The Search Principle blog

What is bioinformatics – and its associated concepts genomics, proteomics, metabolomics? (see Bioinformatics)

Bioinformatics is the integration of computers, databases and software into efforts to address large biological questions. Approaches to bioinformatics are often used to generate large sets of information or data. Two large-scale clinical bioinformatics domains are applied genomics, and proteomics, the study of proteins. While bioinformatics describes the use of computers to manage biological information — it is both an information science as well as a biological one. In a sense, the definition used most often is even narrower: bioinformatics is a synonym for computational molecular biology or the use of computers to understand living things at a molecular level. (For an introduction to this topic, see this Bioinformatics primer).

Genomics is the branch of molecular biology concerned with the structure, function, evolution and mapping of genomes. The totality of all genetic material (deoxyribonucleic acid or DNA) in an organism are organized in a very precise way, though by no means fixed or constant. In the case of viruses, most of them will have ribonucleic acid or RNA as the genetic material.

Proteomics is the large-scale study of proteins, particularly their structures and functions. This term was coined to make an analogy with genomics, and while it is often viewed as the “next step” in bioinformatics, proteomics is more complicated than genomics. The genome is a constant entity, while the proteome differs from cell to cell, and changes constantly through its interactions with the genome and its environment. One organism has radically different protein expressions in different parts of its body, in different stages of its life cycle and in different environmental conditions.

Metabolomics is the scientific study of chemical processes involving metabolites. Metabolomics is the “systematic study of the unique chemical fingerprints specific cellular processes leave behind”, the study of their small-molecule metabolite profiles. The metabolome represents the collection of metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes (Daviss, 2005).

UBC Office for Learning Technology has suggested I go to the shorter URL (without the Google scholar extension): https://blogs.ubc.ca/dean This is where you’ll find me….from now on. ~Dean

Back in late 2004, when Google scholar was first released to the world, the UBC Office of Learning Technology helped me start this blog. They helped me to enter the (at that time) well-established blogosphere in the best way. A shout-out to all the OLT folks.

I had no clue that five years later, I’d still be blogging – and that I’d want to keep blogging. I guess you could say I’ve grown to like it.

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So when OLT decided to move its entire cadre of UBC bloggers over to WordPress, and approached me recently to move Google scholar blog, I had serious doubts about the direction I’d go. Would I use a more minimalist abject learning template? Would I concentrate on my blogging at Open Medicine?

I even contemplated deangiustini.com. On reflection, I realized blogging is an extension of my digital identity as a health librarian working in the Google age. I’m not interested in promoting myself as a speaker or using a blog for commercial purposes. I am very grateful that anyone wants to read what I have to say but am under no delusion it would make me a penny.

Which is to say – stay tuned, a new blog (a rebirthing) of my blog identity is coming soon. My hope is that any content built here will be available over at the new WordPress-enabled blog.

Thanks for the last five years, all. ~Dean

Trying to keep up to Google scholar is hard enough. I began this blog with that lofty goal in mind but at some point started to comment on all things Google.

Now, only into our sixth week of 2009, it seems obvious the search giant isn’t hibernating this winter (or during the recession). New products are coming and going as fast as you can say Obama! (See Google labs).

Yesterday (I think) Google announced a new blog – called Google Social blog – to cover “News and updates about Google products that are helping to make the world more social.” This is apparently Google’s 80th official blog. 

“We are launching this blog for anyone interested or involved in helping to make the web more social. Whether you own a site and want to add social features to increase community engagement, or you’re developing a great social application, this blog is for you.” (See yesterday’s gpeerreview, for an example of what Google is facilitating for the developer community.)

Google is always pushing the proverbial envelope and facilitation of new tools. Recently, a peer review tool was created using Google Code called gpeerreview that reflects the rise of social media. From the point of view of academic libraries, web 2.0and open access, gpeerreview looks interesting and worthy of mention here.

**************************First, what is gpeerreview? GPeerReview is a command-line tool that makes it simple to write a review of someone’s work and digitally link them.

Does a peer review model based on social networking ‘a web of trust’ pose issues of concern for you? On the one hand, someone’s credibility may be enhanced by obtaining multiple reviews beyond what was originally obtained. And a holistic view of research can be useful when groups of reviewers collectively provide assessment – one that reflects the collective intelligence of a community.

This is where groups of respected peers, experts and authority figures are connected over a digital web and can even be visualized using link and graph analysis.

**************************However, will this be a secure system or completely open? Doesn’t this idea sound similar to Pagerank given its emphasis on linkages of popularity? What implications do you see for using a tool like gpeerreview for university libraries, academic publishers and other journal-based organizations? ~Dean

References

1. UBC Health Library wiki – Peer review

Google has announced a new location-based tracking feature that will integrate with Google Maps called Google Latitude. It’s being launched as a maps application for mobile devices such as the Blackberry, Google Android and WinMo. Apple’s iPhone and iPod Touch are said to be enroute and there’s an iGoogle widget.

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But what are the implications of sharing your exact coordinates on a local map online anyway? Why be telling your network of friends where you are? Ain’t this taking social media narcissism and openness to a whole new dangerous level? Simply put, isn’t Google just using this to push more ads at us? ::Le sigh::

Google searchers are already monitored by what they search and ads are already displayed for our delectation based on our IP location. Similarly, contextually-relevant keywords are highlighted in other social media such as Facebook.

Monetization is one of the negatives of Google but only if we let it get to us. About Google Latitude, the question is whether it might have any application in medicine. I keep returning to the simple question: Is it a good idea to be able to track people at all times using technology? Sure we can do it – but do we want to? You decide.

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As we move into Google’s second decade, some of our attention is turning to measuring its impact on how we think. Recent research suggests that the simple act of Google searching (and to some extent other digital, intellectual work) changes patterns of thinking and cognition. To borrow from Peter Morville, it may in fact be true that “what we search changes who we become”.

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To my knowledge, there is very little evidence that Google is having any impact on the way humans think or learn. However, in this month’s American Journal of Geriatric Psychiatry an interesting article was published entitled “Your Brain on Google: Patterns of Cerebral Activation during Internet Searching“.

Researchers at University of California’s Semel Institute for Neuroscience examined twenty-four seniors from 55 to 76 years of age, of whom half had minimal Internet search experience (Net Naive group) and half had extensive experience (Net Savvy group). The groups were asked to perform Google searches while brain pattern activation was measured using MRI technology. The study found that Google searching engages a greater extent of neural circuitry than text-based reading controls.

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While more scientific research is needed, particularly in younger web users, this study comes as I am reading “Proust and the Squid: the Story and Science of the Reading Brain” by American academic Maryanne Wolf. Wolf argues that humans were not born to read but that our brains have adapted over five thousand year of reading text, what she calls the reading brain.

Some questions that arise from her arguments: Is there any difference in the way that we engage with texts online? If so, what are those differences? Does reading online affect our ability to engage with complex texts and ideas? Is the fragmentary, elusive nature of knowledge online detrimental to developing cognitive abilities? The author argues convincingly that a new brain is emerging in the digital age, one that threatens to displace the reading brain.

Clearly, human beings are deeply affected by search and the information they find on Google. Given the central place of search tools in our work, librarians are advised to keep up to emerging research (both scientific and social) in this area. If possible, we should engage in information ‘search’ research ourselves and contribute to better understanding of it at a time when all kinds of tools are competing for our time and attention.