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Re: Time-series spatial data [was: Re: TCGA / Microscopy Imaging Use Case] [SEC=UNCLASSIFIED]

From: Erich Bremer <erich.bremer@stonybrook.edu>
Date: Tue, 10 Mar 2015 10:22:53 -0400
Message-ID: <CAGR3=--YRnKBjYP4-j6UTqaReGUQDuBfgCqG6r5uyVmYdM8Xmw@mail.gmail.com>
To: Kerry.Taylor@csiro.au
Cc: B.Bannerman@bom.gov.au, frans.knibbe@geodan.nl, public-sdw-wg@w3.org
Hi Kerry,

I agree, I think the the use case that I have submitted should fall out of
what is being done.  This area has already benefited from the work done in
the geo-spatial community.  The main component needed to make it more of a
first class citizen is the Cartesian coordinate system as opposed to
lat/long.  I know of one triple store vendor that is adding support for
Cartesian spatial indexing.  I've joined the group already and will try to
make the next call.  - Erich

On Tue, Mar 10, 2015 at 7:39 AM, <Kerry.Taylor@csiro.au> wrote:

>  Frans said> It includes concepts from all scales, from quantum particles
> to the universe itself. Are we ready to take on all these scales?
>
>
>
> IMHO we cannot. However, Bruce’s use case below, should indeed be in scope
> (and I think you will find, Bruce, is addressed by our use cases
> https://www.w3.org/2015/spatial/wiki/Working_Use_Cases, and if it is not,
> it should be!).
>
>
>
> I expect we can also cover Erich’s “morphology of disease at the cellular
> and sub-cellular levels” as that should fall out of what we are doing
> anyway.
>
> Erich, can I encourage you to join up to be sure of that?
>
>
>
> Kerry
>
>
>
>
>
>
>
>
>
> *From:* Bruce Bannerman [mailto:B.Bannerman@bom.gov.au]
> *Sent:* Tuesday, 10 March 2015 12:21 PM
> *To:* Frans Knibbe | Geodan; public-sdw-wg@w3.org
> *Subject:* Time-series spatial data [was: Re: TCGA / Microscopy Imaging
> Use Case] [SEC=UNCLASSIFIED]
>
>
>
> Hi Frans,
>
>
>
> (I’ve been lurking on this list for a little while now…)
>
>
>
> I noted the following in your last comment.
>
>
>
>  “I think that on the human/macroscopic/geographical level space and time
> can be kept separate, in the sense that a model or ontology for space does
> not really need time concepts, and vice versa."
>
>
>
> From my perspective in managing climate data, all of our data is
> time-series spatial data. It is very important to understand the ‘when’ as
> well as there ‘where’ with respect to the data (together with the data
> provenance etc).
>
>
>
> For example, we manage and analyse point-series and gridded distributions
> of say average maximum temperature over a wide range of time periods from
> daily, monthly, yearly, decadal etc periods.
>
>
>
> When using this data, it is **critical** that we understand the temporal
> period that the spatial data refers to.
>
>
>
> For more information on what we mean by climate data, can I refer you to
> WMO No. 1131, Climate Data Management System Specifications [1], Section 4,
> Time Series Climate Data.
>
>
>
> Bruce
>
>
>
> [1]
> http://library.wmo.int/opac/index.php?lvl=notice_display&id=16300#.VP5F9DUu6Fg
>
>
>
>
>
>
>
>
>
>
> *From: *Frans Knibbe | Geodan <frans.knibbe@geodan.nl>
> *Date: *Tuesday, 10 March 2015 11:42
> *To: *"public-sdw-wg@w3.org" <public-sdw-wg@w3.org>
> *Subject: *Re: TCGA / Microscopy Imaging Use Case
> *Resent-From: *<public-sdw-wg@w3.org>
> *Resent-Date: *Tuesday, 10 March 2015 11:42
>
>
>
>
> Wow, that is an interesting use case. Maybe this may calls for a better
> definition of what we mean by 'spatial data'?
>
> I remember the time when geographers started switching from using the
> adjective 'geographic' to using 'spatial', implying a broadening of scope
> and a higher relevance. But still the actual topics were macroscopic
> objects, things that you can plot on a map. And the reference systems still
