MedWorm provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest medical blog items that have been tagged with 'data integration'. Sat, 03 Sep 2011 02:48:40 +0100 http://www.medworm.com/index.php?rid=4455410&cid=t_104433_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2011%2F02%2F09%2Falgorithms-running-day-and-night%2F Warning: contains murky, somewhat unstructured thoughts on large-scale biological data analysis Picture this. It’s based on a true story: names and details altered. Alice, a biomedical researcher, performs an experiment to determine how gene expression in cells from a particular tissue is altered when the cells are exposed to an organic compound, substance Y. She collates a list of the most differentially-expressed genes and notes, in passing, that the expression of Gene X is much lower in the presence of substance Y. Bob, a bioinformatician in the same organisation but in a different city to Alice, is analysing a public dataset. This experiment looks at gene expression in the same tissue but under different conditions: normal compared with a disease state, Z Syndrome. He also notes ... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=4455410 Wed, 09 Feb 2011 03:41:21 +0100 4455410 http://www.medworm.com/index.php?rid=3408575&cid=t_104433_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2010%2F03%2F26%2Fbiomart-and-biomart%2F I’ve been vaguely aware of BioMart for a few years. Inexplicably, I’ve only recently started to use it. It’s one of the most useful applications I’ve ever used. The concept is simple. You have a set of identifiers that describe a biological object, such as a gene. These are called filters. They have values – for example, HGNC symbols. You want to retrieve other identifiers – attributes – for your objects. You can use BioMart as a web application called MartView. However, R users should check out the biomaRt package, part of the Bioconductor suite. Here’s a couple of examples. Example 1: fetch Ensembl gene identifiers given HGNC symbols Let’s start with a simple example. You have a CSV file in which one of the fields is a HGNC symbol (w... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3408575 Fri, 26 Mar 2010 07:23:18 +0100 3408575 http://www.medworm.com/index.php?rid=3048289&cid=t_104433_132_f&fid=35006&url=http%3A%2F%2Fnsaunders.wordpress.com%2F2009%2F12%2F02%2Fhas-our-quest-for-completeness-made-things-too-complicated%2F In my opinion, yes. Let me elaborate. My current job is very much focused on “data integration”. What this means is that we have a large amount of diverse data from different “-omics” experiments: microarrays, protein mass spectrometry, DNA sequencing – really, whatever you like, but it’s all aimed at answering the same question. Namely: which of these biological entities (transcripts, proteins, metabolites) are markers for various human disease states? Somehow, we have to pull all of these data into a common framework so that it can be analysed using statistics. The problem: whilst a lot of effort has gone into designing schema and ontologies that describe the individual data types, less effort has been applied to the question: what do all these things... What You're Doing Is Rather Desperate blogs http://www.medworm.com/rss/comments.php?id=3048289 Wed, 02 Dec 2009 02:38:06 +0100 3048289 http://www.medworm.com/index.php?rid=2046785&cid=t_104433_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Fone-way-for-rdf-to-help-a-bioinformatician-build-a-database-s3db.html%3F_c%3Dfeed-rss This post is part of the PLoS One syncroblogging day, as part of the PLoS ONE @ Two birthday celebrations. Happy Synchroblogging! Here's a link to the paper on the PLoS One website. Biological data: vitally important, determinedly unruly. This... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics) Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=2046785 Thu, 18 Dec 2008 08:34:11 +0100 2046785 http://www.medworm.com/index.php?rid=2033141&cid=t_104433_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Fadding-informative-metadata-to-bioinformatics-services.html%3F_c%3Dfeed-rss [This post has also been copied across to my researchblogging-friendly wordpress site (now completely defunct except for my research blogging efforts, as Vox doesn't play nicely with their aggregator software)]. Carole Goble and the other auth... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics) Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=2033141 Fri, 12 Dec 2008 15:22:43 +0100 2033141 http://www.medworm.com/index.php?rid=2027020&cid=t_104433_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Fthis-site-now-listed-in-nature-blogs-and-the-reason-behind-my-keyword-choices.html%3F_c%3Dfeed-rss Last week when scanning through Friendfeed, someone mentioned Nature Blogs. A number of my friends and fellow friendfeeders (1,2,3,4,5,6,etc.) already have their blogs registered there. I took the plunge and submitted my request last week, and thi... