Fantastic! Can't wait to see the blog post about this.
-ginger
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Today's Topics:
1. Re: Item both subclass and instance? (Thomas Douillard)
2. all human genes are now wikidata items (Benjamin Good)
3. Re: all human genes are now wikidata items (Denny Vrandečić)
4. Re: all human genes are now wikidata items (Andra Waagmeester)
5. Re: all human genes are now wikidata items (Benjamin Good)
6. Re: all human genes are now wikidata items (Lydia Pintscher)
7. Re: all human genes are now wikidata items (Benjamin Good)
8. Re: all human genes are now wikidata items (Lydia Pintscher)
9. Re: all human genes are now wikidata items (Benjamin Good)
10. Re: all human genes are now wikidata items (Luca Martinelli)
----------------------------------------------------------------------
Message: 1
Date: Mon, 6 Oct 2014 17:22:48 +0200
From: Thomas Douillard <thomas.douill...@gmail.com>
To: "Discussion list for the Wikidata project."
<wikidata-l@lists.wikimedia.org>
Cc: Alan Ruttenberg <alanruttenb...@gmail.com>, Janna Hastings
<hasti...@ebi.ac.uk>
Subject: Re: [Wikidata-l] Item both subclass and instance?
Message-ID:
<cahyhspy7om_m4fcfspgvd84j7kgsu4wwdsn2qheeq3-_gdd...@mail.gmail.com>
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Sorry Micru, I read your document, but I can't see a relation beetween ethanol,
negenthropy, and Wikidata's survival :)
2014-10-05 22:48 GMT+02:00 David Cuenca <dacu...@gmail.com>:
> Hi Eric,
>
> The idea is to separate in those edge cases the perceptual model (what
> is
> recognized) from the name given to it. As such you can consider "ethanol"
> and "chemical compound" metaclasses (names) pointing to a label-less
> class that represents the model.
>
> In practical terms what it would entail is:
> - remove the labels from Q153
> - create one item for the label "ethanol" and one item for the label
> "chemical compound"
> - link Q153 with those names using "has name"
> - "ethanol" is no longer an instance, but a class that can take
> different names, "ethanol" being more specific
>
> Do you realize that after this "scrap everything and start again from
> the beginning" the resulting structure is more comprehensive and
> encompasses previous efforts? "Entity" stays as it is, but now it can
> be examined by its qualities and they can be taken apart if needed. The term
> "cognizable"
> is 1:1 compatible with the subclass/instance model, but it emphasizes
> the necessity of having an observer for it to be meaningful. Classes
> do not exist in isolation, it is in fact very naive to keep the notion
> of objectivity when dealing with observation. Even logic needs a
> system to be executed, and based on which reality models? How were
> they produced? And how are those models and the models based on them
> verified? The problem with logicians is that they think themselves
> isolated from the world, however even they were born from a womb.
>
> And have you seen who introduced the term "negentropy"? If you check
> the names behind it you will see that those ideas are in fact standing
> on the shoulders of giants. It is hard to model life without
> understanding first that life itself is survival-oriented.
>
> Those papers are interesting but fail to address basic questions like:
> who decides identity? How does the observer interact with it? Where
> does information come from? And without tackling those questions, and
> by extension, emergent processes, logic seems like a deux ex machina
> that appears from nothingness and acts in nothingness.
>
> Best,
> Micru
>
> On Sun, Oct 5, 2014 at 6:49 PM, Emw <emw.w...@gmail.com> wrote:
>
>> Hi David,
>>
>> How does your treatise relate to the fact that
>> https://www.wikidata.org/wiki/Q153 has statements that entail the
>> following? [1]
>>
>> ethanol
>> *instance of* chemical compound
>> *subclass of* chemical compound
>>
>> How would it resolve that specific problem?
>>
>> Such statements make Wikidata incompatible with ChEBI and other major
>> ontologies, like Gene Ontology and Disease Ontology, which use
>> *instance
>> of* (i.e. rdf:type, P31) and *subclass of* (i.e. rdfs:subClassOf,
>> P279,
>> is_a) as recommended in the Relation Ontology (RO) [2] and the Basic
>> Formal Ontology (BFO).
>>
>> For Wikidata to be interoperable with other major ontologies in the
>> Semantic Web, we cannot "scrap everything and start again from the
>> beginning". We must stand on the shoulders of giants. Doing away
>> with "entity" [3] as a the top of the *subclass of* hierarchy and
>> introducing a raft of idiosyncratic ontological constructs like
>> "identifiables", "cognizables", "negentropy" and "system
>> survival-oriented direction" to Wikidata is probably not the way to go.
