Obviously the current URLs aren't very linked data friendly. E.g.
http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:026
We would most likely end up having the prefix be something under the GO
purl, e.g.
http://purl.obolibrary.org/obo/go/reference/
It hasn't been our highest priority.
The OBO library subset of bio-ontologies have URIs that conform to linked data
norms.
E.g.
http://purl.obolibrary.org/obo/GO_0006264 - mitochondrial DNA replication
http://purl.obolibrary.org/obo/CL_617 - GABAergic neuron
http://purl.obolibrary.org/obo/MP_0002766 - situs inversus
http://pur
Apologies if this has been covered already I haven't been following the whole
discussion.
Genome variant data is just a subset of genome data. My understanding is that
the semweb BioHackathon group looked at a variety of different kinds of genomic
data and came up with FALDO[1]. This model loo
Hi Michael
I can't seem to connect to the triplestore.
Have you considered adding associations between OMIM and phenotype ontology
classes? These can be downloaded from http://www.human-phenotype-ontology.org/
as tab delimited files that can trivially be converted to an rdf model of
choice (we
Hi Bin,
We use OWL reasoning extensively within the GO consortium, primarily
for automated classification of new terms, and for validation of the
ontology and gene associations. For some more background, see
PMID:20152934 and PMID:20973947 (note that in those papers we used
some custom reasoning t
On Nov 7, 2011, at 2:03 PM, M. Scott Marshall wrote:
> Dear BioRDF,
> I've pasted the minutes from our last meeting below. You can find them here:
> http://www.w3.org/2011/10/24-HCLS-minutes.html
> Part of the discussion that isn't available in the minutes below was
> agreement that NGS express
e a general purpose macro language as a W3C standard, from
which these simpler approaches could be defined.
On May 4, 2011, at 2:30 PM, Mark Wilkinson wrote:
> Chris, that's beautiful!! Well done!
>
>
> M
>
>
> On Wed, 04 May 2011 14:27:30 -0700, Chris Mungall wrote:
&
A number of ontologies are starting to use "shortcut" relations. These are
expanded to more complex class expressions prior to OWL reasoning:
http://precedings.nature.com/documents/5292/version/1
http://berkeleybop.org/~cjm/obo2owl/obo-syntax.html#7
On May 4, 2011, at 9:00 AM, Mark Wilkinson wro
On Apr 16, 2009, at 4:06 AM, Matthias Samwald wrote:
__ DBpedia - OBO mapping __
I have created a script that generates a mapping between OBO
ontologies and DBpedia, based on cross-references to Wikipedia
contained in some OBO ontologies. This amounts to a meager ~430
mapping relations.
d this metadata. When OWL2 is
established the official mapping will switch to using axiom
annotations instead of the n-ary relations pattern.
-=Michel=-
-Original Message-
From: public-semweb-lifesci-requ...@w3.org [mailto:public-semweb-
lifesci-requ...@w3.org] On Behalf Of Chr
On Mar 26, 2009, at 8:33 AM, Michel_Dumontier wrote:
The Gene Ontology says a Protein (GO:0003675) is a Thing (the entity
was removed, but then later added so the identifier wouldn't be
reused)
More accurately: very early versions of the GO had a term named
"protein", but this was obsolet
I don't know that much about how DBpedia is generated, but many OBO
Ontologies have reasonably complete xref mappings to Wikipedia.
GO
ENVO
PATO
UBERON
...
plus a few more
It would presumably be a simple syntactic translation to dbpedia URIs
On Mar 25, 2009, at 3:03 PM, Matthias Samwald wr
iProt records for DRs for free.
-Kei
Alan Ruttenberg wrote:
So I count three different sets of URIs for NCBI taxonomy so far. :(
-Alan
On Fri, Feb 27, 2009 at 11:37 AM, Chris Mungall
wrote:
also..
part of the NCBI taxonomy is in NIF Organism:
http://ontology.neuinfo.org/NIF/Biomaterial
!
It'2 240M, but compressed is only 9.
I wonder whether there is some architecture to transparently transfer
compressed ontologies...
Ciao,
Andrea
-Original Message-
From: Chris Mungall [mailto:c...@berkeleybop.org]
Sent: 25 February 2009 20:53
To: andrea splendiani (RRes-Roth)
Cc: p
im. I know others who would be interested in a
similar resource.
Ciao,
Andrea
-Original Message-
From: Chris Mungall [mailto:c...@berkeleybop.org]
Sent: 25 February 2009 20:53
To: andrea splendiani (RRes-Roth)
Cc: public-semweb-lifesci hcls
Subject: Re: Is there an NCBI taxonomy in OWL ?
On Feb 25, 2009, at 11:58 AM, Andrea Splendiani wrote:
Hi,
I was looking for an NCBI Taxnomoy in OWL, but I didn't find it (or
better, could find fragment from other projects...)
