obi-datatrfm-branch

[Obi-datatrfm-branch] Tracker item - proposal to move terms from _unclassified

[Helen P. <par...@eb...>]

Dear dt branch,

please take a look at the proposal in the tracker and comment it if you 
have suggestions or disagree with the proposal to move terms. These will 
be actioned by end Wednesday 9th September unless someone disagrees and 
comes up with an alternate proposal

https://sourceforge.net/search/?group_id=177891&words=_unclass&type_of_search=artifact&pmode=0&words=_unclassified&Search=Search

thanks

Helen

-- 
Helen Parkinson, PhD
ArrayExpress Production Coordinator,
Microarray Informatics Team, 
EBI

EBI 01223 494672
Skype: helen.parkinson.ebi

Re: [Obi-datatrfm-branch] DT visualization and other questions

[Philippe Rocca-S. <ro...@eb...>]

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

Re: [Obi-datatrfm-branch] DT visualization and other questions

[James M. <ma...@eb...>]

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 

[Obi-datatrfm-branch] DT visualization and other questions

[Philippe Rocca-S. <ro...@eb...>]

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...@eb...
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
--

[Obi-datatrfm-branch] Visualizations for DT

[James M. <ma...@eb...>]

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 

Re: [Obi-datatrfm-branch] DT Visualisations

[Frank G. <fg...@gm...>]

James, from the link you gave "*Data visualization* is the study of the
visual representation of data <http://en.wikipedia.org/wiki/Data>" I don't
interpret this as data_visualisation is the process of converting data into
a representation of data that can be visualised. I have no problem with your
definition, as it defines the conversion of data into a form that can be
visualised, but I do think you should consider a label change.

Frank

On Thu, Jul 16, 2009 at 7:35 PM, James Malone <ma...@eb...> wrote:

> Agreed Philippe, what Frank is talking about is something else to that
> which we want to caputure in DT.  That said, personally, I am happy with
> the definition and the label as it meets what I think the world calls
> 'data visualization' http://en.wikipedia.org/wiki/Data_visualization  and
> this is the sense I want to capture with this class.  If this is NOT
> captured in this, then the class I've added is wrong.  Like I said, I am
> more than happy for other people to create the classes for 'visualization'
> or 'visualize' (atually 'rendering' was the original relation I proposed
> to link data to report graphs until it was decided to do this via
> processes) but I have no use case for doing this and it is def outside DT
> scope (Frank mentioned something about some neuroscience experiments he
> has).
>
> I've copied this email onto dev in case anyone is interesting in
> following up Frank and Philippe's suggestions, detailed in the thread
> below.
>
> Thanks,
>
> James
>
>
>
> > Hi James, Frank,
> >
> > I can see valid points from both sides.
> > It seems to me that you are refering to process called 'rendering'. a
> data cluster a rendered as dendrogram
> > the objective of this data transformation = rendering  is visualization
> (I would side with Frank that some you need human eyes to for the
> visualization objective to met ).
> >
> > Cheers
> >
> > Philippe
> >
> >
> >
> >
> > Frank Gibson wrote:
> >> On Thu, Jul 16, 2009 at 5:47 PM, James Malone <ma...@eb...
> <mailto:ma...@eb...>> wrote:
> >>     So the only thing I say is that data visualization is_a data
> transformation, that is the only is_a and in fact that is not quite
> true
> >>     since the input is data but the output is an ICE so really this an
> information processing subclass not a DT - it'll move once I add
> the
> >>     axioms. I don't wish to define 'visualization' here because I have
> no need
> >>     to nor a use case.  By all means we can define the biological
> process if
> >>     necassary but this is not top of my list and I don't think affects
> >> the
> >>     work that is pressing right now for DT.  At the moment I'm happy
> with our
> >>     simple definition below of data visualisation, something that takes
> data
> >>     and produces something 'visual' at the end, i.e. image, report
> graph or
> >>     animation.  I guess the question is would a biological
> visualisation
> >>     process reason to be equivalent (or a subclass of this) and would
> >> that
> >>     cause a problem. I'm happy to cross that bridge if we ever come to
> it, at
> >>     which point we should revisist your point.
> >> That is ok, you used the terms visualised and visualisation process to
> describe data_visualisation. I have no issue with the definition of
> data_visualisation (although I do think it is the wrong label) as long
> as you dont talk about visualised and visualisation process. Eyes
> visualise, machines process and measure and produce information that
> can be visualised.
> >>     Also, no more corny-a jokes please :D (last one)
> >> bloody hell, thats the worst one yet, and I nearly missed it, must get
> my eyes checked
> >> Frank
> >>     James
> >>     > On Thu, Jul 16, 2009 at 5:06 PM, James Malone <ma...@eb...
> >>     <mailto:ma...@eb...>> wrote:
> >>     >
> >>     >> So the class in DT is called "data visualization" definition is
> >>     "Data
> >>     >> visualization is a data transformation that creates images,
> >>     diagrams or
> >>     >> animations from the input data set."
> >>     >>
> >>     >> I personally feel this is distinct enough from the biological
> >>     process
> >>     >> you
> >>     >> outline below. If anyone else can't see the distinction though
> >>     can they
> >>     >> let me know as it may be my own bias is not letting me 'see'
> >>     the problem
> >>     >> ;)
> >>     >>
> >>     >
> >>     > Eye see you..... mention visualised and visulization_process and
> >>     that
> >>     > data_visualisation is a visualisation_process and a data
> >>     transformation.
> >>     > Can
> >>     > you "see your way" to define visualised and
> >>     visualisation_process, to
> >>     > allow
> >>     > me to see the proposal more clearly through your eyes?
> >>     >
> >>     >
> >>     > Frank
> >>     >
> >>     >
> >>     >
> >>     >>
> >>     >> James
> >>     >>
> >>     >>
> >>     >>
> >>     >> > Hi James,
> >>     >> >
> >>     >> > I just wanted to seek clarification on how you are using the
> >> term
> >>     >> > visualisation/visualised. Machines dont visualise, they
