NeuronBank

From W3C Wiki

For Karen Skinner, working from rdf schema and data from http://www.neuronbank.org/

Loading it up into the triple store and asking some questions. Discussion to follow.


Getting it

mkdir neuronbank
cd neuronbank
wget http://www.neuronbank.org:8080/Tritonia/resources/exports/RDF_Export-09-17-07.rdf
wget http://www.neuronbank.org:8080/Tritonia/resources/exports/RDF_Export-09-17-07.rdfs


Loading it into the neurocommons

touch log
perl ~/neuro/product/load-rdf-directory.pl `pwd` http://purl.org/commons/neuronbank-20070918 http://purl.org/commons/neuronbank-20070918 log
cat log

=>
/work/neuronbank/RDF_Export-09-17-07.rdfs Tue Sep 18 16:25:12 EDT 2007
/work/neuronbank/RDF_Export-09-17-07.rdf Tue Sep 18 16:25:23 EDT 2007


Classes

What classes do they define? Lots related to citation. The world *really* needs a standard schema for this. 


prefix tritonia: <http://neuronbank.org/Tritonia#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>

select *
from <http://purl.org/commons/neuronbank-20070918>
where 
 {   ?class rdf:type rdfs:Class.}

=>

http://neuronbank.org/Tritonia#:UI_Class
http://neuronbank.org/Tritonia#_-Neuron_Bank_System_Object
http://neuronbank.org/Tritonia#_-Classification
http://neuronbank.org/Tritonia#_-Article
http://neuronbank.org/Tritonia#_-Conference_Abstract
http://neuronbank.org/Tritonia#_-Neuron_Bank_Core
http://neuronbank.org/Tritonia#_-Neuron
http://neuronbank.org/Tritonia#_-Annotations
http://neuronbank.org/Tritonia#_-User_Defined_Attributes
http://neuronbank.org/Tritonia#_-Reference
http://neuronbank.org/Tritonia#_-Book
http://neuronbank.org/Tritonia#_-Book_Chapter
http://neuronbank.org/Tritonia#_-Journal
http://neuronbank.org/Tritonia#_-Comment
http://neuronbank.org/Tritonia#_-Contributor
http://neuronbank.org/Tritonia#_-WebResource
http://neuronbank.org/Tritonia#_-Brain_Part
http://neuronbank.org/Tritonia#_-Measurement
http://neuronbank.org/Tritonia#_-Chemical_Synapse
http://neuronbank.org/Tritonia#_-Connections
http://neuronbank.org/Tritonia#_-Neuron_Part
http://neuronbank.org/Tritonia#_-Electrical_Synapse
http://neuronbank.org/Tritonia#_-Example
http://neuronbank.org/Tritonia#_-Link
http://neuronbank.org/Tritonia#_-Soma
http://neuronbank.org/Tritonia#_-Modulation
http://neuronbank.org/Tritonia#_-Negative_Connection
http://neuronbank.org/Tritonia#_-Revision


Properties

What properties do they define?. Much of them relate to citations stuff. There are a number of interesting properties that we would like to understand, like what is Loc_x? 


prefix tritonia: <http://neuronbank.org/Tritonia#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix owl: <http://www.w3.org/2002/07/owl#>

select *
from <http://purl.org/commons/neuronbank-20070918>
where 
 {
   ?property rdf:type rdf:Property. 
   optional { ?property rdfs:domain ?domain}
   optional { ?property rdfs:range ?range }
 }

