User:Jkenchel/sandbox
Article evaluation
[edit]Article: Nucleic acid notation
The article is sufficiently concise and covers a number of notation systems for the canonical bases of DNA and RNA. However, it doesn't contain any information about notation of modified or non-canonical bases. Furthermore, the bulk of the article, including the introduction, focus on the IUPAC standardized notation system. Overall, the article reads as if it was created first as an article about the IUPAC system, and later edited to add on information about a few alternative systems at the end. The first sentence of the article essentially equates "nucleic acid notation" with the IUPAC system, which is incorrect. The first sentence of the article should instead define the concept of "nucleic acid notation".
Another glaring issue with the article concerns the apparent bias of the author(s) against the IUPAC system and in favor of other visual representation systems. Many of the statements about the intent of the creators of the systems are not cited, such as "The authors of the notation endeavored to select ambiguity characters with logical mnemonics" and "These creative approaches to visualizing DNA sequences have generally relied on the use of spatially distributed symbols". The author(s) of the article use several terms indicating subjective value judgements, such as "creative approach", "poor legibility", and "far easier". Some of these terms may be neutrally applied, if supported with proper data from references.
About half of the information stated as fact is not cited. This includes such statements as "Despite its broad and nearly universal acceptance, the IUPAC system has a number of limitations, which stem from its reliance on the Roman alphabet" and "these Roman characters are available in the ASCII character set most commonly used in textual communications, which reinforces this system's ubiquity". Only 5 of the 10 references are linked, but those links work. The references themselves seem solid, consisting of primary literature, IUPAC communications, and one interesting rumination on the legibility of print.
Interestingly, the only comment on the Talk page takes note of the bias I noticed: "This whole article is an advertisement for ambiscript. It's disgusting."
In my opinion, in addition to rewriting the article to define "nucleic acid notation" properly and frame each notation system neutrally, rewriting it with a general audience in mind would benefit the quality of the article and make it more accessible. My thinking is that a Wikipedia article shouldn't talk about its subject the way experts in the field would discuss it with each other, or even in the same way the subject would be talked about in a university-level course. The language should be made simpler so that a broad audience can understand it. One example from this article is the sentence "These are used to encode the consensus sequence of a population of aligned sequences and are used for example in phylogenetic analysis to summarise into one multiple sequences or for BLAST searches..." The sheer density of jargon in this sentence would render it illegible to anyone without experience in the field. At the very least, BLAST could be defined or spelled out.
Possible article topics
[edit]RNA spike-in
[edit]Article: RNA-spike-in
This article is only five sentences long and does not contain details about how RNA spike-ins are made or their use in DNA microarrays. I would also expect it not to make sense to anyone without molecular biology knowledge; the language could be simplified and/or the article could link to articles that define specialized terms used in the article.
Ribotyping
[edit]Article: Ribotyping
This article is a bit longer, but could similarly be fleshed out by adding sections describing different applications of ribotyping: for example, the 16S rRNA used to classify bacteria.
Selected article
[edit]Article: RNA-spike-in
I plan to flesh out the article with divided sections about separate kinds of assays in which RNA spike-ins are used and what applications those assays have. I also plan to describe the history of RNA spike-ins and how they are made. If such information is available, I will write about speculated future directions that the technology could take. I will add sources and cite them properly, as well as checking the existing sources for accuracy. I will make sure to write in language that is easily accessible to a wide audience, as much as possible. Where it is not possible and short definitions or general terms cannot be substituted for specialist language, I will link to other articles that explain the terms. Finally, I will add one or more pictures, if I can find relevant ones.
Proposed bibliography:[1][2][3]
References
[edit]- ^ Jiang, Lichun; Schlesinger, Felix; Davis, Carrie A.; Zhang, Yu; Li, Renhua; Salit, Marc; Gingeras, Thomas R.; Oliver, Brian (2011-09-01). "Synthetic spike-in standards for RNA-seq experiments". Genome Research. 21 (9): 1543–1551. doi:10.1101/gr.121095.111. ISSN 1088-9051. PMID 21816910.
- ^ Qing, Tao; Yu, Ying; Du, TingTing; Shi, LeMing (2013-02-01). "mRNA enrichment protocols determine the quantification characteristics of external RNA spike-in controls in RNA-Seq studies". Science China Life Sciences. 56 (2): 134–142. doi:10.1007/s11427-013-4437-9. ISSN 1674-7305.
- ^ Zook, Justin M.; Samarov, Daniel; McDaniel, Jennifer; Sen, Shurjo K.; Salit, Marc (2012-07-31). "Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing". PLOS ONE. 7 (7): e41356. doi:10.1371/journal.pone.0041356. ISSN 1932-6203.
{{cite journal}}: CS1 maint: unflagged free DOI (link)
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