> >>     measure and
> >>     >> > process
> >>     >> > information. A vizulisation_process is something (for
> >>     example) a human
> >>     >> eye
> >>     >> > does, not a machine. A machine would process some information
> >> to
> >>     >> another
> >>     >> > form of information that then data_output could be
> >>     visualised. The
> >>     >> process
> >>     >> > of converting some information into another type of
> >>     infromation could
> >>     >> be
> >>     >> > called something like visual_representation_processing which
> >>     would
> >>     >> produce
> >>     >> > and output that had the potential to be visualised.
> >>     >> >
> >>     >> > This probably is just a label change, but I think it is
> >> important
> >>     >> enough
> >>     >> > to
> >>     >> > seek clairification on, as "visualisation" is definately
> >>     something
> >>     >> that
> >>     >> > can
> >>     >> > be investigated in a biological experiment, irrespective of
> >>     >> information
> >>     >> > processing..
> >>     >> >
> >>     >> > Frank
> >>     >> >
> >>     >> > On Thu, Jul 16, 2009 at 4:18 PM, James Malone
> >>     <ma...@eb... <mailto:ma...@eb...>>
> >>     >> wrote:
> >>     >> >
> >>     >> >> Hi All,
> >>     >> >>
> >>     >> >> As promised, OBI is working again so here is my email.  We
> >>     want to
> >>     >> add
> >>     >> >> some data visualisation processes to DT.  They are to take
> >>     the form
> >>     >> as
> >>     >> >> follows:
> >>     >> >>
> >>     >> >> input x data
> >>     >> >> is visualised in visualization process 'x data visualisation
> '
> >>     >> >> output a, b or c report graphs (where a, b or c are the types
> >> of
> >>     >> graphs
> >>     >> >> that x can be validly visualized as)
> >>     >> >>
> >>     >> >> for example:
> >>     >> >>
> >>     >> >> clustered data visualization
> >>     >> >> has input only clustered data
> >>     >> >> has output dot plot or dendrogram
> >>     >> >>
> >>     >> >> So, we have a list which I've added to the google doc here:
> >>     >> >>
> >>
> http://spreadsheets.google.com/ccc?key=tgoAKj9c9uPcszxN72icObA&hl=en
> <http://spreadsheets.google.com/ccc?key=tgoAKj9c9uPcszxN72icObA&hl=en>
> >>     >> >>
> >>     >> >> What I would like to do is enlist anyone who like to curate
> >> the
> >>     >> >> visualizations by adding the outputs to the visualizations I
> >>     have
> >>     >> added
> >>     >> >> to
> >>     >> >> the spreadsheet.  Presently, these outputs are:
> >>     >> >>
> >>     >> >> contour plot
> >>     >> >> dendrogram
> >>     >> >> density plot
> >>     >> >> dot plot
> >>     >> >> heatmap
> >>     >> >> histogram
> >>     >> >> scatter plot
> >>     >> >> survival curve
> >>     >> >> Venn diagram
> >>     >> >>
> >>     >> >> Though if you can think of more please just add them to the
> >>     >> spreadsheet
> >>     >> >> and I will add them to the ontology.  I've completed moost
> >>     of the
> >>     >> >> processes we need in row a and b so what I'm looking for are
> >>     >> volunteers
> >>     >> >> for column c. Column d can be used for any notes you may
> >>     have. Then I
> >>     >> >> will
> >>     >> >> code these up into the ontology.  Any volunteers? :)
> >>     >> >>
> >>     >> >> Many thanks!
> >>     >> >>
> >>     >> >> James
> >>     >> >>
> >>     >> >>
> >>     >> >> --
> >>     >> >> European Bioinformatics Institute,
> >>     >> >> Wellcome Trust Genome Campus,
> >>     >> >> Hinxton,
> >>     >> >> Cambridge, CB10 1SD,
> >>     >> >> United Kingdom
> >>     >> >> Fax: + 44 (0) 1223 492 468
> >>     >> >>
> >>     >> >>
> >>     >> >>
> >>     >> >>
> >>     >> >>
> >>     >> >>
> >>     >> >>
> >>     >> >>
> >>     >> >>
> >>     >>
> >>
> ------------------------------------------------------------------------------
> >>     >> >> Enter the BlackBerry Developer Challenge
> >>     >> >> This is your chance to win up to $100,000 in prizes! For a
> >>     limited
> >>     >> time,
> >>     >> >> vendors submitting new applications to BlackBerry App
> >>     World(TM) will
> >>     >> >> have
> >>     >> >> the opportunity to enter the BlackBerry Developer Challenge.
> >>     See full
> >>     >> >> prize
> >>     >> >> details at: http://p.sf.net/sfu/Challenge
> >>     >> >> _______________________________________________
> >>     >> >> Obi-datatrfm-branch mailing list
> >>     >> >> Obi...@li...
> >>     <mailto:Obi...@li...>
> >>     >> >>
> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch
> >>     >> >>
> >>     >> >
> >>     >> >
> >>     >> >
> >>     >> > --
> >>     >> > Frank Gibson, PhD
> >>     >> > http://peanutbutter.wordpress.com/
> >>     >> >
> >>     >>
> >>     >>
> >>     >> --
> >>     >> EMBL Outstation - Hinxton,
> >>     >> European Bioinformatics Institute,
> >>     >> Wellcome Trust Genome Campus,
> >>     >> Hinxton,
> >>     >> Cambridge, CB10 1SD,
> >>     >> United Kingdom
> >>     >> Fax: + 44 (0) 1223 492 468
> >>     >>
> >>     >>
> >>     >
> >>     >
> >>     > --
> >>     > Frank Gibson, PhD
> >>     > http://peanutbutter.wordpress.com/
> >>     >
> >>     --
> >>     EMBL Outstation - Hinxton,
> >>     European Bioinformatics Institute,
> >>     Wellcome Trust Genome Campus,
> >>     Hinxton,
> >>     Cambridge, CB10 1SD,
> >>     United Kingdom
> >>     Fax: + 44 (0) 1223 492 468
> >> --
> >> Frank Gibson, PhD
> >> http://peanutbutter.wordpress.com/
> >> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge
> >> This is your chance to win up to $100,000 in prizes! For a limited
> time,
> >> vendors submitting new applications to BlackBerry App World(TM) will
> have
> >> the opportunity to enter the BlackBerry Developer Challenge. See full
> prize
> >> details at: http://p.sf.net/sfu/Challenge
> >> ------------------------------------------------------------------------
> _______________________________________________
> >> Obi-datatrfm-branch mailing list
> >> Obi...@li...
> >> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch
> >
> >
> > --
> > Philippe Rocca-Serra, PhD
> >
> > Technical Coordinator
> > www.ebi.ac.uk/net-project
> >
> > The European Bioinformatics Institute   email:  ro...@eb...
> > 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
> > --
> >
>
>
> --
> EMBL Outstation - Hinxton,
> European Bioinformatics Institute,
> Wellcome Trust Genome Campus,
> Hinxton,
> Cambridge, CB10 1SD,
> United Kingdom
> Fax: + 44 (0) 1223 492 468
>
>
>
>
>


