hi david and renalto,
it's been an interesting, and good, discussion.
> Some common reasons why health data is legitimately published:
i just wanted to add one more reason that has occurred often for me, and
that is with-in an organization health data can be exchanged, and, more
importantly, with
https://isatools.wordpress.com/
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Oya Deniz Beyan [mailto:be...@dbis.rwth-aachen.de]
*Sent:* Wednesday, May 25, 2016 9:08 AM
*To:* 'Brochhausen, Mathias'; 'Richard Boyce'; public-semweb-lifesci@w3.org;
linik...@gmail.com;
ce control. people working on
different sections won't collide in the merges.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Richard Boyce [mailto:rd...@pitt.edu]
*Sent:* Thursday, March 31, 2016 1:26 PM
*To:* public-semweb-lifesci@w3.org; lin
hi all,
regrets, will be traveling
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Marc Twagirumukiza [mailto:marc.twagirumuk...@agfa.com]
*Sent:* Wednesday, December 09, 2015 7:47 AM
*To:* Jim Marks; David Portnoy; public-sche...@w3.org; w3c
hi all,
thought some of you might be interested in this! i'm hopeful of adding a
sparql endpt. to this at some point, particularly the metadata (see the
clinical and biospecimen bigquery tables) and would welcome, thoughts, help
from anyone.
cheers,
michael
Michael Miller
Sof
hi all,
apologies, a conflict has come up. great work, all, on the note
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: M. Scott Marshall [mailto:mscottmarsh...@gmail.com]
> Sent: Friday, March 06, 2015 6:49 AM
&
hi michel,
i've entered issue #101 for this but don't have permission to add labels or
assign it to myself, at least it looks that way. i'll try to get to this in
the next few weeks.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> ---
ntioning that other
representations would have appropriate statistics for the representation?
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Michel Dumontier [mailto:michel.dumont...@gmail.com]
> Sent: Monday, January
based? i had
thought that any kind of data file would be appropriate
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: M. Scott Marshall [mailto:mscottmarsh...@gmail.com]
> Sent: Monday, January 26, 2015 5:15 AM
> T
hi all,
regrets, a busy morning. good news is that i'll be working on the model to
represent the TCGA DCC repository
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: M. Scott Marshall [mailto:mscottmarsh...@gmail.
hi all,
i also hope to have the TCGA dataset example sketched out/done in the next
few weeks
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Gray, Alasdair [mailto:a.j.g.g...@hw.ac.uk]
*Sent:* Monday, November 03, 2014 8:36 AM
*To:* public
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Vipul Kashyap [mailto:kashyap.vi...@gmail.com]
*Sent:* Wednesday, September 10, 2014 3:24 PM
*To:* peter.hend...@kp.org; da...@dbooth.org
*Cc:* public-semweb-lifesci@w3.org; kashyap.vi...@gmail.com
*Subject:* RE: HCLS
hi all,
i just added issue #84 to github for the TCGA dcc-repository example but
find i can't assign myself to it or add labels, probably because i'm not an
official contributor. can some one do this for me?
cheers and thanks,
michael
Michael Miller
Software Engineer
Institute f
so i would lean towards import
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Joachim Baran [mailto:joachim.ba...@gmail.com]
*Sent:* Wednesday, August 27, 2014 5:49 PM
*To:* Stian Soiland-Reyes
*Cc:* Michael Miller; Alasdair J G Gray; w3c semweb
e gene names are not duplicated, they are
the row headers. so no values are changed, just a bit of modest
reformatting and filtering.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
[1] https://confluence.broadinstitute.org/display/GDAC/Dashboard-Stdda
pull request. hope to make the call next week.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Joachim Baran [mailto:joachim.ba...@gmail.com]
*Sent:* Monday, August 11, 2014 8:00 AM
*To:* Michael Miller
*Cc:* Stian Soiland-Reyes; w3c semweb hcls
PROV.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Joachim Baran [mailto:joachim.ba...@gmail.com]
*Sent:* Monday, August 11, 2014 8:00 AM
*To:* Michael Miller
*Cc:* Stian Soiland-Reyes; w3c semweb hcls
*Subject:* Re: hcls dataset description com
hi kim,
i've made decent progress and expect to have something mid-week, if all goes
well (as a pull request, tho no guarantee on the formatting!)
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Jo
hi stian,
thanks much, very useful!
