misc_feature

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misc_feature

cgandini
Hello!

Is there any way to annotate something as misc_feature???

Thanks 

Carolina




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Re: misc_feature

nathandunn

Carolina,

Can you provide a bit more context?  

Its not hard to add specific feature types, but I don’t know if its necessarily a good idea to add features without some information / evidence.  

You can change the annotation type later if you are unsure of the initial feature type.  

Nathan

> On Jul 29, 2017, at 12:14 PM, Carolina Gandini <[hidden email]> wrote:
>
> Hello!
>
> Is there any way to annotate something as misc_feature???
>
> Thanks
>
> Carolina
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: misc_feature

cgandini
HI Nathan,

For example in plant mitochondrial genomes is common to find plastidial insertions, and these are annotated as "misc_feature: plastid derived-sequence" for example. 

Thanks!

Carolina

On Sat, Jul 29, 2017 at 4:22 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

Can you provide a bit more context?

Its not hard to add specific feature types, but I don’t know if its necessarily a good idea to add features without some information / evidence.

You can change the annotation type later if you are unsure of the initial feature type.

Nathan

> On Jul 29, 2017, at 12:14 PM, Carolina Gandini <[hidden email]> wrote:
>
> Hello!
>
> Is there any way to annotate something as misc_feature???
>
> Thanks
>
> Carolina
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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Re: misc_feature

nathandunn

Carolina,

I think that the best approach would be to add it directly to Apollo with a defined SO type.  

I think that this was what you were looking for (thanks Suzi): http://www.sequenceontology.org/browser/current_svn/term/SO:0000740

I think the steps to follow are:

1 - make sure that this is the ontology term you want
2 - update the definition of the term if so (the site should show you how to request an update
3 - open up a GitHub issue in Apollo: https://github.com/GMOD/Apollo/issues/  and we’ll try to get that added (or if you want to issue you’re own PR we would be happy to help you out)

If there is a term missing that you want to annotate (e.g, plastidial insertion), please request it from the SO and we will try to get it in as soon as we are able with the proper SO reference. 

If there are multiple terms you want (e.g., all of the children of organelle_sequence) we might handle it differently (so add those details to the GH issue), but all terms should be backed by the SO.  

Thanks,

Nathan


On Jul 30, 2017, at 7:01 AM, Carolina Gandini <[hidden email]> wrote:

HI Nathan,

For example in plant mitochondrial genomes is common to find plastidial insertions, and these are annotated as "misc_feature: plastid derived-sequence" for example. 

Thanks!

Carolina

On Sat, Jul 29, 2017 at 4:22 PM, Nathan Dunn <[hidden email]> wrote:

Carolina,

Can you provide a bit more context?

Its not hard to add specific feature types, but I don’t know if its necessarily a good idea to add features without some information / evidence.

You can change the annotation type later if you are unsure of the initial feature type.

Nathan

> On Jul 29, 2017, at 12:14 PM, Carolina Gandini <[hidden email]> wrote:
>
> Hello!
>
> Is there any way to annotate something as misc_feature???
>
> Thanks
>
> Carolina
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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