Editing plugin for HPO

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Editing plugin for HPO

Peter Robinson-2
Hi everybody,
I am looking to develop a simple plugin for editing new terms for the
Human Phenotype Ontology (https://hpo.jax.org/app/). Basically, when
 we create new terms, we add a label, definition, comment, synonyms and a few xrefs.
I would like to add these using a form rather than manually entering the fields, and also
have a few convenience functions, such as showing any terms whose labels are close to the new label to avoid inadvertent duplication.

I am wondering if anybody can suggest a good example plugin that might serve as a model for this sort of thing?

thanks, Peter



Peter Robinson
Professor and Donald A. Roux Chair, Genomics and Computational Biology
The Jackson Laboratory for Genomic Medicine
860.837.2095 t | [hidden email] | https://robinsongroup.github.io/
Peter Robinson
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Re: Editing plugin for HPO

Lorenz B.
Hello Peter,

I'd start with the plugin examples in the Github repo [1]. That said, you have to decide on the plugin type but probably a view component would be the way to go.

Or how does the workflow look like?




Hi everybody,
I am looking to develop a simple plugin for editing new terms for the
Human Phenotype Ontology (https://hpo.jax.org/app/). Basically, when
 we create new terms, we add a label, definition, comment, synonyms and a few xrefs.
I would like to add these using a form rather than manually entering the fields, and also
have a few convenience functions, such as showing any terms whose labels are close to the new label to avoid inadvertent duplication.

I am wondering if anybody can suggest a good example plugin that might serve as a model for this sort of thing?

thanks, Peter



Peter Robinson
Professor and Donald A. Roux Chair, Genomics and Computational Biology
The Jackson Laboratory for Genomic Medicine
860.837.2095 t | [hidden email] | https://robinsongroup.github.io/
Peter Robinson
---

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Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center

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Re: Editing plugin for HPO

Peter Robinson-2

Thanks,  Lorenz & besten Gruss nach Leipzig!

I thought I would need a "Tab" component (what exactly is the difference?).

But mainly I want the user to see a new Tab which would have five fields for the new term

1. label

2. definition

3. Citation(s) (PubMed id) for the definition

4. Comment

5. Synonym list


There would be one button that would check whether the term label is similar to any existing labels, and another button that would add the new term to the ontology file.

I have been playing around with the examples, but going the next step is still a little unclear :-0.

thanks Peter




Hello Peter,

I'd start with the plugin examples in the Github repo [1]. That said, you have to decide on the plugin type but probably a view component would be the way to go.

Or how does the workflow look like?




Hi everybody,
I am looking to develop a simple plugin for editing new terms for the
Human Phenotype Ontology (https://hpo.jax.org/app/). Basically, when
 we create new terms, we add a label, definition, comment, synonyms and a few xrefs.
I would like to add these using a form rather than manually entering the fields, and also
have a few convenience functions, such as showing any terms whose labels are close to the new label to avoid inadvertent duplication.

I am wondering if anybody can suggest a good example plugin that might serve as a model for this sort of thing?

thanks, Peter



Peter Robinson
Professor and Donald A. Roux Chair, Genomics and Computational Biology
The Jackson Laboratory for Genomic Medicine
860.837.2095 t | [hidden email] | https://robinsongroup.github.io/
Peter Robinson
---

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_______________________________________________
protege-dev mailing list
[hidden email]
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-- 
Lorenz Bühmann
AKSW group, University of Leipzig
Group: http://aksw.org - semantic web research center
---

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Re: Editing plugin for HPO

Balhoff, James Patrick
Hi Peter,

We have an OBO Annotations Editor plugin which provides most of this (at least for the field entry features). It should be available in the plugins list that you see when you select File > Check for plugins… We could update it if something is missing. I ported it to Protege 5 a while back, and the GO editors are using it, but otherwise it doesn’t get too much attention.

