>Date: Thu, 11 May 2006 09:58:37 -0400
>From: "Xiaoshu Wang" <[EMAIL PROTECTED]>
>Subject: RE: proposal for standard NCBI database URI
>To:
>
>
>--Chris
>> Genes should have their own URIs? That's some 10^16 or so
>> URIs just for t
I may be completely missing the point of this discussion, but I don't see
the point of this discussion :-)
What is represented by a URI is not defined by any convention or standard,
and we shouldn't be trying to define it in this group. rdfs:type can tell
us what the situation is at the
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.
> 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.
My point is: the existence of an URI doesn't imply th
> 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.
>
> in your example I presume the ID gene/123 was intend
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
Hi Guys:
Shouldn't bang on about this, so will shut up now. But was again reminded of
the INFO work (RFC 4452 - http://www.ietf.org/rfc/rfc4452.txt) where one of
the use cases we advance in the RFC is Dewey Decimal Classification (and
which we are still talking to OCLC about). The INFO namespace
--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 ourself from living or learning or working?
The number of
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
> MS> Ultimately, we should only have to talk about the biological
> MS> things (and apply URIs to real world resources)
> Aye, right, laudable aim. But 150 years down the line, we still
> don't
> have a workable definition of gene, species, organism or even
> life.
That is an exaggeration. Sur
> "MS" == Matthias Samwald <[EMAIL PROTECTED]> writes:
>> 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.
>> Or probably "different record,
Hi Phil,
I'm not sure I
understand why having a class DataBank makes this owl full, perhaps you
could explain a bit more. But in general, not much about these ontologies
was deliberate so any discovered oversites like the potential one you pointed
out are appreciated.
- Ben
Phillip Lor
--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
> able to state "different records, but sa
Matthias Samwald wrote:
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.
Or probably "different record, but same gene, according to some criteria"
C
> 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.
> Or probably "different record, but same gene, according to some criteria"
Clearly, there should be different UR
> "MH" == Matt Halstead <[EMAIL PROTECTED]> writes:
>> We would not be happy to have huge amounts of redundant resources
>> linked with owl:sameAs. owl:sameAs is nice when it only needs to
>> be used sparingly, but having two different naming schemes of a
>> large protein database lin
On 9/05/2006, at 8:46 PM, Matthias Samwald wrote:
Hi Alan,
As far as I know there is no standard URI for a resource at NCBI. I
would like to propose that there be one, since we will all need
them to use when we refer to these resources in our RDF. (and I
need one *now*)
I think we sh
Hi All,
I'm new to this list and I only did
a cursory reading of the archives so I apologize if I add anything that
has already been addressed. As some of you know, Stephen Evanchik
and myself are the lead developers on the LSID Toolkit. I have implemented
a prototype LSID Resolution Service
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?
On Tue, 2006-05-09 at 10:12 -0700, Mark Wilkinson wrote:
> Are there limits on the number of retrievals that can be done in a day
> on these URLs? i.e. will my domain get blacklisted if I pull in 100K
> records every hour?
Yes. Here are the rules:
http://eutils.ncbi.nlm.nih.gov/entrez/query/s
On 09 May 2006, at 13:12, Mark Wilkinson wrote:
I stand corrected :-)
Are there limits on the number of retrievals that can be done in a day
on these URLs? i.e. will my domain get blacklisted if I pull in 100K
records every hour?
# Run retrieval scripts on weekends or between 9 pm and 5 am
Thanks, I like this proposal, Larry. You are right - it works now and
satisfies the requirement.
I amend my proposal to be:
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=
DATABASE_GOES_HERE>&
e.g.
http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=gene&id=596
http:
> http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?
>
> which just brings back the raw data. Details here:
>
> http://eutils.ncbi.nlm.nih.gov/entrez/query/static/efetch_help.html
These kinds of URIs are more used as API. It will be difficult to use them
in the context of SW to
I stand corrected :-)
Are there limits on the number of retrievals that can be done in a day
on these URLs? i.e. will my domain get blacklisted if I pull in 100K
records every hour?
M
On Tue, 2006-05-09 at 10:58 -0600, Larry Hunter wrote:
> On Tue, 2006-05-09 at 09:16 -0700, Mark Wilkinson w
On Tue, 2006-05-09 at 09:16 -0700, Mark Wilkinson wrote:
> H yeah, that's true... but my "gut" does a back-flip when I am
> forced to use a URI that refers to a web page, complete with fancy NCBI
> decorations and menu's
You're mistaken about that. If you don't want the decorations, the
H yeah, that's true... but my "gut" does a back-flip when I am
forced to use a URI that refers to a web page, complete with fancy NCBI
decorations and menu's :-)
I think what we are REALLY looking for is an identifier of a data-
entity, independent of its representation. This is what t
On Tue, 2006-05-09 at 00:00 -0400, Alan Ruttenberg wrote:
> As far as I know there is no standard URI for a resource at NCBI.
Ah, but there is:
http://www.ncbi.nlm.nih.gov/entrez/query/static/linking.html
Given that this structure covers many quite distinct databases, it's a
bit more complic
Xiaoshu Wang wrote:
To propose a standard URI for a domain that we don't own is like proposing
Iran to drop their nuclear program. It is wishful thinking.
In this particular case it seems more like Iran proposing that the United
States drop their nuclear program :-)
> As far as I know there is no standard URI for a resource at
> NCBI. I would like to propose that there be one, since we
> will all need them to use when we refer to these resources
> in our RDF. (and I need one
> *now*)
It is useless for us to propose without NCBI's participation. The prob
Not sure of the relevance here but see you might like to consider also this:
http://info-uri.info/registry/OAIHandler?verb=GetRecord&metadataPrefix=reg&i
dentifier=info:pmid/
PubMed identifiers are already registered under the INFO URI namespace (RFC
4452 - http://www.ietf.org/rfc/rfc4452.tx
Hi Alan,
> As far as I know there is no standard URI for a resource at NCBI. I
> would like to propose that there be one, since we will all need
> them to use when we refer to these resources in our RDF. (and I
> need one *now*)
I think we should be aware that this could be a VERY important dec
Alan Ruttenberg wrote:
As far as I know there is no standard URI for a resource at NCBI. I
would like to propose that there be one, since we will all need them to
use when we refer to these resources in our RDF. (and I need one *now*)
Next you'll probably also need standard URL's for all the
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