umont...@gmail.com]
> Sent: Thursday, April 26, 2012 2:31 PM
> To: M. Scott Marshall
> Cc: Mark; Jim McCusker; HCLS
> Subject: Re: Minutes from Monday's Linked Life Data (BioRDF / LODD)
> teleconference
>
> Hi from a rest stop in Vermont with tasty coffee and wifi :)
>
Mark
good question. There could be subproperties. However, in practice as we
are trying to detect these relationships across several databases and
millions of samples the underlying individual data models make it
challenging to detect derived from, so having any confidence and in sub
properti
Would there be sub-properties of "derived-from": "extracted-from" and
"adapted-from"?
M
On Fri, 27 Apr 2012 10:54:21 +0200, Helen Parkinson
wrote:
Derived-from can be used to model e.g. DNAs derived from a cell line, a
blood derived from a person etc. We will be using this in the Bio
Dear Scott and HCLS people
we have a new format for BioSamples database at the EBI which models
these relationships more precisely as derived-from. I agree that has
characteristic is rather weak modelling of this reln. Derived-from can
be used to model e.g. DNAs derived from a cell line, a blo
Hi from a rest stop in Vermont with tasty coffee and wifi :)
So SIO features a few information relations of interest. The most basic is
'refers to',
http://semanticscience.org/resource/SIO_000628
which is to say that an entity is mentioned. If there is an actual
description, then we can
Hmm. Michel suggested that "set" of relations in November:
Michel wrote: " there are some basic relations that we can look at,
for instance, i have defined a wider set of relations as part of my
SIO ontology: "
What we were looking for was a way to describe that a given dataset
might have to do wi
I think Michel deprecated "is related to" DURING the Hackathon! (out of
disgust, if I recall correctly...) "not enough semantics"!
So... He's forcing us to be more clever :-)
M
"M. Scott Marshall" wrote:
On Monday, Jim's description reminded me about a recent discussion in
the biohackathon d
On Monday, Jim's description reminded me about a recent discussion in
the biohackathon dbcatalog group about the best predicate for
indicating that a dataset has 'something to do with', for example, mus
musculus (not unlike Mark's example). I remembered some is_about
predicate from SIO. The predica
No problem, this was something that was added after the telecon, and I
hadn't mentioned it to anyone outside of my immediate collaborators.
Jim
On Thu, Apr 26, 2012 at 3:22 PM, Mark wrote:
> (apologies for not looking it up myself - I'm still stuck without internet
> access at home, and my cell
(apologies for not looking it up myself - I'm still stuck without internet
access at home, and my cell provider in Spain cut me off from high-speed cell
access too, due to over-use... So I'm basically dial-up speed on my phone...
And this little seen isn't great for exploring ontologies!)
Jim
Fantastic! :-)
Jim McCusker wrote:
Actually, we've switched over to generating subproperties of
sio:has_predicate, so I'm glad you suggested the same thing.
Jim
On Thu, Apr 26, 2012 at 2:07 PM, Mark wrote:
> H... what's the range of that predicate? It's a bit like the SIO "has
> attribute
Actually, we've switched over to generating subproperties of
sio:has_predicate, so I'm glad you suggested the same thing.
Jim
On Thu, Apr 26, 2012 at 2:07 PM, Mark wrote:
> H... what's the range of that predicate? It's a bit like the SIO "has
> attribute", where you need to be sure to explic
H... what's the range of that predicate? It's a bit like the SIO "has
attribute", where you need to be sure to explicitly type what's at the other
end to do "useful" reasoning. We're just concluding a project where we use
species-of-origin to restrict the choices the SHARE query resolver can
We had an interesting discussion with Jim McCusker about Linked Data /
RDF representations of MAGE-TAB and some issues, such as choices of
predicates to make describe a human sample.
how to encode "is a sample originating from human"
closest now is "has characteristic"
Jim showed us some linked d
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