==>
Property Domain
`http://neuronbank.org/Tritonia#_-Abstract` `http://neuronbank.org/Tritonia#_-Conference_Abstract`
`http://neuronbank.org/Tritonia#_-Abstract` `http://neuronbank.org/Tritonia#_-Article`
`http://neuronbank.org/Tritonia#_-AccessionID` `http://neuronbank.org/Tritonia#_-Neuron_Bank_Core`
`http://neuronbank.org/Tritonia#_-UI_Level` `http://neuronbank.org/Tritonia#:UI_Class`
`http://neuronbank.org/Tritonia#_-UI_Category` `http://neuronbank.org/Tritonia#:UI_Class`
`http://neuronbank.org/Tritonia#_-Alias` `http://neuronbank.org/Tritonia#_-Neuron`
`http://neuronbank.org/Tritonia#_-Annotates` `http://neuronbank.org/Tritonia#_-Annotations`
`http://neuronbank.org/Tritonia#_-My_Annotations` `http://neuronbank.org/Tritonia#_-Neuron_Bank_Core`
`http://neuronbank.org/Tritonia#_-Articles` `http://neuronbank.org/Tritonia#_-Journal`
`http://neuronbank.org/Tritonia#_-Articles` `http://neuronbank.org/Tritonia#_-Book`
`http://neuronbank.org/Tritonia#_-Source` `http://neuronbank.org/Tritonia#_-Book_Chapter`
`http://neuronbank.org/Tritonia#_-Source` `http://neuronbank.org/Tritonia#_-Article`
`http://neuronbank.org/Tritonia#_-Authors` `http://neuronbank.org/Tritonia#_-Comment`
`http://neuronbank.org/Tritonia#_-Authors` `http://neuronbank.org/Tritonia#_-Reference`
`http://neuronbank.org/Tritonia#_-Publications` `http://neuronbank.org/Tritonia#_-Contributor`
`http://neuronbank.org/Tritonia#_-Base_URL` `http://neuronbank.org/Tritonia#_-WebResource`
`http://neuronbank.org/Tritonia#_-Category`
`http://neuronbank.org/Tritonia#_-City` `http://neuronbank.org/Tritonia#_-Book`
`http://neuronbank.org/Tritonia#_-City` `http://neuronbank.org/Tritonia#_-Conference_Abstract`
`http://neuronbank.org/Tritonia#_-Comment_Text` `http://neuronbank.org/Tritonia#_-Comment`
`http://neuronbank.org/Tritonia#_-Conference` `http://neuronbank.org/Tritonia#_-Conference_Abstract`
`http://neuronbank.org/Tritonia#_-Units` `http://neuronbank.org/Tritonia#:UI_Class`
`http://neuronbank.org/Tritonia#_-Contains` `http://neuronbank.org/Tritonia#_-Brain_Part`
`http://neuronbank.org/Tritonia#_-Located_In` `http://neuronbank.org/Tritonia#_-Neuron_Part`
`http://neuronbank.org/Tritonia#_-Definition` `http://neuronbank.org/Tritonia#_-Neuron`
`http://neuronbank.org/Tritonia#_-Describes` `http://neuronbank.org/Tritonia#_-User_Defined_Attributes`
`http://neuronbank.org/Tritonia#_-My_Properties` `http://neuronbank.org/Tritonia#_-Connections`
`http://neuronbank.org/Tritonia#_-My_Properties` `http://neuronbank.org/Tritonia#_-Neuron`
`http://neuronbank.org/Tritonia#_-Has_A` `http://neuronbank.org/Tritonia#_-Neuron`
`http://neuronbank.org/Tritonia#_-Part_Of` `http://neuronbank.org/Tritonia#_-Neuron_Part`
`http://neuronbank.org/Tritonia#_-Inputs` `http://neuronbank.org/Tritonia#_-Neuron`
`http://neuronbank.org/Tritonia#_-Post` `http://neuronbank.org/Tritonia#_-Connections`
`http://neuronbank.org/Tritonia#_-Level` `http://neuronbank.org/Tritonia#_-Classification`
`http://neuronbank.org/Tritonia#_-Link_Outs` `http://neuronbank.org/Tritonia#_-WebResource`
`http://neuronbank.org/Tritonia#_-Resource` `http://neuronbank.org/Tritonia#_-Link`
`http://neuronbank.org/Tritonia#_-Loc_layer` `http://neuronbank.org/Tritonia#_-Soma`
`http://neuronbank.org/Tritonia#_-Loc_x` `http://neuronbank.org/Tritonia#_-Soma`
`http://neuronbank.org/Tritonia#_-Loc_y` `http://neuronbank.org/Tritonia#_-Soma`
`http://neuronbank.org/Tritonia#_-Outputs` `http://neuronbank.org/Tritonia#_-Neuron`
`http://neuronbank.org/Tritonia#_-Pre` `http://neuronbank.org/Tritonia#_-Connections`
`http://neuronbank.org/Tritonia#_-PMID` `http://neuronbank.org/Tritonia#_-Article`
`http://neuronbank.org/Tritonia#_-Pages` `http://neuronbank.org/Tritonia#_-Book_Chapter`
`http://neuronbank.org/Tritonia#_-Pages` `http://neuronbank.org/Tritonia#_-Article`
`http://neuronbank.org/Tritonia#_-Path` `http://neuronbank.org/Tritonia#_-Example`
`http://neuronbank.org/Tritonia#_-Path` `http://neuronbank.org/Tritonia#_-Brain_Part`
`http://neuronbank.org/Tritonia#_-Publisher` `http://neuronbank.org/Tritonia#_-Book`
`http://neuronbank.org/Tritonia#_-Radius` `http://neuronbank.org/Tritonia#_-Soma`
`http://neuronbank.org/Tritonia#_-Revisions_Made` `http://neuronbank.org/Tritonia#_-Revision`
`http://neuronbank.org/Tritonia#_-Side` `http://neuronbank.org/Tritonia#_-Brain_Part`
`http://neuronbank.org/Tritonia#_-UI_Group` `http://neuronbank.org/Tritonia#:UI_Class`

Articles

The articles they cite. I only ask for two, in order to limit space. 


