[apollo] Keep feature's attributes when creating a new annotation

[Loraine Guéguen]

Hi,

I have a track with automatic annotations on features (GO terms, protein
domains, EC numbers, visible in section "Attributes" in the "View
details" panel). This functional information need to be modified/corrected.
Unfortunately, when creating a new annotation from one of these features
(right click and selecting "Create new annotation"), all functional
information is lost.

Webapollo version : 1.0.4

Is there a way to keep (and edit) the existing attributes when creating
a new annotation ?

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/

[Colin]

Hi Loraine
Technically, the features that are dragged and dropped are sort of created
"from scratch" and don't retain their metadata.

We have discussed this issue for retaining the metadata for the dragged and
dropped annotations, and we have a github page for that here:
https://github.com/GMOD/Apollo/issues/52

While the github issue isn't fixed yet, we do currently have a bulk import
command line script that can retain the metadata for the User-created
annotations. It is in the tools directory, and called
add_transcripts_from_gff3_to_annotations.pl. Note that it is for importing
a funn GFF into the annotation track.

Hope that helps!
-Colin

Post by Loraine Guéguen
Hi,
I have a track with automatic annotations on features (GO terms, protein
domains, EC numbers, visible in section "Attributes" in the "View details"
panel). This functional information need to be modified/corrected.
Unfortunately, when creating a new annotation from one of these features
(right click and selecting "Create new annotation"), all functional
information is lost.
Webapollo version : 1.0.4
Is there a way to keep (and edit) the existing attributes when creating a
new annotation ?
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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.

[Colin]

Typo correction: "it is for importing a full GFF into the annotation track."



-Colin

Post by Colin
Hi Loraine
Technically, the features that are dragged and dropped are sort of created
"from scratch" and don't retain their metadata.
We have discussed this issue for retaining the metadata for the dragged
https://github.com/GMOD/Apollo/issues/52
While the github issue isn't fixed yet, we do currently have a bulk import
command line script that can retain the metadata for the User-created
annotations. It is in the tools directory, and called
add_transcripts_from_gff3_to_annotations.pl. Note that it is for
importing a funn GFF into the annotation track.
Hope that helps!
-Colin

Post by Loraine Guéguen
Hi,
I have a track with automatic annotations on features (GO terms, protein
domains, EC numbers, visible in section "Attributes" in the "View details"
panel). This functional information need to be modified/corrected.
Unfortunately, when creating a new annotation from one of these features
(right click and selecting "Create new annotation"), all functional
information is lost.
Webapollo version : 1.0.4
Is there a way to keep (and edit) the existing attributes when creating a
new annotation ?
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
| 2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.

[Loraine Guéguen]

Thanks a lot for your answer!
I didn't know the perl script. It seems to do the job. We will load the
gff directly into the annotation track, so that all metadata will be
displayed and can be modified.


Loraine

Post by Colin
Typo correction: "it is for importing a full GFF into the annotation track."
-Colin
Hi Loraine
Technically, the features that are dragged and dropped are sort of
created "from scratch" and don't retain their metadata.
We have discussed this issue for retaining the metadata for the
dragged and dropped annotations, and we have a github page for
https://github.com/GMOD/Apollo/issues/52
While the github issue isn't fixed yet, we do currently have a
bulk import command line script that can retain the metadata for
the User-created annotations. It is in the tools directory, and
called add_transcripts_from_gff3_to_annotations.pl
<http://add_transcripts_from_gff3_to_annotations.pl>. Note that it
is for importing a funn GFF into the annotation track.
Hope that helps!
-Colin
On Tue, May 19, 2015 at 8:19 AM, Loraine Guéguen
Hi,
I have a track with automatic annotations on features (GO
terms, protein domains, EC numbers, visible in section
"Attributes" in the "View details" panel). This functional
information need to be modified/corrected.
Unfortunately, when creating a new annotation from one of
these features (right click and selecting "Create new
annotation"), all functional information is lost.
Webapollo version : 1.0.4
Is there a way to keep (and edit) the existing attributes when
creating a new annotation ?
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
<tel:%2B%2B33%20%280%292%2098%2029%2056%2046> (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
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/

--
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/

[Loraine Guéguen]

Dear apollo team,

This message to let you know about an issue we ran into with the
add_transcripts_from_gff3_to_annotations.pl script with version 2.0.2.

