- From: June Kinoshita <junekino@media.mit.edu>
- Date: Tue, 23 Jan 2007 09:49:38 -0500
- To: Tim Clark <twclark@nmr.mgh.harvard.edu>
- Cc: Alan Ruttenberg <alanruttenberg@gmail.com>, public-semweb-lifesci <public-semweb-lifesci@w3.org>
Sorry for the delayed reply on this. There's now an entry for an ADDL antibody in the Alzforum Antibody database. Does that help? June On Jan 21, 2007, at 4:33 PM, Tim Clark wrote: > 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 Tuesday, 23 January 2007 14:49:32 UTC