hi helen,
can you elaborate a bit more on this, i'm not sure exactly what you
mean. what makes the overhead high and for who and what kind of errors
does the text mining produce? what's the metric for performance?
cheers,
michael
Michael Miller
Lead Software Developer
Rosetta Biosoftware Busin
hi all,
yes, at http://bioportal.bioontology.org/ontologies/40510. one odd
thing is that the link to the latest 1.3 is there three times and the
topmost explore link caused an error.
cheers,
michael
Michael Miller
Lead Software Developer
Rosetta Biosoftware Business Unit
www.rosettabio.com
> -
hi kei,
there is already something better than RDFa tags in MAGE-ML, the
OntologyEntry tags. Their purpose is exactly to provide the information
to link to the semantic web. The examples you provided from NIH are
well annotated with those tags.
cheers,
michael
Michael Miller
Lead Software Deve
lude the originating BioSource annotations
that aren't necessarily factor values?
cheers,
michael
> -Original Message-
> From: Helen Parkinson [mailto:parki...@ebi.ac.uk]
> Sent: Thursday, July 23, 2009 11:11 AM
> To: Miller, Michael D (Rosetta)
> Cc: Kei Cheung;
hi kei and helen,
like helen, i've been following the HCLS working groups with great
interest. as one of the designers, with helen, of the MAGE-ML and
MAGE-TAB specs i might be able to provide a little technical insight
into the formats.
(from helen)
"This is probably as we don't have data - her
hi all,
i agree strongly with Chimezie, there are much better methodologies to
do quantitative science. but once a result is arrived at (the measured
distance between two cities as opposed to the process of measuring the
distance), that can be captured by ontologies.
cheers,
michael
Michael Mil
hi all,
samw...@gmx.at wrote:
>> Can any one name a real world example of where confusion between an
>> entity and its record was issue?
>>
>
> I would say that 80% of the RDF/OWL ontologies lingering somewhere on the web
> are examples. They are just so ill-designed that nobody wants to u
hi eric,
this is probably a bit naive but i can think of two examples.
one is that i often do paper examples (i'm a bit of a luddite) when i'm
working out ideas so i might sketch out some object that i will then
annotate from OWL ontologies to 'see how it works.' this might even be
in a group
hi all,
i've also been lurking, even more so than phil. priorities prevent me
from being more active but without access to this list i would not be
the proponent of SW at my work that i am.
(if the list is restricted, will public be removed from the list name?)
cheers,
michael
Michael Miller
hi all,
i agree with michel's second point ("Concrete suggestions welcome.") but
i also think it is important, since this document can be used as a guide
by others, to point out pitfalls and problems that a new user will face.
in that vein it might be good, as suggested, to provide examples of
hi all,
yes, i also agree that these are great points, except for a quibble.
"Data models like schemas, structures, and data formats are
implementation details"
in Model Driven Architecture (MDA), the Platform Independent Model data
model is free of implementation details. as a developer who
hi all,
here is the link to the RFI:
http://www.omg.org/cgi-bin/doc?ontology/2008-02-01
cheers,
michael
From: Miller, Michael D (Rosetta)
Sent: Friday, February 22, 2008 7:49 AM
To: public-semweb-lifesci@w3.org hcls
Subject
hi all,
this may be of interest to some, it's an OMG Ontology RFI on "Ontology
Management Information" which is still in draft form but solicits
comments.
cheers,
michael
Michael Miller
Lead Software Developer
Rosetta Biosoftware Business Unit
www.rosettabio.com
hi susie,
> The folks at Lilly who developed the ontology did review a number of
> existing ontologies, but they didn't meet our needs.
this is the hard part of getting standardization accepted. "but they didn't
meet our needs" will always seem to be true because the most expedient way to
or
hi all,
i agree with much of what matthias has to say, including
> Many of the datatype properties in this ontology look very
> interesting and
> might provide requirements for other ontologies.
having been one of the editors of FuGE, i'm wondering if there are any
tools that can translate U
G spec apply.
cheers,
michael
> -Original Message-
> From: Hilmar Lapp [mailto:[EMAIL PROTECTED]
> Sent: Sunday, August 26, 2007 8:40 AM
> To: [EMAIL PROTECTED]
> Cc: Miller, Michael D (Rosetta); Eric Jain; Ricardo Pereira;
> public-semweb-lifesci; Sean Martin
> Subject: Re: [
hi all,
i forgot the URL (or is it a URI or URN?)
