terms for DENRIE call Monday May 11 at noon EDT
Chris Stoeckert
Here are follow ups from last call:
1. Parameter.
From James:
> I bounced the differences off a few different people and had a few
> different answers. I think one of the biggest issues is that is it a
> social issue? I can see the argument that parameters, like all data,
> are input to DTs, however the difference is that certain parts of
> those DTs are considered to be parameters and not the data. This is
> what has led me to think parameter could be best modelled as a role.
> I can certainly add some under ICE but actually the issue would still
> stand and it would still mean I can't answer the competency question
> "what are the parameters for k-means?". Alan had some suggestion
> about how we might do this via specification the other day, I can't
> recall what it was now. Presently I favour role for ICE, but I also
> like the idea of a relation has_input_parameter as a subtype of
> has_input. I do definitely agree with you though, we shouldn't delay
> parameter waiting for roles for ICE to be green lighted - to that end
> I would favour just doing it since Barry has already agreed in
> principle to this under BFO IIRC (and there are no ontological
> restrictions preventing this in OBI).
2. genome sequence version (label): is_about some (assembled genome
sequence is_output_of some assembly of nucleic acid sequences).
- assembled genome sequence is a data item that is generated from
multiple sequences and is about the sequence of deoxyribonucleotides
found in a representative (or set of representative) organisms of one
species (or strain of species).
- assembly of nucleic acid sequences is a data transformation that
takes as input multiple nucleic acid sequences and orders and orients
them to generate a consensus sequence or set of consensus sequences
according to some algorithm. The input may be previously assembled
sequences such as scaffolds or contigs o generate an assembled genome
or may be individual sequence reads such as ESTs to generate an
assembled transcript.
3. tree model: is a data representational model in which there are one
or more layers of nodes attached in a hierarchical
manner and there may be a top or root node. The leaf nodes are about
entities such as genes or investigation samples and the relationships
are about the (dis)similarity typically between pairs of nodes. The
tree model is distinct in having nodes that are about inferred
entities such as evolutionary precedents or common ancestors to
related nodes. A node can only be in one branch of a tree (i.e., a
tree model does not represent fuzzy clustering).
Here are remaining terms from the tracker to discuss:
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
Thanks,
Chris