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Re: adding pubmed ids to BAMS

From: John Barkley <jbarkley@nist.gov>
Date: Thu, 19 Apr 2007 14:53:56 -0400
Message-ID: <170701c782b4$17699cb0$8a3a0681@ncsl.nist.gov>
To: "Alan Ruttenberg" <alanruttenberg@gmail.com>
Cc: "Jonathan Rees" <jar@mumble.net>, "chris mungall" <cjm@fruitfly.org>, "public-semweb-lifesci hcls" <public-semweb-lifesci@w3.org>, "Suzanna Lewis" <suzi@berkeleybop.org>, "Judith Blake" <jblake@informatics.jax.org>, "Barry Smith" <phismith@buffalo.edu>, <jbarkley@nist.gov>

Hows about:

<owl:Class rdf:ID="article"/>
<owl:Class rdf:ID="pubmedRecord"/>

<owl:ObjectProperty rdf:ID="definedByPMID">
    <rdf:type 
rdf:resource="http://www.w3.org/2002/07/owl#InverseFunctionalProperty"/>
    <rdfs:domain rdf:resource="#article"/>
    <rdfs:range rdf:resource="#pubmedRecord"/>
</owl:ObjectProperty>

<owl:ObjectProperty rdf:ID="isMentionedBy">
    <rdf:type 
rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
</owl:ObjectProperty>

<pubmedRecord rdf:about="http://purl.org/commons/pubmed/PMID_3327422"/>
<pubmedRecord rdf:about="http://purl.org/commons/pubmed/PMID_7451682"/>


<article rdf:ID="pubmed_3327422">
    <definedByPMID 
rdf:resource="http://purl.org/commons/pubmed/PMID_3327422"/>
</article>
<article rdf:ID="pubmed_7451682">
    <definedByPMID 
rdf:resource="http://purl.org/commons/pubmed/PMID_7451682"/>
</article>

<owl:Class rdf:ID="c101">
    <rdfs:subClassOf>
        <owl:Restriction>
            <owl:onProperty rdf:resource="#classId"/>
            <owl:hasValue 
rdf:datatype="http://www.w3.org/2001/XMLSchema#int">101</owl:hasValue>
        </owl:Restriction>
    </rdfs:subClassOf>
    <rdfs:subClassOf 
rdf:resource="http://purl.org/obo/owl/CARO#CARO_0000013"/>
    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
            >motor neuroendocrine magnocellular oxytocin neuron</rdfs:label>
    <isMentionedBy rdf:resource="#pubmed_7451682"/>
</owl:Class>

<owl:Class rdf:ID="Cellc101HasMoleculem3Within">
    <rdfs:subClassOf rdf:resource="#c101"/>
    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
            >the cell motor neuroendocrine magnocellular oxytocin neuron has 
the molecule oxytocin within</rdfs:label>
    <isMentionedBy rdf:resource="#pubmed_3327422"/>
</owl:Class>

jb


----- Original Message ----- 
From: "Alan Ruttenberg" <alanruttenberg@gmail.com>
To: "John Barkley" <jbarkley@nist.gov>
Cc: "Jonathan Rees" <jar@mumble.net>; "chris mungall" <cjm@fruitfly.org>; 
"public-semweb-lifesci hcls" <public-semweb-lifesci@w3.org>; "Suzanna Lewis" 
<suzi@berkeleybop.org>; "Judith Blake" <jblake@informatics.jax.org>; "Barry 
Smith" <phismith@buffalo.edu>
Sent: Thursday, April 19, 2007 11:46 AM
Subject: Re: adding pubmed ids to BAMS


