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Re: adding pubmed ids to BAMS

From: Alan Ruttenberg <alanruttenberg@gmail.com>
Date: Thu, 19 Apr 2007 00:24:18 -0400
Message-Id: <0D926997-7754-45AB-82AB-9BE2AAB8BA51@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>

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 04:24:39 GMT

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