Parameter
James Malone
types is the much sought after roles for data. In many ways, this
would be my preference as it would enable the input data to be
considered as a parameter for a given DT process specifically because
of the context of that process (in much the same way as other roles).
This would remove any possible problems with multiple parentage as
well, which could arise from asserting a parent class parameter where
children of this class may also be types of other things. I could
attempt to code this up for a couple of DT classes and could keep it
all in the DT OWL file is desired so I don't interfere with other
branches. This would probably serve as an obvious example of roles
for data we could send Barry perhaps?
James
On Wed, Apr 29, 2009 at 4:57 PM, Chris Stoeckert
<stoe...@pcbi.upenn.edu> wrote:
>
> Hi James,
> I asked Elisabetta (former DTer and a mathematician by training) what she
> thought a parameter was without giving any background first.
> Her first example was the base of log used such as the 2 in Log base 2.
> Another examples was specifying the variables in a function such as x in
> f(x).
> I then filled her in on the discussion and she thought both points of view
> had merit.
> Two use cases for her are:
> 1. Setting the vaiues of software to be run (e.g., processing microarray
> data for normalization and analysis) so that the software can be run the
> same way on different data sets.
> 2. Often when reporting microarray data processing, the individual steps are
> clumped together so that a bunch of things happen to the data and you need
> to list the settings (parameters) used along the way but their relation to
> the original input data set is unclear (or not important). What you want to
> track is the input data set and the resulting output data set. So these
> datasets seem different from settings (parameters).
>
> Cheers,
> Chris
> On Apr 29, 2009, at 7:18 AM, James Malone wrote:
>
>>
>> Hi All,
>>
>> I have fed back some of the discussion on parameter to the DT branch
>> mailing list to see if anyone has any thoughts. Will cross post if
>> anything important comes up. Thanks for discussion last night, was
>> useful.
>>
>> James
>>
>>
>> On Tue, Apr 28, 2009 at 7:02 PM, Chris Stoeckert
>> <stoe...@pcbi.upenn.edu> wrote:
>>>
>>> having trouble connecting - hope to be on soon!
>>> Chris
>>> On Apr 28, 2009, at 12:44 PM, Bjoern Peters wrote:
>>>
>>>>
>>>> I won't be able to make the call, as I got a new deadline this morning
>>>> for
>>>> a grant proposal due at noon. That is as much fun as it sounds. I hate
>>>> to
>>>> miss this call.
>>>>
>>>>
>>>> ----- Original Message -----
>>>> From: "Chris Stoeckert" <stoe...@pcbi.upenn.edu>
>>>> To: obi-denr...@googlegroups.com
>>>> Sent: Tuesday, April 28, 2009 7:39:10 AM GMT -08:00 US/Canada Pacific
>>>> Subject: [obi-denrie] Reminder: DENRIE call today at 2PM EDT, Tuesday
>>>> April 28th
>>>>
>>>>
>>>>
>>>>
>>>> On Apr 24, 2009, at 5:08 PM, Chris Stoeckert wrote:
>>>>
>>>>
>>>>
>>>> Dear All,
>>>> Here are some suggestions for terms to be discussed at the next DENRIE
>>>> call.
>>>>
>>>>
>>>> term: data transformation parameter specification
>>>> definition: a data transformation parameter specification is an
>>>> information entity about a realizeable that is used in a data
>>>> transformation
>>>> to refer to specific kinds of values.
>>>> definition source: BP, JM, DENRIE
>>>> examples: The integer k in 'k-means clustering', The window size in a
>>>> 'moving average'; The values for p, T, w, m in a 's transformation'
>>>> restrictions:
>>>>
>>>> is_a 'information entity about a realizable'
>>>> is_concretized_as (is_realized by only data transformation)
>>>> is_about some (information_content entity participates_in some data
>>>> transformation)
>>>> editor note: There are other meanings of parameter such as population
>>>> characteristic that may still need to be addressed.
>>>>
>>>>
>>>> term: genome sequence version
>>>> definition: genome sequence version is a label that is used to specify
>>>> the
>>>> representation of the assembled genome sequence contained in a file or
>>>> used
>>>> in an analysis.