cheers,
michael
http://www.omg.org/technology/documents/formal/life_sciences.htm
> -Original Message-
> From: [EMAIL PROTECTED]
> [mailto:[EMAIL PROTECTED] On Behalf Of
> Miller, Michael D (Rosetta)
> Sent: Saturday,
hi all,
> Is there any chance that this will find it's way back into
> the LSID spec?
great thought but...
the spec is an OMG spec through the Life Sciences working group. i3c
worked on it in collaboration with this group but i3c is dead and the
members of the Life Sciences group most interes
> -Original Message-
> From: Kei Cheung [mailto:[EMAIL PROTECTED]
> Sent: Saturday, June 02, 2007 7:26 AM
> To: Miller, Michael D (Rosetta)
> Cc: William Bug; Smith, Barry; Kashyap, Vipul;
> [EMAIL PROTECTED]; public-semweb-lifesci@w3.org;
> [EMAIL PROTECTED]; Pau
hi bill and kei,
i've changed the subject, since this is moving away from the original
topic.
"Yes - you are right, of course - right now the TGEN infrastructure for
the consortium is committed to providing MAGE-ML instances [1]."
that's great.
"the FuGE-stk [2] will provide a means to "con
Hi Xiaoshu,
Getting back to an earlier point in this discussion...
> Well, how can a computer knows my intension about the parts
> that I don't
> "use/disagree"? But, I think, if I disagree one portion of
> the ontology, I
> certainly would not use the other part of the ontology at all
> sin
Hi Alan,
What you are describing is described in MAGE-OM/MAGE-ML, as a UML model
to capture the real world aspects of running a microarray experiment.
Typically at the end of this process a set of genes is identified as
being interesting for some reason and one wants to know more about this
set
Title: Message
Hi
Sean,
Thanks
for your clarification, exactly what John's e-mail brought to my mind but much
better explained.
A
similar use case might be a gene _expression_ experiment that is sent into
ArrayExpress. At some point someone who downloads the experiment discovers
that
Hi John,
Another version of this problem has existed in the relational world when
importing records from the outside world, which is 'when should an
existing record be updated and when should a new record be created.'
Because the record is coming from the outside world, an alternative key
must be
2006 6:55 PM
> To: Miller, Michael D (Rosetta)
> Cc: Alan Ruttenberg; Mark Wilkinson;
> public-semweb-lifesci@w3.org; [EMAIL PROTECTED]
> Subject: RE: A precedent suggesting a compromise for the
> SWHCLS IG Best Practices (ARK)
>
>
> Quoting "Miller, Michael D (Rosetta)&quo
Hi All,
> I frequently see genes, transcripts, dna and mrna and their
> sequences, proteins, protein sequences, transcripts, and peptides
> all confusedly identified by overlapping identifiers. I don't
> see how
> any identifier scheme, in itself, lsid's included, currently fixes
> this
Hi Kei,
> It means that things might not overlap at
> the same level, but may overlap at different levels between different
> ontologies (entity modeled at a higher level of granularity may be
> mapped to one modeled at a lower level of granularity) .
Excellent point, and I just want to add
cheers,
Michael
(but the blog is interesting!)
> -Original Message-
> From: Henry Story [mailto:[EMAIL PROTECTED]
> Sent: Wednesday, July 26, 2006 8:50 AM
> To: Miller, Michael D (Rosetta)
> Cc: w3c hcls semweb; Semantic Web
> Subject: Re: Semantic content negot
Hi Xiaoshu,
I think many excellent points and discussions are being made but I'm
feeling frustrated because, in the 80/20 paradigm (80% is easy to
implement the last 20% is much harder), these discussions are in the
20%, I might even venture that they are in the top 5%.
The vast majority of the
Hi Xiaoshu,
> because the
> designer of one ontology would have no idea how it is going
> to be used.
I agree with you here but ...
> And I think how to treat a set of RDF
> triples, i.e., in what kind of closure is a consumer's issue
... I believe this is a semantic web issue also, but at a
Hi Tim,
"We wrote a note to Michael Miller about this, but he wasn't very
interested"
Not so much not interested as 1) I barely have the time to keep up with
the e-mail threads (which are very useful and thought provoking) and 2)
it's not germane to my priorities here.