>
>
> On Apr 19, 2007, at 9:20 AM, John Barkley wrote:
>
>> hi alan,
>>
>> Here is a mock up of  what I think you had in mind in the case of  BAMS 
>> (sorry for the rdf/xml, I wanted to be precise):
>>
>> Given:
>>
>> <owl:Class rdf:ID="article"/>
>> <owl:Class rdf:ID="pubmedRecord"/>
>>
>> <pubmedRecord rdf:about="http://purl.org/commons/pubmed/_3327422"/>
>> <pubmedRecord rdf:about="http://purl.org/commons/pubmed/_7451682"/>
>>
>> <owl:ObjectProperty rdf:ID="definedByPMID">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/ 
>> owl#InverseFunctionalProperty"/>
>>    <rdfs:domain rdf:resource="#article"/>
>>    <rdfs:range rdf:resource="#pubmedRecord"/>
>> </owl:ObjectProperty>
>>
>> <owl:ObjectProperty rdf:ID="isMentionedBy">
>>    <rdf:type rdf:resource="http://www.w3.org/2002/07/ 
>> owl#AnnotationProperty"/>
>> </owl:ObjectProperty>
>>
>> Then, for each cell and cell/molecule pubmed reference, you would  have 
>> the following (the first is a cell example for c101 and the  second is a 
>> cell/molecule example for c101):
>>
>> <owl:Class rdf:ID="c101">
>>    <rdfs:subClassOf rdf:resource="http://purl.org/obo/owl/ 
>> CARO#CARO_0000013"/>
>>    <rdfs:subClassOf>
>>        <owl:Restriction>
>>            <owl:onProperty rdf:resource="#classId"/>
>>            <owl:hasValue rdf:datatype="http://www.w3.org/2001/ 
>> XMLSchema#int">101</owl:hasValue>
>>        </owl:Restriction>
>>    </rdfs:subClassOf>
>>    <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string"
>>            >motor neuroendocrine magnocellular oxytocin neuron</ 
>> rdfs:label>
>>    <isMentionedBy rdf:resource="http://purl.org/commons/pubmed/ 
>> _7451682"/>
>> </owl:Class>
>
> isMentionedBy should point to an instance of article
> article identifiedByPMID http://purl.org/commons/pubmed/_7451682
>
> I don't like the underscore but Jonathan thinks it is necessary. But  this 
> is minor. I would say using PMID_7451652 or some similar variant  is more 
> appealing. (no accounting for taste)
> We might also want
> http://purl.org/commons/pubmed/_7451682 hasId "7451682", but I'm not 
> sure.
> Anyways, neither of these are essential for progress.
>
>
>> <owl:Class rdf:ID="Cellc101HasMoleculem3Within">
> Would be nice to have an english readable rdfs:label here.
>>    <rdfs:subClassOf rdf:resource="#c101"/>
>>    <rdfs:subClassOf>
>>        <owl:Restriction>
>>            <owl:onProperty rdf:resource="#cell_has_molecule_within"/>
>>            <owl:someValuesFrom rdf:resource="#m3"/>
>>        </owl:Restriction>
>>    </rdfs:subClassOf>
>>    <isMentionedBy rdf:resource="http://purl.org/commons/pubmed/ 
>> _3327422"/>
>> </owl:Class>
>
> This class would be used in place of the restriction if there is a 
> definition that  would otherwise use the restriction.
>
> Thanks for the quick response!
>
>>
>> jb
>>
>>
>> ----- Original Message ----- From: "Alan Ruttenberg" 
>> <alanruttenberg@gmail.com>
>> To: "John Barkley" <jbarkley@nist.gov>
>> Cc: "Jonathan Rees" <jar@mumble.net>; "chris mungall" 
>> <cjm@fruitfly.org>; "public-semweb-lifesci hcls" <public-semweb- 
>> lifesci@w3.org>; "Suzanna Lewis" <suzi@berkeleybop.org>; "Judith  Blake" 
>> <jblake@informatics.jax.org>; "Barry Smith"  <phismith@buffalo.edu>
>> Sent: Thursday, April 19, 2007 12:24 AM
>> Subject: Re: adding pubmed ids to BAMS
>>
>>
>>>
>>> Here is an idea I am exploring. Perhaps you might mock this up:
>>>
>>> The essential idea is that evidence and other annotation is about 
>>> named classes. In those cases where one might think of annotating   some 
>>> axiom, or piece of axiom, we would instead look for the  class  that is 
>>> the referent of the annotation and name that class.
>>> Then, we can connect that class, using an annotation property,  to 
>>> whatever kind of annotation or evidence we think appropriate.
>>>
>>> Suppose we have a class HumanP53Protein, which we will define as: 