>>>> definition source: CS, DENRIE
>>>> examples: mm8, The March 2006 human reference sequence (NCBI Build 36.1)
>>>> restrictions:
>>>> is_about some (genome sequence <output of some data transformation of
>>>> sequence data into a genome sequence>)
>>>> editor note: need to create 'genome sequence' and/or 'data
>>>> transformation
>>>> of sequence data into a genome sequence' or something like it.
>>>> original request from Nicole Washington:
>>>>
>>>> for a data analysis protocol where an entire genomic sequence might be a
>>>> specified parameter, it would be useful to be able to specify the
>>>> genomic
>>>> version.
>>>>
>>>> for example, i have an algorithm that takes a genomic sequence as an
>>>> input,
>>>> say like a gene-model prediction algorithm, and outputs some
>>>> transformation
>>>> of the data. the results of the algorithm would be different depending
>>>> on
>>>> which genomic sequence was in the input parameter.
>>>>
>>>>
>>>> term: tree model
>>>> definition: a tree model is a data representational model in which there
>>>> are one or more layers of leaf nodes attached in a hierarchical manner
>>>> and
>>>> there may be a top or root node.
>>>> definition source: CS, DENRIE
>>>> examples: tree models are use in phylogenetic trees, gene clusters based
>>>> on microarray data
>>>> restrictions: ??
>>>> editor note: not sure how to logically define hierarchical structure
>>>> which
>>>> is what distinguishes this from other models.
>>>> original request from James:
>>>>
>>>>
>>>> Tree as a set of linked nodes. (such as here
>>>> http://en.wikipedia.org/wiki/Tree_data_structure) . Presumably a DENRIE
>>>> branch concept.
>>>>
>>>>
>>>> term: time series collection
>>>> definition: a time series collection is a data collection that is a
>>>> sequence of data points, measured typically at successive times, spaced
>>>> at
>>>> (often uniform) time intervals.
>>>> definition source: Wikipedia
>>>> examples: gene expression measurements of cells taken from a culture
>>>> over
>>>> a series of days.
>>>> restrictions:
>>>> is_output_of some measurement
>>>> is_input_to some data transformation
>>>>
>>>> original request from James:
>>>>
>>>>
>>>> DT requires the concept of 'time series' which would serve as input to
>>>> some
>>>> of the DTs that deal with this. As a starting point for time series,
>>>> here
>>>> is the wikipedia def: "A time series is a sequence of data points,
>>>> measured
>>>> typically at successive times, spaced at (often uniform) time
>>>> intervals".
>>>>
>>>> term: heatmap
>>>> definition: a heatmap is a report element which is a graphical
>>>> representation of data where the values taken by a variable in a
>>>> two-dimensional map are represented as colors.
>>>> definition source: Wikipedia
>>>> examples: representation of microarray data for expression values of
>>>> many
>>>> genes across multiple samples or conditions.
>>>> original request from James:
>>>>
>>>>
>>>> -heatmap http://en.wikipedia.org/wiki/Heat_map
>>>>
>>>>
>>>> term: survival curve
>>>> definition: a survival curve is a report element which plot percent
>>>> survival as a function of time.
>>>> definition source: Graphpad.com
>>>>
>>>> original request from James:
>>>>
>>>>
>>>> -survival curve http://www.graphpad.com/www/book/survive.htm
>>>>
>>>>
>>>> term: venn diagram
>>>> definition: a venn diagram is a report element which is constructed with
>>>> a
>>>> collection of simple closed curves drawn in the plane.
>>>> definition source: Wikipedia
>>>>
>>>> original request from James:
>>>>
>>>>
>>>> -venn diagram http://en.wikipedia.org/wiki/Venn_diagram
>>>>
>>>>
>>>> term: graph diagram
>>>> definition: a graph diagram is a report element which is a collection of
>>>> points and lines connecting some (possibly empty) subset of them.
>>>> definition source: http://mathworld.wolfram.com/Graph.html
>>>>
>>>> original request from James:
>>>>
>>>>
>>>> -graph (in the sense of V=vertices, E=edges, not in the sense of graph
>>>> of
>>>> a function.) See second definition here
>>>> http://mathworld.wolfram.com/Graph.html
>>>>
>>>>
>>>
>>>
>
>