-- 
Frank Gibson, PhD
http://peanutbutter.wordpress.com/

Re: [Obi-datatrfm-branch] DT Visualisations

[James M. <ma...@eb...>]

Agreed Philippe, what Frank is talking about is something else to that
which we want to caputure in DT.  That said, personally, I am happy with
the definition and the label as it meets what I think the world calls
'data visualization' http://en.wikipedia.org/wiki/Data_visualization  and
this is the sense I want to capture with this class.  If this is NOT
captured in this, then the class I've added is wrong.  Like I said, I am
more than happy for other people to create the classes for 'visualization'
or 'visualize' (atually 'rendering' was the original relation I proposed
to link data to report graphs until it was decided to do this via
processes) but I have no use case for doing this and it is def outside DT
scope (Frank mentioned something about some neuroscience experiments he
has).

I've copied this email onto dev in case anyone is interesting in
following up Frank and Philippe's suggestions, detailed in the thread below.

Thanks,

James



> Hi James, Frank,
>
> I can see valid points from both sides.
> It seems to me that you are refering to process called 'rendering'. a
data cluster a rendered as dendrogram
> the objective of this data transformation = rendering  is visualization
(I would side with Frank that some you need human eyes to for the
visualization objective to met ).
>
> Cheers
>
> Philippe
>
>
>
>
> Frank Gibson wrote:
>> On Thu, Jul 16, 2009 at 5:47 PM, James Malone <ma...@eb...
<mailto:ma...@eb...>> wrote:
>>     So the only thing I say is that data visualization is_a data
transformation, that is the only is_a and in fact that is not quite
true
>>     since the input is data but the output is an ICE so really this an
information processing subclass not a DT - it'll move once I add
the
>>     axioms. I don't wish to define 'visualization' here because I have
no need
>>     to nor a use case.  By all means we can define the biological
process if
>>     necassary but this is not top of my list and I don't think affects
>> the
>>     work that is pressing right now for DT.  At the moment I'm happy
with our
>>     simple definition below of data visualisation, something that takes
data
>>     and produces something 'visual' at the end, i.e. image, report
graph or
>>     animation.  I guess the question is would a biological
visualisation
>>     process reason to be equivalent (or a subclass of this) and would
>> that
>>     cause a problem. I'm happy to cross that bridge if we ever come to
it, at
>>     which point we should revisist your point.
>> That is ok, you used the terms visualised and visualisation process to
describe data_visualisation. I have no issue with the definition of
data_visualisation (although I do think it is the wrong label) as long
as you dont talk about visualised and visualisation process. Eyes
visualise, machines process and measure and produce information that
can be visualised.
>>     Also, no more corny-a jokes please :D (last one)
>> bloody hell, thats the worst one yet, and I nearly missed it, must get
my eyes checked
>> Frank
>>     James
>>     > On Thu, Jul 16, 2009 at 5:06 PM, James Malone <ma...@eb...
>>     <mailto:ma...@eb...>> wrote:
>>     >
>>     >> So the class in DT is called "data visualization" definition is
>>     "Data
>>     >> visualization is a data transformation that creates images,
>>     diagrams or
>>     >> animations from the input data set."
>>     >>
>>     >> I personally feel this is distinct enough from the biological
>>     process
>>     >> you
>>     >> outline below. If anyone else can't see the distinction though
>>     can they
>>     >> let me know as it may be my own bias is not letting me 'see'
>>     the problem
>>     >> ;)
>>     >>
>>     >
>>     > Eye see you..... mention visualised and visulization_process and
>>     that
>>     > data_visualisation is a visualisation_process and a data
>>     transformation.
>>     > Can
>>     > you "see your way" to define visualised and
>>     visualisation_process, to
>>     > allow
>>     > me to see the proposal more clearly through your eyes?
>>     >
>>     >
>>     > Frank
>>     >
>>     >
>>     >
>>     >>
>>     >> James
>>     >>
>>     >>
>>     >>
>>     >> > Hi James,
>>     >> >
>>     >> > I just wanted to seek clarification on how you are using the
>> term
>>     >> > visualisation/visualised. Machines dont visualise, they
>>     measure and
>>     >> > process
>>     >> > information. A vizulisation_process is something (for
>>     example) a human
>>     >> eye
>>     >> > does, not a machine. A machine would process some information
>> to
>>     >> another
>>     >> > form of information that then data_output could be
>>     visualised. The
>>     >> process
>>     >> > of converting some information into another type of
>>     infromation could
>>     >> be
>>     >> > called something like visual_representation_processing which
>>     would
>>     >> produce
>>     >> > and output that had the potential to be visualised.
>>     >> >
>>     >> > This probably is just a label change, but I think it is
>> important
>>     >> enough
>>     >> > to
>>     >> > seek clairification on, as "visualisation" is definately
>>     something
>>     >> that
>>     >> > can
>>     >> > be investigated in a biological experiment, irrespective of
>>     >> information
>>     >> > processing..
>>     >> >
>>     >> > Frank
>>     >> >
>>     >> > On Thu, Jul 16, 2009 at 4:18 PM, James Malone
>>     <ma...@eb... <mailto:ma...@eb...>>
>>     >> wrote:
>>     >> >
>>     >> >> Hi All,
>>     >> >>
>>     >> >> As promised, OBI is working again so here is my email.  We
>>     want to
>>     >> add
>>     >> >> some data visualisation processes to DT.  They are to take
>>     the form
>>     >> as
>>     >> >> follows:
>>     >> >>
>>     >> >> input x data
>>     >> >> is visualised in visualization process 'x data visualisation
'
>>     >> >> output a, b or c report graphs (where a, b or c are the types
>> of
>>     >> graphs
>>     >> >> that x can be validly visualized as)
>>     >> >>
>>     >> >> for example:
>>     >> >>
>>     >> >> clustered data visualization
>>     >> >> has input only clustered data
>>     >> >> has output dot plot or dendrogram
>>     >> >>
>>     >> >> So, we have a list which I've added to the google doc here:
>>     >> >>
>>     http://spreadsheets.google.com/ccc?key=tgoAKj9c9uPcszxN72icObA&hl=en
<http://spreadsheets.google.com/ccc?key=tgoAKj9c9uPcszxN72icObA&hl=en>
>>     >> >>
>>     >> >> What I would like to do is enlist anyone who like to curate
>> the
>>     >> >> visualizations by adding the outputs to the visualizations I
>>     have
>>     >> added
>>     >> >> to
>>     >> >> the spreadsheet.  Presently, these outputs are:
>>     >> >>
>>     >> >> contour plot
>>     >> >> dendrogram
>>     >> >> density plot
>>     >> >> dot plot
>>     >> >> heatmap
>>     >> >> histogram
>>     >> >> scatter plot
>>     >> >> survival curve
>>     >> >> Venn diagram
>>     >> >>
>>     >> >> Though if you can think of more please just add them to the
>>     >> spreadsheet
>>     >> >> and I will add them to the ontology.  I've completed moost
>>     of the
>>     >> >> processes we need in row a and b so what I'm looking for are
>>     >> volunteers
>>     >> >> for column c. Column d can be used for any notes you may
>>     have. Then I
>>     >> >> will
>>     >> >> code these up into the ontology.  Any volunteers? :)
>>     >> >>
>>     >> >> Many thanks!
>>     >> >>
>>     >> >> James
>>     >> >>
>>     >> >>
>>     >> >> --
>>     >> >> European Bioinformatics Institute,
>>     >> >> Wellcome Trust Genome Campus,
>>     >> >> Hinxton,
>>     >> >> Cambridge, CB10 1SD,
>>     >> >> United Kingdom
>>     >> >> Fax: + 44 (0) 1223 492 468
>>     >> >>
>>     >> >>
>>     >> >>
>>     >> >>
>>     >> >>
>>     >> >>
>>     >> >>
>>     >> >>
>>     >> >>
>>     >>
>>     ------------------------------------------------------------------------------
>>     >> >> Enter the BlackBerry Developer Challenge
>>     >> >> This is your chance to win up to $100,000 in prizes! For a
>>     limited
>>     >> time,
>>     >> >> vendors submitting new applications to BlackBerry App
>>     World(TM) will
>>     >> >> have
>>     >> >> the opportunity to enter the BlackBerry Developer Challenge.
>>     See full
>>     >> >> prize
>>     >> >> details at: http://p.sf.net/sfu/Challenge
>>     >> >> _______________________________________________
>>     >> >> Obi-datatrfm-branch mailing list
>>     >> >> Obi...@li...
>>     <mailto:Obi...@li...>
>>     >> >> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch
>>     >> >>
>>     >> >
>>     >> >
>>     >> >
>>     >> > --
>>     >> > Frank Gibson, PhD
>>     >> > http://peanutbutter.wordpress.com/
>>     >> >
>>     >>
>>     >>
>>     >> --
>>     >> EMBL Outstation - Hinxton,
>>     >> European Bioinformatics Institute,
>>     >> Wellcome Trust Genome Campus,
>>     >> Hinxton,
>>     >> Cambridge, CB10 1SD,
>>     >> United Kingdom
>>     >> Fax: + 44 (0) 1223 492 468
>>     >>
>>     >>
>>     >
>>     >
>>     > --
>>     > Frank Gibson, PhD
>>     > http://peanutbutter.wordpress.com/
>>     >
>>     --
>>     EMBL Outstation - Hinxton,
>>     European Bioinformatics Institute,
>>     Wellcome Trust Genome Campus,
>>     Hinxton,
>>     Cambridge, CB10 1SD,
>>     United Kingdom
>>     Fax: + 44 (0) 1223 492 468
>> --
>> Frank Gibson, PhD
>> http://peanutbutter.wordpress.com/
>> ------------------------------------------------------------------------
------------------------------------------------------------------------------
Enter the BlackBerry Developer Challenge
>> This is your chance to win up to $100,000 in prizes! For a limited
time,
>> vendors submitting new applications to BlackBerry App World(TM) will have
>> the opportunity to enter the BlackBerry Developer Challenge. See full
prize
>> details at: http://p.sf.net/sfu/Challenge
>> ------------------------------------------------------------------------
_______________________________________________
>> Obi-datatrfm-branch mailing list
>> Obi...@li...
>> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch
>
>
> --
> Philippe Rocca-Serra, PhD
>
> Technical Coordinator
> www.ebi.ac.uk/net-project
>
> The European Bioinformatics Institute   email:  ro...@eb...
> 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
> --
>


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

Re: [Obi-datatrfm-branch] DT Visualisations

[Philippe Rocca-S. <ro...@eb...>]

Hi James, Frank,

I can see valid points from both sides.
It seems to me that you are refering to process called 'rendering'.
a data cluster a rendered as dendrogram
the objective of this data transformation = rendering  is visualization 
(I would side with Frank that some you need human eyes to for the 
visualization objective to met ).

