- From: June Kinoshita <junekino@media.mit.edu>
- Date: Sun, 21 Jan 2007 15:52:00 -0500
- To: Tim Clark <twclark@nmr.mgh.harvard.edu>
- Cc: Alan Ruttenberg <alanruttenberg@gmail.com>, public-semweb-lifesci <public-semweb-lifesci@w3.org>
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 20:52:09 UTC