>>
>> Regarding your concerns about the ability of existing approaches to
>> represent emergent properties and natural language, I recommend
>> perusing [4], an influential paper that informs DOLCE and BFO --
>> particularly the section on "The Role of Identity Criteria". I also
>> highly recommend lectures 3 and 1 in
>> http://ontology.buffalo.edu/smith/IntroOntology_Course.html for
>> gaining a perspective on how BFO maintainers think about things like
>> distinguishing objects and representations, and that upper ontology's
>> philosophical roots. Given your interest in phenomenology and
>> Husserl, you may also be interested in what BFO maintainers have written on
>> those subjects in e.g.
>> [5] with regard to ontology.
>>
>> Best,
>> Eric
>>
>> [1] https://www.wikidata.org/wiki/Q153 currently states "ethanol
>> *subclass
>> of* alcohol", but given "alcohol *subclass of* organic compound" and
>> "organic compound *subclass of* chemical compound", it is entailed
>> that "ethanol *subclass of* chemical compound".
>> [2] Barry Smith et al. (2005). *Relations in Biomedical Ontologies*.
>> http://genomebiology.com/2005/6/5/r46
>> [3] "Entity" item on Wikidata. https://www.wikidata.org/wiki/Q35120.
>> Mapped to owl:Thing.
>> [4] Nicola Guarino (1998). *Some Ontological Principles for Designing
>> Upper Level Lexical Resources*.
>> http://arxiv.org/pdf/cmp-lg/9809002v1
>> [5] Barry Smith (1989). *Husserl: Logic and Formal Ontology*.
>> http://ontology.buffalo.edu/smith/articles/lfo.html
>>
>
>
>
> --
> Etiamsi omnes, ego non
>
> _______________________________________________
> Wikidata-l mailing list
> Wikidata-l@lists.wikimedia.org
> https://lists.wikimedia.org/mailman/listinfo/wikidata-l
>
>
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Message: 2
Date: Mon, 6 Oct 2014 13:21:50 -0700
From: Benjamin Good <ben.mcgee.g...@gmail.com>
To: "Discussion list for the Wikidata project."
<wikidata-l@lists.wikimedia.org>
Cc: Marco Roos <marco.roos...@gmail.com>
Subject: [Wikidata-l] all human genes are now wikidata items
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I thought folks might like to know that every human gene (according to the
United States National Center for Biotechnology Information) now has a
representative entity on wikidata. I hope that these are the seeds for some
amazing applications in biology and medicine.
Well done Andra and ProteinBoxBot !
For example:
Here is one (of approximately 40,000) called "spinocerebellar ataxia 37"
https://www.wikidata.org/wiki/Q18081265
-Ben
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Message: 3
Date: Mon, 06 Oct 2014 20:23:55 +0000
From: Denny Vrandečić <vrande...@google.com>
To: "Discussion list for the Wikidata project."
<wikidata-l@lists.wikimedia.org>
Cc: Marco Roos <marco.roos...@gmail.com>
Subject: Re: [Wikidata-l] all human genes are now wikidata items
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Wow! That's pretty cool work!
Do you have any plans to keep the data fresh?
On Mon Oct 06 2014 at 1:22:12 PM Benjamin Good <ben.mcgee.g...@gmail.com>
wrote:
> I thought folks might like to know that every human gene (according to
> the United States National Center for Biotechnology Information) now
> has a representative entity on wikidata. I hope that these are the
> seeds for some amazing applications in biology and medicine.
>
> Well done Andra and ProteinBoxBot !
>
> For example:
> Here is one (of approximately 40,000) called "spinocerebellar ataxia 37"
> https://www.wikidata.org/wiki/Q18081265
>
> -Ben
> _______________________________________________
> Wikidata-l mailing list
> Wikidata-l@lists.wikimedia.org
> https://lists.wikimedia.org/mailman/listinfo/wikidata-l
>
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Message: 4
Date: Mon, 6 Oct 2014 22:29:03 +0200
From: Andra Waagmeester <an...@micelio.be>
To: "Discussion list for the Wikidata project."
