InterMine 2.0 model changes - update

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InterMine 2.0 model changes - update

Julie Sullivan-2
Hi all!

We had a productive discussion on the data model yesterday, here is my
write-up:

https://intermineorg.wordpress.com/2017/07/07/intermine-2-0-proposed-model-changes-ii/

Please read! Not sure I got everything.

Summary:

1. Synteny - agreement
2. Organism.variety - agreement but not on name
3. GO evidence codes - don't use ECO just add description and optional
URL instead
4. Joel brought up how Ontology Annotations can only annotate proteins
sequence features, but they really should accommodate everything.

The next call is pretty much booked up, so we'll can discuss the model
again on the following call - 3 August.

Thanks everyone!!
Julie
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Re: InterMine 2.0 model changes - update

joe carlson
Hello,

I'm sorry I missed the call yesterday. I updated my calendar but must
have slept through the notification. If there was one.

I had a question about the ontology annotation remarks in the summary.
Your document specifically mentions that you'd like to have the ability
to annotation protein domains, but from what I can see, you can do this
already.

The core model connects OntologyAnnotation to a BioEntity. The standard
interpro loader makes protein domains a subclass of BioEntity and the
standard interpro-go loader attaches GO annotations to these.

Is there a sense that protein domains should not be a subclass of
BioEntity? Is there another use case of something else that needs to be
annotatable?

Thanks,

Joe

On 07/07/2017 06:10 AM, Julie Sullivan wrote:

> Hi all!
>
> We had a productive discussion on the data model yesterday, here is my
> write-up:
>
> https://intermineorg.wordpress.com/2017/07/07/intermine-2-0-proposed-model-changes-ii/ 
>
>
> Please read! Not sure I got everything.
>
> Summary:
>
> 1. Synteny - agreement
> 2. Organism.variety - agreement but not on name
> 3. GO evidence codes - don't use ECO just add description and optional
> URL instead
> 4. Joel brought up how Ontology Annotations can only annotate proteins
> sequence features, but they really should accommodate everything.
>
> The next call is pretty much booked up, so we'll can discuss the model
> again on the following call - 3 August.
>
> Thanks everyone!!
> Julie
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev

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Re: InterMine 2.0 model changes - update

Joel Richardson-2

Hi Joe,

One immediate use case we have is loading disease/phenotype associations
from MGI. These are modeled (in MGI) as ontology annotations, in which
phenotypes (HPO terms) are annotated to diseases (DO terms). This won¹t
fit the InterMine model because OntologyTerm is not a BioEntity. Of
course, there are lots of ways one could approach this problem, each with
pros and cons, and email is too clunky (along with my typing skills) to
get into all that. Suffice it to say that easing the restriction on
OntologyAnnotations only applying to BioEntities seems like a good idea.


Joel

--
Joel E. Richardson, Ph.D.
Sr. Research Scientist
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, Maine 04609
207-288-6435
[hidden email]





On 7/7/17, 12:53 PM, "dev on behalf of Joe Carlson"
<[hidden email] on behalf of [hidden email]> wrote:

>Hello,
>
>I'm sorry I missed the call yesterday. I updated my calendar but must
>have slept through the notification. If there was one.
>
>I had a question about the ontology annotation remarks in the summary.
>Your document specifically mentions that you'd like to have the ability
>to annotation protein domains, but from what I can see, you can do this
>already.
>
>The core model connects OntologyAnnotation to a BioEntity. The standard
>interpro loader makes protein domains a subclass of BioEntity and the
>standard interpro-go loader attaches GO annotations to these.
>
>Is there a sense that protein domains should not be a subclass of
>BioEntity? Is there another use case of something else that needs to be
>annotatable?
>
>Thanks,
>
>Joe
>
>On 07/07/2017 06:10 AM, Julie Sullivan wrote:
>> Hi all!
>>
>> We had a productive discussion on the data model yesterday, here is my
>> write-up:
>>
>>
>>https://intermineorg.wordpress.com/2017/07/07/intermine-2-0-proposed-mode
>>l-changes-ii/
>>
>>
>> Please read! Not sure I got everything.
>>
>> Summary:
>>
>> 1. Synteny - agreement
>> 2. Organism.variety - agreement but not on name
>> 3. GO evidence codes - don't use ECO just add description and optional
>> URL instead
>> 4. Joel brought up how Ontology Annotations can only annotate proteins
>> sequence features, but they really should accommodate everything.
>>
>> The next call is pretty much booked up, so we'll can discuss the model
>> again on the following call - 3 August.
>>
>> Thanks everyone!!
>> Julie
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>
>_______________________________________________
>dev mailing list
>[hidden email]
>https://lists.intermine.org/mailman/listinfo/dev

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