This is a reminder of the Clinical Pharmacogenomics Teleconference on Wednesday
at 10:15 Eastern Time (16:15 Central European Time). Here is the suggested
agendaa.. Simon Lin (Marshfield Clinic) to present/discuss "Big Data Needs in
Clinical Genomics". Simon aims to work with the group to collab
3rd try now without attachments as some SPAM filter seems to reject this
mail.
Hope not everyone gets 4 copies now :(
Regards,
Jerven
-- Forwarded message --
From: Jerven Bolleman
Date: Mon, Jun 3, 2013 at 9:57 PM
Subject: Fwd: Question about Semantic Web
To: public-semweb-lifes
i'm willing to comprise to "should", as it it is generally seen as a good
practice to use void:inDataset for linking data items to datasets. We can
bring this discussion to the semantic-web mailing list, if you want to
additional feedback.
m.
On Tue, Jun 4, 2013 at 5:14 PM, Jerven Bolleman wr
On Tue, Jun 4, 2013 at 3:47 PM, Michel Dumontier wrote:
> Hi Jerven,
>
> First: Bio2RDF's current datasets are listed here:
>
> http://bio2rdf.org/datasets
>
> as i mentioned, and has been presented [1] those that are in Bio2RDF
> release 2 have provenance. e.g.
> http://bio2rdf.org/geneid:123
>
We load the entire dataset into a named graph, then use the graph URI for
provenance. I'm with Jerven in that we don't want to add void:inDataset links
in the source data for the many million resources we index, however, I have no
problem including this information when you request information a
Hi folks,
we're are postponing the HCLS call for July.
Best,
m.
--
Michel Dumontier
Associate Professor of Bioinformatics, Carleton University
Chair, W3C Semantic Web for Health Care and the Life Sciences Interest Group
http://dumontierlab.com
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On Tue, Jun 4, 2013 at 11:10 AM, Alasdair J G Gray <
alasdair.g...@manchester.ac.uk> wrote:
> Hi,
>
> Splitting Jerven's points into separate bite sized chunks.
>
> On 3 Jun 2013, at 17:51, Michel Dumontier
> wrote:
>
> Hi Jerven,
>
>
> On Mon, Jun 3, 2013 at 6:30 PM, Jerven Bolleman wrote:
>
>>
Hi all,
sorry for following this a bit lightly.
If you have multiple validation patterns in a dataset you need to be able to
specify what applies to what, otherwise is too weak.
Perhaps it makes more sense to see the problem from the opposite point of view:
This dataset has the URI collection un
Hi Jerven,
First: Bio2RDF's current datasets are listed here:
http://bio2rdf.org/datasets
as i mentioned, and has been presented [1] those that are in Bio2RDF
release 2 have provenance. e.g.
http://bio2rdf.org/geneid:123
(we did not provide updates to uniprot, genbank, refseq, pubmed in releas
On Tue, Jun 4, 2013 at 3:39 PM, Alasdair J G Gray <
alasdair.g...@manchester.ac.uk> wrote:
>
> On 4 Jun 2013, at 14:20, Jerven Bolleman wrote:
>
>
>
>
> On Tue, Jun 4, 2013 at 3:08 PM, Michel Dumontier <
> michel.dumont...@gmail.com> wrote:
>
>> The point here is simple. if you provide a URI unip
On Tue, Jun 4, 2013 at 3:20 PM, Jerven Bolleman wrote:
>
>
>
> On Tue, Jun 4, 2013 at 3:08 PM, Michel Dumontier <
> michel.dumont...@gmail.com> wrote:
>
>> The point here is simple. if you provide a URI uniprot:1.2.3.4, i would
>> like to know that this is incorrect.
>>
>> m.
>>
> Yes, but the mo
On 4 Jun 2013, at 14:20, Jerven Bolleman wrote:
>
>
>
> On Tue, Jun 4, 2013 at 3:08 PM, Michel Dumontier
> wrote:
> The point here is simple. if you provide a URI uniprot:1.2.3.4, i would like
> to know that this is incorrect.
>
> m.
> Yes, but the model needs to be good enough to tell yo
On 4 June 2013 09:20, Jerven Bolleman wrote:
> The void uriRegexPattern might be good enough.
>
There is also xsd:pattern that can be applied to a xsd:anyURI. That makes
URIs OWL datatypes though, which might not be desirable.
But I am thinking that we can have stronger validation patterns if
On Tue, Jun 4, 2013 at 3:05 PM, Michel Dumontier wrote:
>
>
>
> On Tue, Jun 4, 2013 at 2:40 PM, Jerven Bolleman wrote:
>
>>
>>
>>
>> On Tue, Jun 4, 2013 at 11:36 AM, Alasdair J G Gray <
>> alasdair.g...@manchester.ac.uk> wrote:
>>
>>>
>>> On 3 Jun 2013, at 17:51, Michel Dumontier
>>> wrote:
>>>
On Tue, Jun 4, 2013 at 3:08 PM, Michel Dumontier wrote:
> The point here is simple. if you provide a URI uniprot:1.2.3.4, i would
> like to know that this is incorrect.
