OBO files and annotation

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OBO files and annotation

Paulo Nuin
Hi everyone

We are trying to substitute on XML file that loads anatomy terms by an OBO file connected to an annotation one (extension WB for us). I was able to easily create code necessary to load the OBO file, but the annotation is turning a little bit trickier. Documentation is quite slim for this, is there any resource that would help me with this?

Do we need to generate our own class or we can use a generic annotation loader? What is the preferred configuration strategy?

Any help appreciated

Thanks

Paulo
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Re: OBO files and annotation

Julie Sullivan-2
Paulo,

OBO is a standard file format, that's why we can have a central
InterMine parser for OBO files. GO's annotation file format (GAF) is
also standard, so we have a central file parser for that.

Does the file you have have a standard as well? Or is it a custom file
format? We have parsers for most standard biological file formats:

        http://intermine.readthedocs.io/en/latest/

Click on "Data Sources" > "Core InterMine sources"

If you have a custom file format, you'll have to write your own data
parser. If the file format is close to the GAF, you can use that parser
to start from, and edit as needed. And here's a pretty simple source for
human phenotype annotation:

https://github.com/intermine/intermine/tree/dev/bio/sources/human/hpo-annotation

Again, a custom file from the HPO people, but might be a useful starting
point! Maybe.

Here are the docs on how to write your own source:

        http://intermine.readthedocs.io/en/latest/

Click on "Data Sources" > "Writing your own data source"

You'll use one of our APIs to load the data. We have Java and Perl:

        http://intermine.readthedocs.io/en/latest/

Click on "Data Sources" > "APIs"

Justin's started on a Python API as well.

Good luck! :)

Cheers
Julie

On 27/06/18 05:13, Paulo Nuin wrote:

> Hi everyone
>
> We are trying to substitute on XML file that loads anatomy terms by an OBO file connected to an annotation one (extension WB for us). I was able to easily create code necessary to load the OBO file, but the annotation is turning a little bit trickier. Documentation is quite slim for this, is there any resource that would help me with this?
>
> Do we need to generate our own class or we can use a generic annotation loader? What is the preferred configuration strategy?
>
> Any help appreciated
>
> Thanks
>
> Paulo
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
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Re: OBO files and annotation

Sam Hokin-3
In reply to this post by Paulo Nuin
Hi, Paulo! Just FYI, I do my GO annotations in a post-processor, so in case you decide to do that (load the OBO and WB independently
during integrate and then link them up in postprocess) here's an example:

https://github.com/LegumeFederation/legfed-bio-postprocess/blob/gradle/legfed-create-go-annotations/src/main/java/org/intermine/bio/postprocess/CreateGOAnnotationsProcess.java

I do it this way because I load genes from all over the place and felt that annotation is more of a post-process, linking GO terms
listed in the gene descriptions with GO terms. (Yes, funky, but that's how we roll.)

On 06/26/2018 10:13 PM, Paulo Nuin wrote:

> Hi everyone
>
> We are trying to substitute on XML file that loads anatomy terms by an OBO file connected to an annotation one (extension WB for
> us). I was able to easily create code necessary to load the OBO file, but the annotation is turning a little bit trickier.
> Documentation is quite slim for this, is there any resource that would help me with this?
>
> Do we need to generate our own class or we can use a generic annotation loader? What is the preferred configuration strategy?
>
> Any help appreciated
>
> Thanks
>
> Paulo
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Re: OBO files and annotation

Paulo Nuin
Thanks Julie and Sam.

Indeed our WB files are GAF2.0 format, so I am guessing just adapt the code for the regular GO Annotation step should be enough.

!gaf-version: 2.0
!Project_name: WormBase
!Contact Email: [hidden email]
WB      WBGene00000001  aap-1   Certain WBbt:0003679    WB_REF:WBPaper00005614  IDA     WB:Expr2275     A               Y110A7A.10      gene    taxon:6239      20180416
WB
WB      WBGene00000001  aap-1   Enriched        WBbt:0003679    WB_REF:WBPaper00030839  IDA     WB:WBPaper00030839:Larval_Pan_Neuronal  A               Y110A7A.10      gene
taxon:6239      20180416        WB

Probably the most important change would be the _keys.properties file. I am assuming the keys in the file are connected to each column in the file, is that correct?

Thanks again

Paulo



> On Jun 29, 2018, at 6:28 AM, Sam Hokin <[hidden email]> wrote:
>
> Hi, Paulo! Just FYI, I do my GO annotations in a post-processor, so in case you decide to do that (load the OBO and WB independently during integrate and then link them up in postprocess) here's an example:
>
> https://github.com/LegumeFederation/legfed-bio-postprocess/blob/gradle/legfed-create-go-annotations/src/main/java/org/intermine/bio/postprocess/CreateGOAnnotationsProcess.java
>
> I do it this way because I load genes from all over the place and felt that annotation is more of a post-process, linking GO terms listed in the gene descriptions with GO terms. (Yes, funky, but that's how we roll.)
>
> On 06/26/2018 10:13 PM, Paulo Nuin wrote:
>> Hi everyone
>> We are trying to substitute on XML file that loads anatomy terms by an OBO file connected to an annotation one (extension WB for
>> us). I was able to easily create code necessary to load the OBO file, but the annotation is turning a little bit trickier.
>> Documentation is quite slim for this, is there any resource that would help me with this?
>> Do we need to generate our own class or we can use a generic annotation loader? What is the preferred configuration strategy?
>> Any help appreciated
>> Thanks
>> Paulo
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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