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: st...@mygrid.org.uk [mailto:st...@mygrid.org.uk] On Behalf Of Stian
> Soiland-Reyes
> Sent: Tuesday, August 05, 2014 5:38 AM
&
nd come up with a potential
example of how the two can be used together.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Michel Dumontier [mailto:michel.dumont...@gmail.com]
> Sent: Monday, August 04, 2014 10:14 AM
&
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,
micha
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Joachim Baran [mailto:joachim.ba...@gmail.com]
*Sent:* Thursday, July 31, 2014 3:43 PM
*To:* Michael Miller
*Cc:* w3c semweb hcls
*Subject:* Re: hcls dataset description comments
Hi!
I w
were probably
written by the groups themselves? if i have permission, i can certainly
add them as issues.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Joachim Baran [mailto:joachim.ba...@gmail.com]
*Sent:* Tuesday, July 29, 2014 11:56 AM
*To:* M
hi kim,
thanks for the pointer, i've updated my comments based on this newer draft
below. many fewer and i especially like the complete example in 10.1!
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
general comments:
· s4.4 'Datas
ed'?
· there are two s6.2.3 sections
· s6.2.4: 'Creation: ... The date of authorship' should be '...The
date of creation' and 'Curation:... The date of authorship' should be '...The
date of curation'?
· s8.5: the author
curated
datasets, one for researchers and one for pharma perhaps.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Gray, Alasdair J G [mailto:a.j.g.g...@hw.ac.uk]
*Sent:* Monday, June 16, 2014 8:45 AM
*To:* Jerven Bolleman
*Cc:* HCLS IG
*Subject
hi david and michel,
i agree with your initial effort, david, my experience with the HL7 is that
the charters for the WGs in HL7 are broad and short, but once the WG is
charted then a roadmap is the first order of business. that's where
michel's suggestions would fit in
michael
Mich
hi james,
congrats on getting done with a big chunk of work! tremendous resource
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* James Malone [mailto:mal...@ebi.ac.uk]
*Sent:* Tuesday, October 08, 2013 6:45 AM
*To:* public-semweb-lifesci@w3
hi simon,
i was just looking at this page this morning:
http://wiki.hl7.org/index.php?title=FHIR
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Lin MD, Simon [mailto:linmd.si...@mcrf.mfldclin.edu]
*Sent:* Friday, July 12, 2013 11:52 AM
chael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* KANZAKI Masahide [mailto:mkanz...@gmail.com]
*Sent:* Monday, July 01, 2013 7:19 PM
*To:* John Erickson
*Cc:* Bernadette Hyland; W3C public GLD WG WG; Linked Data community;
egov-ig mailing list; HCLS
*Subject:* Re: L
liability and responsibility.
http://en.wikipedia.org/wiki/Software_license
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Alasdair J G Gray [mailto:alasdair.g...@manchester.ac.uk]
*Sent:* Tuesday, May 28, 2013 9:05 AM
*To:* public-semweb-
ion of RDF?
thanks,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Eric Prud'hommeaux [mailto:eric...@gmail.com] On Behalf Of Eric
> Prud'hommeaux
> Sent: Monday, May 06, 2013 5:42 PM
> To: public-semweb-lifesci@w3.org
hi all,
phillip, not to mention a name (like mine!) is not particularly unique.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Phillip Lord [mailto:phillip.l...@newcastle.ac.uk]
> Sent: Monday, April 08, 2013 9:5
hi amrapali,
for human genes,
http://www.genenames.org/
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Bhat, Talapady N. [mailto:talapady.b...@nist.gov]
*Sent:* Monday, April 08, 2013 7:26 AM
*To:* Amrapali J Zaveri; w3.h...@gmail.com
rom analysis. especially after the analysis,
it becomes even less useful since that analysis will not include any
results it didn't think passed QC
cheers,
michael
*From:* Jeremy J Carroll [mailto:j...@syapse.com]
*Sent:* Wednesday, April 03, 2013 3:39 PM
*To:* Michael Miller
*Cc:* Kin
ariants can
then form a basis to go back to the filtered variants to look for
similarity.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Jeremy J Carroll [mailto:j...@syapse.com]
*Sent:* Tuesday, April 02, 2013 2:22 PM
*To:* Michael Miller
*Cc:
y do what most would do, use a base
class to handle most of the parsing then have a derived class per provider
and try to drive everything through a configuration file.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Jere
hi scott,
although it is in XML, it might be worthwhile to consider translating the
TCGA clinical and sample information on the patients into RDF (if it
hasn't been done already!).
cheers,
michael
> -Original Message-
> From: M. Scott Marshall [mailto:mscottmarsh...@gmail.com]
> Sent: We
also another
nice discussion of neo4j [2]
cheers,
michael
[1] http://link.springer.com/chapter/10.1007%2F978-3-642-16720-1_4?LI=true
[2] http://www.infoq.com/articles/graph-nosql-neo4j
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: King
nce boost using sharding
cheers,
michael
[1] http://docs.neo4j.org/chunked/snapshot/capabilities-
capacity.html#capabilities-data
> -Original Message-
> From: Andrea Splendiani [mailto:andrea.splendi...@deri.org]
> Sent: Saturday, January 19, 2013 4:24 AM
> To: Michael M
y 17, 2013 1:38 PM
> To: public-semweb-lifesci@w3.org
> Subject: Re: Facebook's new Graph Search: An endorsement of the RDF
> approach to healthcare data?
>
> On 1/17/13 1:45 PM, Michael Miller wrote:
> > the developer who wrote the app looked at RDF but settled on
cov
ery.pdf&ei=b0X4ULTdKonUiwLe-IDYAQ&usg=AFQjCNEYpPBbBxvnQGVWmxls8nsRXSrWpw
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Lin MD, Simon [mailto:linmd.si...@mcrf.mfldclin.edu]
> Sent: Thursday, January 17, 2013 10:06 AM
> To: Kingsley Idehen; pub
hi charlie,
that's great, thanks
michael
> -Original Message-
> From: Mead, Charlie (NIH/NCI) [C] [mailto:mea...@mail.nih.gov]
> Sent: Wednesday, January 16, 2013 10:01 AM
> To: Michael Miller
> Cc: David Booth; public-semweb-lifesci
> Subject: RE: Opening Walle
hi charlie,
and is OWL able to capture everything about the MIF so no information is
lost? (i would be surprised if it didn't)
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Mead, Charlie (NIH/NCI) [C] [mailto:mea...@m
t out that this allows organizations the opportunity to keep the data
in the way they want internally and convert to/from RDF on import/export.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Joanne Luciano [mailto:jluci...@g
fragment, leave out the 'of' or elaborate briefly?
i noticed that the 'of' is still there?
cheers,
michael
> -Original Message-
> From: Eric Prud'hommeaux [mailto:eric...@gmail.com] On Behalf Of Eric
> Prud'hommeaux
> Sent: Monday, December 0
or
further details)'
need the outer parentheses?
· in Q11, Figure 2 caption, 'DbPedia' should be 'DBPedia' (it is
elsewhere)?
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* M. Scott Marshall [mailto:mscottmarsh...@
this looks useful, please add me to the list of contributors, thanks!)
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: linkedlifedatapracticesn...@googlegroups.com
> [mailto:linkedlifedatapracticesn...@googlegroups.com
n OMG specification[1] that describes a
way to map from UML to OWL/RDF and there are always less rigorous
formulations that would do, along the lines of transforming a database
schema to RDF.
michael
Michael Miller
Software Engineer
Institute for Systems Biology
[1] http://www.omg.org/spec/OD
ut, it means 'go ahead and implement a custom web application to view
linked data'? i've probably been being dense.
thanks,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: expression...@googlegroups.com
> [
let's finish up what we have
then move on to newer and brighter -omics to come.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Suzanna Lewis [mailto:sele...@lbl.gov] On Behalf Of Suzanna Lewis
> Sent: Saturday, Se
hi michel and all,
this looks like a good overview of where IMPD is and is going, SPL is
mentioned [1]
cheers,
michael
[1]
http://www.diahome.org/productfiles/25038/s5_brosch_integration%20of%20iso.pdf
*From:* Michel Dumontier [mailto:michel.dumont...@gmail.com]
*Sent:* Tuesday, Sept
laced by NGS gene expression studies and there has been no
confusion.
so for the note i think it will be much clearer to stay with gene
expression and, as part of the systems biology working group, begin to move
into these other -omics and how they can be used together to form a model.
my
hi all,
> Note, I brought up wanting to integrate some definitions that Michel
> had brought up.