<wikidata-l@lists.wikimedia.org>
Cc: Marco Roos <marco.roos...@gmail.com>
Subject: Re: [Wikidata-l] all human genes are now wikidata items
Message-ID:
<camnm0fwjucerv51fxcr7birwy6h2cbx_tzjo-bcbtsl_m+p...@mail.gmail.com>
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Yes we plan to keep the data fresh. We are currently looking into optimising
the current bot to increase the throughput and also in ways to automate the
update process.
On Mon, Oct 6, 2014 at 10:23 PM, Denny Vrandečić <vrande...@google.com>
wrote:
> Wow! That's pretty cool work!
>
> Do you have any plans to keep the data fresh?
>
> On Mon Oct 06 2014 at 1:22:12 PM Benjamin Good
> <ben.mcgee.g...@gmail.com>
> wrote:
>
>> I thought folks might like to know that every human gene (according
>> to the United States National Center for Biotechnology Information)
>> now has a representative entity on wikidata. I hope that these are
>> the seeds for some amazing applications in biology and medicine.
>>
>> Well done Andra and ProteinBoxBot !
>>
>> For example:
>> Here is one (of approximately 40,000) called "spinocerebellar ataxia 37"
>> https://www.wikidata.org/wiki/Q18081265
>>
>> -Ben
>> _______________________________________________
>> Wikidata-l mailing list
>> Wikidata-l@lists.wikimedia.org
>> https://lists.wikimedia.org/mailman/listinfo/wikidata-l
>>
>
> _______________________________________________
> Wikidata-l mailing list
> Wikidata-l@lists.wikimedia.org
> https://lists.wikimedia.org/mailman/listinfo/wikidata-l
>
>
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Message: 5
Date: Mon, 6 Oct 2014 13:30:59 -0700
From: Benjamin Good <ben.mcgee.g...@gmail.com>
To: "Discussion list for the Wikidata project."
<wikidata-l@lists.wikimedia.org>
Cc: Marco Roos <marco.roos...@gmail.com>
Subject: Re: [Wikidata-l] all human genes are now wikidata items
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<CALNM3Ep7d3KS7QSLLAG9uD5SoU-PyOxdwP=O_AX_QxK=bhK=q...@mail.gmail.com>
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Yes indeed we do. Andra is working on a scheduler for the update bot now.
(And thanks to the tips about wbeditentity function it should go faster
now...)
We have a grant to expand the scope of the original gene wiki project (
https://en.wikipedia.org/wiki/Gene_Wiki) to a) use wikidata as its structural
foundation and b) expand into other areas such as genes and diseases.
Looking forward to continuing to work with the community to make wikidata a key
hub of open biological and medical information on the Web.
-Ben
On Mon, Oct 6, 2014 at 1:23 PM, Denny Vrandečić <vrande...@google.com>
wrote:
> Wow! That's pretty cool work!
>
> Do you have any plans to keep the data fresh?
>
> On Mon Oct 06 2014 at 1:22:12 PM Benjamin Good
> <ben.mcgee.g...@gmail.com>
> wrote:
>
>> I thought folks might like to know that every human gene (according
>> to the United States National Center for Biotechnology Information)
>> now has a representative entity on wikidata. I hope that these are
>> the seeds for some amazing applications in biology and medicine.
>>
>> Well done Andra and ProteinBoxBot !
>>
>> For example:
>> Here is one (of approximately 40,000) called "spinocerebellar ataxia 37"
>> https://www.wikidata.org/wiki/Q18081265
>>
>> -Ben
>> _______________________________________________
>> Wikidata-l mailing list
>> Wikidata-l@lists.wikimedia.org
>> https://lists.wikimedia.org/mailman/listinfo/wikidata-l
>>
>
> _______________________________________________
> Wikidata-l mailing list
> Wikidata-l@lists.wikimedia.org
> https://lists.wikimedia.org/mailman/listinfo/wikidata-l
>
>
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Message: 6
Date: Mon, 6 Oct 2014 22:40:19 +0200
From: Lydia Pintscher <lydia.pintsc...@wikimedia.de>
To: "Discussion list for the Wikidata project."
<wikidata-l@lists.wikimedia.org>, Jens Ohlig <jens.oh...@wikimedia.de>
Cc: Marco Roos <marco.roos...@gmail.com>
Subject: Re: [Wikidata-l] all human genes are now wikidata items
Message-ID:
<cabfqugkmt2e5tccnera1kpzaepviadsbomhn_jhlcwn6wlt...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
Hey Ben and Andra,
On Mon, Oct 6, 2014 at 10:30 PM, Benjamin Good <ben.mcgee.g...@gmail.com> wrote:
> Yes indeed we do. Andra is working on a scheduler for the update bot now.
