Fantastic! Can't wait to see the blog post about this. -ginger
-----Original Message----- From: wikidata-l-bounces@lists.wikimedia.org [mailto:wikidata-l-bounces@lists.wikimedia.org] On Behalf Of wikidata-l-request@lists.wikimedia.org Sent: Tuesday, October 07, 2014 5:01 AM To: wikidata-l@lists.wikimedia.org Subject: Wikidata-l Digest, Vol 35, Issue 7
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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)
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Message: 1 Date: Mon, 6 Oct 2014 17:22:48 +0200 From: Thomas Douillard thomas.douillard@gmail.com To: "Discussion list for the Wikidata project." wikidata-l@lists.wikimedia.org Cc: Alan Ruttenberg alanruttenberg@gmail.com, Janna Hastings hastings@ebi.ac.uk Subject: Re: [Wikidata-l] Item both subclass and instance? Message-ID: CAHYhspY7OM_M4fcfspGVD84J7kgsu4WWdsN2qhEEq3-_GdDCJg@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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 dacuetu@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.wiki@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
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Message: 2 Date: Mon, 6 Oct 2014 13:21:50 -0700 From: Benjamin Good ben.mcgee.good@gmail.com To: "Discussion list for the Wikidata project." wikidata-l@lists.wikimedia.org Cc: Marco Roos marco.roos.nl@gmail.com Subject: [Wikidata-l] all human genes are now wikidata items Message-ID: CALNM3EpJhc7xsxda8tKp1WRUh9WSS+vpj5m8UsGEg8gF=p6+TA@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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
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Message: 3 Date: Mon, 06 Oct 2014 20:23:55 +0000 From: Denny Vrandečić vrandecic@google.com To: "Discussion list for the Wikidata project." wikidata-l@lists.wikimedia.org Cc: Marco Roos marco.roos.nl@gmail.com Subject: Re: [Wikidata-l] all human genes are now wikidata items Message-ID: CAFXBQpGdYOU06wKE_5wxYL7LHz8eocty8CcyoS3gV8N9rBbFDg@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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.good@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 andra@micelio.be To: "Discussion list for the Wikidata project." wikidata-l@lists.wikimedia.org Cc: Marco Roos marco.roos.nl@gmail.com Subject: Re: [Wikidata-l] all human genes are now wikidata items Message-ID: CAMNM0fWjucERv51FxCR7BiRwY6H2cBx_TZJO-bCBTsL_M+pRxA@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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 vrandecic@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.good@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.good@gmail.com To: "Discussion list for the Wikidata project." wikidata-l@lists.wikimedia.org Cc: Marco Roos marco.roos.nl@gmail.com Subject: Re: [Wikidata-l] all human genes are now wikidata items Message-ID: CALNM3Ep7d3KS7QSLLAG9uD5SoU-PyOxdwP=O_AX_QxK=bhK=qg@mail.gmail.com Content-Type: text/plain; charset="utf-8"
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 vrandecic@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.good@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.pintscher@wikimedia.de To: "Discussion list for the Wikidata project." wikidata-l@lists.wikimedia.org, Jens Ohlig jens.ohlig@wikimedia.de Cc: Marco Roos marco.roos.nl@gmail.com Subject: Re: [Wikidata-l] all human genes are now wikidata items Message-ID: CABfqUgKMt2e5tCcnera1KPzaePviADSbOmHn_JHLcWN6WLTyrQ@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.good@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.good@gmail.com To: "Discussion list for the Wikidata project." wikidata-l@lists.wikimedia.org Cc: Marco Roos marco.roos.nl@gmail.com Subject: Re: [Wikidata-l] all human genes are now wikidata items Message-ID: CALNM3EpDR0=rWAkQ6xXhb1EZQM19z5bdz3ifWu6CZO5wk4BU1Q@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.pintscher@wikimedia.de> wrote:
Hey Ben and Andra,
On Mon, Oct 6, 2014 at 10:30 PM, Benjamin Good ben.mcgee.good@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.pintscher@wikimedia.de To: "Discussion list for the Wikidata project." wikidata-l@lists.wikimedia.org Cc: Marco Roos marco.roos.nl@gmail.com Subject: Re: [Wikidata-l] all human genes are now wikidata items Message-ID: CABfqUgJ44Y9jKfsTpHVd35k50TkuDHuZn6U52wcXt2AnNZpRQw@mail.gmail.com Content-Type: text/plain; charset=UTF-8
On Mon, Oct 6, 2014 at 10:48 PM, Benjamin Good ben.mcgee.good@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.good@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: CALNM3Eorng21XaiHrsjcS2LtXdvObqnHH8P41TNR6BU40iC1EQ@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.pintscher@wikimedia.de> wrote:
On Mon, Oct 6, 2014 at 10:48 PM, Benjamin Good ben.mcgee.good@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 martinelliluca@gmail.com To: "Discussion list for the Wikidata project." wikidata-l@lists.wikimedia.org Cc: Marco Roos marco.roos.nl@gmail.com Subject: Re: [Wikidata-l] all human genes are now wikidata items Message-ID: CADmzhVTQLD_u-Muyah_k1DhciWH2Q0ubtmvc4jQZOcR_Mz8LbA@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.good@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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End of Wikidata-l Digest, Vol 35, Issue 7 *****************************************
This sounds important, but what sort of queries might someone want to run on this data? Despite working at a bio-lab, I am actually not terribly familiar with the human genome and therefore the types of questions having this data on Wikidata can answer.
