[ensembl-dev] Manual curation tools

[Michael Paulini]

I don't think the EnsEMBL API lets you edit gene models anyway, so
Apollo or not, it wouldn't work.
Didn't even Otter rather replace gene models than actually edit existing
ones?

M

On 23/04/13 14:21, Marc Hoeppner wrote:
> That would be an option, of course. But you lose the ability to
> curate/modify annotations in place or just flip/browse through
> multiple databases without having to dump flat files and load them
> into a software.
>
>> Just to play devil's advocate:
>> what speaks against dumping it in GFF(3) and loading it into
>> Apollo/Artemis/JBrowse/GBrowse/...
>> ... as kind of intermediate format or data layer?
>>
>> M
>>
>> On 23/04/13 12:52, Matthew Astley wrote:
>>> On Tue, Apr 23, 2013 at 09:22:45AM +0200, Marc Hoeppner wrote:
>>>
>>>> [...] one thing I am missing is a tool for inspecting the different
>>>> outputs and progress of the pipeline graphically. The documentation
>>>> suggests Apollo as a useful tool, but I had very mixed results
>>> I think some people do still use it for this purpose, possibly with
>>> locally modified source.
>>>
>>> I don't know how Apollo and its Ensembl interface are maintained, but
>>> they have recent activity on their websites.
>>>
>>>
>>>> [...] it seems to have some problems with some not-so-recent updates
>>>> in the database schema (like the gene_stable_id table, which I think
>>>> was deprecated?)
>>> (According to my notes, but not checking the version history) It was
>>> deprecated in 63 or 64, removed in 65 and the backwards compatibility
>>> views removed in 67.
>>>
>>>
>>>> Otterlace seems to be an attractive alternative, but I think that
>>>> one is designed to only work within EnsEMBL/Sanger?
>>> Otterlace includes ZMap, Blixem and Dotter.  Together these make the
>>> desktop client part of the application.  Otterlace needs an Otter
>>> Server with associated Ensembl-schema databases to supply the data for
>>> regions to edit.
>>>
>>> Both Otterlace and the Otter Server are _designed_ to work anywhere
>>> that can support the necessary databases and webserver back-end.
>>> However the server isn't currently installed anywhere else as far as
>>> we know.
>>>
>>> As with any unused software, the ability to work elsewhere is at risk
>>> of becoming vestigial.
>>>
>>>> Any way around that and adopt it to my local setup?
>>> With the current state of the Otter code, I suspect it would be more
>>> work to get Otterlace displaying your pipeline output than Apollo.
>>>
>>>
>>> However ZMap itself should be usable as a stand-alone viewer for gene
>>> builds.  It may not be in a state where you can do this conveniently
>>> now, but it is the direction we are taking it.
>>>
>>> If you are interested in this, we should perhaps continue off the
>>> dev at ensembl list.
>>>
>>>
>>>> I guess my questions is what other people are using - and if there
>>>> is nothing else out there that can talk to an EnsEMBL core DB, what
>>>> I could try to get either of the two options above to work properly.
>>> As developers of Otterlace we need to verify that it is displaying
>>> data correctly.  We tend to look at the ensembl data via SQL or the
>>> API, or the GFF and other underlying data.
>>>
>>> I think we may have used Apollo for the purpose, but not recently.
>>>
>>