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User talk:Jlick

From SNPedia

A magazine reporter working on an upcoming article would like to speak with one or more dedicated SNPedia contributors. We appreciate your involvement and would like to personally invite you to consider speaking to this writer. If you might be willing, or have questions about this, let us know by email (info@snpedia.com) – thanks. Greg (talk) 03:32, 21 August 2014 (UTC)Greg

What is Jlickbot doing?[edit]

Why did it do this? [1]

I think it's broken, and it has messed up half the mitochondrial SNPs. CarlKenner (talk) 10:00, 15 October 2013 (UTC)

So the error is that METTL21D is on Chrom 14, not MT. James any idea what's going on? --- cariaso 16:07, 15 October 2013 (UTC)
Thanks, Jlick! Since you have an SNPedia bot, and you have an mthap application that converts rs numbers into the more common mitochondrial SNP names, and that works out what haplogroup someone is based on that... it would be really awesome if you could make a bot that will automatically do the following on SNPedia: 1. add the common name to every rs# on the mitochondrial chromosome. 2. add any PMIDs for pubmed articles that mention that common SNP name (or rarely rs#) and also mention "mitochondria", "mitochondrial", "mitochondrion", "mtDNA", etc. (since SNPs on other chromosomes can occasionally have the same common name, although it's less common since they normally use rs numbers) and add them to that page 3. For mitochondrial genes that define a haplogroup, mention that, create the appropriate alelle subpages for the two valid combinations, and assign an appropriate (low) magnitude if it doesn't already have one. 4. Create the genosets and criteria for all mitochondrial haplogroups, with magnitudes highest for the most specific and lowest for the least specific. Preferably using the existing pre-defined mitochondrial haplogroup genoset numbers here: http://snpedia.com/index.php/MtDNA_Haplogroup or creating new ones for haplogroups not listed. It should be very easy for a bot to do all those things, but a nightmare for a human (such as myself) to do it manually. And it would be a huge benefit. Otherwise I'll have to program a bot to do that myself, but I've never done that, so I'm not sure exactly where to start (I am a programmer though). And is the common name just the position on the mitochondrial "chromosome" according to the latest version, followed by the minor allele and optionally preceded by the ancestral allele? CarlKenner (talk) 06:39, 21 October 2013 (UTC)
1) Currently the position field already contains the same positioning used for the rCRS and RSRS standards, so this is already there. (This was not true when human genome build 36 was used but is now in sync with build 37.) 2) cariaso's bot is the one which does pubmed stuff, so you're better off asking him. 3) Something like this has been on my todo list for a while but I've not gotten around to it yet. 4) I originally wanted to do something like this for being able to determine haplogroups, but eventually gave up on it as being too complex to solve with a simple model. The problem is that most people have incomplete mtDNA results, so there will be too many holes and exceptions to do this at all accurately in genosets. This is even worse with chip-based genotyping where you will have no-calls and miscalls to deal with. Even with full sequencing results there are problems such as reversions, optional markers, and indels which can be called in a variety of ways. Also most markers are found in multiple haplogroups. I eventually gave up on this idea as unworkable and wrote mthap instead which takes a more algorithmic fuzzy match approach to determining haplogroups. You're welcome to take a stab at this yourself but I think you'll run into the same issues and give up on it eventually. -- Jlick (talk) 09:37, 21 October 2013 (UTC)

I found another surprise. notice the gene name at rs1154155. Here is the edit. Perhaps you'll find a systemic source for others? --- cariaso 21:15, 21 November 2013 (UTC)

deletes as requested. --- cariaso 16:24, 21 February 2016 (UTC)