[Data-modeling] help
François Lamotte
paperjam at gmail.com
Thu Jun 12 20:48:01 UTC 2008
On Thu, Jun 12, 2008 at 10:26 PM, <data-modeling-request at freebase.com> wrote:
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> Today's Topics:
>
> 1. Re: Tweaks to the food domain (Kirrily Robert)
> 2. Re: Tweaks to the food domain (Kirrily Robert)
> 3. Re: Thoughts on disease/treatment (Benjamin Good)
> 4. Re: Tweaks to the food domain (Jeff Prucher)
> 5. Re: Tweaks to the food domain (Tom Morris)
> 6. Re: Tweaks to the food domain (John Giannandrea)
> 7. Re: Thoughts on disease/treatment (Dan Ruderman)
> 8. Re: Thoughts on disease/treatment (Benjamin Good)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 11 Jun 2008 16:24:38 -0700
> From: Kirrily Robert <kirrily at metaweb.com>
> Subject: Re: [Data-modeling] Tweaks to the food domain
> To: Freebase data modeling mailing list <data-modeling at freebase.com>
> Message-ID: <2805EFC2-6E39-4779-91B8-570F032793E6 at metaweb.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> On Jun 11, 2008, at 3:17 PM, Jeff Prucher wrote:
>
>> Does anyone have any thoughts on the second part of my question,
>> regarding
>> the design of the whisk(e)y type? I'm in favor of splitting a
>> "distillery"
>> type of off "whisky" (current instances are a mix of both), similar
>> to the
>> beer/brewery and wine/wine producer types.
>
>
> +1
>
>
> --
> Kirrily Robert
> Freebase Community Director
> kirrily at metaweb.com
> http://freebase.com/
>
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 11 Jun 2008 16:25:08 -0700
> From: Kirrily Robert <kirrily at metaweb.com>
> Subject: Re: [Data-modeling] Tweaks to the food domain
> To: Freebase data modeling mailing list <data-modeling at freebase.com>
> Message-ID: <11C71AAD-3246-4EBD-9595-36AF9338782C at metaweb.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> On Jun 11, 2008, at 3:26 PM, Christopher R. Maden wrote:
>
>> Jeff Prucher wrote:
>>> Does anyone have any thoughts on the second part of my question,
>>> regarding
>>> the design of the whisk(e)y type? I'm in favor of splitting a
>>> "distillery"
>>> type of off "whisky" (current instances are a mix of both), similar
>>> to the
>>> beer/brewery and wine/wine producer types.
>>
>> +2
>
>
> Hey!
>
> --
> Kirrily Robert
> Freebase Community Director
> kirrily at metaweb.com
> http://freebase.com/
>
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 11 Jun 2008 16:52:11 -0700
> From: Benjamin Good <ben.mcgee.good at gmail.com>
> Subject: Re: [Data-modeling] Thoughts on disease/treatment
> To: Freebase data modeling mailing list <data-modeling at freebase.com>
> Message-ID: <8F301606-D6B6-431A-A443-7EEFBFC69218 at gmail.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
> They do indeed have and OWL version of this anatomical beast, though
> its native representation is Protege frames. There is a link to a
> "lite" version of this ontology here http://obofoundry.org/cgi-bin/detail.cgi?id=fma_lite
>
> I mention this here on the main list rather than in the Medicine
> discussion forum because its yet another example of a problem that I
> think everyone in the semantic web community that is interested in
> freebase (which really should be everyone) really needs an answer to.
> What is a good protocol for moving OWL ontologies into and out of
> freebase ? Can this problem be dealt with in a domain/ontology
> independent manner?
>
> I am facing this problem directly in my work on the entity describer (www.entitydescriber.org
> ). One of the greatest selling points I've had within the
> bioinformatics community is that I can use it as a generic Gene
> Ontology (GO) annotation service by pointing the topic lookup at the
> GO group type (http://www.freebase.com/view/biology/
> gene_ontology_group) (and that, as an indication of the already
> extensive community, someone unknown to me had already imported the
> GO). However, there are a number of problems:
>
> 1) the GO import could be made much useful through better integration
> with the rest of freebase. For example, http://www.freebase.com/view/en/biological_reproduction
> should very likely be linked to GO:reproduction (http://www.freebase.com/view/guid/9202a8c04000641f800000000520ead4
> ). How might this be automated ?
