From dan.bolser at gmail.com  Sun Dec 25 09:28:57 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Sun, 25 Dec 2011 14:28:57 +0000
Subject: [Pdbwiki-devel] taking and updating wikipedia genes to PDBwiki
In-Reply-To: <AANLkTi=7kPc7tqKq6TWENW_7kguRDR1XpUQFmSCoDD7P@mail.gmail.com>
References: <AANLkTikifTNoYFz6nrp7EwW_twV3VGHhPwQbLYgzUPcp@mail.gmail.com>
	<AANLkTin=h=x27eCcKK+rhRYmAx31uCNNSDPx+aVLbT-6@mail.gmail.com>
	<AANLkTi=7kPc7tqKq6TWENW_7kguRDR1XpUQFmSCoDD7P@mail.gmail.com>
Message-ID: <CAPBO=2k_XYz9dzFJQFqEWXDxSAWUJq__BE+yAfyP3GPhM4Q56Q@mail.gmail.com>

Wow, two years have passed already, and I haven't looked at doing any of
this! We need an international PDBWiki week once a year to focus our
attention!

Maybe some time in March?

Happy Christmas!
Dan.
On 27 Dec 2010 04:05, "Jong Bhak" <jongbhak at gmail.com> wrote:

> Thanks. Also, Jmol on the site will be good. To turn them
> around a bit.
> Cheers
>
> Jong
>
>
>
>
>
>
>
>
> On Mon, Dec 27, 2010 at 6:56 AM, Dan Bolser <dan.bolser at gmail.com> wrote:
>
>> Hi Jong,
>>
>> Yup, all this is possible. I like the idea to add links to Wikipedia
>> from PDBWiki.
>>
>> We do have the EC terms in PDBWiki as categories, but we didn't add GO
>> because its a 'different kind of category'... for this we were
>> thinking of developing PDBWiki using the functionality of Semantic
>> MediaWiki, but we haven't really worked out how to do that 'properly'.
>> I guess we should rather do it piecemeal and see what works?
>>
>>
>> Happy X-mass and new-year to you too!
>>
>>
>> Dan.
>>
>> On 26 December 2010 16:47, Jong Bhak <jongbhak at gmail.com> wrote:
>> > Hi Dan,
>> >
>> > Can you copy wikipedia's gene and protein names that appear in PDBwiki
>> > and actually store them in PDBwiki? And make a script that automates
>> > the text every month?
>> >
>> > Also, can you add Wikipedia's link to PDB entries under Links section?
>> >
>> > Also, can you make a fuctional category in PDBwiki using GO?
>> > and put lists of genes/proteins in the category so that I can
>> > browser functionally linked 3D domains with annotated information?
>> >
>> > Thanks
>> >
>> > Happy new year!
>> > Jong
>> >
>> >
>> >
>> >
>> >
>> >
>>
>
>
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From dan.bolser at gmail.com  Mon Dec 26 11:06:41 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 26 Dec 2011 16:06:41 +0000
Subject: [Pdbwiki-devel] taking and updating wikipedia genes to PDBwiki
In-Reply-To: <1324830736.55273.YahooMailNeo@web112403.mail.gq1.yahoo.com>
References: <AANLkTikifTNoYFz6nrp7EwW_twV3VGHhPwQbLYgzUPcp@mail.gmail.com>
	<AANLkTin=h=x27eCcKK+rhRYmAx31uCNNSDPx+aVLbT-6@mail.gmail.com>
	<AANLkTi=7kPc7tqKq6TWENW_7kguRDR1XpUQFmSCoDD7P@mail.gmail.com>
	<CAPBO=2k_XYz9dzFJQFqEWXDxSAWUJq__BE+yAfyP3GPhM4Q56Q@mail.gmail.com>
	<1324830736.55273.YahooMailNeo@web112403.mail.gq1.yahoo.com>
Message-ID: <CAPBO=2kvXQNGf8-99=-z877mHOzti+pSjM91wpogeSxFjbZJ2w@mail.gmail.com>

23rd looks OK for me provisionally.

I'd love to attend another bioconference, but it seems a long way to
go just to talk about PDBWiki!

Could be really fun though!

