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" <[EMAIL PROTECTED]>
To: "John Barkley" <[EMAIL PROTECTED]>
Cc: "Jonathan Rees" <[EMAIL PROTECTED]>; "chris mungall" <[EMAIL PROTECTED]>;
"public-semweb-lifesci hcls" <public-semweb-lifesci@w3.org>; "Suzanna Lewis"
<[EMAIL PROTECTED]>; "Judith Blake" <[EMAIL PROTECTED]>; "Barry
Smith" <[EMAIL PROTECTED]>
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"
<[EMAIL PROTECTED]>
To: "John Barkley" <[EMAIL PROTECTED]>
Cc: "Jonathan Rees" <[EMAIL PROTECTED]>; "chris mungall"
<[EMAIL PROTECTED]>; "public-semweb-lifesci hcls" <public-semweb-
[EMAIL PROTECTED]>; "Suzanna Lewis" <[EMAIL PROTECTED]>; "Judith Blake"
<[EMAIL PROTECTED]>; "Barry Smith" <[EMAIL PROTECTED]>
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, [EMAIL PROTECTED] 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 <[EMAIL PROTECTED]>
To: John Barkley <[EMAIL PROTECTED]>
Cc: Jonathan A Rees <[EMAIL PROTECTED]>
Subject: Re: adding pubmed ids to BAMS
Quoting Alan Ruttenberg <[EMAIL PROTECTED]>:
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"
<[EMAIL PROTECTED]>
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