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics) Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=2027020 Thu, 11 Dec 2008 08:03:23 +0100 2027020 http://www.medworm.com/index.php?rid=1859507&cid=t_104433_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Ftwo-journal-special-issues-big-data-and-semantic-mashups-for-bioinformatics.html%3F_c%3Dfeed-rss Both of these special issues are worth a look, as some of the papers look pretty interesting. I'll spend a little time in a later post on any articles I find particularly relevant. Semantic Mashup of Biomedical Data Special Issue of the Journal... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics) Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=1859507 Tue, 07 Oct 2008 12:55:42 +0100 1859507 http://www.medworm.com/index.php?rid=933996&cid=t_104433_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Fof-gelml-and-mfo.html%3F_c%3Dfeed-rss A couple of papers from here at Newcastle University have appeared over the past couple of weeks. Here's a summary of them both. Data Standards From "An Update on Data Standards for Gel Electrophoresis" in Practical Proteomics Issue 1, Septembe... Read and post comments | Send to a friend (Source: Systems Biology & Bioinformatics) Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=933996 Mon, 08 Oct 2007 12:05:48 +0100 933996 http://www.medworm.com/index.php?rid=602049&cid=t_104433_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Fnewcastle-university-technical-report-cisban-dpi.html A Technical Report for the School of Computing Science of Newcastle University was released last month describing the CISBAN DPI, an implementation of the FuGE Milestone 3 STK. You can find and download that technical report here:http://www.cs.ncl.ac.uk/research/pubs/trs/abstract.php?number=1016 The Abstract follows:The Centre for Integrated Systems Biology of Ageing and Nutrition has developed a Data Portal and Integrator (CISBAN DPI) that is based on the FuGE Object Model and which archives, stores, and retrieves raw high-throughput data. Until now, few published systems have successfully integrated multiple omics data types and information about experiments in a single database. The CISBAN DPI is the first published implementation of FuGE that includes a database back-end, expert and s... Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=602049 Thu, 10 May 2007 17:22:01 +0100 602049 http://www.medworm.com/index.php?rid=490872&cid=t_104433_132_f&fid=35011&url=http%3A%2F%2Ffeeds.feedburner.com%2F%7Er%2Fmndoci%2F%7E3%2F103577468%2F Via Techmeme I found this short post by Dave Winer in which he quotes Peter Rip The Web today still resembles MS-DOS more than MS-Windows. Every website is an island, an island that knows nothing about any other website. This is no different than the world before the Windows Clipboard. All 640KB of memory was available to whatever application was running. The point of integration was the User. As it is today. This quote really hits home. With exceptions the world of biological information is exactly that, an island. The integrated web of information is a misnomer. Just because Google indexes the web doesn’t make it integrated. So how does this change? That’s why I am intrigued by the semantic web, Freebase, microformats, etc. In the software business we talk about about develop... business|bytes|genes|molecules blogs http://www.medworm.com/rss/comments.php?id=490872 Thu, 22 Mar 2007 16:11:54 +0100 490872 http://www.medworm.com/index.php?rid=485533&cid=t_104433_132_f&fid=35028&url=http%3A%2F%2Flurena.vox.com%2Flibrary%2Fpost%2Fbeta-release-cisban-data-portal-and-integrator.html The Centre for Integrated Systems Biology of Ageing and Nutrition has developed a Data Portal and Integrator (CISBAN DPI) based on Milestone 3 of the Functional Genomics Experiment (FuGE) Object Model (FuGE-OM), and which archives, stores, and retrieves raw high-throughput data. We are pleased to announce that the CISBAN Data Portal and Integrator is now available in a public sandbox version. Please note that this release is still at an early beta stage, and any data you may upload to the server may be deleted at any time. You will need a logon to access this database, which you may request from the helpdesk. This is a low-level of security that will only serve to prevent anonymous load on the database and to keep your sandbox area separate from others. For more inform... Systems Biology & Bioinformatics blogs http://www.medworm.com/rss/comments.php?id=485533 Fri, 16 Mar 2007 16:40:12 +0100 485533