O'Really?

July 1, 2016

Dear Europeans, do you know who your MEP is and what they do?

eu-flagAlong with 16 million other people on the 23rd June 2016 I voted to remain in the European Union (EU). I believe the benefits of EU membership exceed the costs. Free trade and free movement have been beneficial to me personally, many of those around me, as well as the wider UK economy [1]. I even married an EU migrant too, so I love Europe in more ways that one. Life outside the EU is very difficult to imagine, professionally, financially, culturally and personally.

So when I woke up to Brexit EuroDoom last Friday, to find I was in a minority outnumbered by 17 million leavers who disagreed, I felt sick. After a gloomy week of miserable soul searching, I realised I didn’t have the foggiest notion who my Member of European Parliament (MEP) was or how they got elected. Although not a student of (or expert in) politics or economics, I don’t believe I am apathetic or unaware. I follow the news, vote in general elections and write letters to my MP. I try to understand what is going on in politics and bend my head around the dismal science of economics. But until this week, I had little or no idea how the European Parliament (EP), let alone the European Commission (EC) or lots of other acronyms starting with E, actually work in practice.

Now if you are also a participant in the failing (?) European project, do YOU know who your MEP is? Any idea what they actually do? The chances are you don’t because Euroignorance is widespread [2]. Fortunately, Professor Google can help us. In Manchester, the MEPs for the North West Region of the UK comprising Cumbria, Lancashire, Merseyside, Greater Manchester and Cheshire are:

Unfortunately, I’d only heard of two of those MEPs beforehand, and neither of them because of their activity during the EU referendum. Nuttall I’d heard of because the comedian Stewart Lee performed a brilliant satirical piece mocking Nuttall’s views on immigration [3]. Woolfe I’d heard of because his campaign leaflet came through my letterbox during the 2015 general election. How did they get elected as MEPs because I can’t remember seeing their names on a ballot paper?

MEPs are elected using the D’Hondt method [4], a form of proportional representation (PR) used in the European elections in 2014 and elsewhere. As of 2016, the three largest UK parties in the European Parliament are: UKIP (24 MEPs), Labour (20 MEPs) and The Conservatives (19 MEPs). Isn’t it remarkable that so many of these MEPS were neither seen or heard during the almost entirely fact-free® debate [1] preceding the UK EU referendum?

So what is the nature of an MEPs power? Back in 1998, a politician by the name of Tony Benn proposed five democratic questions to understand the powerful:

“If one meets a powerful person–Rupert Murdoch, perhaps, or Joe Stalin or Hitler–one can ask five questions:

  1. what power do you have?
  2. where did you get it?
  3. in whose interests do you exercise it?
  4. to whom are you accountable?
  5. how can we get rid of you?”

According to Benn, anyone who cannot answer the last of those questions does not live in a democratic system. [5] Personally, I’d like to get rid of UKIP from the European parliament. How can I do this? While I can’t vote for individuals, I can vote for political parties. However, turnout in european elections is often embarrassingly low, in the UK a pathetic 35.6% showed up in 2014. Which means two thirds of UK voters were unaware or didn’t care who their MEP was, including me. My bad. You could call this democratic deficit, not one where people can’t vote but one where people are unaware or don’t bother.

Right now, it is really hard to see how any good can come of what is unfolding in Great Britain and Europe. Brexit leaves the sector I work in, and many others, facing huge uncertainty [6,7,8]. Let’s hope one thing will happen, a reformed EU where those in power are more engaged and accountable to the people they claim to represent. Personally, I am not in a position to judge if the European Union has a democratic deficit or not [9,10]. Neither can I judge if the European Union is as anti-democratic as some eurosceptics have suggested [11, 12,13]. But I do know something has gone badly wrong with the EU if many europeans have no idea of who their parliamentary representatives are and how they can exercise their democratic rights to get rid of them using the ballot box.

If you are staying in the European Union you have a duty to find out who your MEP is and ask them the five democratic questions above. You better do it quickly before risking a Frexit, Czechout, Swexit, Departugal, Grexit, Bygium, Italeave or bidding Austria La Vista.

