Is there a log anywhere that might help a user know which pages have
been updated and when?
tx, -R
On 07/31/2012 12:11 PM, Jona Christopher Sahnwaldt wrote:
Live extracts data from pages as soon as they change on Wikipedia.
http://en.wikipedia.org/wiki/Desomorphine and
http://en.wikipedia.org/wiki/Metoclopramide have changed recently, the
other pages using the template probably haven't.
I think I read somewhere that live also re-extracts unchanged pages
when a template they use or its mapping change, but with lower
priority. Mohamed would know the details.
JC
On Jul 31, 2012 4:29 PM, "Pablo N. Mendes" <[email protected]
<mailto:[email protected]>> wrote:
Whoops... sorry... I was testing the Linked Data URIs and didn't
even check the SPARQL for typos.
This is what puzzles me. I can see extraction samples for
fdaUniiCode showing: Amoxicillin, Amphetamine, etc.
http://mappings.dbpedia.org/server/mappings/en/extractionSamples/Mapping_en:Drugbox
But I cannot see them on live.dbpedia.org <http://live.dbpedia.org>:
http://live.dbpedia.org/page/Amoxicillin
http://live.dbpedia.org/page/Amphetamine
What gives?
Cheers,
Pablo
On Tue, Jul 31, 2012 at 4:19 PM, Jona Christopher Sahnwaldt
<[email protected] <mailto:[email protected]>> wrote:
On Jul 31, 2012 3:08 PM, "Richard Boyce" <[email protected]
<mailto:[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
<http://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 <http://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] <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> 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] <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 (*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 (*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
