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Wait, if she knows how to avoid the issue, how is it still an issue?
by qayxc 5y ago
Wait, if she knows how to avoid the issue, how is it still an issue?
- acomjean 5y agoI work in bioinformatics and have seen the issue. You get data from a lot of sources, and people (like me) just sometimes forget to check the spreadsheet. Often a csv file so it’s not clear it’s been generated by excel. It’s also only a problem for gene symbols (not entrez gene IDs or flybase gene numbers). Also the datasets are big, so there are 15 genes in error over the whole dataset it can be hard to spot. Honestly genes are a constantly moving target and are kinda a pain to write software for. They get new names, split and merge over time…
- qayxc 5y agoWhat really interests me is why your field is still using untyped CSV data for exchanging information, instead of say XML. And why hasn't there been a collaboration between professionals to fix this on an organisational level (like agreeing on a spreadsheet template or sane method for data exchange)? Is it really every lab for themselves with MS Excel and CSV of all things being the lowest common denominator?
- acomjean 5y agoFile sizes are an issue and xml won’t help. The file formats are wierd (fasta?) but they are at least kinda standard. There are groups dedicated to organizing/ annotating genes. They’re quite organized and have highly structured databases. http://gmod.org/wiki/Introduction_to_Chado http://gmod.org/wiki/Introduction_to_Chado A lot of the model orgainism species have gotten together to make thinks more uniform. https://www.alliancegenome.org/ https://www.alliancegenome.org/ Also most people in this field are using free software.