prefix tritonia: <http://neuronbank.org/Tritonia#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix owl: <http://www.w3.org/2002/07/owl#>

select ?label ?pmid ?abstract
from <http://purl.org/commons/neuronbank-20070918>
where 
 {
   ?ta rdf:type tritonia:_-Article. 
   ?ta tritonia:_-PMID ?pmid.
   ?ta tritonia:_-Abstract ?abstract.
   ?ta rdfs:label ?label.
 }
Limit 2

=>

citation pmid
{Frost WN, Wang J, Hoppe TA, Mongeluzi DL, Tian LM} (2003) 14659097
{Willows AO, Masinovsky B, Kempf SC} (1987) 3572391

Chemical Synapses

A query that I wrote after browsing a bit, trying to get some insight into the contents of the resource. 


prefix tritonia: <http://neuronbank.org/Tritonia#>
prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix owl: <http://www.w3.org/2002/07/owl#>

select   ?pre ?post  ?property ?pmid
from <http://purl.org/commons/neuronbank-20070918>
where 
 {
   ?cs rdf:type tritonia:_-Chemical_Synapse. 
   ?cs tritonia:_-Pre ?prei.
   ?cs tritonia:_-Post ?posti.
   ?prei rdfs:label ?pre.
   ?posti rdfs:label ?post. 
   ?cs tritonia:_-My_Annotations ?annotation.
   ?annotation tritonia:_-PMID ?pmid.
   optional {
     ?cs tritonia:_-My_Properties ?propi.
     ?propi rdfs:label ?property
    }
 }

=>


Pre Post Property
Pl10 DSI -Synaptic_Component - Inhibitory
Pl10 DSI -Monosynapticity - polysynaptic
Pl10 Pl5 -Monosynapticity - monosynaptic
Pl10 Pl5 -Synaptic_Component - Excitatory - Fast
Pl10 Pl6 -Synaptic_Component - Excitatory - Fast
Pl10 Pl6 -Monosynapticity - monosynaptic
Pl10 Pl7 -Monosynapticity - monosynaptic
Pl10 Pl7 -Synaptic_Component - Excitatory - Fast
Pl10 Pl8 -Synaptic_Component - Excitatory - Fast
Pl10 Pl8 -Monosynapticity - monosynaptic
Pl10 Pl9 -Monosynapticity - monosynaptic
Pl10 Pl9 -Synaptic_Component - Excitatory
Pl9 Pl6 -Synaptic_Component - Excitatory - Slow
Pl9 Pl8 -Synaptic_Component - Excitatory - Slow
Pl9 Pl7 -Synaptic_Component - Excitatory - Slow
Pl9 S-Cell -Laterality - Bilateral
Pl9 S-Cell -Monosynapticity - monosynaptic
Pl9 S-Cell -Connection_Probability - 100
Pl9 S-Cell -Synaptic_Component - Inhibitory -Fast
Pl9 DRI -Laterality - Bilateral
Pl9 DRI -Synaptic_Component - Inhibitory
Pl9 DRI -Monosynapticity - monosynaptic
Pl9 Tr1 -Monosynapticity - monosynaptic
Pl9 Tr1 -Laterality - Bilateral
Pl9 Tr1 -Synaptic_Component - Inhibitory
S-Cell Pl7 -Synaptic_Component - Excitatory - Fast
S-Cell Pl8 -Synaptic_Component - Excitatory - Fast
S-Cell Pl6 -Synaptic_Component - Excitatory - Fast
S-Cell Pl5 -Synaptic_Component - Excitatory - Fast
S-Cell Pl10 -Synaptic_Component - Excitatory - Fast
S-Cell Pl9 -Monosynapticity - monosynaptic
S-Cell Pl9 -Synaptic_Component - Excitatory - Fast
S-Cell Pl9 -Laterality - Ipsilateral
C2 Pd10 -Laterality - Contralateral
C2 Pd10 -Monosynapticity - monosynaptic
C2 Pd10 -Synaptic_Component - Inhibitory -Fast
C2 Pd10 -Synaptic_Component - Excitatory - Slow
C2 Pd10 -Synaptic_Component - Inhibitory - Slow
C2 Pd10 -Synaptic_Component - Excitatory - Slow
C2 Pd11 -Synaptic_Component - Excitatory - Fast
C2 Pd11 -Laterality - Contralateral
C2 Pd11 -Monosynapticity - monosynaptic
C2 Pd3 -Monosynapticity - monosynaptic
C2 Pd3 -Laterality - Contralateral
C2 Pd3 -Synaptic_Component - Inhibitory -Fast
C2 Pd3 -Synaptic_Component - Inhibitory - Slow
C2 Pd5 -Laterality - Contralateral
C2 Pd5 -Monosynapticity - monosynaptic
C2 Pd5 -Synaptic_Component - Excitatory - Fast
C2 Pd5 -Synaptic_Component - Inhibitory -Fast

General assessment: It's in RDF, which is great, and looks like a valuable resource. Documenting the classes and properties should be a first priority, to enable reuse. Ideally a revision to the standards of the OBO Foundry would be ideal.

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