Re: MIBBI and ISA tools
Karen Cranston
On Thu, Oct 20, 2011 at 9:49 AM, Karen Cranston
<karen.c...@gmail.com> wrote:
> At the MIAPA workshop at the TDWG meetings, we got a great demo from
> Chris Fields about MIBBI [1] and the interface with the ISA Tools [2]
> (specifically about how simple it is to create an annotation interface
> once MIAPA is registered with the MIBBI Foundary). I've been getting
> some additional detail from Chris, and thought that everyone might be
> interested in this thread.
>
> I'll note that my statement about Arlin taking charge of an annotation
> was apparently overly optimistic. ;)
>
> Cheers,
> Karen
>
> [1] http://mibbi.org/index.php/Main_Page
> [2] http://isa-tools.org/
>
>
>
> ---------- Forwarded message ----------
> From: Chris Taylor <chris....@ebi.ac.uk>
> Date: Thu, Oct 20, 2011 at 8:08 AM
> Subject: Re: MIBBI and ISA tools
> To: Karen Cranston <karen.c...@nescent.org>
> Cc: Arlin Stoltzfus <ar...@umd.edu>, Dawn Field
> <fie...@googlemail.com>, Susanna-Assunta Sansone
> <sa.sa...@gmail.com>
>
>
> Hi Karen, Arlin,
>
> I hope you don't mind my expanding the cc list a little to bring Dawn
> Field and Susanna Sansone (ISA team lead) into the discussion...
>
>> Skyping with a room full of strangers can't be entirely fun. :)
>
> It was though :) It always is when a really engaged set of people are
> on a mission like that. My only worry with Skyping in was that I'd end
> up running rough shod over the discussion and cutting in too much.
> Hope I didn't...
>
> Thanks wrt the demo comment. One of the things decided at the last
> MIBBI meeting was that we should gear up to be able to support new
> projects properly, so it is something of a vindication to hear that.
>
> As for the plan, that's what I would have suggested, yes. At the point
> where you've settled the next draft (in text form) I can type that up
> or I can point you at the edit tool and from there everything else is
> more or less automatic in terms of rendering it various ways.
>
> With one exception, as things stand, which is a web-based data entry
> form: There's nothing available right now, but I could look into doing
> that, or working with someone perhaps. It really depends on the level
> of sophistication required. Stone simple forms = easy/quick(ish); lots
> of scripting/logic, not so much.
>
> Great to hear the interest in contributing to and using the Foundry
> modules. All for that. Again once the draft is settled we can revisit
> that. In the meantime, feel free to comment on anything you see at
> http://mibbi.org/index.php/MIBBI_foundry_modules
>
> Incidentally, and again once a settled version emerges; the database
> component of the suite around ISAcreator would be easy to set up
> somewhere to start collecting MIAPA-compliant descriptions (to
> encourage others, etc.). It's even fairly straightforward (given that
> some talked of coding up importers, implying available person-hours)
> to conceive of exporters to wherever (particularly wrt 'split'
> submissions, where the ISA-based metadata DB acts as an index into
> other data-focused repositories -- trees, or perhaps sequence
> [collections] as was discussed) -- ensuring large assemblages of data
> stay coherent.
>
> Thanks again for having me.
>
> Cheers, Chris.
>
>
> On 19/10/2011 15:24, Karen Cranston wrote:
>>
>> Hi Chris,
>> Thanks for taking the time to participate in the MIAPA workshop
>> yesterday and Monday. Skyping with a room full of strangers can't be
>> entirely fun. :)
>>
>> I was really impressed with the MIBBI / ISA demo. It seems that
>> producing a draft interface is going to be extremely straightforward
>> once we have the standard in place. I think that Arlin is taking the
>> lead role on the MIAPA annotation tools, but I wanted to ask a few
>> more questions about the infrastructure. My understanding of how this
>> would work (which may be entirely wrong) is:
>>
>> * in consultation with the phylogenetic community, develop our list of
>> MIAPA components
>> * publish the MIAPA standard on the MIBBI portal (table, list and xml formats )
>> * publish the unique MIAPA components as MIBBI Foundry modules
>> (recognizing that some of the components may already exist as modules)
>> * import the (XML file? XML schema?) into ISA creator to produce a
>> basic data annotation interface. Could we embed this within another
>> web-based software platform? Is it easy to customize the interface?
>>
>> Let me know what I am missing (and sorry for the naive questions).
>>
>> Cheers,
>> Karen
>>
>
> --
> _______________________
> chris....@ebi.ac.uk
> http://mibbi.org/
>
>
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~
> karen.c...@gmail.com
> ~~~~~~~~~~~~~~~~~~~~~~~
>
--
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karen.c...@gmail.com
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