tag:blogger.com,1999:blog-10781944.post5180193707292285483..comments2024-03-28T00:36:36.460-07:00Comments on The Tree of Life: Story behind the paper guest post on "Resolving the ortholog conjecture"Jonathan Eisenhttp://www.blogger.com/profile/07953790938128734305noreply@blogger.comBlogger7125tag:blogger.com,1999:blog-10781944.post-64063083852612300492013-01-02T04:37:36.147-08:002013-01-02T04:37:36.147-08:00Great post, thanks. It has certainly helped me cla...Great post, thanks. It has certainly helped me clarify some of the nuances of the "orthologue conjecture" in my own mind and hopefully my lectures will be clearer and more explicit as a result. That authorship bias thing is fascinating too - worthy of a paper in its own right, I think! I wonder how many users of GO are aware of it. I've certainly always thought about ascertainment bias in GO as an issue of coverage rather than differential annotation.Richard Edwardshttps://www.blogger.com/profile/16115218690707131186noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-17682808524578040572012-12-13T09:19:15.623-08:002012-12-13T09:19:15.623-08:00Thank you for posting this!Thank you for posting this!Tonihttps://www.blogger.com/profile/03001880189572009935noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-16908401751270695712012-05-25T02:10:01.995-07:002012-05-25T02:10:01.995-07:00I posted a French translation of this post, slight...I posted a French translation of this post, slightly edited, on my blog:<br />http://toutsepassecommesi.cafe-sciences.org/2012/05/25/histoire-dun-article-la-solution-de-la-conjecture-orthologue/mrrhttps://www.blogger.com/profile/03739692453151019735noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-43369873871466832772012-05-20T11:17:53.119-07:002012-05-20T11:17:53.119-07:00I agree, this is the big challenge in (bio)datamin...I agree, this is the big challenge in (bio)datamining. From a philosophical perspective, I find it interesting that data can be experimental in one context and observational in another. I hadn't really thought about this (or the author bias) before. In general, one of the important advances from your paper and the Nehrt paper is that the underlying biases in GO are being studied directly in a way that the functional genomics community has not really sunk its teeth as deeply. I wouldn't be surprised if these papers kick start a cottage industry in this direction that will help catalyze the ability to get more meaning from GO in the long run.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-10781944.post-36224368582912062042012-05-20T09:00:41.025-07:002012-05-20T09:00:41.025-07:00Defining observational data as "data lying ar...Defining observational data as "data lying around" was perhaps a bit too derisive, but this does not imply that they are inherently flawed. As you correctly point out, a subset of the GO annotations is derived from experimental evidence (this is the subset we considered in our analysis); such annotations are as reliable as it gets. The challenge lies in inferring causality from observational data.Christophe Dessimozhttps://www.blogger.com/profile/06599363465221194317noreply@blogger.comtag:blogger.com,1999:blog-10781944.post-88202982845558787232012-05-20T07:44:12.973-07:002012-05-20T07:44:12.973-07:00Thanks for this excellent summary, Christophe. Gla...Thanks for this excellent summary, Christophe. Glad to see progress on this important issue. <br /><br />One small thing, when you say "Data pulled from the GO database clearly falls into the second category: observational data" I think you mean that GO data used in a datamining context is observational - not that the data in the GO database itself is observational. While many GO annotations are computationally inferred, the source of these annotations flows back to experimental evidence, and many GO annotations are based on direct experimental evidence.Anonymousnoreply@blogger.comtag:blogger.com,1999:blog-10781944.post-29955447546214891722012-05-18T08:40:30.137-07:002012-05-18T08:40:30.137-07:00Excellent, this had been bothering me for ages and...Excellent, this had been bothering me for ages and now we know the answer. Quite an important issue for anyone performing studies that mine online databases of observational data.<br /><br />The link to the article at the top is wrong, it should be:<br />http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002514Nick Lomanhttps://www.blogger.com/profile/12121179953421841062noreply@blogger.com