Hi Pablo, Mohamed, and JC,
1) I added two drugbox mappings (bioavailability and ChEBI) per the
example - would you please confirm that these are acceptable?
2) Still no luck with querying FDA UNIIs in live.dbpedia.org:
------
PREFIX dbpprop: <http://live.dbpedia.org/property/>
PREFIX dbpedia-owl: <http://live.dbpedia.org/ontology/>
select distinct ?s ?unii
where {
?s dbpedia-owl:fdaUniiCode ?unii.
}
LIMIT 100
------
Did you find any incompatibility between the live and the new extraction
code?
thanks,
-Rich
On 07/21/2012 05:09 PM, Pablo N. Mendes wrote:
Hi Richard,
Please check if you now have editor rights. Otherwise, please send us
your username.
Unfortunately my mapping is not showing up at DBpedia Live yet. This
makes me thing that this is some kind of incompatibility between the
live and the new extraction code.
Mohamed, JC, can you guys confirm this please?
in the meantime, here are a stab at a couple of mappings that
might be helpful
Great! Thanks. They will definitely be helpful. But unfortunately the
mapping system might not be smart enough to handle what you have input
there. You would probably have to split that content into a few
entries. The rdfs:label, rdfs:domain, rdfs:range go to ontology pages
[1], while templateProperty and ontologyProperty go to Mapping pages
[2]. Please let me know if the difference is not easy to spot by
looking at these two examples:
[1]
http://mappings.dbpedia.org/index.php?title=OntologyProperty:FdaUniiCode&action=edit
[2]
http://mappings.dbpedia.org/index.php?title=Mapping_en:Drugbox&action=edit
The way the system is set up now, I think you would have to create one
page for each ontology property (you can copy+paste stuff from [1] and
modify accordingly), then find the Infobox where the data appears and
add the mapping from that infobox to the ontology property (just like
we did in [2]).
Perhaps these links will be helpful:
http://mappings.dbpedia.org/index.php/Main_Page#Detailed_Information
Cheers,
Pablo
On Sat, Jul 21, 2012 at 1:24 PM, Richard Boyce <[email protected]
<mailto:[email protected]>> wrote:
Hi Pablo....
On 07/20/2012 07:51 AM, Pablo N. Mendes wrote:
Hi Richard,
It seems that the URL broke when you shortened it:
http://tinyurl.com/cpq58z3
Sorry about that....
But in general if there is a 0 value for dbprop:unii it is
*probably* because the value was parsed wrongly from the infobox.
I looked at:
http://en.wikipedia.org/w/index.php?title=Dimercaprol&action=edit
And I can see this:
| UNII = 0CPP32S55X
Perhaps the parser though that anything that starts with 0 is a
number. This might be solvable with a mapping to inform the
parser that the value is a string.
That what I think was happening. A query of
<http://dbpedia.org/sparql> <http://dbpedia.org/sparql> suggest
that it happens for all UNIIs that start with numbers:
----------
PREFIX dbpprop: <http://dbpedia.org/property/>
<http://dbpedia.org/property/>
PREFIX dbpedia-owl: <http://dbpedia.org/ontology/>
<http://dbpedia.org/ontology/>
select distinct ?s ?unii
where {
?s dbpprop:unii ?unii.
}
OFFSET 200
LIMIT 100
----------
Have you had a look at the mappings for drugs?
e.g.http://mappings.dbpedia.org/index.php/Mapping_en:Drugbox
This mapping connects the infobox Drugbox [1] to our ontology. It
seems that UNII was not yet mapped to the ontology. I've added a
mapping and a property. It seems to work:
http://mappings.dbpedia.org/server/mappings/en/extractionSamples/Mapping_en:Drugbox
That is great! I had not seen those mappings nor dbpedia's
distributed ontology maintenance approach before....
I hope that data will show up in DBpedia Live soon.
http://live.dbpedia.org/page/Dimercaprol
Once it shows up, would you expect the following SPARQL query to
work at <http://live.dbpedia.org/sparql>
<http://live.dbpedia.org/sparql>?
----------
PREFIX dbpprop: <http://live.dbpedia.org/property/>
<http://live.dbpedia.org/property/>
PREFIX dbpedia-owl: <http://live.dbpedia.org/ontology/>
<http://live.dbpedia.org/ontology/>
select distinct ?s ?unii
where {
?s dbpedia-owl:fdaUniiCode ?unii.
}
LIMIT 100
----------
Perhaps somebody from your group wants to help with more mappings?
Sure. I now have an account at <http://mappings.dbpedia.org>
<http://mappings.dbpedia.org> and will look closely at what we can
contribute based on
<http://mappings.dbpedia.org/server/templatestatistics/en/?template=Drugbox>
<http://mappings.dbpedia.org/server/templatestatistics/en/?template=Drugbox>.