On 25 December 2011 16:32, Jong Bhak <jongbhak at yahoo.com> wrote:
> Hi,
>
> I fully agree.
> Can you come to Korea on 23rd Feb?
> I have the second bioconference and you
> can talk about it.
>
> Take care
>
>
>
> Jong Bhak,
>
> \(^o^)/
> Tel: 031-888-9311, Fax: 031-888-9314, Mobile: 010 9944 6754
>
> From: Dan Bolser <dan.bolser at gmail.com>
> To: Jong Bhak <jongbhak at gmail.com>
> Cc: pdbwiki-devel at bioinformatics.org
> Sent: Sunday, December 25, 2011 11:28 PM
> Subject: Re: taking and updating wikipedia genes to PDBwiki
>
> Wow, two years have passed already, and I haven't looked at doing any of
> this! We need an international PDBWiki week once a year to focus our
> attention!
> Maybe some time in March?
> Happy Christmas!
> Dan.
> On 27 Dec 2010 04:05, "Jong Bhak" <jongbhak at gmail.com> wrote:
>
> Thanks. Also, Jmol on the site will be good. To turn them
> around?a bit.
> Cheers
>
> Jong
>
>
>
>
>
>
>
>
> On Mon, Dec 27, 2010 at 6:56 AM, Dan Bolser <dan.bolser at gmail.com> wrote:
>
> Hi Jong,
>
> Yup, all this is possible. I like the idea to add links to Wikipedia
> from PDBWiki.
>
> We do have the EC terms in PDBWiki as categories, but we didn't add GO
> because its a 'different kind of category'... for this we were
> thinking of developing PDBWiki using the functionality of Semantic
> MediaWiki, but we haven't really worked out how to do that 'properly'.
> I guess we should rather do it piecemeal and see what works?
>
>
> Happy X-mass and new-year to you too!
>
>
> Dan.
>
> On 26 December 2010 16:47, Jong Bhak <jongbhak at gmail.com> wrote:
>> Hi Dan,
>>
>> Can you copy wikipedia's gene and protein names that appear in PDBwiki
>> and actually store them in PDBwiki? And make a script that automates
>> the text every month?
>>
>> Also, can you add Wikipedia's link to PDB entries under Links section?
>>
>> Also, can you make a fuctional category in PDBwiki using GO?
>> and put lists of genes/proteins in the category so that I can
>> browser functionally linked 3D domains with annotated information?
>>
>> Thanks
>>
>> Happy new year!
>> Jong
>>
>>
>>
>>
>>
>>
>
>
>
>

From dan.bolser at gmail.com  Mon Dec 26 11:35:11 2011
From: dan.bolser at gmail.com (Dan Bolser)
Date: Mon, 26 Dec 2011 16:35:11 +0000
Subject: [Pdbwiki-devel] Here is some example SPARQL from DBpedia
Message-ID: <CAPBO=2k_EtU4X0KcQcVy1=W-e5EmZVDGJRGSCsf-z_s+u8f2_A@mail.gmail.com>

Just for your interest,

Dan.


---------- Forwarded message ----------
From: Sebastian Hellmann <hellmann at informatik.uni-leipzig.de>
Date: 24 December 2011 07:32
Subject: Re: [Wiki-research-l] how to query WIkipedia for a list of
people who	died in a given year
To: Research into Wikimedia content and communities
<wiki-research-l at lists.wikimedia.org>


Dear Alek, dear list,
exactly for this use case DBpedia (http://dbpedia.org ) was created, so
you can query Wikipedia like a database. DBpedia already does the
rollout to a "semantic engine", which you can query.
Below I drafted some queries. These will give you all the Persons in
Wikipedia that have a "deathDate". Totally there are 187739, which
should be the most complete list you will find.
Then the queries is refined to all persons, which died in 1941 (yielding
1318 persons), then all artists that died in 1941 and then all artists
and their works!

Note that there is a static database which uses the latest dump:
http://dbpedia.org/sparql
http://dbpedia.org/snorql
as well as a live version, which is synchronized directly (each edit is
loaded into the engine)
http://live.dbpedia.org/sparql
Also for some of the other Wikipedias besides the English one, language
specific versions exist:
Polish: http://pl.dbpedia.org/
German: http://de.dbpedia.org
Greek: http://el.dbpedia.org

DBpedia has quite a large community, I would estimate that over 1000
volunteers from the area of computer science and Semantic Web ?worked on
or with it since 2006. (This does not account for industry partners or a
like) .

