Learning from tech - Better APIs

September 19, 2007

Another post that I started writing a while ago, but never quite managed to pin down. Well, a post by Neil Saunders expressing frustration with the state of bioinformatics services was just the inspiration required.

Historically, centralized data repositories like the NCBI, EBI, PDB, etc have been sources of data, but have also provided the most commonly used search interfaces and web services that people use to access that data. A number of services built on local copies of the data have been developed, often for internal use at companies (and I’ve been part of some fantastic ones), and while APIs are available, the trend to provide documented, usable APIs pervasive in the tech world these days is not quite the norm in the life sciences. Assuming that we have excellent public data repositories, with rich APIs and data structures, it would be nice if a mix of application developers, designers and data geeks could start developing visual experiences and web services that enhance the utility of these sites. Unfortunately, as Neil’s and Hari’s experiences have shown, that is simply not the case.

In my own experience, from conferences, etc, it is clear that the world of bioinformatics (all life science informatics actually) faces a major problem. One where too much time is spent moving data back and forth and in formatting/reformatting and just in work that I would call “grunt work”. A decade ago that might have been somewhat acceptable, as the field was still young, but not when bioinformatics becomes a core part of research. It is critical that various biological resources need to do a better job of allowing their customers (and I use the word deliberately) to be more effective using their resources. One of the best comments about Pipeline Pilot came from the head of informatics at a pharma company. He said that using it had made it possible for his informaticians to focus on developing new methods and deploying them to other scientists, since Pipeline Pilot did such a good job of gluing things together. We need to make this process even more simple, and allow the Neil’s of the world to focus on data analysis, software development and methodology and not data munging.

Let me take this thought one step further. I believe that there is a business model to be explored here as well. Philosophically, I believe that knowledge lies in what can be done with data, rather than the data itself. If everyone has equal access to the data, monetizing processes that generate useful information from the data is perfectly fair and square. The one caveat, and perhaps someone can share their thoughts on this, is whether the data producers should be compensated somehow, or is that addressed by the funding, etc they get? Alternatively, data produces are well placed to develop services on top of the data as they have intimate scientific knowledge. And I am not just talking about the AJAX-ification of genome browsers. It is a well known fact that Google and others have built their empire on top of open source software. Others have leveraged services and APIs to provide useful services, e.g. Lijit uses Google Custom search and one of the genome browsers mentioned above uses the Google maps API. Would it be appropriate to take publicly available services, and using them as a backend, develop commercial services? If yes, what are the kinds of businesses that can be built on top of that? What kind of licensing policies would be prevalent? Food for thought and the subject of another post some day.

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Posted by Deepak Singh | Filed Under Informatics, Software & Internet 

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