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molbiodiv / biojs-io-biom

Parses biom files
MIT License
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Improve introduction (better cover historical context) #28

Closed iimog closed 7 years ago

iimog commented 7 years ago

As a referee to our f1000 article notes:

There is a historical context that Ankenbrand et al. miss in discussing biom-format and subsequently imply that the biom-format is more widely adopted than being field specific format. If the authors leave the introduction more general, then I would suggest they include more background on the history of high-throughput data storage and reproducibility in programmatic languages, perhaps starting with the Minimum Information About a Microarray Experiment - MIAME format [1] and exprSet classes developed in R about 15 years ago before the genomics standards consortium (formed in 2005), for which biom-format is a member.

Paulson J. Referee Report For: biojs-io-biom, a BioJS component for handling data in Biological Observation Matrix (BIOM) format [version 1; referees: 3 approved with reservations]. F1000Research 2016, 5:2348 (doi: 10.5256/f1000research.10362.r16545)

[1] Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C, Aach J, Ansorge W, Ball CA, Causton HC, Gaasterland T, Glenisson P, Holstege FC, Kim IF, Markowitz V, Matese JC, Parkinson H, Robinson A, Sarkans U, Schulze-Kremer S, Stewart J, Taylor R, Vilo J, Vingron M: Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.Nat Genet. 2001; 29 (4): 365-71

iimog commented 7 years ago

Added a little historical background as suggested by the reviewer.