>>> Those proteins whose sequence of amino acids are described by the 
>>> sequence in the sequence information field of the Uniprot  P53_Human 
>>> Record, or which are derived from such a protein. (I'm  open to 
>>> discussion on what this definitions should be, BTW, but I  think we 
>>> should have one)
>>>
>>> One gene ontology annotation to P53 is:
>>> GO:0000739; Molecular function: DNA strand annealing activity 
>>> (inferred from direct assay from UniProtKB).
>>>
>>> GO:0000739 is defined as in OBO, as a class, a subclass of function.
>>>
>>> We will say that the referent of this annotation is the class
>>>
>>> HumanP53ProteinWithFunctionDNAStrandAnnealing:  HumanP53Protein  and 
>>> has_function some GO:0000739
>>>
>>> The annotation property itself might be called  "ExistsAccordingTo",  by 
>>> which we mean that this class has instances
>>>
>>> The thing it exists according is
>>>
>>> Inference001
>>>    type InferredFromDirectAssay
>>>    describedInPaper theArticlePMID1234Describes
>>>
>>> So our annotation is
>>>
>>> HumanP53ProteinWithFunctionDNAStrandAnnealing ExistsAccordingTo 
>>> Inference001
>>>
>>> Up to this point we have been conservative. We haven't made any 
>>> statement about P53 in general. Here, we will overstate (our only 
>>> choice, if we want to make a statement about biology from which  some 
>>> useful inference can be done, given the evidence we have)
>>>
>>> HumanP53Protein subclassOf 
>>> HumanP53ProteinWithFunctionDNAStrandAnnealing
>>>
>>> This may be wrong. For instance, it may be the case that only  that  P53 
>>> phosphorylated in some way actually has this function.
>>> I hope that by some other statement, a contradiction is inferred  that 
>>> will force us (or the curators) to be more specific.
>>>
>>> ----
>>>
>>> What's nice about this?
>>>
>>>
>>> 1) We are making statements about biology (better than making 
>>> statements about "terms")
>>> 2) There is no RDF reification involved - the main contender for 
>>> representing this sort of thing.
>>> 3) We have been (relatively) conservative about what we say there  is 
>>> evidence for
>>> 4) We are owning the fact that we are making an overstatement
>>> 5) We are enabling some inference to take place.
>>>
>>> What's the cost?
>>>
>>> 1) One extra triple, in which we name the class 
>>> HumanP53ProteinInvolvedInDNADamageResponse
>>> Where we previously would have used a restriction to introduce the 
>>> participation, we now use the named class.
>>> 2) When querying about what the evidence is for, we need to query  the 
>>> asserted (or told) assertions only. That's because after  inference  has 
>>> been done, new assertions may be known about 
>>> HumanP53ProteinWithFunctionDNAStrandAnnealing and we won't be able  to 
>>> tell the difference between what was asserted and what is  inferred, 
>>> given that we have associated the only the class name  with the evidence
>>>
>>> ---
>>>
>>> Taking this to BAMS it means that we associate the paper with the   cell 
>>> class for which we already have an name.
>>> For the molecule is found in cell cases, we create the named  class  for 
>>> the cell contains some molecule class, use that
>>> class in place of the restriction, and associate the paper to  that 
>>> named class.
>>>
>>> You can define
>>>
>>> Class(article :partial)
>>> Class(pubmedRecord :partial)
>>> ObjectProperty(definedByPMID inversefunctional)
>>>
>>> Represent the pubmed record as an instance of pubmedRecord named 
>>> http://purl.org/commons/pubmed/1234
>>>
>>> The last issue is the nature of the relationship between the  paper  and 
>>> the class. If we can't easily distinguish between whether
>>> these annotations are evidence or simply discussion we could use  the 
>>> relation "isMentionedBy", which we will mean to say that the  class  (or 
>>> some instances of the class) are discussed in the paper.
>>>
>>> ---
>>>
>>> Call me if you want to discuss this. Admittedly this may seem   involved 