Cheers

Philippe




Frank Gibson wrote:
>
>
> On Thu, Jul 16, 2009 at 5:47 PM, James Malone <ma...@eb... 
> <mailto:ma...@eb...>> wrote:
>
>     So the only thing I say is that data visualization is_a data
>     transformation, that is the only is_a and in fact that is not
>     quite true
>     since the input is data but the output is an ICE so really this an
>     information processing subclass not a DT - it'll move once I add the
>     axioms. I don't wish to define 'visualization' here because I have
>     no need
>     to nor a use case.  By all means we can define the biological
>     process if
>     necassary but this is not top of my list and I don't think affects the
>     work that is pressing right now for DT.  At the moment I'm happy
>     with our
>     simple definition below of data visualisation, something that
>     takes data
>     and produces something 'visual' at the end, i.e. image, report
>     graph or
>     animation.  I guess the question is would a biological visualisation
>     process reason to be equivalent (or a subclass of this) and would that
>     cause a problem. I'm happy to cross that bridge if we ever come to
>     it, at
>     which point we should revisist your point.
>
>
> That is ok, you used the terms visualised and visualisation process to 
> describe data_visualisation. I have no issue with the definition of 
> data_visualisation (although I do think it is the wrong label) as long 
> as you dont talk about visualised and visualisation process. Eyes 
> visualise, machines process and measure and produce information that 
> can be visualised.
>
>  
>
>
>
>     Also, no more corny-a jokes please :D (last one)
>
>
> bloody hell, thats the worst one yet, and I nearly missed it, must get 
> my eyes checked
>
> Frank
>
>  
>
>
>
>     James
>
>
>
>     > On Thu, Jul 16, 2009 at 5:06 PM, James Malone <ma...@eb...
>     <mailto:ma...@eb...>> wrote:
>     >
>     >> So the class in DT is called "data visualization" definition is
>     "Data
>     >> visualization is a data transformation that creates images,
>     diagrams or
>     >> animations from the input data set."
>     >>
>     >> I personally feel this is distinct enough from the biological
>     process
>     >> you
>     >> outline below. If anyone else can't see the distinction though
>     can they
>     >> let me know as it may be my own bias is not letting me 'see'
>     the problem
>     >> ;)
>     >>
>     >
>     > Eye see you..... mention visualised and visulization_process and
>     that
>     > data_visualisation is a visualisation_process and a data
>     transformation.
>     > Can
>     > you "see your way" to define visualised and
>     visualisation_process, to
>     > allow
>     > me to see the proposal more clearly through your eyes?
>     >
>     >
>     > Frank
>     >
>     >
>     >
>     >>
>     >> James
>     >>
>     >>
>     >>
>     >> > Hi James,
>     >> >
>     >> > I just wanted to seek clarification on how you are using the term
>     >> > visualisation/visualised. Machines dont visualise, they
>     measure and
>     >> > process
>     >> > information. A vizulisation_process is something (for
>     example) a human
>     >> eye
>     >> > does, not a machine. A machine would process some information to
>     >> another
>     >> > form of information that then data_output could be
>     visualised. The
>     >> process
>     >> > of converting some information into another type of
>     infromation could
>     >> be
>     >> > called something like visual_representation_processing which
>     would
>     >> produce
>     >> > and output that had the potential to be visualised.
>     >> >
>     >> > This probably is just a label change, but I think it is important
>     >> enough
>     >> > to
>     >> > seek clairification on, as "visualisation" is definately
>     something
>     >> that
>     >> > can
>     >> > be investigated in a biological experiment, irrespective of
>     >> information
>     >> > processing..
>     >> >
>     >> > Frank
>     >> >
>     >> > On Thu, Jul 16, 2009 at 4:18 PM, James Malone
>     <ma...@eb... <mailto:ma...@eb...>>
>     >> wrote:
>     >> >
>     >> >> Hi All,
>     >> >>
>     >> >> As promised, OBI is working again so here is my email.  We
>     want to
>     >> add
>     >> >> some data visualisation processes to DT.  They are to take
>     the form
>     >> as
>     >> >> follows:
>     >> >>
>     >> >> input x data
>     >> >> is visualised in visualization process 'x data visualisation '
>     >> >> output a, b or c report graphs (where a, b or c are the types of
>     >> graphs
>     >> >> that x can be validly visualized as)
>     >> >>
>     >> >> for example:
>     >> >>
>     >> >> clustered data visualization
>     >> >> has input only clustered data
>     >> >> has output dot plot or dendrogram
>     >> >>
>     >> >> So, we have a list which I've added to the google doc here:
>     >> >>
>     http://spreadsheets.google.com/ccc?key=tgoAKj9c9uPcszxN72icObA&hl=en
>     <http://spreadsheets.google.com/ccc?key=tgoAKj9c9uPcszxN72icObA&hl=en>
>     >> >>
>     >> >> What I would like to do is enlist anyone who like to curate the
>     >> >> visualizations by adding the outputs to the visualizations I
>     have
>     >> added
>     >> >> to
>     >> >> the spreadsheet.  Presently, these outputs are:
>     >> >>
>     >> >> contour plot
>     >> >> dendrogram
>     >> >> density plot
>     >> >> dot plot
>     >> >> heatmap
>     >> >> histogram
>     >> >> scatter plot
>     >> >> survival curve
>     >> >> Venn diagram
>     >> >>
>     >> >> Though if you can think of more please just add them to the
>     >> spreadsheet
>     >> >> and I will add them to the ontology.  I've completed moost
>     of the
>     >> >> processes we need in row a and b so what I'm looking for are
>     >> volunteers
>     >> >> for column c. Column d can be used for any notes you may
>     have. Then I
>     >> >> will
>     >> >> code these up into the ontology.  Any volunteers? :)
>     >> >>
>     >> >> Many thanks!
>     >> >>
>     >> >> James
>     >> >>
>     >> >>
>     >> >> --
>     >> >> European Bioinformatics Institute,
>     >> >> Wellcome Trust Genome Campus,
>     >> >> Hinxton,
>     >> >> Cambridge, CB10 1SD,
>     >> >> United Kingdom
>     >> >> Fax: + 44 (0) 1223 492 468
>     >> >>
>     >> >>
>     >> >>
>     >> >>
>     >> >>
>     >> >>
>     >> >>
>     >> >>
>     >> >>
>     >>
>     ------------------------------------------------------------------------------
>     >> >> Enter the BlackBerry Developer Challenge
>     >> >> This is your chance to win up to $100,000 in prizes! For a
>     limited
>     >> time,
>     >> >> vendors submitting new applications to BlackBerry App
>     World(TM) will
>     >> >> have
>     >> >> the opportunity to enter the BlackBerry Developer Challenge.
>     See full
>     >> >> prize
>     >> >> details at: http://p.sf.net/sfu/Challenge
>     >> >> _______________________________________________
>     >> >> Obi-datatrfm-branch mailing list
>     >> >> Obi...@li...
>     <mailto:Obi...@li...>
>     >> >> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch
>     >> >>
>     >> >
>     >> >
>     >> >
>     >> > --
>     >> > Frank Gibson, PhD
>     >> > http://peanutbutter.wordpress.com/
>     >> >
>     >>
>     >>
>     >> --
>     >> EMBL Outstation - Hinxton,
>     >> European Bioinformatics Institute,
>     >> Wellcome Trust Genome Campus,
>     >> Hinxton,
>     >> Cambridge, CB10 1SD,
>     >> United Kingdom
>     >> Fax: + 44 (0) 1223 492 468
>     >>
>     >>
>     >
>     >
>     > --
>     > Frank Gibson, PhD
>     > http://peanutbutter.wordpress.com/
>     >
>
>
>     --
>     EMBL Outstation - Hinxton,
>     European Bioinformatics Institute,
>     Wellcome Trust Genome Campus,
>     Hinxton,
>     Cambridge, CB10 1SD,
>     United Kingdom
>     Fax: + 44 (0) 1223 492 468
>
>
>
>
> -- 
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge  
> This is your chance to win up to $100,000 in prizes! For a limited time, 
> vendors submitting new applications to BlackBerry App World(TM) will have
> the opportunity to enter the BlackBerry Developer Challenge. See full prize  
> details at: http://p.sf.net/sfu/Challenge
> ------------------------------------------------------------------------
>
> _______________________________________________
> Obi-datatrfm-branch mailing list
> Obi...@li...
> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch
>   


-- 
Philippe Rocca-Serra, PhD

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

The European Bioinformatics Institute   email:  ro...@eb...
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
--

Re: [Obi-datatrfm-branch] DT Visualisations

[Frank G. <fg...@gm...>]

On Thu, Jul 16, 2009 at 5:47 PM, James Malone <ma...@eb...> wrote:

> So the only thing I say is that data visualization is_a data
> transformation, that is the only is_a and in fact that is not quite true
> since the input is data but the output is an ICE so really this an
> information processing subclass not a DT - it'll move once I add the
> axioms. I don't wish to define 'visualization' here because I have no need
> to nor a use case.  By all means we can define the biological process if
> necassary but this is not top of my list and I don't think affects the
> work that is pressing right now for DT.  At the moment I'm happy with our
> simple definition below of data visualisation, something that takes data
> and produces something 'visual' at the end, i.e. image, report graph or
> animation.  I guess the question is would a biological visualisation
> process reason to be equivalent (or a subclass of this) and would that
> cause a problem. I'm happy to cross that bridge if we ever come to it, at
> which point we should revisist your point.


That is ok, you used the terms visualised and visualisation process to
describe data_visualisation. I have no issue with the definition of
data_visualisation (although I do think it is the wrong label) as long as
you dont talk about visualised and visualisation process. Eyes visualise,
machines process and measure and produce information that can be visualised.