>
> 2) is there a mechanism to try to update the freebase data when the GO
> is updated ?
> 3) users of things like the GO really expect and depend on inferences
> - especially hierarchical ones (isa, partof). What is a good pattern
> for representing hierarchy and executing queries across hierarchies
> within the context of freebase?
>
> For the entity describer project we are currently debating whether to
> establish (or find) a queriable repository of ontologies like the GO
> for the purpose of answering queries that require inference or trying
> to get everything done in the context of freebase.
>
> -Ben
>
>
>
>
>
>
>
>
> On Jun 6, 2008, at 2:03 PM, Dan Ruderman wrote:
>
>> Hi Faye,
>>
>> Faye Li wrote:
>>> I have a to-do item regarding anatomical structures affected by
>>> diseases
>>> on my whiteboard but didn't get to it this time. The type "Anatomical
>>> structure" exists today without any properties (see
>>> http://www.freebase.com/tools/schema/medicine/anatomical_structure)
>>> and
>>> the plan was to try to flesh out the schema there. Any properties
>>> you'd
>>> suggest?
>>>
>> The fundamental concept I would add is a
>> contains/part-of hierarchy to the structures. I found
>> this web site which has thought a lot of this through and
>> may have an ontology which is importable (e.g. they
>> have an OWL version):
>> http://sig.biostr.washington.edu/projects/fm/AboutFM.html
>> Populating the hierarchy might be tricky, though, unless
>> the anatomical names are consistent with the freebase ones.
>> My biggest concern would be that the hierarchy would be
>> different in different organisms (e.g. cerebral cortex is part of the
>> mammalian brain but not part of the reptilian brain), and
>> I'm not sure if there is a ready source for that information.
>> Because of these complexities I'd probably leave the properties
>> as they are.
>>
>>
>>> As for "Disease Cause" (which will be renamed etiology shortly,
>>> with the
>>> original name saved as an alias), I was thinking about refactoring
>>> the
>>> type. Each cause needs to be qualified with evidence level, something
>>> along the lines of "evident, probable, possible". I was also
>>> considering
>>> adding an enumeration property/new type for etiology category that
>>> would
>>> list, "bacterial, viral, chemical, parasitic", etc. I would
>>> appreciate
>>> your expertise if you have time to talk about this offline.
>>>
>> My knowledge is somewhat limited, but I enjoy thinking about
>> these things and would be glad to chat about them.
>>
>> Dan
>>
>> _______________________________________________
>> Data-modeling mailing list
>> Data-modeling at freebase.com
>> http://lists.freebase.com/mailman/listinfo/data-modeling
>
>
>
> ------------------------------
>
> Message: 4
> Date: Wed, 11 Jun 2008 17:02:45 -0700
> From: "Jeff Prucher" <jeff at metaweb.com>
> Subject: Re: [Data-modeling] Tweaks to the food domain
> To: "'Freebase data modeling mailing list'"
> <data-modeling at freebase.com>
> Message-ID: <003201c8cc1f$a4277180$bc01a8c0 at p4>
> Content-Type: text/plain; charset="US-ASCII"
>
> OK then! Try this on for size:
> http://sandbox.freebase.com/tools/schema/food/whisky
>
> (The big problem is really going to be reconciling with the topics derived
> from Wikipedia -- most of the topics currently typed as "whisky" are either
> distilleries or a combination article about both a whisky and its
> distillery.)
>
> Jeff
>
>> -----Original Message-----
>> From: data-modeling-bounces at freebase.com
>> [mailto:data-modeling-bounces at freebase.com] On Behalf Of
>> Christopher R. Maden
>> Sent: Wednesday, June 11, 2008 3:26 PM
>> To: Freebase data modeling mailing list
>> Subject: Re: [Data-modeling] Tweaks to the food domain
>>
>> Jeff Prucher wrote:
>> > Does anyone have any thoughts on the second part of my question,
>> > regarding the design of the whisk(e)y type? I'm in favor
>> of splitting a "distillery"
>> > type of off "whisky" (current instances are a mix of both),
>> similar to
>> > the beer/brewery and wine/wine producer types.
>>
>> +2
>>
>>
>> --
>> Christopher R. Maden
>> Data Architect
>> Metaweb Technologies, Inc.
