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="ht
tp://purl.org/commons/pubmed/_3327422"/>
> <pubmedRecord rdf:about="ht
tp://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/commo
ns/pubmed/ 
> _7451682"/>
> </owl:Class>

isMentionedBy should point to an instance of article
article identifiedByPMID http://purl.o
rg/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.o
rg/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/commo
ns/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"  
> <alanruttenberggmail.com>
> To: "John Barkley" <jbarkleynist.gov>
> Cc: "Jonathan Rees" <jarmumble.net>; "chris mungall"  
> <cjmfruitfly.org>; "public-semweb-lifesci
hcls" <public-semweb- 
> lifesciw3.org>; "Suzanna Lewis" <suziberkeleybop.org>; "Judith  
> Blake" <jblakeinformatics.jax.org>;
"Barry Smith"  
> <phismithbuffalo.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/c
ommons/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, jbarkleynist.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 <alanruttenberggmail.com>
>>> To:  John Barkley <jbarkleynist.gov>
>>> Cc:  Jonathan A Rees <jarmumble.net>
>>> Subject:  Re: adding pubmed ids to BAMS
>>> Quoting Alan Ruttenberg <alanruttenberggmail.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"
>>>>> <alanruttenberggmail.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
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>
>

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#InverseFunctiona
lProperty"/>
    <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" <alanruttenberggmail.com>
To: "John Barkley" <jbarkleynist.gov>
Cc: "Jonathan Rees" <jarmumble.net>; "chris
mungall" <cjmfruitfly.org>; 
"public-semweb-lifesci hcls"
<public-semweb-lifesciw3.org>; "Suzanna
Lewis" 
<suziberkeleybop.org>; "Judith Blake"
<jblakeinformatics.jax.org>; "Barry 
Smith" <phismithbuffalo.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="ht
tp://purl.org/commons/pubmed/_3327422"/>
>> <pubmedRecord rdf:about="ht
tp://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/commo
ns/pubmed/ 
>> _7451682"/>
>> </owl:Class>
>
> isMentionedBy should point to an instance of article
> article identifiedByPMID http://purl.o
rg/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.o
rg/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/commo
ns/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" 
>> <alanruttenberggmail.com>
>> To: "John Barkley" <jbarkleynist.gov>
>> Cc: "Jonathan Rees" <jarmumble.net>; "chris mungall" 
>> <cjmfruitfly.org>;
"public-semweb-lifesci hcls" <public-semweb- 
>> lifesciw3.org>; "Suzanna Lewis"
<suziberkeleybop.org>; "Judith  Blake" 
>> <jblakeinformatics.jax.org>; "Barry
Smith"  <phismithbuffalo.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/c
ommons/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, jbarkleynist.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
<alanruttenberggmail.com>
>>>> To:  John Barkley <jbarkleynist.gov>
>>>> Cc:  Jonathan A Rees <jarmumble.net>
>>>> Subject:  Re: adding pubmed ids to BAMS
>>>> Quoting Alan Ruttenberg
<alanruttenberggmail.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"
>>>>>> <alanruttenberggmail.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
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>>
>>
>>
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