>>> and odd, since it is a new idea, though I will blame  Chris  and 
>>> Jonathan, who I bounced it off of, for not telling me  straight  off it 
>>> didn't make sense :)
>>>
>>> But how about we give it a go and see what it feels like. I'm   planning 
>>> to use this translation for the GO annotations and the  rest  of the 
>>> similar sources, unless somebody comes forth with  some  arguments about 
>>> what would be a better idea.
>>>
>>> Best,
>>> Alan
>>>
>>>
>>> On Apr 18, 2007, at 3:49 PM, jbarkley@nist.gov wrote:
>>>
>>>>
>>>>> From what Mihai sent me, the pubmed refs are about:
>>>>
>>>>> the cell and
>>>>> the fact the molecule is found in cell
>>>>
>>>> Pending your recomendation, I had tentatively suggested the   following 
>>>> for
>>>> representing this as:
>>>>
>>>> pubmedID has "<id>" or
>>>> cell_has_molecule_within some (<cell> and (pubmedID has "<id>"))
>>>>
>>>> where one of more of these is associated with a cell. I was under  the
>>>> impression that you were thinking about a general representation   that 
>>>> everyone
>>>> would use for pubmedID. So, I haven't yet added these to the  BAMS  OWL 
>>>> version.
>>>>
>>>>> OK. Can you send me this for a quick look?
>>>>
>>>> I'm not sure what you are asking to see. Do you want to see the 
>>>> original
>>>> tables Mihai sent me?
>>>>
>>>> thanks,
>>>>
>>>> jb
>>>>
>>>>
>>>>
>>>> Date:  Wed, 18 Apr 2007 12:30:17 -0400
>>>> From:  Alan Ruttenberg <alanruttenberg@gmail.com>
>>>> To:  John Barkley <jbarkley@nist.gov>
>>>> Cc:  Jonathan A Rees <jar@mumble.net>
>>>> Subject:  Re: adding pubmed ids to BAMS
>>>> Quoting Alan Ruttenberg <alanruttenberg@gmail.com>:
>>>>
>>>>>
>>>>> On Apr 13, 2007, at 1:51 PM, John Barkley wrote:
>>>>>
>>>>>> I have confirmed from Mihai that all of the pubmed references in
>>>>>> BAMS are evidence for or elaboration about.
>>>>>
>>>>> OK. Can you send me this for a quick look?
>>>>> Is it clear what the they are about
>>>>> i.e.
>>>>>
>>>>> the cell
>>>>> the part
>>>>> the fact that cell is located in part
>>>>> the fact the molecule is found in cell
>>>>> the fact the molecule is found in part
>>>>> the fact the molecule is found in cell in part
>>>>> etc.
>>>>>
>>>>> ?
>>>>>
>>>>>>
>>>>>>
>>>>>> ----- Original Message ----- From: "Alan Ruttenberg"
>>>>>> <alanruttenberg@gmail.com>
>>>>>>
>>>>>>> Don't have time at this moment, but I think that generally you
>>>>>>> want  to state the the article is either evidence for, or
>>>>>>> elaboration about  the scientific statement involving the cells,
>>>>>>> molecules, etc. Then  then use the pubmed id in some standard URI
>>>>>>> form (maybe neurocommons  record url style) or
>>>>>>> Jonathan's purl.org suggestion. In other words the pubmed id is
>>>>>>> the identifier for a thing (the article, or the abstract,
>>>>>>> depending on  one's point of view).
>>>>>>>
>>>>>>> More details later.
>>>>>>>
>>>>>>> You could look and see how Gene ontology represents evidence.
>>>>>>>
>>>>>>> -Alan
>>>>>>>
>>>>>>> On Apr 11, 2007, at 3:46 PM, John Barkley wrote:
>>>>>>>
>>>>>>>> hi alan,
>>>>>>>>
>>>>>>>> I recieved spreadsheets from Mihai relating cells & pubmed ids,
>>>>>>>> and cells, molecules, & pubmed ids. I wanted to consult with you
>>>>>>>> about  your preferences for how to integrate this into BAMS.  I am
>>>>>>>> thinking  something like defining a datatype property pubmedID
>>>>>>>> from owl:thing  to string. Then for cells, you would have:
>>>>>>>>
>>>>>>>> pubmedID has "<id>"
>>>>>>>>
>>>>>>>> and for cells with molecules within, you would have:
>>>>>>>>
>>>>>>>> cell_has_molecule_within some (<cell> and (pubmedID has "<id>"))
>>>>>>>>
>>>>>>>> Please let me know.
>>>>>>>>
>>>>>>>> thanks,
>>>>>>>>
>>>>>>>> jb
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>
> 
Received on Thursday, 19 April 2007 18:54:49 GMT

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