>> <URL: http://www.metaweb.com/ >
>> _______________________________________________
>> Data-modeling mailing list
>> Data-modeling at freebase.com
>> http://lists.freebase.com/mailman/listinfo/data-modeling
>>
>
>
>
> ------------------------------
>
> Message: 5
> Date: Wed, 11 Jun 2008 21:00:47 -0400
> From: "Tom Morris" <tfmorris at gmail.com>
> Subject: Re: [Data-modeling] Tweaks to the food domain
> To: "Freebase data modeling mailing list" <data-modeling at freebase.com>
> Message-ID:
> <c5f3f16f0806111800m27925fe2x5ef1e6b802801428 at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> I think the separation is useful, but are we talking about
> distilleries or companies or brands. Leaving aside for a minute the
> fact that purists might not consider blended "whisky" to be whiskys at
> all, have a look at http://www.scotlandwhisky.com/about/brands. The
> Johnnie Walker brand's "spiritual home" is the Cardhu distillery, but
> Ballantine has no identifiable distillery associated with it. Neither
> of them actually distill any spirits.
>
> Tom
>
> On Wed, Jun 11, 2008 at 8:02 PM, Jeff Prucher <jeff at metaweb.com> wrote:
>> OK then! Try this on for size:
>> http://sandbox.freebase.com/tools/schema/food/whisky
>>
>> (The big problem is really going to be reconciling with the topics derived
>> from Wikipedia -- most of the topics currently typed as "whisky" are either
>> distilleries or a combination article about both a whisky and its
>> distillery.)
>>
>> Jeff
>
>
> ------------------------------
>
> Message: 6
> Date: Wed, 11 Jun 2008 22:48:44 -0700
> From: John Giannandrea <jg at metaweb.com>
> Subject: Re: [Data-modeling] Tweaks to the food domain
> To: Freebase data modeling mailing list <data-modeling at freebase.com>
> Message-ID: <56BADC2D-3C60-4D21-97FC-2829A448148A at metaweb.com>
> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>
>
> Id suggest that the whisky is the brand and if its a blend it may or
> may not list some of the contributing distilleries.
> whisky as a food or beverage will presumably acquire manufacturer or
> distributer properties from elsewhere.
> -jg
>
> Tom Morris wrote:
>> I think the separation is useful, but are we talking about
>> distilleries or companies or brands. Leaving aside for a minute the
>> fact that purists might not consider blended "whisky" to be whiskys at
>> all, have a look at http://www.scotlandwhisky.com/about/brands. The
>> Johnnie Walker brand's "spiritual home" is the Cardhu distillery, but
>> Ballantine has no identifiable distillery associated with it. Neither
>> of them actually distill any spirits.
>
>
> ------------------------------
>
> Message: 7
> Date: Thu, 12 Jun 2008 11:16:35 -0700
> From: Dan Ruderman <dan at appliedproteomics.com>
> Subject: Re: [Data-modeling] Thoughts on disease/treatment
> To: Freebase data modeling mailing list <data-modeling at freebase.com>
> Message-ID: <48516803.3040207 at appliedproteomics.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Ben,
>
>
> Benjamin Good wrote:
>> 1) the GO import could be made much useful through better integration
>> with the rest of freebase. For example, http://www.freebase.com/view/en/biological_reproduction
>> should very likely be linked to GO:reproduction (http://www.freebase.com/view/guid/9202a8c04000641f800000000520ead4
>> ). How might this be automated ?
>>
> I think this lies at the core of the reconciliation problem, and may
> require curation by hand unless we can find some organization which
> has already placed GO in this broader context.
>> 2) is there a mechanism to try to update the freebase data when the GO
>> is updated ?
>>
> I had uploaded what was current as of 2007-02-18. I had attempted to
> track version information through the "Data Source" property on
> each GO group, but it looks like that did not work as I had expected.
> It would probably not be that difficult to determine the changes in
> the GO since then and add/deprecate groups (and hopefully reference
> information about the new version somehow).
>
>> 3) users of things like the GO really expect and depend on inferences
>> - especially hierarchical ones (isa, partof). What is a good pattern
>> for representing hierarchy and executing queries across hierarchies
>> within the context of freebase?
>>
> One of the most attractive features of Freebase is the ease
> with which hierarchies can be represented in terms of
> properties. I leveraged this concept when creating the
> schema for GO. This mechanism extends naturally to queries.
> Could you be a bit more specific in stating the type of hierarchy
> and queries which interest you? Perhaps that could help the
> list participants to generate some specific examples.
