Hi Martin, this is great. it will be good enough for us. Joachim: did you have any luck with collecting use cases for this project?
a On Fri, Aug 26, 2011 at 1:16 AM, Martin Gerner <[email protected]> wrote: > Hi Arek, > > I can make sample data available for each of the entity types, if you are > still interested. It's in an SQL table at the moment, so it'd be formatted > as a simple tab-separated value file I imagine. > > -- Martin > > On 26/08/2011 02:16, Arek Kasprzyk wrote: >> >> Hi Goran, >> is there are test dataset available right now that we could use for >> quick prototyping? >> >> a >> >> >> On Thu, Aug 25, 2011 at 1:03 PM, Goran Nenadic >> <[email protected]> wrote: >>> >>>>>> As for the data, we are finalising a datastore of mentions of genes, >>>>>> proteins, species etc. for the entire Medline and (open-access) PMC - >>>>>> e.g. some 80 million mentions of genes/proteins, associated with >>>>>> anatomical location where available. >>>>> >>>>> Sounds great! Will that be a continuation of www.pubmed2ensembl.org? >>> >>> The aim of pubmed2ensembl is to directly link genomic data (Ensembl) and >>> biological literature (PubMed) on a large scale. There are links between >>> over 2 million articles and nearly 150,000 genes from 50 species, and >>> these >>> are then integrated with other Ensembl data on these genes for integrated >>> querying. One can query both PubMed for a particular term (e.g. disease, >>> process) and get associated genomic data directly, or the other way >>> around - >>> e.g. use genomic coordinates as input and get associated papers. The data >>> is >>> available for browsing or download at www.pubmed2ensembl.org, and the >>> associated paper was accepted two days ago (PLOS ONE), and is in >>> production >>> now :). >>> >>> The new dataset that Martin mentioned will be much larger, including >>> links >>> from some 200 million mentions of various 'things' in both PubMed and >>> PubMed >>> Central - from genes, species, anatomical terms etc., many of them linked >>> to >>> relevant databases and processes they are involved in. As I said, this >>> dataset will be available very soon and it could be also potentially >>> integrated in a biomart. I guess with all Joachim's efforts one would be >>> also able to use SPARQL to query this data (if or once it's available via >>> BioMart 0.8). >>> >>> Best, >>> Goran >>> >>> >>> > > > _______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
