[ensembl-dev] Manual curation tools

[Healy, Matthew]

I actually used Apollo with flat files for a different project -- not involving ENSEMBL -- a while back, and liked it very much.  Was easier for us to dump GFF files than it would have been to write hooks into the particular mapping database that we were building.

________________________________________
From: dev-bounces at ensembl.org [dev-bounces at ensembl.org] On Behalf Of Marc Hoeppner [mphoeppner at gmail.com]
Sent: Tuesday, April 23, 2013 9:21 AM
To: Ensembl developers list
Subject: Re: [ensembl-dev] Manual curation tools

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.
>>
>
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