Thanks,
Jim


> On Jan 7, 2019, at 5:36 AM, Peter Robinson <[hidden email]> wrote:
>
> Thanks,  Lorenz & besten Gruss nach Leipzig!
> I thought I would need a "Tab" component (what exactly is the difference?).
> But mainly I want the user to see a new Tab which would have five fields for the new term
> 1. label
> 2. definition
> 3. Citation(s) (PubMed id) for the definition
> 4. Comment
> 5. Synonym list
>
> There would be one button that would check whether the term label is similar to any existing labels, and another button that would add the new term to the ontology file.
> I have been playing around with the examples, but going the next step is still a little unclear :-0.
> thanks Peter
>
>
>
> Hello Peter,
>
> I'd start with the plugin examples in the Github repo [1]. That said, you have to decide on the plugin type but probably a view component would be the way to go.
> Or how does the workflow look like?
>
>
> [1] https://github.com/protegeproject/protege-plugin-examples
>
>> Hi everybody,
>> I am looking to develop a simple plugin for editing new terms for the
>> Human Phenotype Ontology (https://hpo.jax.org/app/). Basically, when
>>  we create new terms, we add a label, definition, comment, synonyms and a few xrefs.
>> I would like to add these using a form rather than manually entering the fields, and also
>> have a few convenience functions, such as showing any terms whose labels are close to the new label to avoid inadvertent duplication.
>>
>> I am wondering if anybody can suggest a good example plugin that might serve as a model for this sort of thing?
>>
>> thanks, Peter
>>
>>
>>
>> Peter Robinson
>> Professor and Donald A. Roux Chair, Genomics and Computational Biology
>> The Jackson Laboratory for Genomic Medicine
>> 860.837.2095 t | [hidden email] | https://robinsongroup.github.io/
>> Peter Robinson
>> ---
>>
>> 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.
>>
>> _______________________________________________
>> protege-dev mailing list
>>
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-dev
> --
> Lorenz Bühmann
> AKSW group, University of Leipzig
> Group:
> http://aksw.org - semantic web research center
> ---
>
> 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._______________________________________________
> protege-dev mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-dev

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Re: Editing plugin for HPO

Peter Robinson-2
Thanks, didn't realize -- I will fork this!
-Peter

Peter Robinson
Professor and Donald A. Roux Chair, Genomics and Computational Biology
The Jackson Laboratory for Genomic Medicine
860.837.2095 t | [hidden email] | https://robinsongroup.github.io/
Peter Robinson

________________________________________
From: protege-dev <[hidden email]> on behalf of Balhoff, James Patrick <[hidden email]>
Sent: Monday, January 7, 2019 9:43 AM
To: Developer support for WebProtege and Protege Desktop
Cc: [hidden email]
Subject: Re: [protege-dev] Editing plugin for HPO

Hi Peter,

We have an OBO Annotations Editor plugin which provides most of this (at least for the field entry features). It should be available in the plugins list that you see when you select File > Check for plugins… We could update it if something is missing. I ported it to Protege 5 a while back, and the GO editors are using it, but otherwise it doesn’t get too much attention.