What is strange though, is that on the obo foundry website
(berkeleybop.org/ontologies) there are notes on th
Hi Alistair
The UI is very nice!
I'm curious that you don't include any ontologies. The source datasets
are quite ontology-centric (the Chado database in particular). The
BDGP data includes annotation of each individual image with terms from
fly_anatomy. This allows you to query for genes
On May 15, 2008, at 4:39 PM, Kei Cheung wrote:
Hi Vipul,
Take the snomed term "Alzheimer's disease" (AD), for example. One
axis may be used to indicate the progression of the disease. For
example, http://www.memorystudy.org/alzheimers_stages.htm lists 7
stages of Alzheimer's disease: n
On Mar 12, 2008, at 9:06 PM, Tore Eriksson wrote:
Hi,
I am contemplating how to represent biochemical reactions in RDF,
and I
have some questions about properties and subproperties that I hope
anyone could shed some light on. What I want to do is to model
reactions
and the involved ent
On Feb 13, 2008, at 2:14 PM, M. Scott Marshall wrote:
Dear Matt,
I see 'trust' as a 'view' that can be produced by running a filter
over
the data (provenance). The filter would implement my trust policy, or
one of them. In other words, my trust in a given 'agent' can be due to
the fact th
On Feb 12, 2008, at 8:31 PM, Alan Ruttenberg wrote:
On Feb 12, 2008, at 8:59 AM, Colin Batchelor wrote:
How do you propose we cope with hedging, that is "It is not
impossible
that bananas are green", "Taken together, these results would
indicate
that bananas are blue" and so forth? This
Sorry to repost something from a list many of you are already
subscribed to; however, this seems like it warrants some specific
discussion on this list.
I know many of you have been wrapping various biological datasources
as RDF - I have been doing the same, using the usual suspects such
On Sep 14, 2007, at 10:04 AM, Alan Ruttenberg wrote:
Seen on the gofriends list:
On Sep 12, 2007, at 1:20 PM, Chris Mungall wrote:
Let me also give you some information on the results of our
experiments using OWL and Sesame, as part of a different project
outside GO. Triplestores such
Hi Matthias
This is very nice. Not sure about the name though. Shouldn't it be
L33TSP34K?
What group are you targeting? SPARQL syntax isn't bad enough to put
off hardcore data miners. And for the less techie folks I think the
main stumbling block isn't so much the syntax as the semantics
On Jul 17, 2007, at 1:44 AM, Eric Jain wrote:
Chris Mungall wrote:
We have also switched from talk of defining specific proteins to
rules to automatically annotate protein records.
You're right, small digression, hope it's of interest anyway :-)
Definitely - although I don&#
On Jul 16, 2007, at 10:29 AM, Eric Jain wrote:
Bijan Parsia wrote:
Eric, I would be very much interested in some more details about
the sort of rules used and how they are used. I personally tend to
distinguish between the use of rules in modeling and the use of
rules for data munging t
On Jul 4, 2007, at 8:27 PM, Kei Cheung wrote:
As a follow-up example, a study for estimating the error rate of
Gene Ontology (GO) was done:
http://www.pubmedcentral.nih.gov/articlerender.fcgi?
artid=1892569#id2674403
The study showed that the GO term annotation error rate estimates
f
On Jun 21, 2007, at 2:57 PM, Pat Hayes wrote:
Which simplifies things enormously and means that busy, practical
biologists don't have to keep wondering whether the Krebs cycle or
a computer program is a continuant or an occurrent
Why would a busy, practical biologist ever wonder if a comp
Hi Matthias
I don't know much about EOL other than what is available on their
website.
I do know that the ATOL (assembling the tree of life project) and
NESCENT have made a lot of progress addressing a lot of the tricky
ontological issues regarding anatomy, homology and phylogeny, which
On Jun 1, 2007, at 3:31 AM, Bijan Parsia wrote:
Looking at some of the queries in:
http://esw.w3.org/topic/HCLS/Banff2007Demo?
action=AttachFile&do=get&target=Banff2007Part2.pdf
I am reminded again of the practice of using gensyms for the URIs
of terms, e.g.,:
?class rdfs:subCl
27, 2007, at 10:01 AM, Alan Ruttenberg wrote:
lsw *is* aware of OBO in OWL and uses, e.g. OBO definitions for
comments when formatting display text such as tooltips :)
-Alan
On May 25, 2007, at 5:28 PM, Chris Mungall wrote:
..but of course this doesn't help if you're using p4, swoo
On May 25, 2007, at 8:44 AM, [EMAIL PROTECTED] wrote:
[2] For instance, definitions in the PATO OWL file (quality.owl) are
not visible in Protege. The OWL version of PATO has an
AnnotationProperty called "oboInOwl:hasDefintion" that has the value
"@_:A4843".
