Re: PROV-ISSUE-6 (define-location): Definition for Concept 'Location' [Provenance Terminology]

I think the notion of location should be as generic as possible.

To this end, I'd like to pose an additional example, which comes from a real 
scenario I've worked with, which suggests possible further uses of location 
provenance.

I raise this because I think it's important that whatever definition we adopt 
for location does not rule out using the information suggested by this use case 
as part of a record of provenance information.

...

Researcher H is investigating genomics in Drosophila (fruit flies), specifically 
genetic factors affecting spermatogenesis that may cause sterility.  To this 
end, she creates in situ hybridization 
(http://en.wikipedia.org/wiki/In_situ_hybridization) images of Drosophila 
testes.  Location information arises in a number of different ways:

(1) starting from a microscopic image of testes treated to reveal gene 
expression, the researcher looks for occurrences of interesting and clearly 
exposed gene expression patterns.  These occurrences are recorded as a slide 
number and a coordinate location within the slide image.

(2) the spatial location of the gene expression within the testis structure 
gives a direct visual indication of the sperm development stage at which a 
target gene is being expressed.  This location is observed and recorded as a 
keyword from a controlled vocabulary that relates the gene expression to a 
developmental stage.

As well as creating microscopic images, the tissue samples are subjected to a 
real-time PCR process (http://en.wikipedia.org/wiki/Polymerase_chain_reaction) 
that gives a quantitative indication of the levels of a particular gene 
expression product present in a sample.  PCR is a batch process, where 
preparations based on different samples (targetting different genes, or 
different Drosophila species) are placed into different wells in a tray.  This 
leads to:

(3) The PCR analyzer presents by reference to the location of the various wells 
(identified by label or row/column position).  The well locations are in turn 
linked to details of the sample that has been placed in that well.

Of these examples, I think that (1) and (3) are definitely part of the 
provenance information for a result.  (2) is less clear, and I'd judge it to be 
part of the data rather than provenance information.  But researcher H has also 
performed some follow-on research to analyzes particular spatial patterns of 
gene expression, in which the location-based developmental stage might 
conceivably be considered to be provenance information, in the sense of where 
the phenomenon was observed to occur.

#g
--


Carl Reed wrote:
> 
> Martin -
>  
> A shorter version as defined in ISO 19112 and used by the OGC (since 
> this was a jointly developed definition) is:
>  
> Location: Identifiable geographic place [ISO 19112]. Typically a 
> location is a physically fixed point, typically on the surface of the 
> Earth, though locations can be relative to other, non-earth centric 
> coordinate reference systems.
>  
> I also noticed that the the European INSPIRE community working on 
> cultural heritage sites are using CIDOC/21127 as well as additional OGC 
> references, such as the URN syntax for spatial reference systems.
>  
> Suffice to say, the definition for location in 21127 is a community 
> elaboration of the more general OGC/ISO definition. We may need some 
> such additional clarification for the provenance work - such as dealing 
> with data provenance for articles, maps, charts, etc for the moon, Mars, 
> and so forth.
>  
> Regards
>  
> Carl

Received on Tuesday, 24 May 2011 10:36:20 UTC