Thanks,
Jim


> On Jan 7, 2019, at 5:36 AM, Peter Robinson <[hidden email]> wrote:
>
> Thanks,  Lorenz & besten Gruss nach Leipzig!
> I thought I would need a "Tab" component (what exactly is the difference?).
> But mainly I want the user to see a new Tab which would have five fields for the new term
> 1. label
> 2. definition
> 3. Citation(s) (PubMed id) for the definition
> 4. Comment
> 5. Synonym list
>
> There would be one button that would check whether the term label is similar to any existing labels, and another button that would add the new term to the ontology file.
> I have been playing around with the examples, but going the next step is still a little unclear :-0.
> thanks Peter
>
>
>
> Hello Peter,
>
> I'd start with the plugin examples in the Github repo [1]. That said, you have to decide on the plugin type but probably a view component would be the way to go.
> Or how does the workflow look like?
>
>
> [1] https://github.com/protegeproject/protege-plugin-examples
>
>> Hi everybody,
>> I am looking to develop a simple plugin for editing new terms for the
>> Human Phenotype Ontology (https://hpo.jax.org/app/). Basically, when
>>  we create new terms, we add a label, definition, comment, synonyms and a few xrefs.
>> I would like to add these using a form rather than manually entering the fields, and also
>> have a few convenience functions, such as showing any terms whose labels are close to the new label to avoid inadvertent duplication.
>>
>> I am wondering if anybody can suggest a good example plugin that might serve as a model for this sort of thing?
>>
>> thanks, Peter
>>
>>
>>
>> Peter Robinson
>> Professor and Donald A. Roux Chair, Genomics and Computational Biology
>> The Jackson Laboratory for Genomic Medicine
>> 860.837.2095 t | [hidden email] | https://robinsongroup.github.io/
>> Peter Robinson
>> ---
>>
>> 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.
>>
>> _______________________________________________
>> protege-dev mailing list
>>
>> [hidden email]
>> https://mailman.stanford.edu/mailman/listinfo/protege-dev
> --
> Lorenz Bühmann
> AKSW group, University of Leipzig
> Group:
> http://aksw.org - semantic web research center
> ---
>
> 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._______________________________________________
> protege-dev mailing list
> [hidden email]
> https://mailman.stanford.edu/mailman/listinfo/protege-dev

_______________________________________________
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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
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Re: Editing plugin for HPO

Balhoff, James Patrick
Great, please feel free to contribute changes directly to the project: https://github.com/owlcollab/protege-obo-plugin 

I expect the features you’re looking for will be useful to anyone using it.


On Jan 7, 2019, at 9:50 AM, Peter Robinson <[hidden email]> wrote:

Thanks, didn't realize -- I will fork this!
-Peter

Peter Robinson
Professor and Donald A. Roux Chair, Genomics and Computational Biology
The Jackson Laboratory for Genomic Medicine
860.837.2095 t | [hidden email] | https://robinsongroup.github.io/
Peter Robinson

________________________________________
From: protege-dev <[hidden email]> on behalf of Balhoff, James Patrick <[hidden email]>
Sent: Monday, January 7, 2019 9:43 AM
To: Developer support for WebProtege and Protege Desktop
Cc: [hidden email]
Subject: Re: [protege-dev] Editing plugin for HPO

Hi Peter,

We have an OBO Annotations Editor plugin which provides most of this (at least for the field entry features). It should be available in the plugins list that you see when you select File > Check for plugins… We could update it if something is missing. I ported it to Protege 5 a while back, and the GO editors are using it, but otherwise it doesn’t get too much attention.

Thanks,
Jim


On Jan 7, 2019, at 5:36 AM, Peter Robinson <[hidden email]> wrote:

Thanks,  Lorenz & besten Gruss nach Leipzig!
I thought I would need a "Tab" component (what exactly is the difference?).
But mainly I want the user to see a new Tab which would have five fields for the new term
1. label
2. definition
3. Citation(s) (PubMed id) for the definition
4. Comment
5. Synonym list

There would be one button that would check whether the term label is similar to any existing labels, and another button that would add the new term to the ontology file.
I have been playing around with the examples, but going the next step is still a little unclear :-0.
thanks Peter



Hello Peter,

I'd start with the plugin examples in the Github repo [1]. That said, you have to decide on the plugin type but probably a view component would be the way to go.
Or how does the workflow look like?


[1] https://github.com/protegeproject/protege-plugin-examples

Hi everybody,
I am looking to develop a simple plugin for editing new terms for the
Human Phenotype Ontology (https://hpo.jax.org/app/). Basically, when
we create new terms, we add a label, definition, comment, synonyms and a few xrefs.
I would like to add these using a form rather than manually entering the fields, and also
have a few convenience functions, such as showing any terms whose labels are close to the new label to avoid inadvertent duplication.