For the 1.0.4 apollo version, the
add_transcripts_from_gff3_to_annotations.pl script did pretty well, thanks.
For a new project, we used the 2.0.2 version. We had the same
problematic that was to keep the metadata and be able to edit them, so
we loaded again the gff directly into the annotation track. However, for
the 2.0.2 version, the "Note" attributes from the gff3 file are
unfortunately not imported into the "comment" section of the
"information editor" panel, but in the "attribute" section, with no tag.
This display is not optimal, and what is more problematic : such an
attribute with no tag is not exported when doing "get gff3".
I noticed that the json script output seems right with the "Note"
attribute typed as "comment". The problem comes probably from the apollo
web service code.

Regards,

Loraine Guéguen

Post by Loraine Guéguen
Thanks a lot for your answer!
I didn't know the perl script. It seems to do the job. We will load
the gff directly into the annotation track, so that all metadata will
be displayed and can be modified.
Loraine

Post by Colin
Typo correction: "it is for importing a full GFF into the annotation track."
-Colin
Hi Loraine
Technically, the features that are dragged and dropped are sort
of created "from scratch" and don't retain their metadata.
We have discussed this issue for retaining the metadata for the
dragged and dropped annotations, and we have a github page for
https://github.com/GMOD/Apollo/issues/52
While the github issue isn't fixed yet, we do currently have a
bulk import command line script that can retain the metadata for
the User-created annotations. It is in the tools directory, and
called add_transcripts_from_gff3_to_annotations.pl
<http://add_transcripts_from_gff3_to_annotations.pl>. Note that
it is for importing a funn GFF into the annotation track.
Hope that helps!
-Colin
On Tue, May 19, 2015 at 8:19 AM, Loraine Guéguen
Hi,
I have a track with automatic annotations on features (GO
terms, protein domains, EC numbers, visible in section
"Attributes" in the "View details" panel). This functional
information need to be modified/corrected.
Unfortunately, when creating a new annotation from one of
these features (right click and selecting "Create new
annotation"), all functional information is lost.
Webapollo version : 1.0.4
Is there a way to keep (and edit) the existing attributes
when creating a new annotation ?
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
<tel:%2B%2B33%20%280%292%2098%2029%2056%2046> (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
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 athttp://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]

Thanks for reporting this.

I created an issue for it here:

https://github.com/GMOD/Apollo/issues/1146 <https://github.com/GMOD/Apollo/issues/1146>

If you have an easy way to test it in 2.0.3 that would be helpful, though I don’t know if we’d specifically looked at this problem though.

If you have any sample data to send directly, that would help expedite things (or you can attach it to the issue), but is not necessary. Feel free to share directly as well if private data.

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory

Post by Loraine Guéguen
Dear apollo team,
This message to let you know about an issue we ran into with the add_transcripts_from_gff3_to_annotations.pl script with version 2.0.2.
For the 1.0.4 apollo version, the add_transcripts_from_gff3_to_annotations.pl script did pretty well, thanks.
For a new project, we used the 2.0.2 version. We had the same problematic that was to keep the metadata and be able to edit them, so we loaded again the gff directly into the annotation track. However, for the 2.0.2 version, the "Note" attributes from the gff3 file are unfortunately not imported into the "comment" section of the "information editor" panel, but in the "attribute" section, with no tag. This display is not optimal, and what is more problematic : such an attribute with no tag is not exported when doing "get gff3".
I noticed that the json script output seems right with the "Note" attribute typed as "comment". The problem comes probably from the apollo web service code.
Regards,
Loraine Guéguen

Post by Loraine Guéguen
Thanks a lot for your answer!
I didn't know the perl script. It seems to do the job. We will load the gff directly into the annotation track, so that all metadata will be displayed and can be modified.
Loraine

Post by Colin
Typo correction: "it is for importing a full GFF into the annotation track."
-Colin
Hi Loraine
Technically, the features that are dragged and dropped are sort of created "from scratch" and don't retain their metadata.
https://github.com/GMOD/Apollo/issues/52 <https://github.com/GMOD/Apollo/issues/52>
While the github issue isn't fixed yet, we do currently have a bulk import command line script that can retain the metadata for the User-created annotations. It is in the tools directory, and calledadd_transcripts_from_gff3_to_annotations.pl <http://add_transcripts_from_gff3_to_annotations.pl/>. Note that it is for importing a funn GFF into the annotation track.
Hope that helps!
-Colin
Hi,
I have a track with automatic annotations on features (GO terms, protein domains, EC numbers, visible in section "Attributes" in the "View details" panel). This functional information need to be modified/corrected.
Unfortunately, when creating a new annotation from one of these features (right click and selecting "Create new annotation"), all functional information is lost.
Webapollo version : 1.0.4
Is there a way to keep (and edit) the existing attributes when creating a new annotation ?
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 <tel:%2B%2B33%20%280%292%2098%2029%2056%2046> (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/