[apollo] Unable to create a new annotation with a new feature type

[Loraine Guéguen]

Dear apollo list,

We have created a new feature type with the admin panel.
But this new type is not available when right clicking on an exiting
feature ("change annotation type") in the User-created annotation or
when right clicking on a feature in the evidence panel ("create new
annotation").

Is there something more to do in order to make this new feature type
available ?

We use Apollo 2.0.4

Thanks in advance

Loraine Guéguen
--
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/

[Nathan Dunn]

Sorry, this isn’t documented properly. Those FeatureType’s are used by the CannedKey, CannedComment, etc. for filtering canned comments. e.g., some Canned Comments (e.g., replaces gene) would only be available to genes and not Repeat Regions, etc.


However, I really like this idea. We have some unused “Custom” Types that could inherit appropriate functionality, but still support the proper annotation.

https://github.com/GMOD/Apollo/issues/1239 <https://github.com/GMOD/Apollo/issues/1239>


What type / type(s) are you trying to add? We can also add custom types as first-class citizens, as well (just create a GH issue).

Nathan

Post by Loraine Guéguen
Dear apollo list,
We have created a new feature type with the admin panel.
But this new type is not available when right clicking on an exiting feature ("change annotation type") in the User-created annotation or when right clicking on a feature in the evidence panel ("create new annotation").
Is there something more to do in order to make this new feature type available ?
We use Apollo 2.0.4
Thanks in advance
Loraine Guéguen
--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

[Loraine Guéguen]

In fact, one of our scaffolds contains the mitochondrial genome and we
want to tag this region of the sequence as mitochondrial DNA by adding
an annotation. On the other hand, the mitochondrial genome is about to
be added as a new genome (organism), and will be annotated with genes in
this place. We have the same issue for the chloroplastic genome.

For that, so far, we have created an annotation with feature type
"pseudogene" to tag the region of the sequence.

In the meantime, I added feature types mitochondrial_DNA (SO:0001032)
and chloroplast_DNA (SO:0001033), thinking that they could be used to
tag the mitochondrial and chloroplastic regions on the scaffolds, what
would be more right than the feature type pseudogene.

Never mind, that's not a crucial issue !

What do you mean by "custom Feature Type" ? What is this for ?

Loraine

Post by Nathan Dunn
Sorry, this isn’t documented properly. Those FeatureType’s are used
by the CannedKey, CannedComment, etc. for filtering canned comments.
e.g., some Canned Comments (e.g., replaces gene) would only be
available to genes and not Repeat Regions, etc.
However, I really like this idea. We have some unused “Custom” Types
that could inherit appropriate functionality, but still support the
proper annotation.
https://github.com/GMOD/Apollo/issues/1239
What type / type(s) are you trying to add? We can also add custom
types as first-class citizens, as well (just create a GH issue).
Nathan

Post by Loraine Guéguen
Dear apollo list,
We have created a new feature type with the admin panel.
But this new type is not available when right clicking on an exiting
feature ("change annotation type") in the User-created annotation or
when right clicking on a feature in the evidence panel ("create new
annotation").
Is there something more to do in order to make this new feature type available ?
We use Apollo 2.0.4
Thanks in advance
Loraine Guéguen
--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/
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
unsubscribe apollo | 3. Leave the message body blank.

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

--
Loraine Guéguen

Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/
http://www.sb-roscoff.fr/

[Nathan Dunn]

The Custom Feature Type is currently just a code stub for what we want to do someday, time permitting.

Nathan

In fact, one of our scaffolds contains the mitochondrial genome and we want to tag this region of the sequence as mitochondrial DNA by adding an annotation. On the other hand, the mitochondrial genome is about to be added as a new genome (organism), and will be annotated with genes in this place. We have the same issue for the chloroplastic genome.
For that, so far, we have created an annotation with feature type "pseudogene" to tag the region of the sequence.
In the meantime, I added feature types mitochondrial_DNA (SO:0001032) and chloroplast_DNA (SO:0001033), thinking that they could be used to tag the mitochondrial and chloroplastic regions on the scaffolds, what would be more right than the feature type pseudogene.
Never mind, that's not a crucial issue !
What do you mean by "custom Feature Type" ? What is this for ?
Loraine

Post by Nathan Dunn
Sorry, this isn’t documented properly. Those FeatureType’s are used by the CannedKey, CannedComment, etc. for filtering canned comments. e.g., some Canned Comments (e.g., replaces gene) would only be available to genes and not Repeat Regions, etc.
However, I really like this idea. We have some unused “Custom” Types that could inherit appropriate functionality, but still support the proper annotation.
https://github.com/GMOD/Apollo/issues/1239 <https://github.com/GMOD/Apollo/issues/1239>
What type / type(s) are you trying to add? We can also add custom types as first-class citizens, as well (just create a GH issue).
Nathan

Post by Loraine Guéguen
Dear apollo list,
We have created a new feature type with the admin panel.
But this new type is not available when right clicking on an exiting feature ("change annotation type") in the User-created annotation or when right clicking on a feature in the evidence panel ("create new annotation").
Is there something more to do in order to make this new feature type available ?
We use Apollo 2.0.4
Thanks in advance
Loraine Guéguen
--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/ <http://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>

--
Loraine Guéguen
Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences)
Service Informatique et Bioinformatique
Station Biologique de Roscoff
FR 2424 CNRS UPMC
Place Georges Teissier
CS 90074
29688 Roscoff cedex
tel: ++33 (0)2 98 29 56 46 (interne : 415)
http://abims.sb-roscoff.fr/ <http://abims.sb-roscoff.fr/>
http://www.sb-roscoff.fr/ <http://www.sb-roscoff.fr/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/