What I hope to peck away
Title: Message
Hi
All,
(from
Sean)
"The issues of broken links is a difficult one
because once the primary source at a particular location disappears you have
nothing left to go on to find a copy of the thing named besides what you can
find in the WayBack machine or perhaps a Google
ca
Hi All,
> I would think that an author of an ontology of this size
> would want to consider fragmenting the ontology (perhaps by
> sub-domains) and linking them with owl:imports. In such a
> scenario, the
> terms could simply be identifiers asserted within each
> ontology fragment
> and on
als and for the Experiments that isn't being
exploited yet but could easily to look for interesting matches today
between ArrayExpress, GEO, NCI and other repositories.
cheers,
Michael
> -Original Message-
> From: Alan Rector [mailto:[EMAIL PROTECTED]
> Sent: Saturday, Jul
Title: Message
Hi
All,
"On one end, some researchers want a
quick and easy way to share an experiment, e.g. simply decompose an experiment
to hypothesis, data, results, procedure, protocols used, who did it, what
project it belongs to, etc."
Even
stronger, at a high level this is what a
6th Street, Charlestown, MA 02129
http://www.mindinformatics.org
--
On Jul 5, 2006, at 7:38 PM, Miller, Michael D (Rosetta) wrote:
Hi Eric,
Just wanted to point out how this overlap
Title: Message
Hi
Eric,
Just
wanted to point out how this overlaps with the current FuGE (http://fuge.sourceforge.net/) and FUGO
(http://fugo.sourceforge.net/)
efforts. These are focused on systems biology and are intended to provide
the underpinnings of reporting gene _expression_, gel,
Hi All,
Just to add a quick 2c to what Bill and others have to say about
practical use cases.
Since we at Rosetta Biosoftware develop applications for end users we
are rather neutral to how we can get annotation, we're happy with just
about anything. The key for us is that our users want the
an
r, Michael D (Rosetta)
> Cc: public-semweb-lifesci@w3.org
> Subject: Re: scientific publishing task force update
>
>
> "Eperimental" looks to me like a typo, it should be "Experimental"?
>
> Cheers,
>
> -Kei
>
> Miller, Michael D (Rosetta) wrote:
&
Hi All,
> It might be interesting to compare this with FUGE.
Yes, there's definite overlap.
Also wanted to pass along one of the top-level classes:
"http://www.hozo.jp/owl/EXPOApr19.xml/EperimentalDesignTask";>"
I'm not exactly sure what "Eperimental" means!
cheers,
Michael
> -Original
fesci@w3.org
> Subject: Re: BioRDF [Telcon]: slides for the UMLS presentation
>
>
>
> Miller, Michael D (Rosetta) wrote:
>
> > One other issue is that the actual objects in a microarray
> experiment
> > are for the most part one offs--i.e. a chip is a chip, it
Hi Marco,
I'm hopeful of putting together a usecase for how the annotation of
MAGE-ML documents with ontology terms makes sense for the semantic
web--I usually end by saying that once the ontology information is
loaded into the local data store, knowledge based tools can be used on
them.
It look
> From: kei cheung [mailto:[EMAIL PROTECTED]
> Sent: Tuesday, June 06, 2006 10:34 AM
> To: Miller, Michael D (Rosetta)
> Cc: Alan Ruttenberg; [EMAIL PROTECTED];
> [EMAIL PROTECTED]; Daniel Rubin;
> public-semweb-lifesci@w3.org; Matthew Cockerill
> Subject: Re: MGED/Fu
7;m a believer of
> incrementality, we probably should aim at something small and
> simple to
> begin with and work our way up.
>
> Cheers,
>
> -Kei
>
> Miller, Michael D (Rosetta) wrote:
>
> >Hi Kei and Larry,
> >
> >Well, since I'm on t
Hi All,
> Thanks for pointing us to FuGO. To me, it seems like that the FuGO
> community is currently defining an upper ontology that can be
> universally used to describe different types of genomic/proteomic
> experiments including microarray experiments.
This, I believe, is their goal.
>
as rooms for
> ontological
> improvement. As Larry suggested, we would have a better luck
> if we can
> work with the MGED consortium.
>
> Cheers,
>
> -Kei
>
> Miller, Michael D (Rosetta) wrote:
>
> >Hi Kei,
> >
> >
> >
>
cheers,
Michael
> -Original Message-
> From: kei cheung [mailto:[EMAIL PROTECTED]
> Sent: Tuesday, June 06, 2006 7:54 AM
> To: Miller, Michael D (Rosetta)
> Cc: Alan Ruttenberg; public-semweb-lifesci@w3.org
> Subject: Re: MGED/FuGO. was: Re: BioRDF [Telcon]: slides for
> the UM
l Message-
> From: Benjamin Good [mailto:[EMAIL PROTECTED]
> Sent: Monday, June 05, 2006 10:45 PM
> To: Miller, Michael D (Rosetta)
> Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED]; public-semweb-lifesci
> Subject: Re: BioRDF [Telcon]: slides for the UMLS presentation
>
>
&g
Hi Alan and All,
The MGED Ontology is now available as OWL. There has been a recent
revision to correct some of the formal problems such an early
implementation has had.
