Issues with SO terms

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Issues with SO terms

Paulo Nuin
Hi everyone

I am having trouble adding new terms included in our new GFF3, even though the term was added to /dbmodel/resources/so_terms. In can it is circular_ncRNA and the output of the builddb process from gradle 

 The following terms specified in so_terms are not valid Sequence Ontology terms according to so.obo: circular_ncRNA

I still have some old code from previous version with the so.obo and the circular_ncRNA is not included in the file, but I am guessing this is an older file. I can see the term on the SO website


Is there a way to use another so.obo and make the term accepted?

Thanks

Paulo

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Re: Issues with SO terms

sergio contrino-2
hi paulo,
you can merge the dev branch of intermine, or just update the file
bio/core/src/main/resources/so.obo
(with an updated so.obo from
https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/so.obo)

please let me know if you have still have issues.
thanks
sergio

On 2020-11-18 23:41, Paulo Nuin wrote:

> Hi everyone
>
> I am having trouble adding new terms included in our new GFF3, even
> though the term was added to /dbmodel/resources/so_terms. In can it is
> circular_ncRNA and the output of the builddb process from gradle
>
>  The following terms specified in so_terms are not valid Sequence
> Ontology terms according to so.obo: circular_ncRNA
>
> I still have some old code from previous version with the so.obo and
> the circular_ncRNA is not included in the file, but I am guessing this
> is an older file. I can see the term on the SO website
>
> http://www.sequenceontology.org/browser/current_release/term/SO:0002291
>
> Is there a way to use another so.obo and make the term accepted?
>
> Thanks
>
> Paulo
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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Re: Issues with SO terms

sergio contrino-2
forgot to reply all...
sergio

On 2020-11-19 16:10, [hidden email] wrote:

> hi paulo,
> the modification in dev happened after the 4.2.0 release, so just
> updating won't help.
> to use a locally updated file please install locally. something like
> cd bio && ./gradlew clean install
> should do it in your case, for a complete install see command below.
> thanks!
> sergio
>
>
> (cd plugin && ./gradlew clean install)&&
> (cd intermine && ./gradlew clean install) &&
> (cd bio && ./gradlew clean install) &&
> (cd bio/sources && ./gradlew clean install)  &&
> (cd bio/postprocess/ && ./gradlew clean install)
>
>
> On 2020-11-19 15:54, Paulo Nuin wrote:
>> Hi Sergio
>>
>> Thanks. I am updating to 4.2.0, I guess this one points to the newest
>> OBO.
>>
>> Also, how do I use my own version of InterMine? I don’t get the
>> bio/core/src/main/resources/so.obo locally.
>>
>> Cheers
>>
>> Paulo
>>
>>> On Nov 19, 2020, at 1:57 AM, [hidden email] wrote:
>>>
>>> hi paulo,
>>> you can merge the dev branch of intermine, or just update the file
>>> bio/core/src/main/resources/so.obo
>>> (with an updated so.obo from
>>> https://raw.githubusercontent.com/The-Sequence-Ontology/SO-Ontologies/master/Ontology_Files/so.obo)
>>>
>>> please let me know if you have still have issues.
>>> thanks
>>> sergio
>>>
>>> On 2020-11-18 23:41, Paulo Nuin wrote:
>>>> Hi everyone
>>>> I am having trouble adding new terms included in our new GFF3, even
>>>> though the term was added to /dbmodel/resources/so_terms. In can it
>>>> is
>>>> circular_ncRNA and the output of the builddb process from gradle
>>>> The following terms specified in so_terms are not valid Sequence
>>>> Ontology terms according to so.obo: circular_ncRNA
>>>> I still have some old code from previous version with the so.obo and
>>>> the circular_ncRNA is not included in the file, but I am guessing
>>>> this
>>>> is an older file. I can see the term on the SO website
>>>> http://www.sequenceontology.org/browser/current_release/term/SO:0002291
>>>> Is there a way to use another so.obo and make the term accepted?
>>>> Thanks
>>>> Paulo
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>

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