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

From: matthew perry <matthew.perry@oracle.com>
Date: Tue, 10 Mar 2015 10:46:00 -0400
Message-ID: <54FF03A8.7070801@oracle.com>
To: Erich Bremer <erich.bremer@stonybrook.edu>
CC: public-sdw-wg@w3.org
Hi Erich,

The GeoSPARQL vocabulary allows for different spatial reference systems, 
so you can represent spatial geometries on a Cartesian coordinate system 
with ogc:WKTLiteral or ogc:GMLLiteral. In addition, Oracle has supported 
Cartesian spatial indexing for the RDF Semantic Graph product since 
2011, so there's a few triple store vendors that can support this.

Cheers,
Matt


On 3/10/2015 10:22 AM, Erich Bremer wrote:
> 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 
> <mailto: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
>     <mailto:B.Bannerman@bom.gov.au>]
>     *Sent:* Tuesday, 10 March 2015 12:21 PM
>     *To:* Frans Knibbe | Geodan; public-sdw-wg@w3.org
>     <mailto: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
>     <mailto:frans.knibbe@geodan.nl>>
>     *Date: *Tuesday, 10 March 2015 11:42
>     *To: *"public-sdw-wg@w3.org <mailto:public-sdw-wg@w3.org>"
>     <public-sdw-wg@w3.org <mailto:public-sdw-wg@w3.org>>
>     *Subject: *Re: TCGA / Microscopy Imaging Use Case
>     *Resent-From: *<public-sdw-wg@w3.org <mailto: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 <tel:1-631-444-3560>
>
>             Fax  : 1-631-444-8873 <tel:1-631-444-8873>
>
>             Cell : 1-631-681-6228 <tel:1-631-681-6228>
>
>             erich.bremer@stonybrook.edu
>             <mailto: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 <tel:%2B31%20%280%2920%20-%205711%20347>
>         E frans.knibbe@geodan.nl <mailto:frans.knibbe@geodan.nl>
>         www.geodan.nl <http://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 <mailto:erich.bremer@stonybrook.edu>
> Office Location/Mailing Address
> HSC, L3: Room 119
> Stony Brook, NY 11794-8330
>
Received on Tuesday, 10 March 2015 14:46:42 UTC

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