> (And thanks to the tips about wbeditentity function it should go
> faster
> now...)
>
> We have a grant to expand the scope of the original gene wiki project
> (https://en.wikipedia.org/wiki/Gene_Wiki) to a) use wikidata as its
> structural foundation and b) expand into other areas such as genes and
> diseases.
>
> Looking forward to continuing to work with the community to make
> wikidata a key hub of open biological and medical information on the Web.
That's really great news!
Would you be willing to write a blog post about what you did, your plans for
the future and why this is awesome? Jens can work with you on getting that
published on our blog. We ran a few lately and your project sounds like it
should get a bit ore exposure ;-) http://blog.wikimedia.de/tag/wikidata/
Cheers
Lydia
--
Lydia Pintscher - http://about.me/lydia.pintscher Product Manager for Wikidata
Wikimedia Deutschland e.V.
Tempelhofer Ufer 23-24
10963 Berlin
www.wikimedia.de
Wikimedia Deutschland - Gesellschaft zur Förderung Freien Wissens e. V.
Eingetragen im Vereinsregister des Amtsgerichts Berlin-Charlottenburg unter der
Nummer 23855 Nz. Als gemeinnützig anerkannt durch das Finanzamt für
Körperschaften I Berlin, Steuernummer 27/681/51985.
------------------------------
Message: 7
Date: Mon, 6 Oct 2014 13:48:45 -0700
From: Benjamin Good <ben.mcgee.g...@gmail.com>
To: "Discussion list for the Wikidata project."
<wikidata-l@lists.wikimedia.org>
Cc: Marco Roos <marco.roos...@gmail.com>
Subject: Re: [Wikidata-l] all human genes are now wikidata items
Message-ID:
<CALNM3EpDR0=rwakq6xxhb1ezqm19z5bdz3ifwu6czo5wk4b...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Would be happy to. Let me know suggested size and how to get it over to you.
thanks
-Ben
On Mon, Oct 6, 2014 at 1:40 PM, Lydia Pintscher < lydia.pintsc...@wikimedia.de>
wrote:
> Hey Ben and Andra,
>
> On Mon, Oct 6, 2014 at 10:30 PM, Benjamin Good
> <ben.mcgee.g...@gmail.com>
> wrote:
> > Yes indeed we do. Andra is working on a scheduler for the update
> > bot
> now.
> > (And thanks to the tips about wbeditentity function it should go
> > faster
> > now...)
> >
> > We have a grant to expand the scope of the original gene wiki
> > project
> > (https://en.wikipedia.org/wiki/Gene_Wiki) to a) use wikidata as its
> > structural foundation and b) expand into other areas such as genes
> > and diseases.
> >
> > Looking forward to continuing to work with the community to make
> wikidata a
> > key hub of open biological and medical information on the Web.
>
> That's really great news!
> Would you be willing to write a blog post about what you did, your
> plans for the future and why this is awesome? Jens can work with you
> on getting that published on our blog. We ran a few lately and your
> project sounds like it should get a bit ore exposure ;-)
> http://blog.wikimedia.de/tag/wikidata/
>
>
> Cheers
> Lydia
>
> --
> Lydia Pintscher - http://about.me/lydia.pintscher Product Manager for
> Wikidata
>
> Wikimedia Deutschland e.V.
> Tempelhofer Ufer 23-24
> 10963 Berlin
> www.wikimedia.de
>
> Wikimedia Deutschland - Gesellschaft zur Förderung Freien Wissens e. V.
>
> Eingetragen im Vereinsregister des Amtsgerichts Berlin-Charlottenburg
> unter der Nummer 23855 Nz. Als gemeinnützig anerkannt durch das
> Finanzamt für Körperschaften I Berlin, Steuernummer 27/681/51985.
>
> _______________________________________________
> Wikidata-l mailing list
> Wikidata-l@lists.wikimedia.org
> https://lists.wikimedia.org/mailman/listinfo/wikidata-l
>
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Message: 8
Date: Mon, 6 Oct 2014 22:53:36 +0200
From: Lydia Pintscher <lydia.pintsc...@wikimedia.de>
To: "Discussion list for the Wikidata project."
