- From: Alan Ruttenberg <alanruttenberg@gmail.com>
- Date: Tue, 6 Mar 2007 09:49:26 -0500
- To: Twigger Simon <simont@hmgc.mcw.edu>
- Cc: public-semweb-lifesci@w3.org
Lovely! We would indeed data rather than web pages in order to translate into RDF/OWL and integrate into our queries. I'll contact you off-list to talk about possibilities. -Alan On Mar 6, 2007, at 9:42 AM, Twigger Simon wrote: > Dear All, > > I've been lurking on list for a while and saw this email and wanted > to chime in briefly. I have a few other suggestions for some of > your 'Other Resources' that we have at the Rat Genome Database. We > have rat genes annotated with the Mammalian Phenotype ontology, > along with a disease ontology derived from MeSH, GO and a pathway > ontology we've been putting together in house. We also pull in and > annotate genes from Rat, Mouse and Human where we can to try and > give a broader view from the three species. > > You can search any of the ontologies by starting here: > http://rgd.mcw.edu/tools/ontology/ont_search.cgi > > The Alzheimer's entry via the disease ontology is here: > http://rgd.mcw.edu/tools/ontology/ont_annot.cgi? > term_key=54285&ontology=do > > For this area in particular we also have a Neurological Diseases > portal which gives a different view on the disease data: > http://rgd.mcw.edu/dportal/neurological/ > > This data was derived from a focused curation effort looking at rat > genes involved in neurological diseases and then branching out to > include human and mouse data where available. Much of the human > data came from our curation, Mouse came from MGD. > > To get to the Alzheimer's entry you need to select: > 1. Neurodegenerative Diseases for the disease category in drop down #1 > and then > 2. Alzheimer Disease for the disease in drop down menu #2 (excuse > the typo in the menu's text) > > the page should then refresh giving you graphical views of genes > annotated to Alzheimer's in rat, human and mouse, tables of genes > from these three species and then a GO slim overview of the rat genes. > > If you need raw data instead of web pages or if we can help in any > other way, please let me know. > > Cheers, > > Simon. > > -- > > Simon N. Twigger, Ph.D. > Assistant Professor, Department of Physiology > Medical College of Wisconsin > 8701 Watertown Plank Road, > Milwaukee, WI, USA > tel: 414-456-8802 > fax: 414-456-6595 > AIM/iChat: simontatmcw > > > On Mar 5, 2007, at 9:35 PM, Alan Ruttenberg wrote: > >> >> Summary: >> >> We reviewed the use case, and then, starting in one area of the >> use case - the connection between ADDL and impairment of long term >> potentiation deficits - highlighted on page 2 of the updated use >> case [1] - and started to trace out a series of steps that lead >> towards determining relevant sets of gene and then to images of >> expression of those genes. Along the way we reviewed web pages and >> databases to verify what information was available. We then >> collected a list of on line databases that would enable >> the kinds of queries we were exploring. >> >> [1] http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Demo_Thoughts/ >> Alzheimer%27s_Proposal? >> action=AttachFile&do=get&target=AD_PDUseCase_02-26-07.pdf >> >> Start: >> >> Hypothesis+Abeta -> ADDL (SWAN. Note that these areas of SWAN are >> not yet populated but June and Gwen are working on this). >> >> We attempted to linking ABeta to LTP, but this did not find the >> requisite links. What we did was: >> >> Go to http://senselab.med.yale.edu/senselab/modeldb/. Search for >> "ltp" (could also search for "long term potentiation" >> This is a text search, and the matches are typically against the >> titles of citations. >> Each result links to a model, which lists some cell types, some >> receptor families, some transmitters. >> >> We reviewed the receptors and searched for them in NeuronDB but >> did not find links to processes such as long term potentiation. >> >> --- Starting over >> >> Go to http://senselab.med.yale.edu/BrainPharm/eavData.asp? >> db=1&c=122&o=5904 >> Links from Alzheimer's disease to CA1 Pyramidal Neuron >> >> Click on CA1 Pyramidal Neuron >> Link to http://senselab.med.yale.edu/BrainPharm/NeuronDB/ >> ndbEavSum.asp?id=5588&mo=4&re= >> >> CA1 Pyramidal Neuron Extracellular Elements : Abeta (current I A) >> CA1 Pyramidal Neuron Intrinsic Currents : I A. Click on I A. >> >> http://senselab.med.yale.edu/BrainPharm/eavData.asp?o=5545 >> Links to K+ >> >> Need to know that current of K+ is carried by Potassium Channels. >> >> However, even though some text indicates LTP, there is no explicit >> link. We do have a link from neurons of interest >> to genes however, if we are able to look up proteins associated >> with potassium channel function. >> Browse GO we do find these associations. >> >> ---- Approach using LTP as a key from a different direction. >> >> There is a mesh term >> http://www.nlm.nih.gov/cgi/mesh/2007/MB_cgi?mode=&term=Long-Term >> +Potentiation&field=entry >> >> We can link to pubmed