O'Really?

September 9, 2014

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

Filed under: data mining,Googleology,paperware,publishing,Science,technology — Duncan Hull @ 10:31 am
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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

December 11, 2009

The Semantic Biochemical Journal experiment

Filed under: publishing,semweb — Duncan Hull @ 12:18 am
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utopian documentsThere is an interesting review [1] (and special issue) in the Biochemical Journal today, published by Portland Press Ltd. It provides (quote) “a whirlwind tour of recent projects to transform scholarly publishing paradigms, culminating in Utopia and the Semantic Biochemical Journal experiment”. Here is a quick outline of the publishing projects the review describes and discusses:

  • Blogs for biomedical science
  • Biomedical Ontologies – OBO etc
  • Project Prospect and the Royal Society of Chemistry
  • The Chemspider Journal of Chemistry
  • The FEBS Letters experiment
  • PubMedCentral and BioLit [2]
  • Public Library of Science (PLoS) Neglected Tropical Diseases (NTD) [3]
  • The Elsevier Grand Challenge [4]
  • Liquid Publications
  • The PDF debate: Is PDF a hamburger? Or can we build more useful applications on top of it?
  • The Semantic Biochemical Journal project with Utopia Documents [5]

The review asks what advances these projects have made  and what obstacles to progress still exist. It’s an entertaining tour, dotted with enlightening observations on what is broken in scientific publishing and some of the solutions involving various kinds of semantics.

One conclusion made is that many of the experiments described above are expensive and difficult, but that the costs of not improving scientific publishing with various kinds of semantic markup is high, or as the authors put it:

“If the cost of semantic publishing seems high, then we also need to ask, what is the price of not doing it? From the results of the experiments we have seen to date, there is clearly a need to move forward and still a great deal of scope to innovate. If we fail to move forward in a collaborative way, if we fail to engage the key players, the price will be high. We will continue to bury scientific knowledge, as we routinely do now, in static, unconnected journal articles; to sequester fragments of that knowledge in disparate databases that are largely inaccessible from journal pages; to further waste countless hours of scientists’ time either repeating experiments they didn’t know had been performed before, or worse, trying to verify facts they didn’t know had been shown to be false. In short, we will continue to fail to get the most from our literature, we will continue to fail to know what we know, and will continue to do science a considerable disservice.”

It’s well worth reading the review, and downloading the Utopia software to experience all of the interactive features demonstrated in this special issue, especially the animated molecular viewers and sequence alignments.

Enjoy… the Utopia team would be interested to know what people think, see commentary on friendfeed,  the digital curation blog and youtube video below for more information.

References

  1. Attwood, T., Kell, D., McDermott, P., Marsh, J., Pettifer, S., & Thorne, D. (2009). Calling International Rescue: knowledge lost in literature and data landslide! Biochemical Journal, 424 (3), 317-333 DOI: 10.1042/BJ20091474
  2. Fink, J., Kushch, S., Williams, P., & Bourne, P. (2008). BioLit: integrating biological literature with databases Nucleic Acids Research, 36 (Web Server) DOI: 10.1093/nar/gkn317
  3. Shotton, D., Portwin, K., Klyne, G., & Miles, A. (2009). Adventures in Semantic Publishing: Exemplar Semantic Enhancements of a Research Article PLoS Computational Biology, 5 (4) DOI: 10.1371/journal.pcbi.1000361
  4. Pafilis, E., O’Donoghue, S., Jensen, L., Horn, H., Kuhn, M., Brown, N., & Schneider, R. (2009). Reflect: augmented browsing for the life scientist Nature Biotechnology, 27 (6), 508-510 DOI: 10.1038/nbt0609-508
  5. Pettifer, S., Thorne, D., McDermott, P., Marsh, J., Villéger, A., Kell, D., & Attwood, T. (2009). Visualising biological data: a semantic approach to tool and database integration BMC Bioinformatics, 10 (Suppl 6) DOI: 10.1186/1471-2105-10-S6-S19

October 19, 2007

The Webolution Will Be Televised

Filed under: communication,publishing — Duncan Hull @ 8:42 pm
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The American poet and songwriter Gil Scott-Heron once famously remarked that The Revolution Will Not Be Televised [1]. Science has undergone its own quiet revolution since the invention of the Web back in 1990. This has slowly but surely changed scientific communication, not just a Revolution but a “Webolution” [2] if you like. The recent addition of television to the Web means that, to paraphrase Gil, the Webolution will be televised. You can now watch some of the webolution in science, thanks the likes of JOVE (The Journal Of Visualised Experiments), SciVee.TV, Google Video and YouTube. What are these sites like and is their scientific and technical content any good?

(more…)

April 13, 2007

Collaboration, collaboration, collaboration!

Filed under: Uncategorized — Duncan Hull @ 10:05 pm
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Geldof Blair collaborationWhat should your three main priorities be as a Scientist? Collaboration, collaboration, collaboration. Quentin Vicens and Phil Bourne have just published Ten Simple Rules for a Successful Collaboration [1] to help you do just that, as part of a continuing series [2,3,4,5].

Tony Bliar once said “Ask me my three main priorities for government, and I tell you: education, education, education.” In Science, its not so much about education as collaboration, collaboration, collaboration. The advice in Ten Simple Rules is all useful stuff, but what caught my eye is the fact that collaboration is on the rise, at least according to the number of co-authors on papers published in PNAS. The average number of co-authors has risen from 3.9 in 1981 to 8.4 in 2001. So before you publish or perish, it seems likely that you’ll also need to collaborate or commiserate… less laboratory, more collaboratory!

Photo credit Garret Keogh

References

  1. Quentin Vicens and Phillip Bourne (2007) Ten Simple Rules for a Successful Collaboration PLOS Computational Biology
  2. Phillip Bourne (2006) Ten Simple Rules for Getting Published PLOS Computational Biology
  3. Philip Bourne and Iddo Friedberg (2006) Ten Simple Rules for Selecting a Postdoctoral Position PLOS Computational Biology
  4. Phillip Bourne and Leo Chalupa (2006) Ten Simple Rules for Getting Grants PLOS Computational Biology
  5. Phillip Bourne and Alon Korngreen (2006) Ten Simple Rules for Reviewers PLOS Computational Biology
  6. This post originally published on nodalpoint with comments

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