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Mining Scientific Literature

January 30, 2010 in Education, Science, research by Kris | 7 comments

ResearchBlogging.orgThere’s an interesting piece in the most recent issue of Nature.  Corie Lok discusses how researchers are dealing with the information firehose that is scientific literature.  How big is that firehose?

The 19 million citations and abstracts covered by the US National Library of Medicine’s PubMed search engine include nearly 830,000 articles published in 2009, up from some 814,000 in 2008 and around 772,000 in 2007. That growth rate shows no signs of abating, especially as emerging countries such as China and Brazil continue to ratchet up their research.

With that amount of data overload, how is an established researcher going to keep up with relevant work in their field? Nevermind how a new investigator can get a handle on establishing a research focus, or a midcareer scientist switch tracks.  That’s where literature mining comes in.  There are several start-up services on the web to help scientists find relevant research, make connections, and generate hypotheses. A few of these are discussed in Lok’s article, but there are many others.

PubMed – My default search engine for research papers, this is the first stop for many scientists.  So let’s try a little experiment.  Searching “alcoholism” generates the following – Results: 1 to 20 of 66827. PubMed does have tools to help you narrow your search.  Say I’m interested in the genetics of alcoholism. Searching “alcoholism genetics” returns – Results: 1 to 20 of 5940. A lot of research to go through. Restricting that search to only publications in the last 5 years, in English, and about humans gives Results: 1 to 20 of 1283. Still a lot of literature, even if you’re only reading the abstracts.

That’s where literature mining can really make a difference.

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The Western European Y

January 24, 2010 in Anthropology, Genetics by Kris | 1 comment

ResearchBlogging.orgA new study in PLoS Biology suggests one of the most common Western European Y halplogroups, R1b1b2, might have originated in Turkey and radiated into Europe with the spread of agriculture during the Neolithic.  This is significant because this haplogroup is the most frequent in Western Europe, and has been posited as a signal from Paleolithic populations who were less impacted by the Neolithic Revolution.

The researchers compared STR variance for this haplotype in several European populations and three Turkish groups, and found a significant correlation (R2 = 0.358; p = 0.004) between that variance and the longitude of the population (i.e., how far east the population was located).

Balaresque et al. Figure 1C. Distribution of haplogroup R1b1b STR variance

From the plot, the greatest variance (indicated by the most intense color) within haplogroup R1b1b2 is found in Turkey. They also calculated the time to most recent common ancestor (TMRCA) using STR variance, and found that the oldest lineages, dated between 7,000-7,989 years, are also in Turkey.  The youngest lineage is in Cornwall, dating from 5,460 years ago. The researchers inferred that R1b1b2 originated in Anatolia and spread rapidly into Europe with the spread of agriculture.

Balaresque et al. Figure 1B. Frequency distribution of Haplogroup R1b1b2. More intense color indicate higher frequency.

A couple of things strike me about this study. 1) Haplogroup R1b1b2 reaches it’s highest frequencies in Western Europe, up to 85% of Y-chromosomes in Ireland belong to this haplogroup (Figure 1B). And there are two populations, one in Germany (GE1) and one on the northwest coast of France (FR2), with TMRCA dates in the range of the Turkish dates (7,282 and 7,384 years, respectively). 2) The Turkish data come from Cinnioglu et al. (2004), and consist of samples collected in 90 cities from blood banks, paternity clinics, and university students classified into geographical areas by self-reported “paternal residential heritage” (128).   There is the possibility of introducing error into the sample from this self-reported residence. It’s also possible that the high variance present in the Turkish R1b1b2 lineages reflects more recent immigration.  In addition, TMRCA applies to the molecule, not the populations in which it is found, so while a particular lineage may be 7,000 years old it does not mean that the population has been in that particular location for that length of time. And the authors note, in the supplemental information, “…there is a tendency for TMRCA to be underestimated when single-haplogroup data are considered.”

It’s an interesting hypothesis, though, and I’m curious to see what analyses with additional populations will show.

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Balaresque P, Bowden GR, Adams SM, Leung HY, King TE, Rosser ZH, Goodwin J, Moisan JP, Richard C, Millward A, Demaine AG, Barbujani G, Previderè C, Wilson IJ, Tyler-Smith C, & Jobling MA (2010). A predominantly neolithic origin for European paternal lineages. PLoS biology, 8 (1) PMID: 20087410


Cinnioğlu C, King R, Kivisild T, Kalfoğlu E, Atasoy S, Cavalleri GL, Lillie AS, Roseman CC, Lin AA, Prince K, Oefner PJ, Shen P, Semino O, Cavalli-Sforza LL, & Underhill PA (2004). Excavating Y-chromosome haplotype strata in Anatolia. Human genetics, 114 (2), 127-48 PMID: 14586639

William Stukeley’s Life of Newton Now Online

January 18, 2010 in Critical Thinking, Science by Kris | 4 comments

William Stukeley

Remember the old story of Newton and the apple? Ever wonder where it came from? Now you can read the original, in William Stukeley’s Memoirs of Sir Isaac Newton’s Life (1752). The Royal Society, the “world’s oldest scientific academy in continuous existence,” had made this manuscript (and others) available as part of their Turning the Pages project.

