Question: (Closed) Should Fasta Be Capitalized?
3
gravatar for sanjuro
7.9 years ago by
sanjuro170
sanjuro170 wrote:

This may not be quite the right forum for this but I don't know of another more appropriate one.

In writing about the Fasta format (as opposed to the program), should Fasta be written as FASTA, Fasta, or fasta? From what I understand, the Fasta format originated as part of the (appropriately capitalized) FASTA program, but it seems to me that it has taken on a life of its own. The NCBI fasta format description and the EMBL sequence format page seem to be consistent in using FASTA. A search for the term "fasta" on the PLoS Biology website yielded a mix of FASTA and Fasta capitalizations (and one FastA), though most were FASTA.

I've tried to summarize the arguments for each format below.

FASTA: since it originated with the program, it should be capitalized like the program.

Fasta: as a proper name, it should be capitalized in the same way as other proper names.

fasta: as an informal reference to an unpublished format which has changed over time (see the Wikipedia article discussion), it's not really a proper name at all.

I prefer Fasta but I'm open to arguments. Any suggestions?

fasta subjective • 3.3k views
ADD COMMENTlink modified 7.9 years ago by Lars Juhl Jensen11k • written 7.9 years ago by sanjuro170
7
gravatar for Lars Juhl Jensen
7.9 years ago by
Copenhagen, Denmark
Lars Juhl Jensen11k wrote:

I don't really care, but I would write it FASTA. Wikipedia seems to agree with me.

Edit:

And for those who do not find Wikipedia and Google convincing, Bill Pearson (the developer of FASTA) writes it FASTA (ref, ref, ref, ref, ref, ref).

ADD COMMENTlink modified 7.9 years ago • written 7.9 years ago by Lars Juhl Jensen11k
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Maybe you didn't take the time to read the question? Like the part where I look at sources that are more authoritative than Google or Wikipedia? And I would say it's relevant to anyone who wants to use the word in a publication, which is most scientists. I thought this might be the right forum given that the history of the word would be best understood by people who work with the program/format. Clearly I was wrong.

ADD REPLYlink written 7.9 years ago by sanjuro170
8

In my opinion such behaviors are really rude, and unfortunately I must tell they are also common here. I find really sad to see experienced people lacking the basic of humility. If you care so much about relevancy (but I do not think this is an irrelevant or stupid question) you should first avoid to publish mere mockeries.

ADD REPLYlink written 7.9 years ago by Anima Mundi2.4k
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I don't understand why the question was closed. Etymological conventions involving writing about a term used in bioinformatics is legitimate and interesting - at least for those of us who enjoy language. Also, the posing of the question is an attempt AWAY from subjectivity, and I don't find sanjuro's question argumentative at all. I don't understand the arrogance displayed by others (apathy, triviality). I also think people can afford to thicken their skin a little. Sanjuro, you're checking out terms before writing about them in the literature. It's an important topic.

ADD REPLYlink written 7.9 years ago by seidel6.8k
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I'm sorry if my comments offended you. I just wanted to leave a funny comment.

ADD REPLYlink written 7.9 years ago by Pierre Lindenbaum121k
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+1 for "I don't really care"

ADD REPLYlink written 7.9 years ago by Pierre Lindenbaum121k
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[<] Please, I would be glad to know who removed the comment.

In my opinion the question is relevant and pertinent, as it regards conventions in the bioinformatics community and literature. Also, the rules of biostar state that "No question is too trivial or too "newbie"", so even questions solved by a simple Google search should be fine (however this is not the case in my opinion). In addition, I do not find the question argumentative, the eventual argument arose from the comments: you had the faculty of not answering if for any reasons you disliked the question. [>]

ADD REPLYlink written 7.9 years ago by Anima Mundi2.4k
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How rude... why not say: http://lmgtfy.com/?q=FASTA ;)

ADD REPLYlink written 7.9 years ago by Joachim2.8k
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And how exactly do you find it a rude to answer a question that is trivially answered by a Google search or looking in Wikipedia to find the consensus? Would you prefer that I just downvote the quetions with no comment and no answer? Or close them as off topic?

ADD REPLYlink written 7.9 years ago by Lars Juhl Jensen11k
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I find rude to comment a question with any type of sarcasm: even if you find trivial a question, in my opinion you should just declare your point of view (as you are doing now, and as you mostly made in your first answer). For me, your second comment (that now has been removed) appeared to be a mere mockery, as it added almost null information while using possible offending connotations, thus it main scope could have been just to make fun of a (just arrived) person. Given the fact that the comment is now missing, I guess my interpretation is correct. [>]

ADD REPLYlink written 7.9 years ago by Anima Mundi2.4k
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In all fairness, you should also try: http://lmgtfy.com/?q=Fasta - which of course gives the same result ;)

ADD REPLYlink written 7.9 years ago by Lars Juhl Jensen11k
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Thanks for the insinuation that I don't read before answering. How about the source Bill Pearson who consistently writes it FASTA both referring to the program and the file format? Authoritative enough for you? http://fasta.bioch.virginia.edu http://www.ncbi.nlm.nih.gov/pubmed/3162770 http://www.ncbi.nlm.nih.gov/pubmed/2156132 http://www.ncbi.nlm.nih.gov/pubmed/2059850 http://www.ncbi.nlm.nih.gov/pubmed/1774068 http://www.ncbi.nlm.nih.gov/pubmed/1422882

ADD REPLYlink written 7.9 years ago by Lars Juhl Jensen11k
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[<] Finally, I want to declare my sincere appreciation for Pierre's apologies (always nice to know how to apologize when we are wrong), and I want to welcome sanjuro too.

ADD REPLYlink written 7.9 years ago by Anima Mundi2.4k
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Thanks to Anima for springing to my defense and to Pierre for his (unnecessary but appreciated) apology. I'd like to make one of my own. As Lars noticed, I insinuated that he did not read the question. I was trying to make the point that I had not failed to use Google and Wikipedia in researching the question. I should not have defended my effort by casting aspersions on his.

ADD REPLYlink written 7.9 years ago by sanjuro170
1

Lars, as a moderator you made fun of a new user for asking a proper and regular question, you* removed your comment, you closed the question for unclear (to me) reasons, and instead of feeling sorry for such behavior you say you are disappointed. That is my personal point of view.

*Or at least an unknown moderator, but in my opinion you should have cared of this point, as the missing of the comment impairs deeply the comprehension of the events.

ADD REPLYlink written 7.9 years ago by Anima Mundi2.4k

I totally disagree with you. There was no sarcasm intended, you read something into my response that was never there. Honestly, your attitude is pissing me off and I'll take a break from Biostar.

ADD REPLYlink written 7.9 years ago by Lars Juhl Jensen11k

I totally disagree with you. There was no sarcasm intended, you read something into my response that was never there. Honestly, your attitude is pissing me off and I'll take a break from BioStar as a direct consequence of this. If this is the thanks one gets for answering a question, then I do not want to spend time here.

ADD REPLYlink written 7.9 years ago by Lars Juhl Jensen11k

I really do not understand why you are offended by my answer. There is no sarcasm intended - it is something you read into it. My point is simply that Wikipedia is edited by the community, and I thus use Wikipedia as a source to support that FASTA seems to be the consensus. Google similarly supports the idea that this is the consensus, but I can understand why someone /might/ get offended by suggesting to use Google. However, I have to say that I am disappointed that this is what one gets as thank for spending time on answering questions for free. I will thus take a break from BioStar.

ADD REPLYlink written 7.9 years ago by Lars Juhl Jensen11k
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