OBO loading

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OBO loading

Paulo Nuin
Hi everyone

I have a question regarding loading OBO files that are not exactly from GO. We are loading OBO files with Anatomy terms 

[Term]
id: WBbt:0000101
name: Lineage
def: "pedigree of nuclei, lineal descent from P0, the founder." [WB:RYNL]
xref: WB:RYNL
is_a: WBbt:0000100 ! C. elegans Cell and Anatomy

and we are looking for the possibility of these terms not be grouped in the Ontology Term, Ontology Relation etc. Ideally, we would have Anatomy Ontology Relation, etc in the model. 

The attached image is what we have right now (some classes loaded only, GO, Anatomy Ontology OBO and Anatomy term XML).

Thanks in advance

Paulo



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Re: OBO loading

Joel Richardson-2
Hi Paolo, et al,

We’ve done something similar in MouseMine, where we subclass off the core/GO annotation model for loaded annotation data of all kinds, e.g., phenotype annotations where the ontology is the MP and the annotation targets are mice (genotypes). The pattern we adopted is to define a subclass of OntologyTerm as needed for the specific ontology and use the standard OBO source to load it. Eg at MouseMine we have MPTerm, DOTerm, etc. Each annotation data set gets its own DataSet object, suitably named. The annotations themselves are just OntologyAnnotation objects. Queries use data set names and/or ontology term types as constraints. Unlike the ontology terms, we don’t use the GAF source to load annotations. Instead they are part of a larger MGI-to-MouseMine ETL pipeline, which uses ItemXML format.

Don’t know if any of this helps. It’s been a useful pattern for us.

Cheers,
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

From: dev <[hidden email]> on behalf of Paulo Nuin <[hidden email]>
Date: Monday, July 23, 2018 at 3:57 PM
To: InterMine Devs <[hidden email]>
Subject: [InterMine Dev] OBO loading

Hi everyone

I have a question regarding loading OBO files that are not exactly from GO. We are loading OBO files with Anatomy terms 

[Term]
id: WBbt:0000101
name: Lineage
def: "pedigree of nuclei, lineal descent from P0, the founder." [WB:RYNL]
xref: WB:RYNL
is_a: WBbt:0000100 ! C. elegans Cell and Anatomy

and we are looking for the possibility of these terms not be grouped in the Ontology Term, Ontology Relation etc. Ideally, we would have Anatomy Ontology Relation, etc in the model. 

The attached image is what we have right now (some classes loaded only, GO, Anatomy Ontology OBO and Anatomy term XML).

Thanks in advance

Paulo


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Re: OBO loading

Paulo Nuin
Hi Joel

Thanks for the reply. Do you have an implementation example on MouseMine? I am assuming your code is here


Thanks again

Paulo



On Jul. 23, 2018, at 2:31 p.m., Joel Richardson <[hidden email]> wrote:

Hi Paolo, et al,

We’ve done something similar in MouseMine, where we subclass off the core/GO annotation model for loaded annotation data of all kinds, e.g., phenotype annotations where the ontology is the MP and the annotation targets are mice (genotypes). The pattern we adopted is to define a subclass of OntologyTerm as needed for the specific ontology and use the standard OBO source to load it. Eg at MouseMine we have MPTerm, DOTerm, etc. Each annotation data set gets its own DataSet object, suitably named. The annotations themselves are just OntologyAnnotation objects. Queries use data set names and/or ontology term types as constraints. Unlike the ontology terms, we don’t use the GAF source to load annotations. Instead they are part of a larger MGI-to-MouseMine ETL pipeline, which uses ItemXML format.

Don’t know if any of this helps. It’s been a useful pattern for us.

Cheers,
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

From: dev <[hidden email]> on behalf of Paulo Nuin <[hidden email]>
Date: Monday, July 23, 2018 at 3:57 PM
To: InterMine Devs <[hidden email]>
Subject: [InterMine Dev] OBO loading

Hi everyone

I have a question regarding loading OBO files that are not exactly from GO. We are loading OBO files with Anatomy terms 

[Term]
id: WBbt:0000101
name: Lineage
def: "pedigree of nuclei, lineal descent from P0, the founder." [WB:RYNL]
xref: WB:RYNL
is_a: WBbt:0000100 ! C. elegans Cell and Anatomy

and we are looking for the possibility of these terms not be grouped in the Ontology Term, Ontology Relation etc. Ideally, we would have Anatomy Ontology Relation, etc in the model. 

The attached image is what we have right now (some classes loaded only, GO, Anatomy Ontology OBO and Anatomy term XML).

Thanks in advance

Paulo


<Screen Shot 2018-07-23 at 1.53.48 p.m..png>
---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
<Screen Shot 2018-07-23 at 1.53.48 p.m..png>


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Re: OBO loading

Paulo Nuin
I think I found, checking the Disease Ontology on your bio/sources.

