860.-.*ID=PB22745;Name=PB22745*;Alias=PB22745;
>>>>> scf71pbar1.7mRNA24356122436860.-.ID=PB22745-RA;Name=PB22745-RA;Alias=PB22745-RA
>>>>>
>>>>>
>>>>> Orthodb_config file
>>>>>
>>>>> 144034.geneid=primaryIdentifier
>>>>>
>>>>> Orthodb_keys file
>>>>>
>>>>> Gene.key_primaryidentifier=primaryIdentifier
>>>>>
>>>>>
>>>>> Gff keys file
>>>>>
>>>>> Gene.key_primaryidentifier=primaryIdentifier
>>>>>
>>>>>
>>>>> Thank you
>>>
>>>
>>>
>>
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev