Congratulations! I look forward to working with all of you and others in the
coming years.
-Kei
Quoting Susie M Stephens <[EMAIL PROTECTED]>:
>
>
> Dear HCLSIG folks,
>
> Chime, Scott and I are very excited to be co-chairing the new HCLSIG from
> June 1, and working closely with you all over th
Quoting Alan Ruttenberg <[EMAIL PROTECTED]>:
>
> I wonder if we could include a line remembering Bill Bug in the KB
> note. Something simple along the lines of
> "In memory of our friend and colleague William Bug, Ontological
> Engineer"
>
> -Alan
>
>
>
+1
-Kei
In the context of neuroscience, I hope things like "long-term depression"
(http://en.wikipedia.org/wiki/Long-term_depression) won't get the system
confused. By the way, in mammalian phenotype ontology, there is a term called
"reduced long-term depression"
-Kei
Quoting "Kashyap, Vipul" <[EMAIL PR
Quoting Matthias Samwald <[EMAIL PROTECTED]>:
> Maybe we/you could turn it into a journal publication / review? I guess that
> would cause a sudden increase of interest by HCLSIG members with an academic
> background :)
>
It would be nice if HCLSIG can produce a paper (or more than one paper) in
Hi Tim et al.,
I think it would be great if more details about SWAN can be added. The HCLS
ecosystem consists of scientists, patients, doctors, government agencies,
publishers, etc. Creating/maintaining a balance in this digital age across
national boundaries is challenging/interesting.
Speaking
Hi Scott,
The note looks good. The Alzheimer's disease (AD) use case is interesting. As a
future direction, you and others might consider expanding the AD use case to
make it more realistic and scientifically interesting. In fact, SenseLab is
heading in the direction of studying the molecular mec
Quoting Matthias Samwald <[EMAIL PROTECTED]>:
>
>
> > 1. In the "Future directions and plans" section, I would add the following
> > sentences at the beginning. "In creating an ontology, one may consider
> > using
> > the pre-coordinated approach and/or the post-coordinated approach. It will
> >
Hi Matthias,
To reflect the recent discussions on the SenseLab note, I would like to suggest
the following minor edits:
1. In the "Future directions and plans" section, I would add the following
sentences at the beginning. "In creating an ontology, one may consider using
the pre-coordinated appr
I always remember his long but passionate/knowledgeable emails. He will be
dearly missed.
-Kei
Quoting eric neumann <[EMAIL PROTECTED]>:
> I recently was informed of this sad and unexpected news... Bill contributed
> to many important efforts including HCLSIG-- we will miss him greatly.
>
> -Er
I experienced the same problem initially, but I later found that the URL should
be: http://www.e-mds.com/solutions/drug_database/drugdb.html
Apparently, there is a white space before drugdb.html
-Kei
Quoting Daniel Rubin <[EMAIL PROTECTED]>:
>
> I might be able to help. But I don't seem able t
Hi Eric,
Thanks for your complimemnt. It's really the help and support provided by many
people including you, Carole, Amit, Adam, Susie, Vipul, ... which made the
workshop successful.
Unfortunately, I have to leave Banff in the morning of Thursday. I hope you and
others will have a good follow-u
Hi,
We just finished a round of revision of NeuronDB OWL ontology based on
the feedback from people like Matthias, Alan, Bill, ... (thanks to
them). We also established mapping to other ontologies like BAMS,
Birnlex, BFO, OBI, etc. (thanks to Don for helping to establish mapping
of some of t
Hi Ivan,
First of all, I'd like to congratulate Vipul on his book chapter. For
the HCLS paper, last time I was told that it would be published some
time in April in a supplement issue of BMC Bioinformatics. I'll keep you
and others informed once I know the exact date of publication.
Best,
Alan,
Since CA1 pyramidal neuron was mentioned in the AD/PD use case, I just
wonder at least for educational purposes (especially those who are not
neuroscientists) to see the image or even some animation (aha, cool,
etc) of such a neuron. Also, the neuron morpholoy may have research
value a
Hi Bill,
Thanks for the comments. I look forward to working with you and others
in the community to make NeuronDB (SenseLab in general) as broadly and
semantically usable as possible.
Cheers,
-Kei
William Bug wrote:
Hi Kei,
This is wonderful. It will really help others across the fiel
Hi Eric,
I was the ?. I attended for about 1.5 hours of the call and then I had
to leave quietly (I didn't want to disturb the discussion) for teaching
a class. I think the suggestions are great. It's important to show the
benefits that SW can potentially bring to the healthcare and life
sci
certain June, Gwen, or Elisabeth could help us
identify genes whose expression correlates with high levels of ADDL
species (most interesting question given current AD research) or
with other APP related macromolecules or plaques. I'm not certain
how you'd ask the same question
Alan et al.,
In addition to mapping to brain regions, what seems to be also missing
is some kind of brain coordinates. I thought one major advanatage of
using Google Map is the ability to issue GIS-like queries. With this
type queries, one can potentially query something like finding expresse
Hi Vipul,
Yes, that's exactly what I meant.
-Kei
Kashyap, Vipul wrote:
I think what Kei is asking for (correct me if I got it wrong) is that he would
like the ability to define something of the following sort:
EquivalentClass(X, intersectionOf(Y, Restriction(locatedinBrainRegion
allValuesFr
Just want to clarify that the ontology should be generic enough to
handle different neurological diseases such as AD and PD. Also, it may
be possible to integrate the ontology (although it's not OWL-based) into
the current bioont effort.
Best,
-Kei
kc28 wrote:
Hi June, Don, et al
Hi June, Don, et al,
As part of the BioRDF's SenseLab task, we have recently created an RDFS
ontology for BrainPharm (a subdatabase of SenseLab). The ontology can be
used to model information about the effect of drugs on pathological (or
molecular) mechanisms (which involve neuronal propertie
William Bug wrote:
Here, here.
I also would join Chimezie in saying I don't want to ruffle feathers
on this issue, but if either NCBO and/or NLM/NCBI would start
experimenting with a more broadly deployed LSID Registry & Resolution
Service (NCBO for ontologies and NLM/NCBI for BioRDF data s
Hi,
Are we talking about versioning at a very high granularity level (e.g.,
a URI that points to an entire ontology)? Should we also consider
versioning at finer granularity levels such as the levels of concepts or
terms and their relationships within an ontology? Some of these
concepts, ter
Hi Joanne,
I'll work with Alan and others based on your suggestions.
Thanks,
-Kei
Joanne Luciano wrote:
Hi Kei,
I made my edits on the google page this morning, so this becomes a
belated request for deadline extension.
Included here:
1.3.2. Standards as Applications of Semantic Web Te
of kc28
Sent: Sun 12/10/2006 11:09 PM
To: Tim Clark
Cc: public-semweb-lifesci; Carole Goble
Subject: Re: Book on Semantic Web and Life Sciences published
Thanks for the congrats, Tim. I also thank Carole for introducing the
book to the SWHCLSIG group.
-Kei
Tim Clark wrote:
Congrats, Kei
Hi Marco et al.,
It is also possible that a person can have multiple roles (e.g.,
researcher and teacher). Are there standard vocabularies that we can use
to describe roles, for example? There might be a temporal aspect as
well. For example, a person at one point was a postdoc but later becam
Hi Michael et al,
The following tools, for example, are available for microarray gene
annotation.
SOURCE -- http://nar.oxfordjournals.org/cgi/content/full/31/1/219
KARMA -- http://nar.oxfordjournals.org/cgi/content/full/32/suppl_2/W441
RESOURCERER -- http://pga.tigr.org/tigr-scripts/magic/r1.
Hi All,
As part of the SenseLab task
(ttp://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/SenseLab), we've
recently published a paper in SeS2006 and created a demo called
"AlzPharm", which demonstrates how to use RDF (Oracle) to link
drug-related information between SenseLab/BrainPharm and
Hi Vipul,
For ontology mapping, I can try to talk about the two mapping examples
between NeuronDB and CoCoDat.
Cheers,
-Kei
Kashyap, Vipul wrote:
Phone: +1 617 761 6200, conference 24668 ("BIONT")
IRC: irc://irc.w3.org:6665/hcls
Browser-based IRC client: http://www.w3.org/2001/01/cgi-irc
Hi All,
I second Tim's suggestions. This is a really community effort to move
this important SW component forward.
Best,
-Kei
Tim Clark wrote:
Hi All,
I think Susie is performing a valuable service which we all respect
and which may help to advance the discussion. HOWEVER...
... I S
Forgot to say that I hope your kidney stone issues get resolved much
sooner than these ontological issues. :-)
-Kei
John Rumble wrote:
An unwritten rule about higher level ontologies is that they reflect
our knowledge today, not tomorrow. As knowledge evolves, the upper
level ontologies, e
This brings up an interesting issue -- how ontological evolution would
impact mapping or integration of overlapping ontologies. I believe it's
quite a research challenge. We might need to incorporate the notion of
versioning into the ontological structure. For example, what versions of
the pr
International Workshop on Semantic e-Science
4th September, 2006, Beijing, China. (SeS2006), co-located with ASWC2006
http://km.aifb.uni-karlsruhe.de/ws/SeS2006/
===Call for Papers
In the successful series of Semantic Grid and e-Sc
ncecommons.org/resources.
***see the excellent article by Richard Nelson posted by John
Wilbanks on the Science Commons weblog a few months back [http://
sciencecommons.org/weblog/archive/2006/02/15/richard-nelson-on-the-
scientific-commons] for an excellent treatment of how this directly
impedes
- ontology to SKOS (an OWL ontology
used for the representation of taxonomies / theasauri). It will
be added to the extension of the bio-zen ontologies framework
[1]. I will keep you updated.
kind regards,
Matthias Samwald
[1] http://neuroscientific.net/index.php?id=download
On Mon
For more up-to-date information about neuronames and related tools,
please visit: http://braininfo.rprc.washington.edu/. While building our
own open neural anatomy is one option, getting the neuroscientist (e.g.,
braininfo people) involved if possible may be another option (outreach
to the ne
For more up-to-date information about neuronames and related tools,
please visit: http://braininfo.rprc.washington.edu/. While building our
own open neural anatomy is one option, getting the neuroscientist (e.g.,
braininfo people) involved if possible is another option (outreach to
the neuros
Hi,
For those of you who are interested, the powerpoint presentation of our
pilot OWL-based integration of NeuronDB and CoCoDat is available at:
http://twiki.med.yale.edu/kei_web/sw_group/hbp_2006_4_24_sw_neurodb_int2.ppt
-Kei
Donald Doherty wrote:
The Human Brain Project (HBP) meeting las
Hi,
Below is the link to the ppt senselab task description.
http://twiki.med.yale.edu/kei_web/sw_group/Semantic_Web_SenseLab_Task2.ppt
Thanks,
-Kei
Susie Stephens wrote:
Don't forget Monday's BioRDF call.
_Agenda_
- Brian Osborne and Kei Cheung will be giving progress reports on
their t
Hi Davide,
You can download the full article at:
http://twiki.med.yale.edu/kei_web/neurotext_neuroinformatics.pdf
-Kei
Davide Zaccagnini wrote:
Thanks Kei,
I linked it to the NLP-RDF wiki page. Is it possible to have access to the
full paper?
Davide
-Original Message-
From: [EMA
Hi Tim,
I agree with what you said. We should consider Alzforum (Alzheimer
Disease) and come up with a use case that is practical to
neuroscientists. I talked to Gordon Shepherd (who is a neuroscientist
and the PI of SenseLab) about such a use case for our SenseLab task. He
suggested the fo
Hi,
I have written a proposal of the SenseLab task, which is described at
the following URL:
http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Tasks/SenseLab
The SenseLab project (http://senselab.med.yale.edu/senselab/) is a long
term effort that builds integrated, multidisciplinary models of
Hi,
I found the following link interesting, as it describes several ways of
mapping a table to RDF:
http://www.w3.org/2001/sw/Europe/reports/scalable_rdbms_mapping_report/#sec-mapping
YeastHub (http://yeasthub.gersteinlab.org) provides an interactive web
interface to allow the user to regis
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