>
>
> Also, no more corny-a jokes please :D (last one)


bloody hell, thats the worst one yet, and I nearly missed it, must get my
eyes checked

Frank



>
>
> James
>
>
>
> > On Thu, Jul 16, 2009 at 5:06 PM, James Malone <ma...@eb...> wrote:
> >
> >> So the class in DT is called "data visualization" definition is "Data
> >> visualization is a data transformation that creates images, diagrams or
> >> animations from the input data set."
> >>
> >> I personally feel this is distinct enough from the biological process
> >> you
> >> outline below. If anyone else can't see the distinction though can they
> >> let me know as it may be my own bias is not letting me 'see' the problem
> >> ;)
> >>
> >
> > Eye see you..... mention visualised and visulization_process and that
> > data_visualisation is a visualisation_process and a data transformation.
> > Can
> > you "see your way" to define visualised and visualisation_process, to
> > allow
> > me to see the proposal more clearly through your eyes?
> >
> >
> > Frank
> >
> >
> >
> >>
> >> James
> >>
> >>
> >>
> >> > Hi James,
> >> >
> >> > I just wanted to seek clarification on how you are using the term
> >> > visualisation/visualised. Machines dont visualise, they measure and
> >> > process
> >> > information. A vizulisation_process is something (for example) a human
> >> eye
> >> > does, not a machine. A machine would process some information to
> >> another
> >> > form of information that then data_output could be visualised. The
> >> process
> >> > of converting some information into another type of infromation could
> >> be
> >> > called something like visual_representation_processing which would
> >> produce
> >> > and output that had the potential to be visualised.
> >> >
> >> > This probably is just a label change, but I think it is important
> >> enough
> >> > to
> >> > seek clairification on, as "visualisation" is definately something
> >> that
> >> > can
> >> > be investigated in a biological experiment, irrespective of
> >> information
> >> > processing..
> >> >
> >> > Frank
> >> >
> >> > On Thu, Jul 16, 2009 at 4:18 PM, James Malone <ma...@eb...>
> >> wrote:
> >> >
> >> >> Hi All,
> >> >>
> >> >> As promised, OBI is working again so here is my email.  We want to
> >> add
> >> >> some data visualisation processes to DT.  They are to take the form
> >> as
> >> >> follows:
> >> >>
> >> >> input x data
> >> >> is visualised in visualization process 'x data visualisation '
> >> >> output a, b or c report graphs (where a, b or c are the types of
> >> graphs
> >> >> that x can be validly visualized as)
> >> >>
> >> >> for example:
> >> >>
> >> >> clustered data visualization
> >> >> has input only clustered data
> >> >> has output dot plot or dendrogram
> >> >>
> >> >> So, we have a list which I've added to the google doc here:
> >> >> http://spreadsheets.google.com/ccc?key=tgoAKj9c9uPcszxN72icObA&hl=en
> >> >>
> >> >> What I would like to do is enlist anyone who like to curate the
> >> >> visualizations by adding the outputs to the visualizations I have
> >> added
> >> >> to
> >> >> the spreadsheet.  Presently, these outputs are:
> >> >>
> >> >> contour plot
> >> >> dendrogram
> >> >> density plot
> >> >> dot plot
> >> >> heatmap
> >> >> histogram
> >> >> scatter plot
> >> >> survival curve
> >> >> Venn diagram
> >> >>
> >> >> Though if you can think of more please just add them to the
> >> spreadsheet
> >> >> and I will add them to the ontology.  I've completed moost of the
> >> >> processes we need in row a and b so what I'm looking for are
> >> volunteers
> >> >> for column c. Column d can be used for any notes you may have. Then I
> >> >> will
> >> >> code these up into the ontology.  Any volunteers? :)
> >> >>
> >> >> Many thanks!
> >> >>
> >> >> James
> >> >>
> >> >>
> >> >> --
> >> >> European Bioinformatics Institute,
> >> >> Wellcome Trust Genome Campus,
> >> >> Hinxton,
> >> >> Cambridge, CB10 1SD,
> >> >> United Kingdom
> >> >> Fax: + 44 (0) 1223 492 468
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >>
> ------------------------------------------------------------------------------
> >> >> Enter the BlackBerry Developer Challenge
> >> >> This is your chance to win up to $100,000 in prizes! For a limited
> >> time,
> >> >> vendors submitting new applications to BlackBerry App World(TM) will
> >> >> have
> >> >> the opportunity to enter the BlackBerry Developer Challenge. See full
> >> >> prize
> >> >> details at: http://p.sf.net/sfu/Challenge
> >> >> _______________________________________________
> >> >> Obi-datatrfm-branch mailing list
> >> >> Obi...@li...
> >> >> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch
> >> >>
> >> >
> >> >
> >> >
> >> > --
> >> > Frank Gibson, PhD
> >> > http://peanutbutter.wordpress.com/
> >> >
> >>
> >>
> >> --
> >> EMBL Outstation - Hinxton,
> >> European Bioinformatics Institute,
> >> Wellcome Trust Genome Campus,
> >> Hinxton,
> >> Cambridge, CB10 1SD,
> >> United Kingdom
> >> Fax: + 44 (0) 1223 492 468
> >>
> >>
> >
> >
> > --
> > Frank Gibson, PhD
> > http://peanutbutter.wordpress.com/
> >
>
>
> --
> EMBL Outstation - Hinxton,
> European Bioinformatics Institute,
> Wellcome Trust Genome Campus,
> Hinxton,
> Cambridge, CB10 1SD,
> United Kingdom
> Fax: + 44 (0) 1223 492 468
>
>


-- 
Frank Gibson, PhD
http://peanutbutter.wordpress.com/

Re: [Obi-datatrfm-branch] DT Visualisations

[James M. <ma...@eb...>]

So the only thing I say is that data visualization is_a data
transformation, that is the only is_a and in fact that is not quite true
since the input is data but the output is an ICE so really this an
information processing subclass not a DT - it'll move once I add the
axioms. I don't wish to define 'visualization' here because I have no need
to nor a use case.  By all means we can define the biological process if
necassary but this is not top of my list and I don't think affects the
work that is pressing right now for DT.  At the moment I'm happy with our
simple definition below of data visualisation, something that takes data
and produces something 'visual' at the end, i.e. image, report graph or
animation.  I guess the question is would a biological visualisation
process reason to be equivalent (or a subclass of this) and would that
cause a problem. I'm happy to cross that bridge if we ever come to it, at
which point we should revisist your point.

Also, no more corny-a jokes please :D (last one)

James



> On Thu, Jul 16, 2009 at 5:06 PM, James Malone <ma...@eb...> wrote:
>
>> So the class in DT is called "data visualization" definition is "Data
>> visualization is a data transformation that creates images, diagrams or
>> animations from the input data set."
>>
>> I personally feel this is distinct enough from the biological process
>> you
>> outline below. If anyone else can't see the distinction though can they
>> let me know as it may be my own bias is not letting me 'see' the problem
>> ;)
>>
>
> Eye see you..... mention visualised and visulization_process and that
> data_visualisation is a visualisation_process and a data transformation.
> Can
> you "see your way" to define visualised and visualisation_process, to
> allow
> me to see the proposal more clearly through your eyes?
>
>
> Frank
>
>
>
>>
>> James
>>
>>
>>
>> > Hi James,
>> >
>> > I just wanted to seek clarification on how you are using the term
>> > visualisation/visualised. Machines dont visualise, they measure and
>> > process
>> > information. A vizulisation_process is something (for example) a human
>> eye
>> > does, not a machine. A machine would process some information to
>> another
>> > form of information that then data_output could be visualised. The
>> process
>> > of converting some information into another type of infromation could
>> be
>> > called something like visual_representation_processing which would
>> produce
>> > and output that had the potential to be visualised.
>> >
>> > This probably is just a label change, but I think it is important
>> enough
>> > to
>> > seek clairification on, as "visualisation" is definately something
>> that
>> > can
>> > be investigated in a biological experiment, irrespective of
>> information
>> > processing..
>> >
>> > Frank
>> >
>> > On Thu, Jul 16, 2009 at 4:18 PM, James Malone <ma...@eb...>
>> wrote:
>> >
>> >> Hi All,
>> >>
>> >> As promised, OBI is working again so here is my email.  We want to
>> add
>> >> some data visualisation processes to DT.  They are to take the form
>> as
>> >> follows:
>> >>
>> >> input x data
>> >> is visualised in visualization process 'x data visualisation '
>> >> output a, b or c report graphs (where a, b or c are the types of
>> graphs
>> >> that x can be validly visualized as)
>> >>
>> >> for example:
>> >>
>> >> clustered data visualization
>> >> has input only clustered data
>> >> has output dot plot or dendrogram
>> >>
>> >> So, we have a list which I've added to the google doc here:
>> >> http://spreadsheets.google.com/ccc?key=tgoAKj9c9uPcszxN72icObA&hl=en
>> >>
>> >> What I would like to do is enlist anyone who like to curate the
>> >> visualizations by adding the outputs to the visualizations I have
>> added
>> >> to
>> >> the spreadsheet.  Presently, these outputs are:
>> >>
>> >> contour plot
>> >> dendrogram
>> >> density plot
>> >> dot plot
>> >> heatmap
>> >> histogram
>> >> scatter plot
>> >> survival curve
>> >> Venn diagram
>> >>
>> >> Though if you can think of more please just add them to the
>> spreadsheet
>> >> and I will add them to the ontology.  I've completed moost of the
>> >> processes we need in row a and b so what I'm looking for are
>> volunteers
>> >> for column c. Column d can be used for any notes you may have. Then I
>> >> will
>> >> code these up into the ontology.  Any volunteers? :)
>> >>
>> >> Many thanks!
>> >>
>> >> James
>> >>
>> >>
>> >> --
>> >> European Bioinformatics Institute,
>> >> Wellcome Trust Genome Campus,
>> >> Hinxton,
>> >> Cambridge, CB10 1SD,
>> >> United Kingdom
>> >> Fax: + 44 (0) 1223 492 468
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> >>
>> ------------------------------------------------------------------------------
>> >> Enter the BlackBerry Developer Challenge
>> >> This is your chance to win up to $100,000 in prizes! For a limited
>> time,
>> >> vendors submitting new applications to BlackBerry App World(TM) will
>> >> have
>> >> the opportunity to enter the BlackBerry Developer Challenge. See full
>> >> prize
>> >> details at: http://p.sf.net/sfu/Challenge
>> >> _______________________________________________
>> >> Obi-datatrfm-branch mailing list
>> >> Obi...@li...
>> >> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch
>> >>
>> >
>> >
>> >
>> > --
>> > Frank Gibson, PhD
>> > http://peanutbutter.wordpress.com/
>> >
>>
>>
>> --
>> EMBL Outstation - Hinxton,
>> European Bioinformatics Institute,
>> Wellcome Trust Genome Campus,
>> Hinxton,
>> Cambridge, CB10 1SD,
>> United Kingdom
>> Fax: + 44 (0) 1223 492 468
>>
>>
>
>
> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
>


