[Obi-protocol-application-branch] DT visualization and other questions

[Philippe Rocca-Serra]

Hi James,

I am looking at the link and have the following suggestion/request:

i. gene list visualization:

Can we think of a more generic term such as 'molecular entity list
visualization' so that protein lists, metabolite lists could be handled ?

ii. then another question, related to the 'visualization', have you
discussed how to specify what is plotted against what or is it out of
scope for the moment?

for example, I am currently modeling 'glucose tolerance test' and I want
to say that I 'visualizing/plotting' ]glucose concentration values
(realizing/concretizing 'dependent variable specification'] as a
function of [time values (realizing/concretizing 'dependent variable
specification' )].

iii. This is more a term request related question:

Should DT include terms such as 'area calculation' (and corresponding
'area calculation objective') since we have (mean calculation) and then
possibly add 'integration data transformation'

(if this is valid and not causing too much of a scope creep, I would
need terms to cover derivation/differentiation)

Let me know and i'll provide all metadata

cheers

P

James Malone wrote:
> Hi All,
>
> Just a reminder, I'm adding in some of the visualization terms into OBI
> this week as these are urgent for the OBI manuscript. If anyone has
> anything they'd like to contribute please add to the spreadsheet here
> http://spreadsheets.google.com/ccc?key=0Ak22gS-WQteedGdvQUtqOWM5dVBjc3p4TjcyaWNPYkE&hl=en
>
> Cheers,
>
> James
>
>
>

--
Philippe Rocca-Serra, PhD

Technical Coordinator
www.ebi.ac.uk/net-project

The European Bioinformatics Institute email: ro...@ebi.ac.uk
EMBL Outstation - Hinxton direct: +44 (0)1223 492 553
Wellcome Trust Genome Campus fax: +44 (0)1223 492 620
Cambridge CB10 1SD, UK room: A3-141
--

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[James Malone]

Hi Phil,

Answers in line:

Philippe Rocca-Serra wrote:
> Hi James,
>
> I am looking at the link and have the following suggestion/request:
>
> i. gene list visualization:
>
> Can we think of a more generic term such as 'molecular entity list
> visualization' so that protein lists, metabolite lists could be handled ?

Definitely, we can add a parent class to this which is able to visualize
various mol entities we desire.

>
> ii. then another question, related to the 'visualization', have you
> discussed how to specify what is plotted against what or is it out of
> scope for the moment?
>
> for example, I am currently modeling 'glucose tolerance test' and I
> want to say that I 'visualizing/plotting' ]glucose concentration
> values (realizing/concretizing 'dependent variable specification'] as
> a function of [time values (realizing/concretizing 'dependent variable
> specification' )].
>

The scope is derived from what we need for the GenePattern use case. If
you have some use case or examples of things you would want in I think
we should take a look at them. We don't require anything as granular as
you specify here so far, but this is not to say we shouldn't have them
in. For the example above I would probably like to abstract out as much
as possible so we don't get too caught up in the specifics. For glucose
concentration values, it would be good if we could abstract this to a
data item or set by the features that define it and link that class of
data item/set to an appropriate list of data visualizations.

>
> iii. This is more a term request related question:
>
> Should DT include terms such as 'area calculation' (and corresponding
> 'area calculation objective') since we have (mean calculation) and
> then possibly add 'integration data transformation'

Sure let's get these in, I think it would be useful.

Cheers,

James

>
> (if this is valid and not causing too much of a scope creep, I would
> need terms to cover derivation/differentiation)
>
> Let me know and i'll provide all metadata
>
> cheers
>
> P
>
>
> James Malone wrote:
>> Hi All,
>>
>> Just a reminder, I'm adding in some of the visualization terms into
>> OBI this week as these are urgent for the OBI manuscript. If anyone
>> has anything they'd like to contribute please add to the spreadsheet
>> here
>> http://spreadsheets.google.com/ccc?key=0Ak22gS-WQteedGdvQUtqOWM5dVBjc3p4TjcyaWNPYkE&hl=en
>>
>>
>> Cheers,
>>
>> James
>>
>>
>>
>
>

--
European Bioinformatics Institute,
Wellcome Trust Genome Campus,
Hinxton,
Cambridge, CB10 1SD,
United Kingdom
Tel: + 44 (0) 1223 494 676
Fax: + 44 (0) 1223 492 468

[Philippe Rocca-Serra]

Hi James

> The scope is derived from what we need for the GenePattern use case.
> If you have some use case or examples of things you would want in I
> think we should take a look at them. We don't require anything as
> granular as you specify here so far, but this is not to say we
> shouldn't have them in. For the example above I would probably like to
> abstract out as much as possible so we don't get too caught up in the
> specifics. For glucose concentration values, it would be good if we
> could abstract this to a data item or set by the features that define
> it and link that class of data item/set to an appropriate list of data
> visualizations.

I am with you here and have actually used measured data item for that
matter. The modeling should deliver a generic solution .

thx

P