What’s N? It’s the fraction of time that bioinformaticians spend obtaining, formatting and getting raw data ready to use, as opposed to analysing it.
There’ll be a longer post on this topic soon. Suffice to say, I’ve spent the last month evaluating the performance of 5 predictive tools that are available on the web. To do this, a test dataset of 200 or so sequences had to be submitted to each one. Each tool generates a score for particular residues in the sequence. The final output, which is what I require to do some statistical analysis, looks something like this:
P08153 114 method 61.74 0 P08153 522 method 82.10 1
where we have a sequence UniProt accession number, a sequence position, the name of the tool used (method), a score and either 1 (a positive instance) or 0 (a negative instance).
Doesn’t look too hard, does it? Except that:
- None of the web servers provide web services or APIs
- None of them provide standalone software for download
- Most of them don’t generate easily-parsed output (delimited plain text)
- Most of them have limited batch upload and processing capabilities
The solution, as always, is to hack together several hundred lines of poorly-written Perl (using HTML::Form in my case) to send each sequence to the server, grab the HTML that comes back, parse it and write out text files in the format shown above.
That’s 3-4 weeks and 500 lines of throwaway code just to get the raw data in the right state for analysis
When I started out in bioinformatics, I used to joke that at least 50% of my time was spent just obtaining raw data and formatting files. Over the years, I’ve revised my estimate. It’s currently at around 80-90% and I’m not sure that it’s still a joke.
Why is this trend in the wrong direction? When does it become untenable? I’m starting to think that my job title should be “data munger”, not “research officer”. I wouldn’t mind if data munging was perceived as a skill in academia but when funding is results-based, it will only ever be seen as the means to an end. Which it is, of course.