> are earth based.
>
> Taken literally, 'spatial' covers a lot more than 'geographic'. It
> includes concepts from all scales, from quantum particles to the universe
> itself. Are we ready to take on all these scales?
>
> Related to the issue of the scope of scale is the relationship between
> space and time. I think that on the human/macroscopic/geographical level
> space and time can be kept separate, in the sense that a model or ontology
> for space does not really need time concepts, and vice versa. But it could
> well be that such a separation is not possible for very small things (like
> elemental particles) and very big things (like galaxies). On such levels
> time and space tend to be more entangled.
>
> Greetings,
> Frans
>
> On 2015-03-03 21:52, Erich Bremer wrote:
>
>
>
>  Studying the morphology of disease at the cellular and sub-cellular
> levels using high resolution tissue images is extremely important to help
> understand the nature of various cancers. The Cancer Genome Atlas (TCGA) (
> http://cancergenome.nih.gov/) contains over 32,000 de-identified
> whole-slide microscopy images (WSI) of over two dozen cancer types. These
> images can contain between 100K-1M nuclei each.  Biomedical informatics
> researcher have developed (and continue to develop) software to
> automatically segment nuclei for study.  The spatial features of each
> nucleus and groups of nuclei as it relates to other nuclei combined with
> other linked data such as other morphological features (crypts, ducts, etc)
> and/or patient lab results are used in analyzing and categorizing tissues
> and patients into groups and in comparing such groupings to understand
> disease mechanisms in a particular cancer type as well as across cancer
> types.
>
>
>
> Representing nuclear segmentations is often done with binary masks or
> through polygon representations (e.g., the use of Well Known Text (WKT)
> representations) and also by leveraging work from the Geospatial
> community.  However, in the case of nuclear segmentations, coordinate
> systems are 2D & 3D Cartesian based.  Although the majority of work is this
> area is 2D-based, a growing segment of microscopy is also 3D-based as the
> technology develops and become more sophisticated.  As living tissue can
> change over time through growth, infection, cancer, damage, etc, (as well
> as its associated organism’s various properties) it is important that
> spatial locations of features such as nuclear segmentation be also
> represented in a temporal aspect for proper comparisons.
>
>
>
> Samples of TCGA WSI data can be viewed at:
> http://cancer.digitalslidearchive.net
>
>
>
>
>
> --
>
> ==========================================================
>
> Erich Bremer, M.Sc.
>
> Director for Cyberinfrastructure
>
> Health Sciences Division of Applied Informatics
>
> Stony Brook Medicine
>
> Tel. : 1-631-444-3560
>
> Fax  : 1-631-444-8873
>
> Cell : 1-631-681-6228
>
> erich.bremer@stonybrook.edu
>
> Office Location/Mailing Address
>
> HSC, L3: Room 119
>
> Stony Brook, NY 11794-8330
>
>
>
>
>  ------------------------------
>
> Frans Knibbe
> Geodan
> President Kennedylaan 1
> 1079 MB Amsterdam (NL)
>
> T +31 (0)20 - 5711 347
> E frans.knibbe@geodan.nl
> www.geodan.nl | disclaimer <http://www.geodan.nl/disclaimer>
>  ------------------------------
>
>
>
>
>
>


-- 
==========================================================
Erich Bremer, M.Sc.
Director for Cyberinfrastructure
Health Sciences Division of Applied Informatics
Stony Brook Medicine
Tel. : 1-631-444-3560
Fax  : 1-631-444-8873
Cell : 1-631-681-6228
erich.bremer@stonybrook.edu
Office Location/Mailing Address
HSC, L3: Room 119
Stony Brook, NY 11794-8330
Received on Tuesday, 10 March 2015 14:23:21 UTC

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