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Re: HCLS knowledgebase extension: PDSP Ki database uploaded to DERI triplestore

From: Kei Cheung <kei.cheung@yale.edu>
Date: Wed, 07 Nov 2007 08:29:59 -0500
To: Bill Bug <wbug@ncmir.ucsd.edu>
Cc: samwald@gmx.at, "alanruttenberg@gmail.com" <alanruttenberg@gmail.com>, "giovanni.tummarello@deri.org" <giovanni.tummarello@deri.org>, "public-semweb-lifesci@w3.org" <public-semweb-lifesci@w3.org>
Message-id: <4731BDD7.8070607@yale.edu>

Hi Bill, Matthias,

I think it would be great if we can demonstrate how to query across 
these neuroscience ontologies with SW applications like Entrez Neuron ....



Bill Bug wrote:

> This is wonderful, Matthias.
> We need to look at how this jibes with what we've created in BIRN & 
> NIF for the IUPHAR classification for G-protein coupled receptors.  We 
> definitely want our representations to stay commensurate.  We've got 
> this in the ontology driving integration between SenseLab, CCDB, and 
> NeuroMorpho.org.  This includes the complete set of NeuroName brain 
> regions refactored for a BFO+OBO-RO + PATO representation in OWL 
> (BIRNLex-Anatomy), nerve cell types (NIF-Cell.owl) which we are 
> working to make compatible with the OBO CL ontology, and OBI.
> For the IUPHAR representation, I'm using the Sequence ontology, BFO, 
> OBO-RO, and PATO.  I also use NCBI eUtils to draw out multiple 
> organism representations using Homologene, as well as to assemble all 
> the appropriate parts from protein superfamily to the 
> organism-specific protein (think UniProt) on through to transcript, 
> gene, and chromosome, so that you could resolve a SPARQL query that asks:
> What Cav2-type Ca++-Channels are on mouse chromosome 11?
> I've got ligands in there - at least those the IUPHAR group has listed 
> for the receptor families.  It's nothing like the variety in PSPD Ki 
> (7500 test ligands).  There are some blank node problems with my 
> current representation of the ligand interactions that I have to fix, 
> but it does use the BFO dependent continuants to describe a 
> "disposition to bind" a ligand which is then linked to specific 
> ligands (e.g., the many Adenosine analogs that bind to the various 
> Adenosine receptors).  I'm not certain whether disposition is the way 
> to do this - or whether there should be a "ligand role" that inheres 
> in the ligand molecules.  You're still left trying to figure out how 
> to link the ligands to the receptors.  The alternative is to represent 
> the binding process - which you are doing very nicely here using the 
> generic GO "binding" molecular function.  Since IUPHAR is 
> receptor-centric, representing binding as a disposition of the 
> receptors, seemed reasonable as a first pass on IUPHAR.
> The other issue I've still not worked out is in order to be able to 
> infer the set described in the example above, all the classes need to 
> have the proper disjoint relations and closing axioms.  I can easily 
> do this, since this whole representation is algorithmically generated 
> off an algorithmic dump of the IUPHAR spreadsheets using Jena & the 
> NCBI eUtils.  The problem was, when I put the sibling disjoints in 
> there for the mRNAs & genes (essentially 500+ sibling descendants of 
> SO:mRNA and SO:multi-cistronic gene), I couldn't open the file in 
> Protege v3.3.1, so I had to drop those for the time being.
> One comment on the PSPD Ki representation you have:
> Do you have the tissue & organism source fields from PSPD Ki?  If 
> these could be included in the result list (maybe even used to sort 
> the list - in addition to sorting on ligand), then it would be clear 
> why there are multiple entries for some of the ligands.
> Again - very nice work.
> Cheers,
> Bill
> P.S.: We've also run the same conversion on the IUPHAR voltage-gated 