<wikidata-l@lists.wikimedia.org>
Cc: Marco Roos <marco.roos...@gmail.com>
Subject: Re: [Wikidata-l] all human genes are now wikidata items
Message-ID:
<cabfqugj44y9jkfstphvd35k50tkudhuzn6u52wcxt2annzp...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
On Mon, Oct 6, 2014 at 10:48 PM, Benjamin Good <ben.mcgee.g...@gmail.com> wrote:
> Would be happy to. Let me know suggested size and how to get it over
> to you.
Sweet. As long as you want. Don't write a novel ;-) Pictures are a plus. One or
two pages is a good goal.
Just send it to Jens and CC me. We'll get it published asap then.
Cheers
Lydia
--
Lydia Pintscher - http://about.me/lydia.pintscher Product Manager for Wikidata
Wikimedia Deutschland e.V.
Tempelhofer Ufer 23-24
10963 Berlin
www.wikimedia.de
Wikimedia Deutschland - Gesellschaft zur Förderung Freien Wissens e. V.
Eingetragen im Vereinsregister des Amtsgerichts Berlin-Charlottenburg unter der
Nummer 23855 Nz. Als gemeinnützig anerkannt durch das Finanzamt für
Körperschaften I Berlin, Steuernummer 27/681/51985.
------------------------------
Message: 9
Date: Mon, 6 Oct 2014 13:56:47 -0700
From: Benjamin Good <ben.mcgee.g...@gmail.com>
To: "Discussion list for the Wikidata project."
<wikidata-l@lists.wikimedia.org>
Subject: Re: [Wikidata-l] all human genes are now wikidata items
Message-ID:
<calnm3eorng21xaihrsjcs2ltxdvobqnhh8p41tnr6bu40ic...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Sounds good. Will do.
On Mon, Oct 6, 2014 at 1:53 PM, Lydia Pintscher < lydia.pintsc...@wikimedia.de>
wrote:
> On Mon, Oct 6, 2014 at 10:48 PM, Benjamin Good
> <ben.mcgee.g...@gmail.com>
> wrote:
> > Would be happy to. Let me know suggested size and how to get it
> > over to you.
>
> Sweet. As long as you want. Don't write a novel ;-) Pictures are a
> plus. One or two pages is a good goal.
> Just send it to Jens and CC me. We'll get it published asap then.
>
>
> Cheers
> Lydia
>
> --
> Lydia Pintscher - http://about.me/lydia.pintscher Product Manager for
> Wikidata
>
> Wikimedia Deutschland e.V.
> Tempelhofer Ufer 23-24
> 10963 Berlin
> www.wikimedia.de
>
> Wikimedia Deutschland - Gesellschaft zur Förderung Freien Wissens e. V.
>
> Eingetragen im Vereinsregister des Amtsgerichts Berlin-Charlottenburg
> unter der Nummer 23855 Nz. Als gemeinnützig anerkannt durch das
> Finanzamt für Körperschaften I Berlin, Steuernummer 27/681/51985.
>
> _______________________________________________
> Wikidata-l mailing list
> Wikidata-l@lists.wikimedia.org
> https://lists.wikimedia.org/mailman/listinfo/wikidata-l
>
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Message: 10
Date: Tue, 7 Oct 2014 13:56:44 +0200
From: Luca Martinelli <martinellil...@gmail.com>
To: "Discussion list for the Wikidata project."
<wikidata-l@lists.wikimedia.org>
Cc: Marco Roos <marco.roos...@gmail.com>
Subject: Re: [Wikidata-l] all human genes are now wikidata items
Message-ID:
<cadmzhvtqld_u-muyah_k1dhciwh2q0ubtmvc4jqzocr_mz8...@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8
This is absolutely awesome! Congratulations for your work!
L.
2014-10-06 22:21 GMT+02:00 Benjamin Good <ben.mcgee.g...@gmail.com>:
> I thought folks might like to know that every human gene (according to
> the United States National Center for Biotechnology Information) now
> has a representative entity on wikidata. I hope that these are the
> seeds for some amazing applications in biology and medicine.
>
> Well done Andra and ProteinBoxBot !
>
> For example:
> Here is one (of approximately 40,000) called "spinocerebellar ataxia 37"
> https://www.wikidata.org/wiki/Q18081265
>
> -Ben
>
> _______________________________________________
> Wikidata-l mailing list
> Wikidata-l@lists.wikimedia.org
> https://lists.wikimedia.org/mailman/listinfo/wikidata-l
>
--
Luca "Sannita" Martinelli
http://it.wikipedia.org/wiki/Utente:Sannita
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