In Newton’s Life, Stukeley recounts one of the most famous stories in modern science:

After dinner, the weather being warm, we went into the garden and drank tea under the shade of some apple trees; only he and myself. Amidst other discourse, he told me, he was just in the same situation, as when formerly, the notion of gravitation came into his mind. Why should that apple always descend perpendicularly to the ground, thought he to himself; occasioned by the fall of an apple, as he sat in a contemplative mood. Why should it not go sideways, or upwards? But constantly to the earth’s center? Assuredly, the reason is, that the earth draws it. There must be a drawing power in matter. The sum of the drawing power in the matter of the earth must be in the earth’s center, not in any side of the earth. Therefore does this apple fall perpendicularly or toward the center. If matter thus draws matter; it must be in proportion of its quantity. Therefore the apple draws the earth, as well as the earth draws the apple.
Thus by degrees, he began to apply this property of gravitation to the motion of the Earth, and of the heavenly bodies; to consider their distances, their magnitudes, their periodical revolutions: to find out, that this property, conjointly with a progressive motion impressed on them in the beginning, perfectly [soloed] their circular courses; kept the planets from falling upon one another, or dropping all together into one center. And thus he unfolded the universe. This was the birth of those amazing discoveries, whereby he built philosophy on a solid foundation, to the astonishment of Europe (page 16, 42 in the online version).

Sir Isaac Newton

Rather than being conked on the head by an apple while napping, Newton had been thinking in his garden, maybe while drinking tea. Granted, this work was originally published 25 years after Newton’s death, but Stukeley was a friend of Newton, and a fellow member of the Royal Society.

I have waited for this life to be done, as it deserves; and have not been overhasty in printing, what was wrote 27 years ago (page ii, 4 in the online version).

He began recording his memories of Newton before Newton’s death, and now they are available, in their original 18th century manuscript, for anyone with an Internet connection to read.  How fantastic to be able to read the actual account of this most famous story for yourself.

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Images courtesy of Wikimedia Commons.

PhyloTree.org

January 14, 2010 in Anthropology, Genetics by Kris | 1 comment

ResearchBlogging.orgAs a grad student in anthropological genetics, one of the more tedious tasks I had was aligning mtDNA sequences manually, noting the mutations (differences from the revised Cambridge Reference Sequence, which belongs to haplogroup H), and determining the haplogroup (or lineage).  The difficulty was compounded by a lack of comprehensive definitions.  I had a stack of references listing diagnostic mutations, but not for every haplogroup, not even for the subset of haplogroups found in Europe, which was the focus of my research. Part of the problem was that when I started whole genome sequencing wasn’t available. Whenever a new haplogroup was discovered, the authors would name it, and in some cases the same name was given to different sequences because there was no standardized nomenclature. What I needed was a phylogenetic tree, showing the relationships between lineages, and all diagnostic mutations for each haplogroup.

That’s what you can find at PhyloTree.org.  The “updated comprehensive phylogenetic tree of global human mitochondrial DNA variation” lists all mitochondrial haplogroups, with diagnostic mutations from both the coding and control regions, based on full sequences deposited in GenBank. The figure below shows a portion of the tree for Haplogroup H1a:

Haplogroup H1a. Coding region mutations are in black, control region mutations in blue.

Coding region mutations are in black, control region mutations in blue.  Established haplogroup names are in in black at the base of the branches, and proposed haplogroup labels are shown in red.  GenBank accession numbers are provided at the tips of the branches. Assigning haplogroups to your samples is as easy as using the find function in your Internet brower. PhyloTree is continuously updated as new sequences are published; they’re currently on Build 7.0 as of November 2009.

PhyloTree is a valuable and much need resource for the anthropological genetics community, especially poor grad students.
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van Oven, M., & Kayser, M. (2009). Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation Human Mutation, 30 (2) DOI: 10.1002/humu.20921

Tweeting for Science

January 10, 2010 in Science, Technology by Kris | No comments

Heh. So after I wrote my previous post, I noticed a comment in my spam filter.

[...] This post was mentioned on Twitter by link2peer, SFSU Sch. of Nursing. SFSU Sch. of Nursing said: Have to check out the sites mentioned here. http://is.gd/5WDXY I wonder if any would benefit nursing researchers.

A few of my posts have been retweeted. I had no idea (waving at the twitter folks). Congratulations. You’ve convinced me. I think I’ll give twitter a try. If I consider it a communication tool, a way to disseminate information about my science to a broader audience, then I can see the potential benefits.

I think scientists should embrace using the Internet to connect with each other and to advance career goals and technical aspects. There are many exciting possibilities, especially for scientists….” — Jonathan Weissman in “Should you be Tweeting”, Bonetta (2009).

Bluetit 2
Creative Commons License photo credit: ahisgett

Here’s a list of 600 scientwists (coined by science writer David Bradley of Science Base) if, like me, you’re looking for other scientists to follow.
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Bonetta L (2009). Should you be tweeting? Cell, 139 (3), 452-3 PMID: 19879830

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