http://mged.sourceforge.net/ontologies/MGEDOntology.owl
Also, the FuGO project would love any feedback, thanks for pointing
: Benjamin Good [mailto:[EMAIL PROTECTED]
> Sent: Monday, June 05, 2006 12:52 PM
> To: Miller, Michael D (Rosetta)
> Cc: [EMAIL PROTECTED]; [EMAIL PROTECTED];
> public-semweb-lifesci@w3.org
> Subject: Re: BioRDF [Telcon]: slides for the UMLS presentation
>
>
> Hi,
>
>
Hi All,
> But presumably the relations which characterize the structure
> of UMLS could be given their own URIs, no?
> Along with the concepts themselves.
>
> And then UMLS could then be expressed in RDF, using UMLS
> specific relations, rather than standard OWL relations.
This, of course, wo
Hi Mark,
Just to add a bit to Steve's reply...
> > If the only thing that comes from the LSID spec is a notion of an
> > identifier
> > syntax that becomes widely adopted by bioinformatics data
> providers, it
> > would be a huge success, ...
In the gene expression domain, best practice stat
Hi Alan,
Interesting use case.
> are often matches at this level of description. The downside is that
> you lose the superclass relations that you have in taxonomy,
One would think that the intersection/merging of the results from a
query to the wikipedia and a query from taxonomy might do t
Hi All,
> 2. Squeezing legacy identifiers into LSIDs can be tricky; some life
> sciences databases use colons in their identifiers (GO and MGD), or
> separate version numbers with dots (EMBL).
One can use the URI escape sequence syntax for these.
cheers,
Michael
Michael Miller
Lead Software
Hi Roger,
I believe I can provide some comfort for the scalability issue with our
experience with MAGE-ML.
One thing that greatly alleviates the problem is to use compress
writers/readers (Java provides nice ones), for regularly formatted XML
this can compress to 2-10% the original size.
> 3 -
Hi All,
I've also (as I think I've said) found OMG proposed specification
"Ontology Definition Metamodel" very useful for thinking of practical
ways of dealing with Ontologies, especially for referencing from the
non-onotolgy UML FuGE (Functional Genomics) model. I've included an
image of the cla
Title: Message
Hi Jim
and Vipul,
"If all three of us published to the
Web, and used common URIs (or a third party expressed equivalences) then the
system as a whole would have the information..."
Just
to echo what Jim is saying, the Life Science Identifier (LSID), a type of
URI, basical
Title: Message
Hi
Vipul,
Here's
a paper at EBI that illustrates some of what they are thinking about in terms
of the semantic web.
http://www.ebi.ac.uk/mygrid/mygrid.pdf
the
myGrid home page (which I'm sure people are familiar with)
http://www.mygrid.org.uk/
When I
was at a MGED M
Hi All,
For me, my interest was in the transformation of an RDF XML document to
the equivalent (to some measure of equivalent) UML XML document and back
to describe/define an ontology.
The practical problem with the RDF XML notation we ran into for our use
is that many of the XML element names a
Hi Xiaoshu,
http://www.omg.org/docs/ad/05-09-08.pdf
Because it is still being evaluated, this might only be available from
the OMG website to OMG members.
It is a very thorough document, well thought out. They worked with many
of the W3C OWL and RDF experts.
cheers,
Michael
> -Original M
Hi All,
> So RDF = UML 4.0? :-)
At the OMG there is a proposed Ontology Definition Metamodel that IBM
and SandPiper are submitting that takes an excellent look at this issue.
cheers,
Michael
Michael Miller
Lead Software Developer
Rosetta Biosoftware Business Unit
www.rosettabio.com
> -Or
Hi All,
my quick 2c
> I'd argue that most information resources are indeed
> semi-structured. The
> human brain is only able to meta-categorize resources based on its
> structured aspects (markup and structural metadata), its informational
> content (its aboutness), and context (environmental m
Hi Vipul and Adrian,
> However, in order for
> these ontological
> artifacts to be useful to practitioners, we have to adopt the
> "model of use" perspective as well.
>From my (admittedly limited) point of view, for microarray experiments,
our use case for ontologies is that we wish to attach
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