On Jul 31, 2012 3:08 PM, "Richard Boyce" <[email protected]> wrote:
>
> 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
> ------
live.dbpedia.org is just the server, the RDF URIs don't change, they're
still http://dbpedia.org/... This works:
SELECT * WHERE { ?s <http://dbpedia.org/ontology/fdaUniiCode> ?o } LIMIT 10
>
> 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]> 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>
suggest that it happens for all UNIIs that start with numbers:
>>>
>>> ----------
>>> PREFIX dbpprop: <http://dbpedia.org/property/>
>>> PREFIX dbpedia-owl: <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>?
>>>
>>> ----------
>>> 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
>>> ----------
>>>
>>>
>>>> Perhaps somebody from your group wants to help with more mappings?
>>>
>>> Sure. I now have an account at <http://mappings.dbpedia.org> and will
look closely at what we can contribute based on <
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]> 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]
>>>>> 412-648-9219 (W), 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]
>>>>> 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
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ---
>>>> Pablo N. Mendes
>>>> http://pablomendes.com
>>>> Events: 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
>>
>>
>>
>>
>> --
>> ---
>> Pablo N. Mendes
>> http://pablomendes.com
>> Events: 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
