Annotations commenting

[Dmitrii-Romanov]

Commenting of annotations can be useful both in case of an individual and group work (sharing with collaborators). Moreover capability of comments public sharing may be intresting for whole gemonic research community. There is no support for automatically sharing annotations among members of the research team. Groups are constrained by saving files or/and e-mail exchange. Please consider expediency of that feature.

[sidoruka]

@Dmitrii-Romanov thanks for this. But I'm not sure I understood your suggestion. What annotations and comments are you talking about? Do you mean that a user shall be able to leave some generic comment somewhere?

[Dmitrii-Romanov]

@sidoruka thanks for prompt response. You are right. A user can be able to make text comments about some place-of-interesting, in particular about annotations of variations in researched genome.

[sidoruka]

@Dmitrii-Romanov , could you please some use cases on this functionality, how do you imagine that? E.g. what user shall do to place comments, how they are stored, how they are shared..

I believe generic commenting can be implemented in hundreds ways, that is your approach to this?

[kupryashova]

It is a useful feature to make comments on uploaded to NGB files in the Datasets panel that can be seen by any user of the session. It will help to navigate through files in NGB session when a user shares session or when there are many files in the Datasets tab. What about manual genomic regions annotation: It is especially useful when researcher attempts to annotate genome of the newly sequenced organism. After automatic annotation step researcher usually goes to manual edition of generated GFF/GTF file at regions that haven’t been annotated via annotation tool or have been ambiguously annotated. Note that BLAT search of the sequence that researcher can copy-paste from other resource can be very useful in this context (not implemented now). A good example of manual annotation functionality is Apollo plugin for JBrowse https://github.com/GMOD/Apollo, http://genomearchitect.github.io/demo/. It also allows to simultaneously edit the annotation by several people in real time when each of them can see the changes made by others. Here are use cases on this feature:

• Edit information about the selected region at the GTF/GFF track (region type (gene, pseudogene, rRNA, etc), start-end coordinates, name, description, dates of creation and last modification, References to databases where the region is described, attributes, field, Pubmed IDs, Gene Ontology IDs, comments)
• See the history of annotation of the region (date, what was done, if team annotation is supported – who did the change)
• Undo and redo certain actions from the history of annotation of the region.
• Export GTF/GFF file with the edited annotation information of the selected region.
• Create a new (empty) annotation track.
• Save different versions of genome annotations and represent them in the dataset tab.(Making comments on this annotations can be very useful)

More thoughts are here https://github.com/epam/NGB/wiki/Genome-annotation-in-NGB