I and some other people have a
On May 25, 2007, at 8:44 AM, [EMAIL PROTECTED] wrote:
[2] For instance, definitions in the PATO OWL file (quality.owl) are
not visible in Protege. The OWL version of PATO has an
AnnotationProperty called "oboInOwl:hasDefintion" that has the value
"@_:A4843".
note there is a protege3 plugin
On May 24, 2007, at 11:36 AM, William Bug wrote:
Hi Alan,
Here's the GO/NCBO/Berkeley list that Chris Mungall curates (a page
I'm certain you've been to many times):
http://www.berkeleybop.org/ontologies/
As you know, it contains - among a host of other XML-based
On May 22, 2007, at 9:09 AM, [EMAIL PROTECTED] wrote:
In AFO:
-
.
.
-
Of course, cytoplasm probably also be a full temporal part of a
cytoplasm. I did not make that any more explicit, because it does
not matter for this example. It would matter even less when we are
mak
On May 22, 2007, at 8:04 AM, [EMAIL PROTECTED] wrote:
I have changed the title of the mail, since the discussion has
moved away from the BMC Bioinformatics paper.
First of all, RDF and OWL have no special features for n-ary
relations (RDF reification is not practical for that), and in m
On May 22, 2007, at 6:11 AM, Marijke Keet wrote:
The history of computing is the history of "design patterns" at
one level that eventually get built into "higher level
languages" at the next level of abstraction up.
I think I have a less optimistic view of progress in computer
s
On May 21, 2007, at 11:24 AM, Pat Hayes wrote:
>>>>> "CM" == Chris Mungall <[EMAIL PROTECTED]> writes:
>> Out of curiosity, can you describe how different or similar this
>> is to the result that you can achieve in the N-ary relation
>
On May 20, 2007, at 11:49 PM, Alan Rector wrote:
Chris
On 18 May 2007, at 18:10, Chris Mungall wrote:
I'm afraid I'm unclear how to state the OWL n-ary relation pattern
(http://www.w3.org/TR/swbp-n-aryRelations) where I really need it.
In all the examples given, the &qu
On May 17, 2007, at 8:43 AM, Pat Hayes wrote:
On 17 May 2007, at 05:13, Chris Mungall wrote:
[snip]
I've never understood why RDF-reification is so loathed. So the
syntax is ugly - but I think there may be other reasons RDF/XML
hasn't won any beauty contests.
They are fairly u
On May 18, 2007, at 12:55 PM, Dan Brickley wrote:
Matt Williams wrote:
I've been lurking & reading the discussion with interest.
It might be worth pointing out that there is an ongoing attempt to
classify/ represent evidential links/ weight/ etc. started in the
legal domain by people suc
On May 18, 2007, at 1:16 AM, Marijke Keet wrote:
Staying with article comments but going off topic from this thread,
there were two aspects in particular that read oddly and raises
more questions than that it provides information. One about the
BioRDF, the other the ontology working group
On May 18, 2007, at 3:40 AM, Phillip Lord wrote:
"MK" == Marijke Keet <[EMAIL PROTECTED]> writes:
MK> Regarding “reification design patterns” and the reification &
MK> OWL (not the thorny logic-based representation of beliefs et
MK> al), permit me to mention that support for n-ary re
On May 16, 2007, at 12:16 PM, Pat Hayes wrote:
The association is done by the reification using a URI which is
intended to identify the triple. However, there is no 'standard'
way to associate a URI with an RDF triple. This is exactly the
problem that named graphs were proposed as a way t
On Apr 17, 2007, at 10:49 AM, William Bug wrote:
I with Bijan on this issue.
However complex the current OWL representation may appear, it's
considerably more terse than the expression of this same info in a
relational model.
I'm not sure if this is necessarily the case. If we are talki
Looking at "Creating class level relations for easier querying of the
GO"
The problem you are solving is the one of limited inferencing in RDF
engines; in particular, queries such as:
SELECT *
WHERE
{
?whole rdfs:subClassOf ?sub.
?sub rdf:type owl:Restriction.
?sub owl:onProper
On Apr 10, 2007, at 12:15 PM, Elizabeth Wu wrote:
Bio-RDF 9 April 2007 conference call minutes is posted at http://
esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/
2007-04-09_Conference_Call.
I saw mention of the GO MySQL Database; As Alan pointed out, GO is
already available in RDF (b
I have some comments on:
http://esw.w3.org/topic/HCLS/
HCLSIG_DemoHomePage_HCLSIG_Demo#head-50710462ea5aac416fd063dce8621ce0354
d2d5a
Formal Definition of Semantics
OWL and RDF have a formal definition for the semantics of an OWL/
RDF knowledge base, i.e., given a knowledge base, associat
Umm, the OBO Cell ontology? There are a few ontological issues with
OBO-Cell right now, but these are currently being addressed. There
are also efforts within OBO to link cells with the brain regions they
are part of, although these are currently focused on model organisms.