It looks like I need to wait until I have some permissions to
edit...in the meantime, here are a stab at a couple of mappings
that might be helpful:
----------
{{TemplateMapping
| mapToClass = Drug
| mappings =
{{ PropertyMapping | templateProperty = bioavailability | ontologyProperty =
ncbit:bioavailability | rdfs:label@en = "bioavailability" | rdfs:domain = Drug |
rdfs:range = xsd:/float/ | rdfs:comment@en = "The rate and extent to which the active
ingredient or active moiety is absorbed from a drug product and becomes available at the site of
action. For drug products that are not intended to be absorbed into the bloodstream,
bioavailability may be assessed by measurements intended to reflect the rate and extent to which
the active ingredient or active moiety becomes available at the site of action (21CFR320.1)."}}
{{ PropertyMapping | templateProperty = ChEBI | ontologyProperty = ChEBI |
rdfs:label@en = "A unique identifier for the drug in the Chemical Entities of
Biological Interest (ChEBI) ontology" rdfs:domain = Drug | rdfs:range =
xsd:/string/ }}
}}
-----------
kind regards,
-Rich
[1] http://en.wikipedia.org/wiki/Template:Drugbox
[2]
http://mappings.dbpedia.org/index.php/Special:Contributions/Pablomendes
Cheers,
Pablo
On Fri, Jul 20, 2012 at 12:31 PM, Richard Boyce <[email protected]
<mailto:[email protected]>> wrote:
Hello,
There is a property called "dbpprop:unii" which I believe
should provide
an FDA Unique Ingredient Identifier (UNII) code for a dbpedia
drug.
Unfortunately, it appears that a great number of the codes are
incorrect. For example, the following query
<http://tinyurl.com/cpq58z3>
shows numerous repeated "0" values as the uniis for various
drugs. If
you go back to the FDA's official UNII listing
<http://tinyurl.com/6nmge3d> and grep it for the drug names
(upper
cased), it turns out that all of the drugs in the left column
have UNIIs
starting with the integer shown in the right column! This is
not true
for all drugs; this other query returns a correct UNII
<http://tinyurl.com/bw8rpo2>. This looks like it might be a
bug. Does
anyone know how this issue can be addressed?
kind regards,
-Rich
--
Richard Boyce, PhD
Assistant Professor of Biomedical Informatics
Faculty, Geriatric Pharmaceutical Outcomes and
Gero-Informatics Research and Training Program
Scholar, Comparative Effectiveness Research Program
University of Pittsburgh
[email protected] <mailto:[email protected]>
412-648-9219 <tel:412-648-9219> (W), 206-371-6186
<tel:206-371-6186> (C)
Twitter: @bhaapgh
--
Richard Boyce, PhD
Assistant Professor of Biomedical Informatics
Faculty, Geriatric Pharmaceutical Outcomes and
Gero-Informatics Research and Training Program
Scholar, Comparative Effectiveness Research Program
University of Pittsburgh
[email protected] <mailto:[email protected]>
412-648-9219 <tel:412-648-9219> (W), 206-371-6186
<tel:206-371-6186> (C)
Twitter: @bhaapgh
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond.
Discussions
will include endpoint security, mobile security and the
latest in malware
threats.
http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Dbpedia-discussion mailing list
[email protected]
<mailto:[email protected]>
https://lists.sourceforge.net/lists/listinfo/dbpedia-discussion
--
---
Pablo N. Mendes
http://pablomendes.com
Events: http://wole2012.eurecom.fr
<http://wole2012.eurecom.fr/> (*Deadline: July 31st 2012*)
--
Richard Boyce, PhD
Assistant Professor of Biomedical Informatics
Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics Research
and Training Program
Scholar, Comparative Effectiveness Research Program
University of Pittsburgh
[email protected] <mailto:[email protected]>
412-648-9219 <tel:412-648-9219> (W),206-371-6186 <tel:206-371-6186> (C)
Twitter: @bhaapgh
--
---
Pablo N. Mendes
http://pablomendes.com
Events: http://wole2012.eurecom.fr
<http://wole2012.eurecom.fr/> (*Deadline: July 31st 2012*)
--
Richard Boyce, PhD
Assistant Professor of Biomedical Informatics
Faculty, Geriatric Pharmaceutical Outcomes and Gero-Informatics Research and
Training Program
Scholar, Comparative Effectiveness Research Program
University of Pittsburgh
[email protected]
412-648-9219 (W), 206-371-6186 (C)
Twitter: @bhaapgh
------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Dbpedia-discussion mailing list
[email protected]
https://lists.sourceforge.net/lists/listinfo/dbpedia-discussion