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

Re: [Obi-datatrfm-branch] DT Visualisations

[Frank G. <fg...@gm...>]

On Thu, Jul 16, 2009 at 5:06 PM, James Malone <ma...@eb...> wrote:

> So the class in DT is called "data visualization" definition is "Data
> visualization is a data transformation that creates images, diagrams or
> animations from the input data set."
>
> I personally feel this is distinct enough from the biological process you
> outline below. If anyone else can't see the distinction though can they
> let me know as it may be my own bias is not letting me 'see' the problem
> ;)
>

Eye see you..... mention visualised and visulization_process and that
data_visualisation is a visualisation_process and a data transformation. Can
you "see your way" to define visualised and visualisation_process, to allow
me to see the proposal more clearly through your eyes?


Frank



>
> James
>
>
>
> > Hi James,
> >
> > I just wanted to seek clarification on how you are using the term
> > visualisation/visualised. Machines dont visualise, they measure and
> > process
> > information. A vizulisation_process is something (for example) a human
> eye
> > does, not a machine. A machine would process some information to another
> > form of information that then data_output could be visualised. The
> process
> > of converting some information into another type of infromation could be
> > called something like visual_representation_processing which would
> produce
> > and output that had the potential to be visualised.
> >
> > This probably is just a label change, but I think it is important enough
> > to
> > seek clairification on, as "visualisation" is definately something that
> > can
> > be investigated in a biological experiment, irrespective of information
> > processing..
> >
> > Frank
> >
> > On Thu, Jul 16, 2009 at 4:18 PM, James Malone <ma...@eb...> wrote:
> >
> >> Hi All,
> >>
> >> As promised, OBI is working again so here is my email.  We want to add
> >> some data visualisation processes to DT.  They are to take the form as
> >> follows:
> >>
> >> input x data
> >> is visualised in visualization process 'x data visualisation '
> >> output a, b or c report graphs (where a, b or c are the types of graphs
> >> that x can be validly visualized as)
> >>
> >> for example:
> >>
> >> clustered data visualization
> >> has input only clustered data
> >> has output dot plot or dendrogram
> >>
> >> So, we have a list which I've added to the google doc here:
> >> http://spreadsheets.google.com/ccc?key=tgoAKj9c9uPcszxN72icObA&hl=en
> >>
> >> What I would like to do is enlist anyone who like to curate the
> >> visualizations by adding the outputs to the visualizations I have added
> >> to
> >> the spreadsheet.  Presently, these outputs are:
> >>
> >> contour plot
> >> dendrogram
> >> density plot
> >> dot plot
> >> heatmap
> >> histogram
> >> scatter plot
> >> survival curve
> >> Venn diagram
> >>
> >> Though if you can think of more please just add them to the spreadsheet
> >> and I will add them to the ontology.  I've completed moost of the
> >> processes we need in row a and b so what I'm looking for are volunteers
> >> for column c. Column d can be used for any notes you may have. Then I
> >> will
> >> code these up into the ontology.  Any volunteers? :)
> >>
> >> Many thanks!
> >>
> >> James
> >>
> >>
> >> --
> >> European Bioinformatics Institute,
> >> Wellcome Trust Genome Campus,
> >> Hinxton,
> >> Cambridge, CB10 1SD,
> >> United Kingdom
> >> Fax: + 44 (0) 1223 492 468
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >> Enter the BlackBerry Developer Challenge
> >> This is your chance to win up to $100,000 in prizes! For a limited time,
> >> vendors submitting new applications to BlackBerry App World(TM) will
> >> have
> >> the opportunity to enter the BlackBerry Developer Challenge. See full
> >> prize
> >> details at: http://p.sf.net/sfu/Challenge
> >> _______________________________________________
> >> Obi-datatrfm-branch mailing list
> >> Obi...@li...
> >> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch
> >>
> >
> >
> >
> > --
> > Frank Gibson, PhD
> > http://peanutbutter.wordpress.com/
> >
>
>
> --
> EMBL Outstation - Hinxton,
> European Bioinformatics Institute,
> Wellcome Trust Genome Campus,
> Hinxton,
> Cambridge, CB10 1SD,
> United Kingdom
> Fax: + 44 (0) 1223 492 468
>
>


-- 
Frank Gibson, PhD
http://peanutbutter.wordpress.com/

Re: [Obi-datatrfm-branch] DT Visualisations

[James M. <ma...@eb...>]

So the class in DT is called "data visualization" definition is "Data
visualization is a data transformation that creates images, diagrams or
animations from the input data set."

I personally feel this is distinct enough from the biological process you
outline below. If anyone else can't see the distinction though can they
let me know as it may be my own bias is not letting me 'see' the problem
;)

James



> Hi James,
>
> I just wanted to seek clarification on how you are using the term
> visualisation/visualised. Machines dont visualise, they measure and
> process
> information. A vizulisation_process is something (for example) a human eye
> does, not a machine. A machine would process some information to another
> form of information that then data_output could be visualised. The process
> of converting some information into another type of infromation could be
> called something like visual_representation_processing which would produce
> and output that had the potential to be visualised.
>
> This probably is just a label change, but I think it is important enough
> to
> seek clairification on, as "visualisation" is definately something that
> can
> be investigated in a biological experiment, irrespective of information
> processing..
>
> Frank
>
> On Thu, Jul 16, 2009 at 4:18 PM, James Malone <ma...@eb...> wrote:
>
>> Hi All,
>>
>> As promised, OBI is working again so here is my email.  We want to add
>> some data visualisation processes to DT.  They are to take the form as
>> follows:
>>
>> input x data
>> is visualised in visualization process 'x data visualisation '
>> output a, b or c report graphs (where a, b or c are the types of graphs
>> that x can be validly visualized as)
>>
>> for example:
>>
>> clustered data visualization
>> has input only clustered data
>> has output dot plot or dendrogram
>>
>> So, we have a list which I've added to the google doc here:
>> http://spreadsheets.google.com/ccc?key=tgoAKj9c9uPcszxN72icObA&hl=en
>>
>> What I would like to do is enlist anyone who like to curate the
>> visualizations by adding the outputs to the visualizations I have added
>> to
>> the spreadsheet.  Presently, these outputs are:
>>
>> contour plot
>> dendrogram
>> density plot
>> dot plot
>> heatmap
>> histogram
>> scatter plot
>> survival curve
>> Venn diagram
>>
>> Though if you can think of more please just add them to the spreadsheet
>> and I will add them to the ontology.  I've completed moost of the
>> processes we need in row a and b so what I'm looking for are volunteers
>> for column c. Column d can be used for any notes you may have. Then I
>> will
>> code these up into the ontology.  Any volunteers? :)
>>
>> Many thanks!
>>
>> James
>>
>>
>> --
>> European Bioinformatics Institute,
>> Wellcome Trust Genome Campus,
>> Hinxton,
>> Cambridge, CB10 1SD,
>> United Kingdom
>> Fax: + 44 (0) 1223 492 468
>>
>>
>>
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Enter the BlackBerry Developer Challenge
>> This is your chance to win up to $100,000 in prizes! For a limited time,
>> vendors submitting new applications to BlackBerry App World(TM) will
>> have
>> the opportunity to enter the BlackBerry Developer Challenge. See full
>> prize
>> details at: http://p.sf.net/sfu/Challenge
>> _______________________________________________
>> Obi-datatrfm-branch mailing list
>> Obi...@li...
>> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch
>>
>
>
>
> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/
>


