Error on loading GO

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Error on loading GO

Paulo Nuin
Hi everyone

We encountered an error when loading GO data, especially with entries that are annotated as obsolete and have two consider links at the bottom.

The error:


Caused by: Error: Attempted to specify obsolete value obsolete negative regulation of growth of symbiont on or near host surface for consider tag.
on line: 410135
charnum: -1
line: consider: GO:0044140
        at org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1691)
        at org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74)
        at org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:273)
        ... 50 more

The item

[Term]
id: GO:0075309
name: obsolete negative regulation of growth or development of symbiont on or near host surface
namespace: biological_process
def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the increase in the symbiont's size or mass, or its progression from an initial condition to a later condition, on or near the cells or tissues of the host org$
comment: This term was made obsolete because it contained a conjunction (or). It has been replaced with the terms 'negative regulation of development of symbiont on or near host surface ; GO:0044141' and 'negative regulation of growth of symbiont on or $
synonym: "negative regulation of growth or development of symbiont on or near host surface" EXACT []
is_obsolete: true
consider: GO:0044140
consider: GO:0044141

The only solution we found was to remove these items. Is there anything that can be added to the loader that would remedy the situation? We are using InterMine’s GO loader.

Thanks

Paulo


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Re: Error on loading GO

Sam Hokin-3
Which version, Paulo? I made some updates some time ago to deal with errors loading from the official go-basic.obo file, and it's
loading fine for me. Julie punched those updates in the release quite a while ago, though, so perhaps I'm not hitting the same OBO
file that you are. I've attached mine which works so you can compare.

On 12/4/19 10:48 AM, Paulo Nuin wrote:

> Hi everyone
>
> We encountered an error when loading GO data, especially with entries that are annotated as obsolete and have two consider links at the bottom.
>
> The error:
>
>
> Caused by: Error: Attempted to specify obsolete value obsolete negative regulation of growth of symbiont on or near host surface for consider tag.
> on line: 410135
> charnum: -1
> line: consider: GO:0044140
>          at org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1691)
>          at org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74)
>          at org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:273)
>          ... 50 more
>
> The item
>
> [Term]
> id: GO:0075309
> name: obsolete negative regulation of growth or development of symbiont on or near host surface
> namespace: biological_process
> def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the increase in the symbiont's size or mass, or its progression from an initial condition to a later condition, on or near the cells or tissues of the host org$
> comment: This term was made obsolete because it contained a conjunction (or). It has been replaced with the terms 'negative regulation of development of symbiont on or near host surface ; GO:0044141' and 'negative regulation of growth of symbiont on or $
> synonym: "negative regulation of growth or development of symbiont on or near host surface" EXACT []
> is_obsolete: true
> consider: GO:0044140
> consider: GO:0044141
>
> The only solution we found was to remove these items. Is there anything that can be added to the loader that would remedy the situation? We are using InterMine’s GO loader.
>
> Thanks
>
> Paulo
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>

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go-basic.obo.gz (5M) Download Attachment
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Re: Error on loading GO

Paulo Nuin
Hi Sam

We had this problem on our current release with InterMine 3.1 and now on testing with 4.1.

In fact, yours look similar or identical ours, so maybe the error is not on the dual/triple consider, but somewhere else in the item, maybe some offending character.

I will keep digging. Thanks a lot

Cheers

Paulo

> On Dec 4, 2019, at 12:44 PM, Sam Hokin <[hidden email]> wrote:
>
> Which version, Paulo? I made some updates some time ago to deal with errors loading from the official go-basic.obo file, and it's loading fine for me. Julie punched those updates in the release quite a while ago, though, so perhaps I'm not hitting the same OBO file that you are. I've attached mine which works so you can compare.
>
> On 12/4/19 10:48 AM, Paulo Nuin wrote:
>> Hi everyone
>> We encountered an error when loading GO data, especially with entries that are annotated as obsolete and have two consider links at the bottom.
>> The error:
>> Caused by: Error: Attempted to specify obsolete value obsolete negative regulation of growth of symbiont on or near host surface for consider tag.
>> on line: 410135
>> charnum: -1
>> line: consider: GO:0044140
>>         at org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1691)
>>         at org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74)
>>         at org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:273)
>>         ... 50 more
>> The item
>> [Term]
>> id: GO:0075309
>> name: obsolete negative regulation of growth or development of symbiont on or near host surface
>> namespace: biological_process
>> def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the increase in the symbiont's size or mass, or its progression from an initial condition to a later condition, on or near the cells or tissues of the host org$
>> comment: This term was made obsolete because it contained a conjunction (or). It has been replaced with the terms 'negative regulation of development of symbiont on or near host surface ; GO:0044141' and 'negative regulation of growth of symbiont on or $
>> synonym: "negative regulation of growth or development of symbiont on or near host surface" EXACT []
>> is_obsolete: true
>> consider: GO:0044140
>> consider: GO:0044141
>> The only solution we found was to remove these items. Is there anything that can be added to the loader that would remedy the situation? We are using InterMine’s GO loader.
>> Thanks
>> Paulo
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
> <go-basic.obo.gz>_______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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Re: Error on loading GO

Paulo Nuin
In reply to this post by Sam Hokin-3
Hi Sam (and everyone)

This is the explanation of the error we’re getting, an obsolete item linking to another one.


We have to work on our OBO file.

Cheers

Paulo



On Dec 4, 2019, at 12:44 PM, Sam Hokin <[hidden email]> wrote:

Which version, Paulo? I made some updates some time ago to deal with errors loading from the official go-basic.obo file, and it's loading fine for me. Julie punched those updates in the release quite a while ago, though, so perhaps I'm not hitting the same OBO file that you are. I've attached mine which works so you can compare.

On 12/4/19 10:48 AM, Paulo Nuin wrote:
Hi everyone
We encountered an error when loading GO data, especially with entries that are annotated as obsolete and have two consider links at the bottom.
The error:
Caused by: Error: Attempted to specify obsolete value obsolete negative regulation of growth of symbiont on or near host surface for consider tag.
on line: 410135
charnum: -1
line: consider: GO:0044140
        at org.obo.dataadapter.DefaultOBOParser.endParse(DefaultOBOParser.java:1691)
        at org.obo.dataadapter.AbstractParseEngine.parse(AbstractParseEngine.java:74)
        at org.obo.dataadapter.OBOFileAdapter.doOperation(OBOFileAdapter.java:273)
        ... 50 more
The item
[Term]
id: GO:0075309
name: obsolete negative regulation of growth or development of symbiont on or near host surface
namespace: biological_process
def: "OBSOLETE. Any process that stops, prevents, or reduces the frequency, rate or extent of the increase in the symbiont's size or mass, or its progression from an initial condition to a later condition, on or near the cells or tissues of the host org$
comment: This term was made obsolete because it contained a conjunction (or). It has been replaced with the terms 'negative regulation of development of symbiont on or near host surface ; GO:0044141' and 'negative regulation of growth of symbiont on or $
synonym: "negative regulation of growth or development of symbiont on or near host surface" EXACT []
is_obsolete: true
consider: GO:0044140
consider: GO:0044141
The only solution we found was to remove these items. Is there anything that can be added to the loader that would remedy the situation? We are using InterMine’s GO loader.
Thanks
Paulo
_______________________________________________
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<go-basic.obo.gz>_______________________________________________
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[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


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