i might be off base here but :
> 3. semantic interoperability - establish SPARQL-based transformations
> of each source to a global schema
sounds like what the BioRDF paper laid the groundwork for?
hi all,
apologies, i am at a workshop today and tomorrow.
enjoy the talk,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: M. Scott Marshall [mailto:mscottmarsh...@gmail.com]
> Sent: Monday, September 10, 2012 7:16 AM
&
hi scott,
thanks
cheers,
michael
> -Original Message-
> From: M. Scott Marshall [mailto:mscottmarsh...@gmail.com]
> Sent: Thursday, September 06, 2012 9:49 AM
> To: Michael Miller
> Cc: Helena Deus; W3C HCLSIG hcls; laleh.kazemza...@deri.org
> Subject: Re: REMINDER
hi all,
apologies for missing the talk, i look forward to seeing the slides.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Helena Deus [mailto:helenad...@gmail.com]
*Sent:* Thursday, September 06, 2012 7:37 AM
*To:* W3C HCLSIG hcls
://www.omg.org/mda/
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Phillip Lord [mailto:phillip.l...@newcastle.ac.uk]
> Sent: Friday, August 10, 2012 4:44 AM
> To: Alan Ruttenberg
> Cc: Michel Dumontier; Peter Ansell; Robinson, Peter; Chri
sure what you meant
here, rafael?
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Michel Dumontier [mailto:michel.dumont...@gmail.com]
*Sent:* Tuesday, June 26, 2012 9:07 AM
*To:* public-semweb-lifesci@w3.org
*Cc:* rmri...@gmail.com
*Subject
ly does it translate to OWL and
RDF and are people doing that (apparently yes)? and so on...
so i am looking forward to the next call,
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Helena Deus [mailto:helenad...@gmail.com]
*Sent:* Thursday, May 24,
e problem.
cheers,
michael
[1] http://mged.sourceforge.net/ontologies/MOMAGEpolicy.txt
[2]
http://mged.sourceforge.net/ontologies/GilbertoTestAnnotationValidated.xml
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Michel Dumontier [mailto:michel.d
hi scott,
this message ended up in my organization's quarantined email, which means i
don't see it until i get an email (usually the next day) that allows me to
unquarantine it
but i've been seeing some of the others
cheers,
michael
*From:* Health Care Life Sciences [mailto:w3.h...@gma
expressed genes.
can our bioRDF paper be extended to show how gene sets can be created and
compared using semantic web technologies from raw gene expression data?
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: M. Sc
nless canceled or confirmed before
being on doesn't matter, it still requires someone to remember)
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Joanne Luciano [mailto:jluci...@gmail.com]
*Sent:* Thursday, April 19, 2012 12:08 PM
*To:* Elg
hi lena,
here's the reference to pubcrawl: https://www.systemsbiology.org/pubcrawl
there's a link to the google code site from there.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* Joanne Luciano [mailto:jluci...@gmail.
utility of the Web is by documenting
the reliability and performance of information services. In the area of
biomedical information services,..."
* Q14
grammar (delete 'a'?): "... and to use classes as a values in the
metadata for a graph;"
Section 4:
perhaps change &q
ot;
[1] and goes on to describe how confused and certain every one is about the
notions.
cheers,
michael
[1] http://en.wikipedia.org/wiki/A_priori_and_a_posteriori
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: David Booth [mailto:da...
be converted into RDF.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Oliver Ruebenacker [mailto:cur...@gmail.com]
> Sent: Friday, February 24, 2012 12:14 PM
> To: Bob Futrelle
> Cc: Waard, Anita de A (ELS-NY
hi joanne,
interesting article. but do they use RDF? i don't have a subscription so
couldn't read more than the abstract but my impression was that they used
a general network model, not an RDF graph.
cheers,
michael
Michael Miller
Software Engineer
Institute for Syste
ts to life
sciences as they mature.