References

  1. Zanny Minton Beddoes (2016) The Brexit Briefs: The 17 things you need to know before Britain’s #EUref—in one handy guide, The Economist
  2. Oana Lungescu (2001) EU Poll reveals huge ignorance, BBC News
  3. Stewart Lee (2014) Stewart Lee’s Comedy Vehicle, Series 2: England
  4. Jeremy Vine (2009) D’Hondt Explainer, BBC News
  5. Anon (1998)  House of Commons Debates, Hansard, parliament.uk
  6. Anon (2016) Brexit vote sparks huge uncertainty for UK universities, Times Higher Education
  7. Alison Abbott, Daniel Cressey, Richard Van Noorden (2016) UK scientists in limbo after Brexit shock: Researchers organize to lobby for science as country prepares for life outside the EU Nature, Vol. 534, No. 7609., pp. 597-598, DOI:10.1038/534597a
  8. Anon (2016) Brexit vote highlights lack of leaving plan: Scientists — just like everybody else — have little idea what will happen now that the United Kingdom has voted to exit the European Union. Nature, Vol. 534, No. 7609., pp. 589-589, DOI:10.1038/534589a
  9. Andrew Moravcsik (2008) The Myth of Europe’s “Democratic Deficit” Intereconomics, Volume 43, Issue 6, pp 316–340 DOI:10.1007/s10272-008-0266-7
  10. Michael Dougan (2016) The UK’s position following vote to leave the EU, University of Liverpool, School of Law and Social Justice
  11. Tony Benn (2013) Tony Benn speaks at the Oxford Union on Euroscepticism, The Oxford Union.
  12. Martin Durkin (2016) Brexit: The Movie (warning: contains Nigel Farage and dubious opinions europhiles will find offensive, factual content is highly questionable in places)
  13. Tony Benn (1975) Letter from Tony Benn to his constituents about the UK European referendum of 1975, The Spectator, Coffee House

* Disclaimer, like I’ve already said, my grasp of politics and economics is pretty basic. I have made every reasonable effort to get the facts right but correct any mistakes I might have made below. These are personal views, which do not necessarily reflect those of my employer.

September 9, 2014

Punning with the Pub in PubMed: Are there any decent NCBI puns left? #PubMedPuns

PubMedication: do you get your best ideas in the Pub? CC-BY-ND image via trombone65 on Flickr.

Many people claim they get all their best ideas in the pub, but for lots of scientists their best ideas probably come from PubMed.gov – the NCBI’s monster database of biomedical literature. Consequently, the database has spawned a whole slew of tools that riff off the PubMed name, with many puns and portmanteaus (aka “PubManteaus”), and the pub-based wordplays are very common. [1,2]

All of this might make you wonder, are there any decent PubMed puns left? Here’s an incomplete collection:

  • PubCrawler pubcrawler.ie “goes to the library while you go to the pub…” [3,4]
  • PubChase pubchase.com is a “life sciences and medical literature recommendations engine. Search smarter, organize, and discover the articles most important to you.” [5]
  • PubCast scivee.tv/pubcasts allow users to “enliven articles and help drive more views” (to PubMed) [6]
  • PubFig nothing to do with PubMed, but research done on face and image recognition that happens to be indexed by PubMed. [7]
  • PubGet pubget.com is a “comprehensive source for science PDFs, including everything you’d find in Medline.” [8]
  • PubLons publons.com OK, not much to do with PubMed directly but PubLons helps you “you record, showcase, and verify all your peer review activity.”
  • PubMine “supports intelligent knowledge discovery” [9]
  • PubNet pubnet.gersteinlab.org is a “web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks” aka a publication network graph utility. [10]
  • GastroPub repackages and re-sells ordinary PubMed content disguised as high-end luxury data at a higher premium, similar to a Gastropub.
  • PubQuiz is either the new name for NCBI database search www.ncbi.nlm.nih.gov/gquery or a quiz where you’re only allowed to use PubMed to answer questions.
  • PubSearch & PubFetch allows users to “store literature, keyword, and gene information in a relational database, index the literature with keywords and gene names, and provide a Web user interface for annotating the genes from experimental data found in the associated literature” [11]
  • PubScience is either “peer-reviewed drinking” courtesy of pubsci.co.uk or an ambitious publishing project tragically axed by the U.S. Department of Energy (DoE). [12,13]
  • PubSub is anything that makes use of the publish–subscribe pattern, such as NCBI feeds. [14]
  • PubLick as far as I can see, hasn’t been used yet, unless you count this @publick on twitter. If anyone was launching a startup, working in the area of “licking” the tastiest data out of PubMed, that could be a great name for their data-mining business. Alternatively, it could be a catchy new nickname for PubMedCentral (PMC) or Europe PubMedCentral (EuropePMC) [15] – names which don’t exactly trip off the tongue. Since PMC is a free digital archive of publicly accessible full-text scholarly articles, PubLick seems like a appropriate moniker.