On Mar 2, 200
;ll
make contact with the OBI group, since this all falls within the
realm of biomedical investigations, and should be represented in OBI.
I think what Chimezie has done is entirely compatible
Cheers
Chris
On Dec 6, 2006, at 11:20 AM, William Bug wrote:
Hi Trish,
This is a very informal ef
Hi Mary
I invite you to submit your comments to the obo-format list, where we
are close to finalising a new version of the obof->owl mapping
http://www.bioontology.org/wiki/index.php/OboInOwl:Main_Page
On Oct 10, 2006, at 10:08 PM, Mary Montoya wrote:
I have a question about using the Op
On Sep 14, 2006, at 10:26 AM, Phillip Lord wrote:
This paper for example, managed to get the Gene Ontology and, I think,
all of GOA into a DL form and reason over it in a, er, reasonable
amount of time. So scalability to 10's of thousands of T-box and 100's
of thousands of A-Box's is possible.
On Sep 14, 2006, at 10:36 AM, Drew McDermott wrote:
[Chimezie Ogbuji]
Seems to me the biggest barrier is in coming to a consensus on
an appropriate placeholder vocabulary and not neccessarily on
determining
all the various ways in which a person (and their related data)
could be
expre
Note that the GO evidence codes are a subset of the evidence codes
available on OBO:
http://obo.sourceforge.net/cgi-bin/detail.cgi?evidence_code
On Aug 1, 2006, at 11:19 AM, Joanne Luciano wrote:
Hi,
Here's a short list of Evidence Code / Ontology Links/papers:
1. SRI/Peter Karp - the B
On Jul 7, 2006, at 3:35 AM, Phillip Lord wrote:
"TW" == Trish Whetzel <[EMAIL PROTECTED]> writes:
TW> Hi all,
TW> As a terribly simple question, is it possible to take the actual
TW> FuGE-ML that is generated on a per instance reporting of an
TW> experiment/study/investigation and
Hi Bill
Just a minor clarification - the neurodevelopment ontology will not
be distinct from GO, it will be part of the GO biological process
ontology (and thus part of the OBO Foundry) and available as OWL
Cheers
Chris
On Jun 6, 2006, at 7:57 AM, William Bug wrote:
Oops -
I forgot t
On May 11, 2006, at 4:18 PM, Matthias Samwald wrote:
Hmm, the 10^16 genes instantiated in the volume of space occupied
by me are neither irrelevant (to me anyway), nor are they concepts.
They are very real instances of physical material objects - at
least under one definition of gene.
On May 11, 2006, at 6:58 AM, Xiaoshu Wang wrote:
--Chris
Genes should have their own URIs? That's some 10^16 or so
URIs just for the volume of space that I'm occupying right now.
So what is the problem? There are more concepts exist in the world
than
each of us know. Does it limit ourse
On May 10, 2006, at 6:32 AM, Xiaoshu Wang wrote:
--Phil,
Also, it's not clear what it meant by "same thing".
An genbank record and embl record identifying the same piece
of DNA are not the same thing; they are different records.
Given that this is the semantic web, it might be nice to be
a
One other thing to bear in mind is that many of the IDs that are
purported to be NCBI nucleotide sequence IDs are actually NCBI/EMBL/
DDBJ IDs. See http://www.insdc.org/
Presumably the ID scheme should reflect this?
Hi Steve
What's the advantage in using a wikispecies URI over an NCBI Taxon ID?
Of course with the taxon ID we would need a conversion of the NCBI
taxonomy to OWL classes, which is fairly trivial, and there a number
of such conversions around (and ideally there would be some kind of
ontol
On Mar 1, 2006, at 7:33 AM, Duncan Hull wrote:
Matthias Samwald wrote:
XSLT definitly is not sufficient for such conversions, I agree.
XQuery, however, is much more powerful than XSLT and has most
features of a 'full blown programming language'.
If you're trying to decide between XSL
I see OMIM was proposed as a test case. I'm interested in this. I'm not
entirely sure what it means to put OMIM disease descriptions into RDF
though. One approach that springs to mind is simple binary mapping
between OMIM IDs and, say, UMLS IDs. The question of whether RDF is
used here s
Hi Everyone
I'm Chris Mungall, and I'm based at Lawrence Berkeley Labs. I'm part of
the Gene Ontology Consortium, and the National Center for Biomedical
Ontologies. One of the things I'm interested in is storage and querying
of large datasets annotated and modeled u
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