> ion channels.  Both of these will be reviewed at the upcoming Protege 
> Ontology (PRO) meeting to figure out how to make use of Sequence 
> Ontology & the PRO components (ProEvo & ProForm) - as well as the RNA 
> Ontology.
> As I mentioned about 2 months ago, these files are available for 
> review at:
> BIRNLex ontology (some components re-used in NIF ontology):
> http://purl.org/nbirn/birnlex/ontology/birnlex.owl
> NIF ontology:
> http://purl.org/nif/ontology/nif.owl
> On Oct 31, 2007, at 11:10 AM, samwald@gmx.at <mailto:samwald@gmx.at> 
> wrote:
>> I have uploaded the 'beta version' of the OWL conversion of the PDSP 
>> Ki database to the SPARQL endpoint hosted by DERI.
>> The address is:
>> http://hcls.deri.ie/sparql
>> Alternatively, you can also use the SPARQL endpoint of the Yale 
>> Center for Medical Informatics (only contains the SenseLab ontologies):
>> http://neuroweb.med.yale.edu:8890/sparql
>> Since the datasets makes use of the SenseLab URIs for receptors, the 
>> queries can also be connected to further information about neuronal 
>> cell types, cellular properties, brain regions etc.
>> A possible SPARQL query showing some ligands of the serotonin 
>> receptor 5-HT2A, together with their affinity (lower values mean 
>> higher affinity, i.e. the substance is of higher pharmacological 
>> interest):
>> =====
>> PREFIX neurondb: <http://purl.org/ycmi/senselab/neuron_ontology.owl#>
>> PREFIX obo_essentials: <http://purl.org/zen/obo_essentials.owl#>
>> PREFIX ro:
>> <http://www.obofoundry.org/ro/ro.owl#>
>> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
>> SELECT ?name_of_ligand ?ki_value FROM 
>> <http://purl.org/ycmi/ki/core.owl> WHERE  {?nicotinic_receptor a 
>> neurondb:_5-HT2A .
>> ?ligand a ?ligand_class .
>> ?process a obo_essentials:GO_0005488_process .
>> ?process ro:has_participant ?nicotinic_receptor . 
>> ?process ro:has_participant ?ligand .
>> ?ligand_class rdfs:label ?name_of_ligand .
>> ?ligand ro:bearer_of ?quality .
>> ?quality rdf:value ?ki_value .
>>  } 
>> =====
>> First three results:
>> name_of_ligand -- ki_value
>> --------------------------
>> tryptamine -- 218.7761623949
>> (R)-noradrenaline --455970.15
>> yohimbine -- 4790
>> chlorpromazine -- 1.8 
>> Some of the ligands have the name 'null', this still needs to be fixed.
>> The PDSP Ki datasets can be mirrored on other installations of 
>> Virtuoso with the following iSQL command:
>> xml_uri_get('http://neuroweb.med.yale.edu/svn/trunk/ontology/ki/core.owl' 
>> <http://neuroweb.med.yale.edu/svn/trunk/ontology/ki/core.owl%27>, 
>> 'http://neuroweb.med.yale.edu/svn/trunk/ontology/ki/core.owl' 
>> <http://neuroweb.med.yale.edu/svn/trunk/ontology/ki/core.owl%27>), 
>> 'http://purl.org/ycmi/ki/core.owl' 
>> <http://purl.org/ycmi/ki/core.owl%27>, 
>> 'http://purl.org/ycmi/ki/core.owl' <http://purl.org/ycmi/ki/core.owl%27>
>> )
>> Please note that the current HCLS demo knowledge base contains 
>> outdated namespaces for the SenseLab ontologies (we are using PURLs 
>> now), so the PDSP Ki datasets do not readily connect to the rest of 
>> the knowledge base. The namespaces in the demo KB will soon be 
>> updated (at least I would like to do so).
>> cheers,
>> Matthias Samwald
>> -- 
>> Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! 
>> Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer
> William Bug, M.S., M.Phil.                                          
> email: wbug@ncmir.ucsd.edu <mailto:wbug@ncmir.ucsd.edu>
> Ontological Engineer/Programmer Analyst III work: (858) 822-0739
> Biomedical Informatics Research Network
> Dept. of Neuroscience, School of Medicine
> University of California, San Diego
> 9500 Gilman Drive
> La Jolla, CA 92093
> Please note my email has recently changed
Received on Wednesday, 7 November 2007 13:30:39 UTC

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