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

Re: [Obi-datatrfm-branch] DT Visualisations

[Frank G. <fg...@gm...>]

Hi James,

I just wanted to seek clarification on how you are using the term
visualisation/visualised. Machines dont visualise, they measure and process
information. A vizulisation_process is something (for example) a human eye
does, not a machine. A machine would process some information to another
form of information that then data_output could be visualised. The process
of converting some information into another type of infromation could be
called something like visual_representation_processing which would produce
and output that had the potential to be visualised.

This probably is just a label change, but I think it is important enough to
seek clairification on, as "visualisation" is definately something that can
be investigated in a biological experiment, irrespective of information
processing..

Frank

On Thu, Jul 16, 2009 at 4:18 PM, James Malone <ma...@eb...> wrote:

> Hi All,
>
> As promised, OBI is working again so here is my email.  We want to add
> some data visualisation processes to DT.  They are to take the form as
> follows:
>
> input x data
> is visualised in visualization process 'x data visualisation '
> output a, b or c report graphs (where a, b or c are the types of graphs
> that x can be validly visualized as)
>
> for example:
>
> clustered data visualization
> has input only clustered data
> has output dot plot or dendrogram
>
> So, we have a list which I've added to the google doc here:
> http://spreadsheets.google.com/ccc?key=tgoAKj9c9uPcszxN72icObA&hl=en
>
> What I would like to do is enlist anyone who like to curate the
> visualizations by adding the outputs to the visualizations I have added to
> the spreadsheet.  Presently, these outputs are:
>
> contour plot
> dendrogram
> density plot
> dot plot
> heatmap
> histogram
> scatter plot
> survival curve
> Venn diagram
>
> Though if you can think of more please just add them to the spreadsheet
> and I will add them to the ontology.  I've completed moost of the
> processes we need in row a and b so what I'm looking for are volunteers
> for column c. Column d can be used for any notes you may have. Then I will
> code these up into the ontology.  Any volunteers? :)
>
> Many thanks!
>
> James
>
>
> --
> European Bioinformatics Institute,
> Wellcome Trust Genome Campus,
> Hinxton,
> Cambridge, CB10 1SD,
> United Kingdom
> Fax: + 44 (0) 1223 492 468
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge
> This is your chance to win up to $100,000 in prizes! For a limited time,
> vendors submitting new applications to BlackBerry App World(TM) will have
> the opportunity to enter the BlackBerry Developer Challenge. See full prize
> details at: http://p.sf.net/sfu/Challenge
> _______________________________________________
> Obi-datatrfm-branch mailing list
> Obi...@li...
> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch
>



-- 
Frank Gibson, PhD
http://peanutbutter.wordpress.com/

Re: [Obi-datatrfm-branch] DT Visualisations

[James M. <ma...@eb...>]

I should also have added these are some of the thing we need for the
manuscript so are at the top of the DT list of things to do.

Cheers,

James



> Hi All,
>
> As promised, OBI is working again so here is my email.  We want to add
> some data visualisation processes to DT.  They are to take the form as
> follows:
>
> input x data
> is visualised in visualization process 'x data visualisation '
> output a, b or c report graphs (where a, b or c are the types of graphs
> that x can be validly visualized as)
>
> for example:
>
> clustered data visualization
> has input only clustered data
> has output dot plot or dendrogram
>
> So, we have a list which I've added to the google doc here:
> http://spreadsheets.google.com/ccc?key=tgoAKj9c9uPcszxN72icObA&hl=en
>
> What I would like to do is enlist anyone who like to curate the
> visualizations by adding the outputs to the visualizations I have added to
> the spreadsheet.  Presently, these outputs are:
>
> contour plot
> dendrogram
> density plot
> dot plot
> heatmap
> histogram
> scatter plot
> survival curve
> Venn diagram
>
> Though if you can think of more please just add them to the spreadsheet
> and I will add them to the ontology.  I've completed moost of the
> processes we need in row a and b so what I'm looking for are volunteers
> for column c. Column d can be used for any notes you may have. Then I will
> code these up into the ontology.  Any volunteers? :)
>
> Many thanks!
>
> James
>
>
> --
> European Bioinformatics Institute,
> Wellcome Trust Genome Campus,
> Hinxton,
> Cambridge, CB10 1SD,
> United Kingdom
> Fax: + 44 (0) 1223 492 468
>
>
>
>
>
>
>
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge
> This is your chance to win up to $100,000 in prizes! For a limited time,
> vendors submitting new applications to BlackBerry App World(TM) will have
> the opportunity to enter the BlackBerry Developer Challenge. See full
> prize
> details at: http://p.sf.net/sfu/Challenge
> _______________________________________________
> Obi-datatrfm-branch mailing list
> Obi...@li...
> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch
>


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

[Obi-datatrfm-branch] DT Visualisations

[James M. <ma...@eb...>]

Hi All,

As promised, OBI is working again so here is my email.  We want to add
some data visualisation processes to DT.  They are to take the form as
follows:

input x data
is visualised in visualization process 'x data visualisation '
output a, b or c report graphs (where a, b or c are the types of graphs
that x can be validly visualized as)

for example:

clustered data visualization
has input only clustered data
has output dot plot or dendrogram

So, we have a list which I've added to the google doc here:
http://spreadsheets.google.com/ccc?key=tgoAKj9c9uPcszxN72icObA&hl=en

What I would like to do is enlist anyone who like to curate the
visualizations by adding the outputs to the visualizations I have added to
the spreadsheet.  Presently, these outputs are:

contour plot
dendrogram
density plot
dot plot
heatmap
histogram
scatter plot
survival curve
Venn diagram

Though if you can think of more please just add them to the spreadsheet
and I will add them to the ontology.  I've completed moost of the
processes we need in row a and b so what I'm looking for are volunteers
for column c. Column d can be used for any notes you may have. Then I will
code these up into the ontology.  Any volunteers? :)

Many thanks!

James


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

[Obi-datatrfm-branch] No Call and Action Item

[James M. <ma...@eb...>]

Hi All,

Just a reminder - there is no DT call today following the new protocol to
merge branch calls for the time being.

I was hoping to draw up a list of report graphs and data sets and suggest
some visualization processes that we might want to introduce into DT (and
enlist some help making the connections) today but this is going to have
be delayed until the problems after the namespace change are fixed.

James



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

Re: [Obi-datatrfm-branch] No Call Today

[James M. <ma...@eb...>]

We can temporarily suspend calls and see what progress is made I think. 
We'll review this in a few weeks to see if the new development calls are
working.  For Monnie and Pance's benefit - the OBI coordinators decided to
consolodate branch calls for the next few weeks and have joint OBI
development calls where everyone turns up to work on the most pressing OBI
problems.  I'd still be eager to see the OnotoDM Pance, once your server
is back up though.