I am wondering if anybody can suggest a good example plugin that might serve as a model for this sort of thing?

thanks, Peter



Peter Robinson
Professor and Donald A. Roux Chair, Genomics and Computational Biology
The Jackson Laboratory for Genomic Medicine
860.837.2095 t | [hidden email] | https://robinsongroup.github.io/
Peter Robinson
---

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.

_______________________________________________
protege-dev mailing list

[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
--
Lorenz Bühmann
AKSW group, University of Leipzig
Group:
http://aksw.org - semantic web research center
---

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._______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev

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[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
---

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Re: Editing plugin for HPO

Matthew Horridge-2
Administrator
Hi Peter,

We could also add the similar terms look up to the general create entity dialogs in Protege.  I’ve filed an issue for this https://github.com/protegeproject/protege/issues/821

Cheers,

Matthew


On 7 Jan 2019, at 06:56, Balhoff, James Patrick <[hidden email]> wrote:

Great, please feel free to contribute changes directly to the project: https://github.com/owlcollab/protege-obo-plugin 

I expect the features you’re looking for will be useful to anyone using it.


On Jan 7, 2019, at 9:50 AM, Peter Robinson <[hidden email]> wrote:

Thanks, didn't realize -- I will fork this!
-Peter

Peter Robinson
Professor and Donald A. Roux Chair, Genomics and Computational Biology
The Jackson Laboratory for Genomic Medicine
860.837.2095 t | [hidden email] | https://robinsongroup.github.io/
Peter Robinson

________________________________________
From: protege-dev <[hidden email]> on behalf of Balhoff, James Patrick <[hidden email]>
Sent: Monday, January 7, 2019 9:43 AM
To: Developer support for WebProtege and Protege Desktop
Cc: [hidden email]
Subject: Re: [protege-dev] Editing plugin for HPO

Hi Peter,

We have an OBO Annotations Editor plugin which provides most of this (at least for the field entry features). It should be available in the plugins list that you see when you select File > Check for plugins… We could update it if something is missing. I ported it to Protege 5 a while back, and the GO editors are using it, but otherwise it doesn’t get too much attention.

Thanks,
Jim


On Jan 7, 2019, at 5:36 AM, Peter Robinson <[hidden email]> wrote:

Thanks,  Lorenz & besten Gruss nach Leipzig!
I thought I would need a "Tab" component (what exactly is the difference?).
But mainly I want the user to see a new Tab which would have five fields for the new term
1. label
2. definition
3. Citation(s) (PubMed id) for the definition
4. Comment
5. Synonym list

There would be one button that would check whether the term label is similar to any existing labels, and another button that would add the new term to the ontology file.
I have been playing around with the examples, but going the next step is still a little unclear :-0.
thanks Peter



Hello Peter,

I'd start with the plugin examples in the Github repo [1]. That said, you have to decide on the plugin type but probably a view component would be the way to go.
Or how does the workflow look like?


[1] https://github.com/protegeproject/protege-plugin-examples

Hi everybody,
I am looking to develop a simple plugin for editing new terms for the
Human Phenotype Ontology (https://hpo.jax.org/app/). Basically, when
we create new terms, we add a label, definition, comment, synonyms and a few xrefs.
I would like to add these using a form rather than manually entering the fields, and also
have a few convenience functions, such as showing any terms whose labels are close to the new label to avoid inadvertent duplication.

I am wondering if anybody can suggest a good example plugin that might serve as a model for this sort of thing?

thanks, Peter



Peter Robinson
Professor and Donald A. Roux Chair, Genomics and Computational Biology
The Jackson Laboratory for Genomic Medicine
860.837.2095 t | [hidden email] | https://robinsongroup.github.io/
Peter Robinson
---

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.

_______________________________________________
protege-dev mailing list

[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev
--
Lorenz Bühmann
AKSW group, University of Leipzig
Group:
http://aksw.org - semantic web research center
---

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._______________________________________________
protege-dev mailing list
[hidden email]
https://mailman.stanford.edu/mailman/listinfo/protege-dev

_______________________________________________
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---

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