- From: Tim Clark <twclark@nmr.mgh.harvard.edu>
- Date: Sun, 21 Jan 2007 16:33:47 -0500
- To: Alan Ruttenberg <alanruttenberg@gmail.com>
- Cc: June Kinoshita <junekino@media.mit.edu>, public-semweb-lifesci <public-semweb-lifesci@w3.org>
Well, the point here I'd say is to use the identification of ADDL's in the discourse itself - as the starting point. Today that would be, you read a paper. But I am suggesting we use the SWAN "Research Statement" concerning the role of ADDL's as a jumping off point. Tim On SundayJan 21, 2007, at 4:06 PM, Alan Ruttenberg wrote: > > Hi June, > The issue wasn't legal use - rather I was trying to point out that > there aren't public databases that include ADDLs that I was aware of. > So unlike a gene, which we could identify by a URI based on the > Entrez Gene id, I don't know of an analogous resource to identify > ADDLs. This is probably a job for BioONT - either identify an > existing ontology that includes ADDLs, or generate an ontology that > we could use. In some sense this isn't a technical issue in using > the data for the demo, as much as demonstrating how all of it > places in the larger semantic web. > > Best, > Alan > > > > On Jan 21, 2007, at 3:52 PM, June Kinoshita wrote: > >> I think it would be OK to use the antibody date if we include the >> source/credit tag as agreed upon. >> >> June >> >> On Jan 21, 2007, at 9:59 AM, Tim Clark wrote: >> >>> >>> Alan, >>> >>> DS1 can be provided from SWAN beta which we expect to have out by >>> then. At minimum we would give the RDF representation from >>> SWAN. Right June? >>> >>> Tim >>> >>> On SundayJan 21, 2007, at 2:33 AM, Alan Ruttenberg wrote: >>> >>>> >>>> I, among others, took the action item to review the AD use case >>>> and associated data sets. Summary: 7 data sets listed. 2 are >>>> freetext/difficult to convert/query. Wasn't sure how 1 was to be >>>> used. 1 (antibody) has identifier issue for this case. 3 look >>>> usable as specified. >>>> >>>> Please chime in to correct errors, fill in details. >>>> >>>> Regards, >>>> Alan >>>> >>>>> In our use case, an investigator reads about the discovery of a >>>>> new form of Abeta, called Abeta*56, that is reported to cause >>>>> memory impairment in a mouse model of AD. (DS1 - Alzheimer >>>>> Research Forum News) >>>> >>>> It isn't clear in what sense DS1 is a data set to be used in the >>>> use case. Are we expecting that DS1 is to be represented as RDF? >>>> If so, this is something of a challenge, as it is primarily free >>>> text. >>>> >>>>> Question: Is there human data to support that Abeta*56 is >>>>> involved. >>>>> >>>>> A query of PubMed (DS2 - PubMed) finds a paper reporting that a >>>>> form of Abeta with identical molecular weight, called ADDL, is >>>>> elevated by as much as 70-fold in human AD patients' >>>>> cerebrospinal fluid. A hypothesis about ADDL causing memory >>>>> loss in AD is posted on Alzforum. >>>> I'm not sure how to encode pubmed (free text + mesh terms) in >>>> such a way as to successfully make this query. The pmids for the >>>> papers cited in the HCLSIG paper, and their searchable >>>> annotations are below. I've condensed this from the XML >>>> representation of the record, specifically the <ChemicalList >, >>>> and the <MeshHeadingList>. To do this query the annotations >>>> would at least have to mention something to do with memory >>>> impairment and Abeta*56, which neither do. >>>> >>>> PMID:15695586 >>>> >>>> Chemical: Amyloid beta-Protein, Biological Markers, Ligands, DNA >>>> Topic:Alzheimer Disease, *cerebrospinal fluid,diagnosis,genetics >>>> Topic:Amyloid beta-Protein,*cerebrospinal fluid,genetics, >>>> Topic:Base Sequence >>>> Topic:Biological Markers,cerebrospinal fluid >>>> Topic:Case-Control Studies >>>> Topic:DNA,genetics >>>> Topic:Humans >>>> Topic:Ligands >>>> Topic:Nanotechnology >>>> Topic:Polymerase Chain Reaction,methods,statistics & numerical data >>>> Topic:Sensitivity and Specificity >>>> Topic:Solubility >>>> >>>> PMID: 9163350 >>>> >>>> Chemical: Amyloid,Nerve Tissue Proteins,Protein Precursors, >>>> SNCA protein- human,SNCB protein- human,Synucleins,alpha- >>>> Synuclein, >>>> beta-Synuclein,Biotin >>>> Mesh:Amyloid,*metabolism >>>> Mesh:Binding Sites >>>> Mesh:Biotin >>>> Mesh:Electrophoresis, Polyacrylamide Gel >>>> Mesh:Humans >>>> Mesh:Nerve Tissue Proteins,*metabolism >>>> Mesh:Protein Precursors,*metabolism >>>> Mesh:Spectrometry, Mass, Matrix-Assisted Laser Desorption- >>>> Ionization >>>> Mesh:Synucleins >>>> Mesh:alpha-Synuclein >>>> Mesh:beta-Synuclein >>>> >>>>> Question: By what mechanism might Abeta*56 cause memory loss? >>>>> >>>>> The ADDL Hypothesis on Alzforum suggests that ADDL (= >>>>> Abeta*56?) disrupts LTP. >>>> I think we have to parse free text to determine this. I don't >>>> know ho >>>>> Question: What is the mechanism of LTP, in a part of the brain >>>>> that is relevant to AD? >>>>> >>>>> The literature indicates CA1 hippocampal neurons, and A- and D- >>>>> type K channels are involved in LTP. BrainPharm (DS3 - Senselab >>>>> BrainPharm) data state that CA1 hippocampal neurons have A- >>>>> channels. What's more, the A-current is reduced by Abeta. >>>> Verified(second sentence): http://senselab.med.yale.edu/senselab/ >>>> BrainPharm/alzData.asp >>>>> Question: Would an antibody directed against ADDL / Abeta*56 >>>>> restore A-current in the mouse model hippocampal neuron (e.g. >>>>> in an organotypic slice prep)? >>>>> >>>>> A query locates an antibody (DS4 - Alzheimer Research Forum >>>>> Antibody Database) to ADDL and where to obtain it. >>>> Could search here by name, and succeed. However ADDL isn't an >>>> entity that is given an identifier in any of the standard >>>> databases I am aware of, so we do have an issue to deal with >>>> here. Antibody db conversion focuses on proteins whose gene ids >>>> can be found. >>>> >>>>> Our investigator queries pathway databases to identify the gene >>>>> network involved in IFNG regulation, and also SNP databases for >>>>> differences between mouse strains, mouse and human (DS5 - >>>>> GeneNetwork, DS6 - KEGG). He narrows down a group of genes and >>>>> queries the AlzGene (DS7 - AlzGene) database to see if any gene >>>>> association studies have shown a correlation between any of >>>>> these genes and AD risk. >>>> >>>> Verified(IFNG): Could start here for interferon gamma, which >>>> links to several pathways in KEGG. http://www.genome.jp/dbget- >>>> bin/www_bget?hsa+3458 >>>> >>>> Wasn't sure how to use GeneNetwork. Verified that Alzgene links >>>> Gene/SNP to association study. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>> >>> >> > > >
Received on Sunday, 21 January 2007 21:34:09 UTC