@Alek I drafted some queries for you. There are a total of 5 result
formats to choose from. Maybe json, plain or html are the one you are
looking for. Here is a ?link to some user interfaces:
http://wiki.dbpedia.org/OnlineAccess
http://wiki.dbpedia.org/Applications

Feel free to improve the data directly in Wikipedia (and use the live
endpoint 5 minutes later) or tailor the data how you like it at mappings
wiki: http://mappings.dbpedia.org ?. ?Actuallly the information
contained could help to clean up the infoboxes, which would also help
the start of WikiData.
Here is one hook though. The more precise the queries get, the worse
recall will be, as minor errors in the data add up with each constraint.

Hope I could help,
Sebastian

Queries below:
*******************
A count of all persons that have a deathDate [1]:
SELECT count (*) WHERE {
?person <http://dbpedia.org/ontology/deathDate> ?deathDate .
?person <http://xmlns.com/foaf/0.1/page> ?page .
}


All persons that died in 1941. Note that on http:dbpedia.org there is a
given limit of 1000, so you need to use OFFSET:

SELECT * WHERE {
?person <http://dbpedia.org/ontology/deathDate> ?deathDate .
?person <http://xmlns.com/foaf/0.1/page> ?page .
FILTER(?deathDate >= "1941-01-01"^^xsd:date)
FILTER(?deathDate <= "1942-01-01"^^xsd:date)
} order by ?deathDate
Limit 1000
OFFSET 0

SELECT * WHERE {
?person <http://dbpedia.org/ontology/deathDate> ?deathDate .
?person <http://xmlns.com/foaf/0.1/page> ?page .
FILTER(?deathDate >= "1941-01-01"^^xsd:date)
FILTER(?deathDate <= "1942-01-01"^^xsd:date)
} order by ?deathDate
Limit 1000
OFFSET 1000

All artists that died in 1941 [3]
SELECT * WHERE {
?person <http://dbpedia.org/ontology/deathDate> ?deathDate .
?person <http://xmlns.com/foaf/0.1/page> ?page .
?person rdf:type <http://dbpedia.org/ontology/Artist>
FILTER(?deathDate >= "1941-01-01"^^xsd:date)
FILTER(?deathDate <= "1942-01-01"^^xsd:date)
}

All artists and their work[4]:
SELECT * WHERE {
?person <http://dbpedia.org/ontology/deathDate> ?deathDate .
?person rdf:type <http://dbpedia.org/ontology/Artist> .
?person <http://xmlns.com/foaf/0.1/page> ?page .

OPTIONAL {
? ?person ?works ?work .
? FILTER (?works in (<http://dbpedia.org/property/works>,
<http://dbpedia.org/property/notableworks>,
<http://dbpedia.org/property/writer>) )
}
FILTER(?deathDate >= "1941-01-01"^^xsd:date) .
FILTER(?deathDate <= "1942-01-01"^^xsd:date) .
}



[1]
http://dbpedia.org/snorql/?query=SELECT+count+%28*%29+WHERE+{%0D%0A%3Fperson+%3Chttp%3A%2F%2Fdbpedia.org%2Fontology%2FdeathDate%3E+%3FdeathDate+.%0D%0A%3Fperson+%3Chttp%3A%2F%2Fxmlns.com%2Ffoaf%2F0.1%2Fpage%3E+%3Fpage+.%0D%0A}

[2]
http://dbpedia.org/snorql/?query=SELECT+*+WHERE+{%0D%0A%3Fperson+%3Chttp%3A%2F%2Fdbpedia.org%2Fontology%2FdeathDate%3E+%3FdeathDate+.%0D%0A%3Fperson+%3Chttp%3A%2F%2Fxmlns.com%2Ffoaf%2F0.1%2Fpage%3E+%3Fpage+.%0D%0AFILTER%28%3FdeathDate+%3E%3D+%221941-01-01%22^^xsd%3Adate%29+%0D%0AFILTER%28%3FdeathDate+%3C%3D+%221942-01-01%22^^xsd%3Adate%29+%0D%0A}+order+by+%3FdeathDate%0D%0ALimit+1000+%0D%0AOFFSET+0

