I'm happy to help Michael, let me know where I can contribute.
Cheers,
Melissa
On Aug 4, 2014, at 10:19 AM, Michael Miller
mailto:michael.mil...@systemsbiology.org>>
wrote:
hi michel and kim,
yes, i'll take a look at writing something up.
kim, i do see 'wasDerivedFrom' and 'createdWith' which
hi michel and kim,
yes, i'll take a look at writing something up.
kim, i do see 'wasDerivedFrom' and 'createdWith' which, you're right, do
address this issue in part but there is so much more to this, which i think
using PROV terms will address. so i'll try and come up with a potential
example o
On Mon, Aug 4, 2014 at 10:08 AM, Joachim Baran wrote:
> Having said that, our note apparently is not clear on that particular
> aspect. We will see what we can do about this.
We would welcome some prose from you and Melissa so that it
communicates what you feel is necessary for other potential us
Hi!
Relations between dataset descriptions are actually supported and we
addressed derived datasets. Having said that, our note apparently is not clear
on that particular aspect. We will see what we can do about this.
Kim
> On Aug 4, 2014, at 9:44 AM, Michael Miller
> wrote:
>
> hi all,
hi melissa,
'...and ideally we'd be able to automate the display of the provenance
chain...'
we already are close to automating producing our feature matrix given a
snapshot of the dcc repository and this is exactly what we'd like to add to
the pipeline.
thanks,
michael
Michael Miller
Hi all,
I agree Michael, and I had put a note to this effect on the original google doc.
We deal with the same issue all the time, and ideally we'd be able to automate
the display of the provenance chain if such a thing were specified well enough.
Cheers,
Melissa
On Aug 4, 2014, at 9:44 AM, Mic
hi all,
as you are all undoubtedly aware, a major, if not the major TCGA dataset
use cases revolve around taking the 3rd level data from the TCGA dcc
repository and doing analysis, producing 4th level data such as clusters,
pca, etc. one of the things we do here at ISB is produce an intermediat
Yes, I think reasoners that only consider the EL subset are very fast.
>From the site: TrOWL utilises ... a syntactic approximation from OWL2-DL to
OWL2-EL for TBox and ABox reasoning.
best,
Andrea
On Mon, Aug 4, 2014 at 2:40 PM, Matthias Samwald <
matthias.samw...@meduniwien.ac.at> wrote:
> >
Hello All,
Just a reminder of our telco at 8AM PST / 5PM CET.
Relevant docs: - Working draft of W3C Note:
http://htmlpreview.github.io/?https://github.com/joejimbo/HCLSDatasetDescriptions/blob/master/Overview.html
Cheers,
Scott
--
M. Scott Marshall, PhD
MAASTRO clinic, http://www.maastro.nl/en
Hi Andrea,
Those of us who work on the HPO (OWL) use ELK for classification, and most
other ontologies and it works quite well.
Cheers,
Melissa
On Aug 4, 2014, at 5:40 AM, Matthias Samwald
mailto:matthias.samw...@meduniwien.ac.at>>
wrote:
> TrOWL I have tried, but I have the impression it doe
> TrOWL I have tried, but I have the impression it doesn't really make
a classification upfront, but rather incrementally on demand. It's just
an impression, but it classified HP in no time ;)
It is supposed to classify everything. Maybe you don't have a problem at
all. ;)
- Matthias
Am 0
Hi,
I didn't see the BioHackathon ML message. I have just realised my mail
setup is a bit messed up...
TrOWL I have tried, but I have the impression it doesn't really make a
classification upfront, but rather incrementally on demand. It's just an
impression, but it classified HP in no time ;)
I wi
Hi Andrea,
I remember you got the recommendation to try ELK on the Biohackathon
mailing list. Is ELK not working for you?
You might also want to give TrOWL a try if ELK is not working for you
for some reason. Konclude might also be an option as it seems to
outperform most other reasoners, but
Hi all,
I have stumbled onto a problem for which I would like to hear from your
experience.
In a project, I am using the Human Phenotype Ontology (
http://www.human-phenotype-ontology.org/).
For the sake of the project, I really only need the is_a structure of the
ontology, but as an OWL version
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