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Re: adding pubmed ids to BAMS

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Thu, 19 Apr 2007 15:44:41 -0400
Message-Id: <A6386563-5800-45B1-BC2C-0B32521158A4@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>
To: John Barkley <jbarkley@nist.gov>

Looks good.

Tweaks:
Call the article "article 7451682"
Name the pubmed record
http://purl.org/commons/pmid/7451682

Best,
Alan



On Apr 19, 2007, at 2:53 PM, John Barkley wrote:

> 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 19:43:26 GMT

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