[3]
http://dbpedia.org/snorql/?query=SELECT+*+WHERE+{%0D%0A%3Fperson+%3Chttp%3A%2F%2Fdbpedia.org%2Fontology%2FdeathDate%3E+%3FdeathDate+.%0D%0A%3Fperson+%3Chttp%3A%2F%2Fxmlns.com%2Ffoaf%2F0.1%2Fpage%3E+%3Fpage+.%0D%0A%3Fperson+rdf%3Atype+%3Chttp%3A%2F%2Fdbpedia.org%2Fontology%2FArtist%3E+%0D%0AFILTER%28%3FdeathDate+%3E%3D+%221941-01-01%22^^xsd%3Adate%29+%0D%0AFILTER%28%3FdeathDate+%3C%3D+%221942-01-01%22^^xsd%3Adate%29+%0D%0A}+

[4]
http://dbpedia.org/snorql/?query=SELECT+*+WHERE+{%0D%0A%3Fperson+%3Chttp%3A%2F%2Fdbpedia.org%2Fontology%2FdeathDate%3E+%3FdeathDate+.%0D%0A%3Fperson+rdf%3Atype+%3Chttp%3A%2F%2Fdbpedia.org%2Fontology%2FArtist%3E+.%0D%0A%3Fperson+%3Chttp%3A%2F%2Fxmlns.com%2Ffoaf%2F0.1%2Fpage%3E+%3Fpage+.%0D%0A%0D%0AOPTIONAL+{%0D%0A++%3Fperson+%3Fworks+%3Fwork+.%0D%0A++FILTER+%28%3Fworks+in+%28%3Chttp%3A%2F%2Fdbpedia.org%2Fproperty%2Fworks%3E%2C+%3Chttp%3A%2F%2Fdbpedia.org%2Fproperty%2Fnotableworks%3E%2C+%3Chttp%3A%2F%2Fdbpedia.org%2Fproperty%2Fwriter%3E%29+%29%0D%0A}%0D%0AFILTER%28%3FdeathDate+%3E%3D+%221941-01-01%22^^xsd%3Adate%29+.%0D%0AFILTER%28%3FdeathDate+%3C%3D+%221942-01-01%22^^xsd%3Adate%29+.%0D%0A}+%0D%0A


On 12/23/2011 01:35 PM, Alek Tarkowski wrote:
> Hello everyone,
>
> I've been until now a lurker on this list, let me introduce myself - I'm
> a sociologist studying digital technologies, an activist (I run Creative
> Commons Poland) and I run a digital think tank / NGO in Poland.
>
> I'm hoping someone on this list might be able to help me: I'm involved
> in the celebrations of the Public Domain Day - on the 1st of January
> each year works pass into the public domain of authors who've died 70
> years ago (at least in Poland, and in most countries, but it might
> differ in some jurisdictions).
>
> I'm looking for a good way to determine, who died in 1941 - and thought
> that Wikipedia will be a good place to find this out. I know there are
> lists of people who died in a given year, but they are not complete. Is
> there any way to automatically query Wikipedia for such information? I
> know that it's to some extent structured, as this information is
> provided in templates for biographical articles, but I don't know
> whether there is any mechanism for querying?
>
> Any advice will be much appreciated.
>
> All the best,
>
> Alek
>


--
Dipl. Inf. Sebastian Hellmann
Department of Computer Science, University of Leipzig
Projects:http://nlp2rdf.org ?,http://dbpedia.org
Homepage:http://bis.informatik.uni-leipzig.de/SebastianHellmann
Research Group:http://aksw.org


_______________________________________________
Wiki-research-l mailing list
Wiki-research-l at lists.wikimedia.org
https://lists.wikimedia.org/mailman/listinfo/wiki-research-l

From jongbhak at yahoo.com  Mon Dec 26 12:23:19 2011
From: jongbhak at yahoo.com (Jong Bhak)
Date: Mon, 26 Dec 2011 09:23:19 -0800 (PST)
Subject: [Pdbwiki-devel] taking and updating wikipedia genes to PDBwiki
In-Reply-To: <CAPBO=2kvXQNGf8-99=-z877mHOzti+pSjM91wpogeSxFjbZJ2w@mail.gmail.com>
References: <AANLkTikifTNoYFz6nrp7EwW_twV3VGHhPwQbLYgzUPcp@mail.gmail.com>
	<AANLkTin=h=x27eCcKK+rhRYmAx31uCNNSDPx+aVLbT-6@mail.gmail.com>
	<AANLkTi=7kPc7tqKq6TWENW_7kguRDR1XpUQFmSCoDD7P@mail.gmail.com>
	<CAPBO=2k_XYz9dzFJQFqEWXDxSAWUJq__BE+yAfyP3GPhM4Q56Q@mail.gmail.com>
	<1324830736.55273.YahooMailNeo@web112403.mail.gq1.yahoo.com>
	<CAPBO=2kvXQNGf8-99=-z877mHOzti+pSjM91wpogeSxFjbZJ2w@mail.gmail.com>
Message-ID: <1324920199.46382.YahooMailNeo@web112414.mail.gq1.yahoo.com>