JM


> Hi JM,
>
> During the last OBI coordinators call it has been decided to suspend
> separated branch calls and instead meet twice a week to work globally
> on the ontology.
> Do we keep having distinct DT calls or are we suspending those to use
> the 2 "general development" slots instead?
>
> Thanks,
> Melanie
>
>
>
> On 9-Jul-09, at 5:42 AM, James Malone wrote:
>
>> Hi All,
>>
>> As a reminder there will be NO DT CALL today as this is our 'off'
>> week.
>> There will be a call next week if people are able to attend.
>>
>> 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
>>
>>
>> ------------------------------------------------------------------------------
>> Enter the BlackBerry Developer Challenge
>> This is your chance to win up to $100,000 in prizes! For a limited
>> time,
>> vendors submitting new applications to BlackBerry App World(TM) will
>> have
>> the opportunity to enter the BlackBerry Developer Challenge. See
>> full prize
>> details at: http://p.sf.net/sfu/Challenge
>> _______________________________________________
>> Obi-datatrfm-branch mailing list
>> Obi...@li...
>> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch
>
> ---
> Mélanie Courtot
> TFL- BCCRC
> 675 West 10th Avenue
> Vancouver, BC
> V5Z 1L3, Canada
>
>
>
>
>


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

Re: [Obi-datatrfm-branch] No Call Today

[Melanie C. <mco...@gm...>]

Hi JM,

During the last OBI coordinators call it has been decided to suspend  
separated branch calls and instead meet twice a week to work globally  
on the ontology.
Do we keep having distinct DT calls or are we suspending those to use  
the 2 "general development" slots instead?

Thanks,
Melanie



On 9-Jul-09, at 5:42 AM, James Malone wrote:

> Hi All,
>
> As a reminder there will be NO DT CALL today as this is our 'off'  
> week.
> There will be a call next week if people are able to attend.
>
> 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
>
>
> ------------------------------------------------------------------------------
> Enter the BlackBerry Developer Challenge
> This is your chance to win up to $100,000 in prizes! For a limited  
> time,
> vendors submitting new applications to BlackBerry App World(TM) will  
> have
> the opportunity to enter the BlackBerry Developer Challenge. See  
> full prize
> details at: http://p.sf.net/sfu/Challenge
> _______________________________________________
> Obi-datatrfm-branch mailing list
> Obi...@li...
> https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch

---
Mélanie Courtot
TFL- BCCRC
675 West 10th Avenue
Vancouver, BC
V5Z 1L3, Canada

[Obi-datatrfm-branch] No Call Today

[James M. <ma...@eb...>]

Hi All,

As a reminder there will be NO DT CALL today as this is our 'off' week.  
There will be a call next week if people are able to attend.

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 

[Obi-datatrfm-branch] No call this week for DT

[James M. <ma...@eb...>]

Hi All,

Since Sourceforge is behaving very slowly I thought I'd email to say 
this will be our no call week (since we have are now having calls every 
2 weeks).  I will email an update after the coordinator call on 
discussion regarding the information processing ontology.

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 

[Obi-datatrfm-branch] Data Transformation Call ON this Thursday

[James M. <ma...@eb...>]

Hi All,

Since we didn't have a call last week, I'd like to have one this week.  
One thing I'd like to discuss is the possibility of merging the DT 
branch of OBI with the data mining ontology Pance has been working on.  
I think this would be of benefit to DT and hopefully to Pance as well.  
Pance I would very much welcome your thoughts on merging your work with 
ours, I know having spoken to you and Saso, you have been doing some 
alignment tasks already.  I could also envisage this eventually becoming 
a more general information processing ontology with the extra parts the 
data mining ontology would bring which would almost certainly end up 
being a separate effort from OBI.  Again I welcome any thoughts on this.

Otherwise, there are lots of other things to be done, not least tying 
data to report graphs, if anyone fancies taking some on we can dish some 
out tomorrow :)

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 

Re: [Obi-datatrfm-branch] Obi-datatrfm-branch Digest, Vol 27, Issue 2

[Yongqun H. <yon...@me...>]

Hi James,
I don't get Pance's paper since I only get archived Obi-datatrfm-branch emails. Can you send it to me? Thanks!
--Oliver 

>>> <obi...@li...> 6/26/2009 6:28 AM >>>
Send Obi-datatrfm-branch mailing list submissions to
obi...@li... 

To subscribe or unsubscribe via the World Wide Web, visit
https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch 
or, via email, send a message with subject or body 'help' to
obi...@li... 

You can reach the person managing the list at
obi...@li... 

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Obi-datatrfm-branch digest..."


Today's Topics:

   1. Data Transformation branch of OBI (James Malone)
   2. Today's DT Call at 4 (James Malone)
   3. Paper mentioning DT branch of OBI (James Malone)


----------------------------------------------------------------------

Message: 1
Date: Tue, 16 Jun 2009 16:02:23 +0100
From: James Malone <ma...@eb...>
Subject: [Obi-datatrfm-branch] Data Transformation branch of OBI
To: OBI-DataTransform Branch
<Obi...@li...>,OBI Developers
<obi...@li...>
Message-ID: <4A3...@eb...>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi Everyone (including none DTers),

I have quite a lot of things to update on the DT side of OBI following on from the workshop, some of which are quite complex.  It would be useful for me to recruit some new people that are active in this area to help me edit the file, etc. since call attendance is very low and there is a large workload.  It would therefore be useful if people involved with the DT branch could confirm they still wish to contribute to this part of OBI (by this I mean willing to join calls, define classes and edit owl file) as I would intend to call on these people to help me you lucky people  :)    Larissa has already told me she wants to join the branch which is great and I already have interest from an outside party working in the data mining community who I intend to discuss joining the branch.  So action item for anyone interested in maintaining (or in fact beginning) DT involvement, could you email me or Tina please?

Thanks.

James

PS Join now and get a free "I transformed data with OBI" T-shirt.  Limited stock.


-- 
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 





------------------------------

Message: 2
Date: Thu, 18 Jun 2009 09:47:38 +0100
From: James Malone <ma...@eb...>
Subject: [Obi-datatrfm-branch] Today's DT Call at 4
To: OBI-DataTransform Branch
<Obi...@li...>
Message-ID: <4A3...@eb...>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Hi All,

I have another meeting at 4:30 today so will have to keep the call short 
(4-4:30), sorry.  I was going to go over some of the action items we 
have for DT and introduce Pance to the branch.  He will be collaborating 
with us on DT and he knows OWL (hooray!).  I have cc'd him to this email 
so you have his email details.

Speak to you at 4!

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 




------------------------------

Message: 3
Date: Fri, 26 Jun 2009 11:28:04 +0100
From: James Malone <ma...@eb...>
Subject: [Obi-datatrfm-branch] Paper mentioning DT branch of OBI
To: OBI-DataTransform Branch
<Obi...@li...>
Message-ID: <4A4...@eb...>
Content-Type: text/plain; charset="iso-8859-1"

Hi DTers,

This paper from Pance has been accepted for the Discovery Science 2009 
conference in Porto in October and he has given me permission to send it 
around. If you have any comments feel free to bounce them direct to 
Pance pan...@ij... 

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 

-------------- next part --------------
A non-text attachment was scrubbed...
Name: DS09_OntoDM.pdf
Type: application/pdf
Size: 643342 bytes
Desc: not available

------------------------------

------------------------------------------------------------------------------


------------------------------

_______________________________________________
Obi-datatrfm-branch mailing list
Obi...@li... 
https://lists.sourceforge.net/lists/listinfo/obi-datatrfm-branch 


End of Obi-datatrfm-branch Digest, Vol 27, Issue 2
**************************************************

**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

[Obi-datatrfm-branch] Paper mentioning DT branch of OBI

[James M. <ma...@eb...>]

Hi DTers,

This paper from Pance has been accepted for the Discovery Science 2009 
conference in Porto in October and he has given me permission to send it 
around. If you have any comments feel free to bounce them direct to 
Pance pan...@ij...

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 

[Obi-datatrfm-branch] Today's DT Call at 4

[James M. <ma...@eb...>]

Hi All,

I have another meeting at 4:30 today so will have to keep the call short 
(4-4:30), sorry.  I was going to go over some of the action items we 
have for DT and introduce Pance to the branch.  He will be collaborating 
with us on DT and he knows OWL (hooray!).  I have cc'd him to this email 
so you have his email details.

Speak to you at 4!

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 

[Obi-datatrfm-branch] Data Transformation branch of OBI

[James M. <ma...@eb...>]

Hi Everyone (including none DTers),

I have quite a lot of things to update on the DT side of OBI following on from the workshop, some of which are quite complex.  It would be useful for me to recruit some new people that are active in this area to help me edit the file, etc. since call attendance is very low and there is a large workload.  It would therefore be useful if people involved with the DT branch could confirm they still wish to contribute to this part of OBI (by this I mean willing to join calls, define classes and edit owl file) as I would intend to call on these people to help me you lucky people  :)    Larissa has already told me she wants to join the branch which is great and I already have interest from an outside party working in the data mining community who I intend to discuss joining the branch.  So action item for anyone interested in maintaining (or in fact beginning) DT involvement, could you email me or Tina please?

Thanks.

James

PS Join now and get a free "I transformed data with OBI" T-shirt.  Limited stock.


-- 
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