GFF Collection

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GFF Collection

Delmans, Mihails
Hello,

I am trying to load a gff3 file that annotates interpro protein domains. I have the following model:

<class name="Protein" is-interface="true">
        <collection name="proteinDomains" referenced-type="ProteinDomain" reverse-reference="proteins" />
    </class>

    <class name="ProteinDomain" extends="BioEntity" is-interface="true">
        <attribute name="score" type="java.lang.Double"/>
        <attribute name="scoreType" type="java.lang.String"/>
        <attribute name="length" type="java.lang.Integer"/>
        <collection name="proteins" referenced-type="Protein" reverse-reference="proteinDomains"/>
    </class>

In my gff3 record handler I have:

public InterproGffGFF3RecordHandler (Model model) {
        super(model);
        refsAndCollections.put("ProteinDomain", "proteins");
    }

When I do protein domain queries in webapp I have only one protein (first occurrence in the gff3 file) in the collection of proteins associated with each protein domain.

On the contrary, proteins are loaded with the multiple protein domains (apart from those which had been already assigned to some other protein).

I attach my gff3 file with this letter.

Thanks,
Mihails






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cam1TAP.pep.gff3 (1M) Download Attachment
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Re: GFF Collection

Sergio Contrino
hi mihails,
it seems there is a problem when you are not locating the feature on a
chromosome.
could you send us also your (complete) recordhandler?
thanks
sergio


On 23/09/14 15:46, Delmans, Mihails wrote:

> Hello,
>
> I am trying to load a gff3 file that annotates interpro protein domains.
> I have the following model:
>
> <class name="Protein" is-interface="true">
>          <collection name="proteinDomains"
> referenced-type="ProteinDomain" reverse-reference="proteins" />
>      </class>
>
>      <class name="ProteinDomain" extends="BioEntity" is-interface="true">
>          <attribute name="score" type="java.lang.Double"/>
>          <attribute name="scoreType" type="java.lang.String"/>
>          <attribute name="length" type="java.lang.Integer"/>
>          <collection name="proteins" referenced-type="Protein"
> reverse-reference="proteinDomains"/>
>      </class>
>
> In my gff3 record handler I have:
>
> public InterproGffGFF3RecordHandler (Model model) {
>          super(model);
>          refsAndCollections.put("ProteinDomain", "proteins");
>      }
>
> When I do protein domain queries in webapp I have only one protein
> (first occurrence in the gff3 file) in the collection of proteins
> associated with each protein domain.
>
> On the contrary, proteins are loaded with the multiple protein domains
> (apart from those which had been already assigned to some other protein).
>
> I attach my gff3 file with this letter.
>
> Thanks,
> Mihails
>
>
>
>
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

--
sergio contrino                                InterMine, Cambridge
https://sergiocontrino.github.io           http://www.intermine.org

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