[open-science] (Lack of) data sharing for fossil data

Fri Apr 15 14:44:12 UTC 2011

Thank you, Peter. That helps me put what I know a little about in  
perspective with respect to what I don't know anything about.

I would only argue with you that "where" matters in the study of  
fossils, trees and many other objects of study not generally thought  
of as subjects of the geosciences. Studying such objects very often  
requires managing geospatial information, and so students of those  
Earth features would benefit from leveraging the work that I described  
below.

Curiously, lung science (http://www.technologyreview.com/computing/37387/?nlid=4352&a=f 
) and brain science (http://geo.sdsc.edu/ilya/presentations/INCF_Atlas_Services_and_WaxML_version_06pic.doc 
) require, or will require, standard ways of dealing with spatial data  
that are not too different from the OGC's Earth-referencing geospatial  
standards.

Lance

On Apr 15, 2011, at 10:05 AM, Peter Murray-Rust wrote:

> This looks like a good opportunity to discuss different ways of  
> viewing the problem.
>
> On Fri, Apr 15, 2011 at 2:40 PM, Lance McKee <lmckee at opengeospatial.org 
> > wrote:
> re:
>
> The semantic problems you allude to are harder. PDF is an  
> abomination in science - it has no role. We're trying to develop  
> scholarly HTML as the right way to communicate science. It will need  
> critical mass but we are as always optimistic.
>
> PDF, no. HTML, no.
>
> XML, yes.
>
> XML yes as well. FWIW I was one of the early developers of XML in  
> 1997 and ran the XML-DEV mailing list. I have developed (with very  
> few assistants) Chemical Markup Language over the last 17 years. So  
> I support XML for certain domains - chemistry, geoscience, and other  
> physical sciences.
>
> But there are very few absolutes in this area.
>
> Other domains such as bioscience rely much more on words and less on  
> structure. So HTML is a natural way of communicating ideas. It's  
> universal and - with goodwill at both ends of the chain (author and  
> reader) HTML can manage most of what is necessary. The great thing  
> about HTML is that any device can render it and allow reuse. XML  
> usually requires specialist tools. So If I send you a CML file, the  
> first thing that you are likely to do is ask where you can get a  
> toolchain (yes, it exists and there is a lot of my blood in it). If  
> you send me xml-encoded ISO standard metadata I will have to ask for  
> help.
>
> Every domain needs a metadata council.
>
> Probably true. But some are top down (a political activity) and some  
> are bottom up (i.e. the discipline has no interest or insight into  
> doing it). Top down works, often very slowly. Bottom-up often does  
> not work but when it does moves rapidly.
>
> Ultimately, it's about profiles of the ISO metadata standards and  
> web service interfaces for catalogs that enable the xml-encoded ISO  
> standard metadata -- and links to the data (and data processing  
> services) -- to be published, discovered, assessed, accessed and  
> used. See, for example, the Marine Metadata Interoperability Project  
> (http://marinemetadata.org/). Ultimately, this approach enables  
> chaining of web services in models that draw on multiple remote  
> resources.
>
> This model works for geoscience. It does not work for bioscience  
> (fossils, trees). It does not work for chemistry. Each domain is a  
> muddle of designed semantics, evolved semantics, commercial forces,  
> learned societies, etc. Each domain will provide different ways of  
> disseminating their data and metadata.
>
> There is no single one-fits-all solution. For several decades  there  
> are likley to be per-domain solutins with more-or-less funding, more  
> or less volunteer activity. In chemistry it's been a very hard  
> strufggle against the forces of inertia and walled-garden  
> commercialism (who benefit from keeping the subject in the dark ages).
>
> P.
>
>
> -- 
> Peter Murray-Rust
> Reader in Molecular Informatics
> Unilever Centre, Dep. Of Chemistry
> University of Cambridge
> CB2 1EW, UK
> +44-1223-763069