Hi,
?
Think it as a holiday. We can talk about
anything.
If you have any friends you want to invite,
please let me know.


?
Jong Bhak,

\(^o^)/
Tel: 031-888-9311, Fax: 031-888-9314, Mobile: 010 9944 6754


>________________________________
> From: Dan Bolser <dan.bolser at gmail.com>
>To: Jong Bhak <jongbhak at yahoo.com> 
>Cc: Jong Bhak <jongbhak at gmail.com>; "pdbwiki-devel at bioinformatics.org" <pdbwiki-devel at bioinformatics.org> 
>Sent: Tuesday, December 27, 2011 1:06 AM
>Subject: Re: taking and updating wikipedia genes to PDBwiki
> 
>23rd looks OK for me provisionally.
>
>I'd love to attend another bioconference, but it seems a long way to
>go just to talk about PDBWiki!
>
>Could be really fun though!
>
>On 25 December 2011 16:32, Jong Bhak <jongbhak at yahoo.com> wrote:
>> Hi,
>>
>> I fully agree.
>> Can you come to Korea on 23rd Feb?
>> I have the second bioconference and you
>> can talk about it.
>>
>> Take care
>>
>>
>>
>> Jong Bhak,
>>
>> \(^o^)/
>> Tel: 031-888-9311, Fax: 031-888-9314, Mobile: 010 9944 6754
>>
>> From: Dan Bolser <dan.bolser at gmail.com>
>> To: Jong Bhak <jongbhak at gmail.com>
>> Cc: pdbwiki-devel at bioinformatics.org
>> Sent: Sunday, December 25, 2011 11:28 PM
>> Subject: Re: taking and updating wikipedia genes to PDBwiki
>>
>> Wow, two years have passed already, and I haven't looked at doing any of
>> this! We need an international PDBWiki week once a year to focus our
>> attention!
>> Maybe some time in March?
>> Happy Christmas!
>> Dan.
>> On 27 Dec 2010 04:05, "Jong Bhak" <jongbhak at gmail.com> wrote:
>>
>> Thanks. Also, Jmol on the site will be good. To turn them
>> around?a bit.
>> Cheers
>>
>> Jong
>>
>>
>>
>>
>>
>>
>>
>>
>> On Mon, Dec 27, 2010 at 6:56 AM, Dan Bolser <dan.bolser at gmail.com> wrote:
>>
>> Hi Jong,
>>
>> Yup, all this is possible. I like the idea to add links to Wikipedia
>> from PDBWiki.
>>
>> We do have the EC terms in PDBWiki as categories, but we didn't add GO
>> because its a 'different kind of category'... for this we were
>> thinking of developing PDBWiki using the functionality of Semantic
>> MediaWiki, but we haven't really worked out how to do that 'properly'.
>> I guess we should rather do it piecemeal and see what works?
>>
>>
>> Happy X-mass and new-year to you too!
>>
>>
>> Dan.
>>
>> On 26 December 2010 16:47, Jong Bhak <jongbhak at gmail.com> wrote:
>>> Hi Dan,
>>>
>>> Can you copy wikipedia's gene and protein names that appear in PDBwiki
>>> and actually store them in PDBwiki? And make a script that automates
>>> the text every month?
>>>
>>> Also, can you add Wikipedia's link to PDB entries under Links section?
>>>
>>> Also, can you make a fuctional category in PDBwiki using GO?
>>> and put lists of genes/proteins in the category so that I can
>>> browser functionally linked 3D domains with annotated information?
>>>
>>> Thanks
>>>
>>> Happy new year!
>>> Jong
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>>
>>
>
>
>   
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