> Does anybody knows if such a list exists ?
take a look at SEMTECH sponsors[1]! oracle and topquadrant i know have
built strong support and applications. elsevier and deri were sponsors
also.
cheers,
michael
Michael Miller
Software Engineer
Institute for System
hi scott,
in regards to our conversation about the difference between microarrays and
NGS in the teleconference yesterday, if you look at Figure 1 in the paper,
in step 2), if you substitute NGS for Microarray, it is still valid.
cheers,
michael
> -Original Message-
> From: exp
deshna Das [mailto:s...@seas.harvard.edu]
*Sent:* Wednesday, November 30, 2011 12:30 PM
*To:* Michael Miller
*Cc:* Tim Clark; HCLS IG; scidiscou...@googlegroups.com; Alberto Accomazzi;
Bradley P (ELS-SDG) Allen; Sophia Ananiadou; Philip Bourne; Gully Burns;
Ronald (ELS-SDG) Daniel; Rahul Dave;
racteristics of the samples or
protocol parameters but it is difficult to model that relationship. i've
thought that might be some sort of 'is_a' relationship.
cheers,
michael
*From:* Tim Clark [mailto:tim_cl...@harvard.edu]
*Sent:* Wednesday, November 30, 2011 8:30 AM
miRNA forms (in ccase the value is a Y)?
This would enable easy linking to the expression values!!
Ideas? Suggestions?
Best, Lena
On Tue, Nov 29, 2011 at 11:43 PM, Michael Miller <
michael.mil...@systemsbiology.org> wrote:
hi all,
here's what i found as quantitation types f
hi all,
here's what i found as quantitation types from the TCGA MAGE files for next
gene seq from the DESCRIPTION.txt file (from
C:\data\nci\2011_11_28_tcga\blca\cgcc\bcgsc.ca
\illuminahiseq_mirnase\mirnaseq\bcgsc.ca_BLCA.IlluminaHiSeq_miRNASeq.Level_3.1.0.0):
The .mirna.quantification.txt dat
uld be factor values associated with each factor of the study and
each assay would be associated with a set of factor values, one pre factor,
e.g. for dosage and time factors an assay might be associated with 1mg and
10 seconds.
also, is there any desire to track sample processing?
cheers,
mic
hi lena,
if you could send me some sample files (or point me at them) at the
analyzed level, i could take a look. i'm also going to see if i can find
out how TCGA records the information.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
hi lena,
also, if you find a sparql end point for other sequence
databases/repositories often they will have a one-to-one reference into
ensemble.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* public-semweb-lifesci-requ...@w3.org [mailto
my desk today.
>
> Jim
>
> On Mon, Oct 17, 2011 at 11:23 AM, Michael Miller
> wrote:
> > hi jim,
> >
> > does 12:30 edt work for you, sounds like it will work for lena.
> >
> > cheers,
> > michael
> >
> >> -Original Message-
> > join us next week.
> >
> > Cheers,
> > Scott
> >
> > On Mon, Oct 17, 2011 at 5:06 PM, Michael Miller
> > wrote:
> >> hi jim,
> >>
> >> i didn't see any notice for one so i assumed not.
> >>
> >>
hi jim,
i didn't see any notice for one so i assumed not.
cheers,
michael
> -Original Message-
> From: expression...@googlegroups.com
> [mailto:expression...@googlegroups.com] On Behalf Of Jim McCusker
> Sent: Monday, October 17, 2011 8:04 AM
> To: expression...@googlegroups.com
> Cc: HC
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
*From:* public-semweb-lifesci-requ...@w3.org [mailto:
public-semweb-lifesci-requ...@w3.org] *On Behalf Of *David Shotton
*Sent:* Wednesday, October 05, 2011 9:46 AM
*To:* Waard, Anita de A (ELS-AMS)
*Cc:* Tim Clar
hi all,
peter, nice article, it matches well my experience.
one thing to note is that, in this context, that the mapping is
(hopefully) a one shot deal that then can be used into the future without
much change, e.g. the bio* efforts that map to sequence database records.
also if one has a standar
two,
if a museum with a missing piece didn't have authorization from the museum
it came from as part of the provenance, they are obliged to return it. i
would also think it would be important facet for certain queries.
cheers,
michael
Michael Miller
Software Engineer
Institute for
cCusker [mailto:james.mccus...@yale.edu]
> Sent: Wednesday, August 17, 2011 9:35 AM
> To: Helena Deus
> Cc: Michael Miller; W3C HCLSIG hcls
> Subject: Re: "molar" for concentration
>
> Ah, I thought you were looking for predicates for datatype properties.
> This makes m
atype. in programming terms i
define a variable to be of a certain datatype:
int count = 5
what does it mean to say,
Molar solution = ??
cheers,
michael
*From:* Helena Deus [mailto:helenad...@gmail.com]
*Sent:* Tuesday, August 16, 2011 3:17 PM
*To:* Michael Miller
*Cc:* Jim McCusker
hi all,
i did take a quick look at MUO and it does seem sane.
