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RE: adding pubmed ids to BAMS

From: Booth, David (HP Software - Boston) <dbooth@hp.com>
Date: Fri, 20 Apr 2007 15:25:00 -0400
Message-ID: <EBBD956B8A9002479B0C9CE9FE14A6C20285D7C7@tayexc19.americas.cpqcorp.net>
To: "Huajun Chen @ Zhejiang University" <huajunsir@gmail.com>, "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>, "John Barkley" <jbarkley@nist.gov>

My 2 cents: If something is important, it should have a name (a URI).   See the W3C WebArch sec 2.1 "Good practice: Identify with URIs":
http://www.w3.org/TR/webarch/#uri-benefits

David Booth, Ph.D.
HP Software
+1 617 629 8881 office  |  dbooth@hp.com
http://www.hp.com/go/software 

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org 
> [mailto:public-semweb-lifesci-request@w3.org] On Behalf Of 
> Huajun Chen @ Zhejiang University
> Sent: Friday, April 20, 2007 11:12 AM
> To: Alan Ruttenberg
> Cc: Jonathan Rees; chris mungall; public-semweb-lifesci hcls; 
> Suzanna Lewis; Judith Blake; Barry Smith; John Barkley
> Subject: Re: adding pubmed ids to BAMS
> 
> 
> We met similar problems when we tried to relate publications 
> to neurons.
> 
> Check the research notes for CA3 pyramidal neuron:
> http://senselab.med.yale.edu/senselab/NeuronDB/ndbEavSum.asp?i
> d=259&mo=4&re=
> 
> All of the notes are about papers supporting the evidences of being
> present or absent of a receptor/current/transmitter in a specific
> compartment.  The notes can not simply attach to the neurocell class,
> since they are actually annotations that should be attached to
> statements.  All of the notes should be attached to the
> owl:Restriction defined for those receptor/current/transmitter, see
> the definition for CA3 pyramidal neuron in old DL syntax below.
> 
> If taking Alan's approach, we have to create additionally a huge
> number of new named classes. For example, for CA3, we have to create
> extra 30 named classes. And if take it as an average for other cells,
> we have to create nearly 30*33=990 new named classes for all cells in
> neuroDB. Previously we only have less than 50 classes in total.
> 
> We also have to come up new class name for each one which tends to be
> long and somewhat odd. For example, the class name might be
> AMPA_in_DAD_in_CA3_pyramidal_neuron.
> 
> Unnamed class is one of the elegant and neat features of DL,
> especially in the cases where we do not want or do not know how to
> explicitly specify the name.
> Besides, I don't think unnamed class dis-enable the evidential
> inference to take place.  For examples, the inconsistence we've just
> found were inferred out from those unnamed class.
> 
> I've also found protégé does supports annotating unnamed classes, but
> I'm not quite sure if the OWL specification allows us to do that?
> 
> Best all,
> Huajun
> 
> Principal_Neuron AND
> 
> ro:hasPart SOME [(Dad AND
>                   (has_Receptors SOME AMPA) AND
>                   (has_Receptors SOME NMDA) AND
>                   (has_Currents SOME I_p_q) AND
>                   (has_Currents SOME I_K)),
>                  (Dap AND
>                   (has_Receptors SOME Glutamate) AND
>                   (NOT (has_Currents SOME I_Na_t)) AND
>                   (has_Currents SOME I_K) AND
>                   (has_Currents SOME I_p_q)),
>                  (Soma AND
>                   (has_Receptors SOME AMPA) AND
>                   (has_Receptors SOME NMDA) AND
>                   (has_Receptors SOME GabaB) AND
>                   (has_Receptors SOME GabaA) AND
>                   (has_Receptors SOME mGluR) AND
>                   (has_Receptors SOME Gaba) AND
>                   (has_Currents SOME I_p_q) AND
>                   (has_Currents SOME I_K_Ca) AND
>                   (has_Currents SOME I_Na_t) AND
>                   (has_Currents SOME I_N) AND
>                   (has_Currents SOME I_A) AND
>                   (has_Currents SOME I_K) AND
>                   (has_Currents SOME I_IR_Q_h) AND
>                   (has_Currents SOME I_T_low_threshold) AND
>                   (has_Currents SOME I_L_high_threshold)),
>                  (Dam AND
>                   (has_Receptors SOME mGluR) AND
>                   (has_Receptors SOME GabaB) AND
>                   (has_Receptors SOME AMPA) AND
>                   (has_Receptors SOME Gaba) AND
>                   (has_Receptors SOME Glutamate) AND
>                   (has_Receptors SOME NMDA) AND
>                   (has_Receptors SOME GabaA) AND
>                   (has_Currents SOME I_L_high_threshold) AND
>                   (has_Currents SOME I_p_q) AND
>                   (has_Currents SOME I_T_low_threshold) AND
>                   (has_Currents SOME I_K)),
>                  (T AND
>                   (has_Receptors SOME NO) AND
>                   (has_Currents SOME I_N) AND
>                   (has_Transmitters SOME Glutamate)),
>                  (A AND
>                   (has_Currents SOME I_Na_t)),
>                  (AH AND
>                   (has_Currents SOME I_K) AND
>                   (has_Currents SOME I_Na_t))]
Received on Friday, 20 April 2007 19:25:09 GMT

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