PubLick Cat got all the PubMed cream. CC-BY image via dizznbonn on flickr.

There’s probably lots more PubMed puns and portmanteaus out there just waiting to be used. Pubby, Pubsy, PubLican, Pubble, Pubbit, Publy, PubSoft, PubSort, PubBrawl, PubMatch, PubGames, PubGuide, PubWisdom, PubTalk, PubChat, PubShare, PubGrub, PubSnacks and PubLunch could all work. If you’ve know of any other decent (or dodgy) PubMed puns, leave them in the comments below and go and build a scientific twitterbot or cool tool using the same name — if you haven’t already.

References

  1. Lu Z. (2011). PubMed and beyond: a survey of web tools for searching biomedical literature., Database: The Journal of Biological Databases and Curation, http://pubmed.gov/21245076
  2. Hull D., Pettifer S.R. & Kell D.B. (2008). Defrosting the digital library: bibliographic tools for the next generation web., PLOS Computational Biology, PMID: http://pubmed.gov/18974831
  3. Hokamp K. & Wolfe K.H. (2004) PubCrawler: keeping up comfortably with PubMed and GenBank., Nucleic acids research, http://pubmed.gov/15215341
  4. Hokamp K. & Wolfe K. (1999) What’s new in the library? What’s new in GenBank? let PubCrawler tell you., Trends in Genetics, http://pubmed.gov/10529811
  5. Gibney E. (2014). How to tame the flood of literature., Nature, 513 (7516) http://pubmed.gov/25186906
  6. Bourne P. & Chalupa L. (2008). A new approach to scientific dissemination, Materials Today, 11 (6) 48-48. DOI:10.1016/s1369-7021(08)70131-7
  7. Kumar N., Berg A., Belhumeur P.N. & Nayar S. (2011). Describable Visual Attributes for Face Verification and Image Search., IEEE Transactions on Pattern Analysis and Machine Intelligence, http://pubmed.gov/21383395
  8. Featherstone R. & Hersey D. (2010). The quest for full text: an in-depth examination of Pubget for medical searchers., Medical Reference Services Quarterly, 29 (4) 307-319. http://pubmed.gov/21058175
  9. Kim T.K., Wan-Sup Cho, Gun Hwan Ko, Sanghyuk Lee & Bo Kyeng Hou (2011). PubMine: An Ontology-Based Text Mining System for Deducing Relationships among Biological Entities, Interdisciplinary Bio Central, 3 (2) 1-6. DOI:10.4051/ibc.2011.3.2.0007
  10. Douglas S.M., Montelione G.T. & Gerstein M. (2005). PubNet: a flexible system for visualizing literature derived networks., Genome Biology, http://pubmed.gov/16168087
  11. Yoo D., Xu I., Berardini T.Z., Rhee S.Y., Narayanasamy V. & Twigger S. (2006). PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature., Current Protocols in Bioinformatics , http://pubmed.gov/18428773
  12. Seife C. (2002). Electronic publishing. DOE cites competition in killing PubSCIENCE., Science (New York, N.Y.), 297 (5585) 1257-1259. http://pubmed.gov/12193762
  13. Jensen M. (2003). Another loss in the privatisation war: PubScience., Lancet, 361 (9354) 274. http://pubmed.gov/12559859
  14. Dubuque E.M. (2011). Automating academic literature searches with RSS Feeds and Google Reader(™)., Behavior Analysis in Practice, 4 (1) http://pubmed.gov/22532905
  15. McEntyre J.R., Ananiadou S., Andrews S., Black W.J., Boulderstone R., Buttery P., Chaplin D., Chevuru S., Cobley N. & Coleman L.A. & (2010). UKPMC: a full text article resource for the life sciences., Nucleic Acids Research, http://pubmed.gov/21062818