Thanks again

Paulo



On Jul. 23, 2018, at 3:23 p.m., Paulo Nuin <[hidden email]> wrote:

Hi Joel

Thanks for the reply. Do you have an implementation example on MouseMine? I am assuming your code is here


Thanks again

Paulo



On Jul. 23, 2018, at 2:31 p.m., Joel Richardson <[hidden email]> wrote:

Hi Paolo, et al,

We’ve done something similar in MouseMine, where we subclass off the core/GO annotation model for loaded annotation data of all kinds, e.g., phenotype annotations where the ontology is the MP and the annotation targets are mice (genotypes). The pattern we adopted is to define a subclass of OntologyTerm as needed for the specific ontology and use the standard OBO source to load it. Eg at MouseMine we have MPTerm, DOTerm, etc. Each annotation data set gets its own DataSet object, suitably named. The annotations themselves are just OntologyAnnotation objects. Queries use data set names and/or ontology term types as constraints. Unlike the ontology terms, we don’t use the GAF source to load annotations. Instead they are part of a larger MGI-to-MouseMine ETL pipeline, which uses ItemXML format.

Don’t know if any of this helps. It’s been a useful pattern for us.

Cheers,
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

From: dev <[hidden email]> on behalf of Paulo Nuin <[hidden email]>
Date: Monday, July 23, 2018 at 3:57 PM
To: InterMine Devs <[hidden email]>
Subject: [InterMine Dev] OBO loading

Hi everyone

I have a question regarding loading OBO files that are not exactly from GO. We are loading OBO files with Anatomy terms 

[Term]
id: WBbt:0000101
name: Lineage
def: "pedigree of nuclei, lineal descent from P0, the founder." [WB:RYNL]
xref: WB:RYNL
is_a: WBbt:0000100 ! C. elegans Cell and Anatomy

and we are looking for the possibility of these terms not be grouped in the Ontology Term, Ontology Relation etc. Ideally, we would have Anatomy Ontology Relation, etc in the model. 

The attached image is what we have right now (some classes loaded only, GO, Anatomy Ontology OBO and Anatomy term XML).

Thanks in advance

Paulo


<Screen Shot 2018-07-23 at 1.53.48 p.m..png>
---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
<Screen Shot 2018-07-23 at 1.53.48 p.m..png>



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Re: OBO loading

Joel Richardson-2

Yup. Check out the project.properties file to see how the class is set:

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

From: Paulo Nuin <[hidden email]>
Date: Monday, July 23, 2018 at 5:43 PM
To: Joel Richardson <[hidden email]>
Cc: InterMine Devs <[hidden email]>
Subject: Re: [InterMine Dev] OBO loading

I think I found, checking the Disease Ontology on your bio/sources.

Thanks again

Paulo



On Jul. 23, 2018, at 3:23 p.m., Paulo Nuin <[hidden email]> wrote:

Hi Joel

Thanks for the reply. Do you have an implementation example on MouseMine? I am assuming your code is here


Thanks again

Paulo



On Jul. 23, 2018, at 2:31 p.m., Joel Richardson <[hidden email]> wrote:

Hi Paolo, et al,

We’ve done something similar in MouseMine, where we subclass off the core/GO annotation model for loaded annotation data of all kinds, e.g., phenotype annotations where the ontology is the MP and the annotation targets are mice (genotypes). The pattern we adopted is to define a subclass of OntologyTerm as needed for the specific ontology and use the standard OBO source to load it. Eg at MouseMine we have MPTerm, DOTerm, etc. Each annotation data set gets its own DataSet object, suitably named. The annotations themselves are just OntologyAnnotation objects. Queries use data set names and/or ontology term types as constraints. Unlike the ontology terms, we don’t use the GAF source to load annotations. Instead they are part of a larger MGI-to-MouseMine ETL pipeline, which uses ItemXML format.

Don’t know if any of this helps. It’s been a useful pattern for us.

Cheers,
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

From: dev <[hidden email]> on behalf of Paulo Nuin <[hidden email]>
Date: Monday, July 23, 2018 at 3:57 PM
To: InterMine Devs <[hidden email]>
Subject: [InterMine Dev] OBO loading

Hi everyone

I have a question regarding loading OBO files that are not exactly from GO. We are loading OBO files with Anatomy terms 

[Term]
id: WBbt:0000101
name: Lineage
def: "pedigree of nuclei, lineal descent from P0, the founder." [WB:RYNL]
xref: WB:RYNL
is_a: WBbt:0000100 ! C. elegans Cell and Anatomy

and we are looking for the possibility of these terms not be grouped in the Ontology Term, Ontology Relation etc. Ideally, we would have Anatomy Ontology Relation, etc in the model. 

The attached image is what we have right now (some classes loaded only, GO, Anatomy Ontology OBO and Anatomy term XML).

Thanks in advance

Paulo


<Screen Shot 2018-07-23 at 1.53.48 p.m..png>
---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
<Screen Shot 2018-07-23 at 1.53.48 p.m..png>


---

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.
_______________________________________________
dev mailing list
[hidden email]
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