>
> m.
>
Yes, but the model needs to be good enough to tell you that. The model
discussed yesterday with
data item identifer reg
The point here is simple. if you provide a URI uniprot:1.2.3.4, i would
like to know that this is incorrect.
m.
On Tue, Jun 4, 2013 at 3:01 PM, Joachim Baran wrote:
>
> On 4 June 2013 08:56, Jerven Bolleman wrote:
>
>> uniprot:P12345 a up:Protein ;
>>
>>> up:enzyme ec:1
On Tue, Jun 4, 2013 at 2:40 PM, Jerven Bolleman wrote:
>
>
>
> On Tue, Jun 4, 2013 at 11:36 AM, Alasdair J G Gray <
> alasdair.g...@manchester.ac.uk> wrote:
>
>>
>> On 3 Jun 2013, at 17:51, Michel Dumontier
>> wrote:
>>
>> About void:inDataset I personally don't like it. I suspect it would cost
On 4 June 2013 08:56, Jerven Bolleman wrote:
> uniprot:P12345 a up:Protein ;
>
>>up:enzyme ec:1.2.3.4 .
>>> ec:1.2.3.4 a up:Enzyme .
>>> What if my data is
>>>
>>
> uniprot:1.2.3.4 a up:Protein ;
>up:enzyme ec:P12345 .
> ec:P12345 a up:Enzyme .
>
Hi!
On 4 June 2013 07:45, N Juty wrote:
> The GO abbreviations and cross-referencing list is one of a few possible
> lists that could be used, but there would be overlap and inconsistencies in
> coverage and namespace assignments, especially when using more than one
> such list to bridge any gap
On Tue, Jun 4, 2013 at 2:52 PM, Michel Dumontier wrote:
>
>
>
> On Tue, Jun 4, 2013 at 2:47 PM, Jerven Bolleman wrote:
>
>> Hi All,
>>
>> The problem with the current suggested solution is that it does not
>> account for a mix of identifiers in a dataset.
>> This is because in RDF we have resour
On Tue, Jun 4, 2013 at 2:47 PM, Jerven Bolleman wrote:
> Hi All,
>
> The problem with the current suggested solution is that it does not
> account for a mix of identifiers in a dataset.
> This is because in RDF we have resources not data items.
>
> So in case of uniprot.org we have lots of identi
Alasdair,
We have large lists of preferred prefixes for datasets, some of them are
defined by communities (uniprot, ncbi, psi-mi, etc), and others are used in
the scope of specific datasets to refer to other datasets. As part of
Bio2RDF, and in collaboration with identifiers.org, we collect these
Hi All,
The problem with the current suggested solution is that it does not account
for a mix of identifiers in a dataset.
This is because in RDF we have resources not data items.
So in case of uniprot.org we have lots of identifiers in a single dataset.
Identifying annotation, ranges, go terms e
On Tue, Jun 4, 2013 at 11:36 AM, Alasdair J G Gray <
alasdair.g...@manchester.ac.uk> wrote:
>
> On 3 Jun 2013, at 17:51, Michel Dumontier
> wrote:
>
> About void:inDataset I personally don't like it. I suspect it would cost
>> me a 13% growth in triple size for negligible benefits. This also mean
Hi,
The GO abbreviations and cross-referencing list is one of a few possible
lists that could be used, but there would be overlap and inconsistencies
in coverage and namespace assignments, especially when using more than
one such list to bridge any gaps. A lot of these lists are also
'static'
Hello,
On 2013-06-04, at 5:27 AM, Alasdair J G Gray
wrote:
> Again, there is a scoping problem. Prefixes are locally scoped and must be
> defined.
At least in life sciences, there are the Gene Ontology abbreviations for
cross-referenced databases: http://www.geneontology.org/doc/GO.xrf_abbs
On 3 Jun 2013, at 17:51, Michel Dumontier wrote:
> About void:inDataset I personally don't like it. I suspect it would cost me a
> 13% growth in triple size for negligible benefits. This also means that the
> dataset description starts to affect the data. Although I could only present
> this
On 3 Jun 2013, at 17:51, Michel Dumontier wrote:
>
> Also continuing the discussion on e-mail that started on the call.
> We should have a clear definition of data item if we are going to record
> information about such things. e.g. baseURI, what happens if we have 2 data
> item types in a s
Hi,
Splitting Jerven's points into separate bite sized chunks.
On 3 Jun 2013, at 17:51, Michel Dumontier wrote:
> Hi Jerven,
>
>
> On Mon, Jun 3, 2013 at 6:30 PM, Jerven Bolleman wrote:
> Hi All,
>
> I wanted to discuss one more thing that has been decided in an earlier
> meeting.
> And th
thanks for the link. Looks really useful. I'll have a proper look at it later
in the day.
Alasdair
On 3 Jun 2013, at 18:15, Amrapali J Zaveri wrote:
> Hi all,
>
> I just wanted to point you to this checklist: http://goo.gl/K642I, which
> might be helpful.
>
> Thanks.
> Regards,
> Amrapali Z
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