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