Does anyone have a few example queries (don't have to be possible to execute right now) to show what this could be used for?
Thank you, Derric Atzrott
For one thing, they could serve as an alternative, stable identifier.
You can link up different, external identifiers, such as Entrez and HGNC: https://tools.wmflabs.org/wikidata-todo/beacon.php?prop=351&source=354
(you can probably do that elsewhere, but Wikidata should attract more ID systems over time).
You can look up the Entrez ID: https://tools.wmflabs.org/wikidata-todo/autolist2.php?language=en&projec...
You can ask "which genes encode proteins that are involved in cell cycle checkpointing?": https://tools.wmflabs.org/wikidata-todo/autolist2.php?language=en&projec...
Once we get "typed quantities" (how's that coming along??), you can also query on chromosome/region.
On Wed, Oct 8, 2014 at 2:28 PM, Derric Atzrott <datzrott@alizeepathology.com
wrote:
This sounds important, but what sort of queries might someone want to run on this data? Despite working at a bio-lab, I am actually not terribly familiar with the human genome and therefore the types of questions having this data on Wikidata can answer.
Does anyone have a few example queries (don't have to be possible to execute right now) to show what this could be used for?
Thank you, Derric Atzrott
Wikidata-l mailing list Wikidata-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wikidata-l
Magnus is right on here. We are hoping to begin things by establishing wikidata as a central hub for gene identifier lookup and matching. (This is a big a problem in bioinformatics). With this (hopefully fairly bit stable) starting point of wikidata entities, we will be expanding the statements attached to the genes to enable many different kinds of queries. For example, "what genes that encode proteins that are located in the cell membrane are known to be related to alzheimer's disease?". In particular we are hoping to build a network of relationships between genes, drugs, and diseases..
So, for now identifier matching queries, tomorrow the world ;).
And more importantly.. Given these gene starting points in the wikidata entity space, we can do queries over whatever anyone else decides to hook up to them! Go nuts! (but add your evidence please..)
-Ben
On Wed, Oct 8, 2014 at 7:47 AM, Magnus Manske magnusmanske@googlemail.com wrote:
For one thing, they could serve as an alternative, stable identifier.
You can link up different, external identifiers, such as Entrez and HGNC: https://tools.wmflabs.org/wikidata-todo/beacon.php?prop=351&source=354
(you can probably do that elsewhere, but Wikidata should attract more ID systems over time).
You can look up the Entrez ID:
https://tools.wmflabs.org/wikidata-todo/autolist2.php?language=en&projec...
You can ask "which genes encode proteins that are involved in cell cycle checkpointing?":
https://tools.wmflabs.org/wikidata-todo/autolist2.php?language=en&projec...
Once we get "typed quantities" (how's that coming along??), you can also query on chromosome/region.
On Wed, Oct 8, 2014 at 2:28 PM, Derric Atzrott < datzrott@alizeepathology.com> wrote:
This sounds important, but what sort of queries might someone want to run on this data? Despite working at a bio-lab, I am actually not terribly familiar with the human genome and therefore the types of questions having this data on Wikidata can answer.
Does anyone have a few example queries (don't have to be possible to execute right now) to show what this could be used for?
Thank you, Derric Atzrott
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