papers using mesh term headings. >> >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? >> CMD=search&DB=pubmed&term=Long-Term+Potentiation%5Bmh%5D&cmd >> >> There is also Potassium Channel >> http://www.nlm.nih.gov/cgi/mesh/2007/MB_cgi?mode=&term=Potassium >> +Channels&field=entry >> and Pyramidal cells >> http://www.nlm.nih.gov/cgi/mesh/2007/MB_cgi?mode=&term=Pyramidal >> +Cells&field=entry >> >> So if we have a Pubmed -> Mesh mapping, we are able to use this to >> navigate from mesh term to mesh term, >> for example, from LTP to cell types or to channel types. >> >> This also requires that we have the MESH tree encoded. Note, >> however, that this MESH->MESH links are potentially unreliable >> as they could be the product of unrelated discussions in the paper >> used to do the mapping. >> >> --- From pubmed to genes. >> >> We can also go from pubmed to gene. This is seen in the user >> interface via the "links" button on a pubmed abstract page. >> e.g. >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? >> db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=17251421&query_hl= >> 5&itool=pubmed_docsum >> >> Choose links, then gene, then you get: >> >> http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? >> itool=pubmed_AbstractPlus&db=pubmed&cmd=Display&dopt=pubmed_gene&from >> _uid=17251421 >> >> The mapping of pubmed -> gene is not in the pubmed records, but is >> kept on the gene side. >> There are entries in the Entrez gene asn or xml record, as well as >> the generifs, which associate a gene with a paper. >> >> Along with the Gene ontology, we now have two ways to navigate >> from "Potassium channel" to gene. >> >> -- From gene to brain region >> >> We can get BrainRegion from gene in a number of ways: >> >> Using expression data: The Allen Brain Map has, for a select group >> of regions and structures, lists of genes >> expressed in those structures. Some of these are at: >> >> http://community.brain-map.org/confluence/display/DataAnno/Home >> >> Others can be scraped from the results of queries at http://brain- >> map.org/welcome.do (click on the "Anatomic Search" tab) >> (Alan has these) >> >> Similarly, Gensat (ftp://ftp.ncbi.nih.gov/RawData/ >> GENSAT-20050125.xml.gz) Has images associated with genes >> and annotations that say which areas/cell types have which >> patterns of expressions of those genes. >> (Alan has these) >> >> --- From Cell type to brain region. >> >> In addition to the mappings implicit in Gensat, >> BAMS http://brancusi.usc.edu/bkms/xml/swanson-98.xml has mappings >> of cell types to brain regions >> >> -- Another route for getting Alzheimer related genes: >> >> We can also get from Alzheimer to gene via Alzgene >> There is a popup of genes on http://www.alzforum.org/res/com/gen/ >> alzgene/default.asp, which records >> studies which find associations between mutations of these genes >> with Alzheimer disease. >> >> --- Some other resources >> >> We will want human to mouse gene mappings for better navigating >> from pubmed. >> Available at: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi? >> db=homologene >> >> For linking gene to protein and protein products such as cleaved >> proteins, June has started curating these from various sources. >> Uniprot has such mapping, it is only textual. See, e.g., http:// >> www.pir.uniprot.org/cgi-bin/upEntry?id=P05067. Look for the >> "contains" field. >> >> Another resource for relating phenotype, process to genes is the >> JAX Mammalian Phenotype ontology/ >> Associated with each phenotype, are the alleles/genes associated >> with the phenotype. >> >> http://www.informatics.jax.org/searches/MP_form.shtml >> For example, abnormal hippocampus function http:// >> www.informatics.jax.org/javawi2/servlet/WIFetch? >> page=mpAnnotSummary&id=MP:0001895 >> >> Gwen and Don will review the terms to see which would be relevant >> to processes associated with Alzheimers, and this gives us another >> route to narrow/expand genes of interest. >> >> Summarizing data sources which we will use for the next step of >> exploration. Some we have, some we need to acquire/convert to RDF. >> >> Mesh >> Pubmed -> Mesh Term >> GO -> Associations (Genes) >> Entrez Gene -> Pubmed >> Entrez GeneRif (= gene->Pubmed) >> NeuronDB/Brainpharm >> Homologene >> Alzgene (Alzheimer Disease -> Associated Gene) >> JAX: Mouse Phenotpe -> Gene >> Uniprot Gene-> splice form, gene product. >> BAMS swanson-98.xml >> Allen/Gensat gene->image, gene-> regions/expressed >> >> Alan's comment: Process for conversion to RDF should be 2 step >> 1) Propose model, give sample entry for review >> 2) Upon agreement on model translate rests/load into triple store >> for query. >> >> Action: Candidates for doing conversions: Alan, EricP, Matthias, >> Don(?) to talk and split tasks. >> Action: Don and Gwen to review phenotypes >> Action: June to curate trying to write pseudo-triples to make >> conversion to real triples easier. >> >> -Alan >> >> >> >> >
Received on Tuesday, 6 March 2007 14:51:15 UTC