>
> best
> Dan
>
>
>
>
> ------------------------------
>
> Message: 8
> Date: Thu, 12 Jun 2008 13:25:58 -0700
> From: Benjamin Good <ben.mcgee.good at gmail.com>
> Subject: Re: [Data-modeling] Thoughts on disease/treatment
> To: Freebase data modeling mailing list <data-modeling at freebase.com>
> Message-ID: <CE4EE457-DB07-4024-A296-AE3689F2C8FE at gmail.com>
> Content-Type: text/plain; delsp=yes; format=flowed; charset=US-ASCII
>
>
> On Jun 12, 2008, at 11:16 AM, Dan Ruderman wrote:
>
>> Hi Ben,
>>
>>
>> Benjamin Good wrote:
>>> 1) the GO import could be made much useful through better integration
>>> with the rest of freebase. For example, http://www.freebase.com/view/en/biological_reproduction
>>> should very likely be linked to GO:reproduction (http://www.freebase.com/view/guid/9202a8c04000641f800000000520ead4
>>> ). How might this be automated ?
>>>
>> I think this lies at the core of the reconciliation problem, and may
>> require curation by hand unless we can find some organization which
>> has already placed GO in this broader context.
>
> I tend to agree. The ideal case would be for an organization like the
> GO consortium itself or the OBO foundry that it begot to take charge
> of this task. That being said, I bet there are quite a few example
> where direct correspondence could be determined automatically at
> import. (This has got to be something the data harvesting teams at
> freebase know quite a lot about).
>
>
>>
>>> 2) is there a mechanism to try to update the freebase data when the
>>> GO
>>> is updated ?
>>>
>> I had uploaded what was current as of 2007-02-18. I had attempted to
>> track version information through the "Data Source" property on
>> each GO group, but it looks like that did not work as I had expected.
>> It would probably not be that difficult to determine the changes in
>> the GO since then and add/deprecate groups (and hopefully reference
>> information about the new version somehow).
>>
>>> 3) users of things like the GO really expect and depend on inferences
>>> - especially hierarchical ones (isa, partof). What is a good pattern
>>> for representing hierarchy and executing queries across hierarchies
>>> within the context of freebase?
>>>
>> One of the most attractive features of Freebase is the ease
>> with which hierarchies can be represented in terms of
>> properties. I leveraged this concept when creating the
>> schema for GO. This mechanism extends naturally to queries.
>> Could you be a bit more specific in stating the type of hierarchy
>> and queries which interest you? Perhaps that could help the
>> list participants to generate some specific examples.
>
> Sure. I'd like to find all gene groups (and all genes when the
> associations get into freebase) that have been annotated with any
> Cellular Component or, any component of the cytoplasm. This is
> basically the same as a query for all of the organism classifications
> lower-than a particular classification. I can see how to request
> hierarchical chains when I know how many levels I want to traverse,
> but I would also like to be able to handle queries when I don't know
> in advance how far down they will go. This could be solved through an
> iterative request but, as it seems like such a general case, it would
> be great if there was some sort of standard way to deal with it. Here
> is MQL for a getting several levels down from 'bird' or 'Aves'.
>
> [
> {
> "lower_classifications" : [
> {
> "lower_classifications" : [
> {
> "lower_classifications" : [
> {
> "lower_classifications" : [
> {
> "lower_classifications" : []
> }
> ],
> "name" : null
> }
> ],
> "name" : null
> }
> ],
> "name" : null
> }
> ],
> "name" : null,
> "scientific_name" : "Aves",
> "type" : "/biology/organism_classification"
> }
> ]
>
> In an answer to a previous inquiry about subsumption in freebase, John
> Giannandrea said "So why dont we support strict type inheritance?
> Well because real world data is messy." . OK, cool, I'm not
> suggesting that Freebase should support inheritance at the level of
> Types, but why not explicitly support the general case of what he
> calls "phylogeny patterns" ? Though real world data is indeed very
> messy, there is a lot of very valuable, fairly clean data (e.g. the
> GO, the FMA, etc.) that would be much more easily merged into freebase
> given the definition (even just a consensus agreement) on what the
> general-purpose broader-than/narrower-than relationship should be and
> how it should be interacted with in MQL.
>
> -Ben
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> ------------------------------
>
> _______________________________________________
> Data-modeling mailing list
> Data-modeling at freebase.com
> http://lists.freebase.com/mailman/listinfo/data-modeling
>
>
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