June 29, 2012

Impact Factor Boxing 2012

Rocky Balboa  Philadelphia, PA

Rocky Balboa, Philadelphia, PA. Creative Commons licensed picture by seng1011 (steve eng) on Flickr.

[This post is part of an ongoing series about impact factors]

In the world of abused performance metrics, the impact factor is the undisputed heavyweight champion of the (publishing) world.

It has been an eventful year in the boxing ring of scientific publishing since the last set of figures were published by Thomson-Reuters. A brand new journal called PeerJ launched with a radical publish ’til you perish business model [1]. There’s another new journal on the way too in the shape of eLifeSciences – with it’s own significant differences from current publishing models. Then there was the Finch report on Open Access. If that wasn’t enough fun, there’s been the Alternative metrics “Altmetrics” movement gathering pace [2], alongside suggestions that the impact factor may be losing its grip on the supposed “title” [3].

The impact factors below are the most recent, published June 28th 2012, covering data from 2011. Love them or loathe them, use them or abuse them, game them or shame them … here is a tiny selection of impact factors for the 10,675 journals that are tracked in Journal Citation Reports (JCR) ordered by increasing punch power.

WARNING: Abusing these figures can seriously damage your Science – you have been warned! Normal caveats apply, see nature.com/metrics.

Journal 2011 data from isiknowledge.com/JCR Eigenfactor™ Metrics
Total Cites Impact Factor 5-Year Impact Factor Immediacy Index Articles Cited Half-life Eigenfactor™ Score Article Influence™ Score
Russian Journal of Cardiology* 3 0.005 0.000 75 0.00000
BMC Bioinformatics 14268 2.751 3.493 0.293 557 4.2 0.07757 1.314
PLoS ONE 75544 4.092 4.537 0.437 13781 2.4 0.50216 1.797
Briefings in Bioinformatics 2859 5.202 7.749 0.692 65 4.3 0.01129 2.857
PLoS Computational Biology 8924 5.215 5.844 0.710 407 3.1 0.06968 2.722
OUP Bioinformatics 43380 5.468 6.051 0.666 707 6.2 0.15922 2.606
Nucleic Acids Research 106520 8.026 7.417 2.016 1230 7.4 0.30497 3.003
Genome Biology 15556 9.036 7.896 1.550 151 5.2 0.08221 4.124
PLoS Biology 20579 11.452 13.630 2.461 180 4.6 0.14975 7.830
Science 480836 31.201 32.452 6.075 871 9.4 1.41282 17.508
Nature 526505 36.280 36.235 9.690 841 9.4 1.65658 20.353
New England Journal of Medicine 232068 53.298 50.075 11.484 349 7.8 0.66466 21.293
CA – A Cancer Journal for Clinicians** 10976 101.780 67.410 21.263 19 3.8 0.04502 24.502

* The Russian Journal of Cardiology is included here for reference as it has the lowest non-zero impact factor of any science journal. A rather dubious honour…

** The Cancer Journal for Clinicians is the highest ranked journal in science, it is included here for reference. Could it be the first journal to have an impact factor of more than 100?

References

  1. Richard Van Noorden (2012). Journal offers flat fee for ‘all you can publish’, Nature, 486 (7402) 166. DOI: 10.1038/486166a
  2. Jason Priem, Heather Piwowar and Bradley Hemminger (2012).  Altmetrics in the wild: Using social media to explore scholarly impact arxiv.org/abs/1203.4745
  3. George Lozano, Vincent Lariviere and Yves Gingras (2012). The weakening relationship between the Impact Factor and papers’ citations in the digital age arxiv.org/abs/1205.4328

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