"For instance, MUO has the ability to assert units of measure on n-ary
observations, ..."
and MUO appears based on SI.
cheers,
michael
> -Original Message-
> From: public-semweb-lifesci-requ...@w3.org [mailto:public-semweb-
hi all,
how do these ontologies map to SI units? i would pick the one that maps/is
based on most closely.
...across a URI for datatype "M"
lena, did you mean 'unit' instead of 'datatype'?
cheers,
michael
Michael Miller
Software Engineer
Institute
hi all,
my regrets, i'm under deadline pressure for the project i'm currently
working on and am attending a course on the TPP tools for mass spec this
week.
" b) (NCBI gene id vs Ensembl gene id)"
this is an issue that goes beyond just gene expression. the common sequence
databases (to wh
LSIG_BioRDF_Subgroup/MicroarrayExperimentContext.
cheers,
michael
> -Original Message-
> From: Helen Parkinson [mailto:parkin...@ebi.ac.uk]
> Sent: Friday, July 08, 2011 7:44 AM
> To: Michael Miller
> Cc: tomasz.adamus...@ebi.ac.uk; public-semweb-lifesci@w3.org
> Subject: Re: GXA triples
>
>
. is there an overall, across the factors, differential measurement
(e.g. limma) or am i missing something?
are you also planning on RDFizing the information on the experiment (the
idf and sdrf info) that is in ArrayExpress?
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems
n human but can
probably be extended):
http://www.archivesofpathology.org/doi/pdf/10.1043/1543-2165%282007%29131%
5B852%3ACLRIMP%5D2.0.CO%3B2
this came from the HL7 Clinical Genomics mailing list.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
- Original Mes
hi all,
regrets also and +1 to both of lena's points
cheers,
michael
*From:* public-semweb-lifesci-requ...@w3.org [mailto:
public-semweb-lifesci-requ...@w3.org] *On Behalf Of *Helena Deus
*Sent:* Thursday, June 16, 2011 7:56 AM
*To:* Eric Prud'hommeaux
*Cc:* public-semweb-lifesci@w3.org
*
hi paul,
i did a little research on this a little while ago. you should have plenty
of power.
if you're research i hear oracle offers their spatial triple store for free,
running jena on top of a storage system like BigOWLIM is also quite popular
check out Berlin SPARQL benchmark (
http:/
y.html
> 2. and set path to endpoint to: endpoint/gxa
see below for more info.
cheers,
michael
Michael Miller
Software Engineer
Institute for Systems Biology
> -Original Message-
> From: Jun Zhao [mailto:jun.z...@zoo.ox.ac.uk]
> Sent: Thursday, June 09, 2011 5:16 AM
> T
hi all,
> Many of us have expressed interest in personalized medicine in the
> last year. If you define personalized medicine as the application of
> molecular knowledge about a particular patient to tailor therapeutic
> choices for that patient, it is simply the future of medicine. And the
> futu
hi david and matthais,
"(for example, the original idea of BioRDF was mainly to convert biomedical
data to RDF, but over the years this also became a major focus of other task
forces such as LODD)"
along david's point, i would argue that because the problem the two groups
are trying to solve, Bio
hi joanne,
+1!
cheers,
michael
> -Original Message-
> From: Joanne Luciano (gmail) [mailto:jluci...@gmail.com]
> Sent: Thursday, May 26, 2011 9:31 AM
> To: Michael Miller
> Cc: Jim McCusker; Chris Baker; w3c semweb HCLS
> Subject: Re: Minimum information about a mutati
lem space gives us a lot to work
on.
cheers,
michael
*From:* Tim Clark [mailto:twcl...@nmr.mgh.harvard.edu]
*Sent:* Thursday, May 26, 2011 8:56 AM
*To:* Michael Miller
*Cc:* HCLS IG
*Subject:* Re: HCLS chartering/next steps Thur 26 May
HI Michael,
As I said, problem focused activitie
...
michael
> -Original Message-
> From: Jim McCusker [mailto:james.mccus...@yale.edu]
> Sent: Thursday, May 26, 2011 8:45 AM
> To: Michael Miller
> Cc: Chris Baker; w3c semweb HCLS
> Subject: Re: Minimum information about a mutation
>
> I'm looking for an
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