This Site I Like is a new feature, replacing the Editors' WebWatch section of European Science Editing, the EASE journal. The section is a membership-driven resource guiding editors and writers in the sciences to websites and services of interest.

Please send suggestions to Paola de Castro (ese.webwatch@gmail.com), who coordinates this section along with Penny Hubbard.

Work in progress to be published in the journal can be viewed online in the EASE Journal Blog. Website entries are marked 'W' in the blog.

You can join the blog posters by contacting paola.decastro@iss.it.

The article below is from the August 2009 issue of European Science Editing (vol. 35, no. 3). Previous This Site I Like articles are in the Archive.

WebWatch articles from past issues are archived in the Editors' WebWatch Archive page.

This Site I Like

August 2009

Notes from the blogosphere

As a blogger since 2006, approaching my 1000th post, I'm interested in what's going on in the corner of the blogosphere that's concerned with editing and related subjects. Reading blogs is a good way to keep your finger on the pulse, to find out what's new and what the latest thinking is on the current hot topics – and isn't it interesting to be exposed to some quite extreme opinions, sometimes! Here's a list of some of the web logs I read, or at least dip into, to find out what’s going on not just in biomedical editing but more widely.

High on my list is the COPE Council blog – http://publicationethics.org/blogs. Since October 2008, members of the Council of the Committee on Publication Ethics have been writing succinctly about matters of concern and interest to them (and us as ethically-aware editors). Recent topics include: Should all journals have one universal referencing style?; Concern about UK libel laws; When an editor knows that a submitted article omits to reference key works in the area, what should he or she do?

Ben Goldacre’s series of "bad science" articles in the Guardian led me to his blog - http://www.badscience.net. At the time of writing, the latest post is about inaccurate science journalism: "There's nothing like science for giving that objective, white-coat flavoured legitimacy to your prejudices, so it must have been a great day for Telegraph readers when they came across the headline 'Women who dress provocatively more likely to be raped, claim scientists'. Ah, scientists. 'Women who drink alcohol, wear short skirts and are outgoing are more likely to be raped, claim scientists at the University of Leicester.' Well there you go. Oddly, though, the title of the press release for the same research was 'Promiscuous men more likely to rape'." Read the rest at http://www.badscience.net/2009/07/asking-for-it.

After all those years of working at BMJ, I hasten to mention its blog, http://blogs.bmj.com/bmj – which has a variety of writers from the journal and from the BMA writing on current biomedical concerns. The list of categories on the BMJ blog consists mostly of the names of regular writers, but also  includes some topics: carbon, conferences, credit crunch, digital media, flu pandemic updates, junior doctors, students, swine flu – and 245 posts by guest bloggers.

Nor is the BMJ the only journal with daily posts on topics of interest to its readers (often related to articles they have just published, or are about to – and why not?). Since the Wall Street Journal started in 1998 (blogs.wsj.com), every magazine and newspaper has hopped on  the bandwagon, and as journals have gone online, they've often found they "need" to add a blog. Keeping up with them all will keep you busy; I can list only a few from well-known international journals: www.biomedicaleditor.com/biomedical-editor-blog.html; http://blogs.sciencemag.org;  http://everyone.plos.org.

The best "one stop shop" must be http://blogs.nature.com. It's busy with "tracking blogs from nature.com and beyond. Find great science blogs, keep up to date with the latest buzz and read the latest posts from our editorial staff" – and yes, it does what it says on the tin, in the subject areas of Bioinformatics, Chemistry, Clinical Practice & Research, Earth & Environment, Life Sciences, Neuroscience, Physics, Science and Society. Some of the blogs it includes are Gobbledygook, Martin Fenner's blog on scientific publishing in the internet age (http://network.nature.com/people/mfenner/blog); Journalology: science publishing trends, ethics, peer review, and open access (http://journalology.blogspot.com/), 80beats "news aggregator, weaving together the choicest tidbits from the best articles covering the day's most compelling topics" (http://blogs.discovermagazine.com/80beats), and blogs for NPG authors (http://blogs.nature.com/nautilus) and peer reviewers (http://blogs.nature.com/peer-to-peer).

Blogs are available in many languages, and I hope readers will share their non-English favourites. Being educated in Canada, I'm not uncomfortable with reading French and am glad to know about the blog of ESE's former editor-in-chief, Hervé Maissoneuve. At http://redactionmedicale.typepad.com/redactionmedicale (also accessible as www.h2mw.eu) he writes punchy posts about current stories in the biomedical field.

The blogs of practising editors are often on their professional websites, and pass on grammar and style tips (for example, www.biomedicaleditor.com/biomedical-editor-blog.html) or generously give general writing and publishing advice (http://lillieammann.com/blog).

If you're new to the blogosphere, you'll find a plethora of blogs for any topic of interest. Apart from the writing and opinions of the writer, characteristics of the blogs themselves make some more pleasant than others . An uncluttered layout, and use of black text on a pale background (not vice versa) , make it easier to focus on the words, the argument. Visual material  can be important – those without photos can use the catchiness of the headline, and the words highlighted with clickable links. Categories and tags are useful for finding similar items in the archives; a list of related blogs is useful for "joining the community" – as reader or as blogger. We'd be interested to hear from EASE members involved in blogging on their journal’s website: what's your experience?

Margaret Cooter
mcooter@bmj.com
(http://margaret-cooter.blogspot.com)

February 2009

Regular expressions
http://office.microsoft.com/en-us/help/HA010873051033.aspx
http://office.microsoft.com/en-us/help/HA010873041033.aspx
http://wiki.services.openoffice.org/wiki/Documentation/How_Tos/Regular_Expressions_in_Writer

One of the most powerful features of any text-editing package is its support for regular expressions. Using regular expressions as part of a find-and-replace operation enables you to make systematic edits to a document with remarkable speed.

Querying a search engine for something like "regular expressions" produces lots of helpful results, but in Microsoft Word and OpenOffice the syntax used for regular expressions, or regexes for short, is rather different.

Say one wanted to change "vapor" into "vapour", but only in those cases where it was a word on its own, not, for example, in "vaporous" or "evaporate". <(vapor)> (Word) and \<vapor\> (OOo) catch these cases, where the < and \< stand for the beginning of a word. Likewise, word-final "-ize" can be identified by (ize)> (Word) and ize\> (OOo). This, however, would be an unwise thing to do as it would also catch "size", "prize", "seize" and so forth. One can restrict the search to words longer than, say, six letters by writing [a-z]{3,}(ize)> (Word) and [a-z]{3,}(ize)\> (OOo), where the square brackets introduce a set of characters to be matched (this can be as simple as a single character, [n], or a range, [A-Z], or a mixture, [aeiou0-9]), and the braces indicate the number of characters to be matched, in this case at least three.

In general, the trickier the task being asked of the regular expression, the more similar the syntax in Word, OOo, and in programming languages such as Perl.

The above examples might seem somewhat contrived, but regular expressions come into their own for tasks such as rearranging formulaic subject matter such as addresses and bibliographies, and the Microsoft Word-specific pages are particularly focused on the tasks of rearranging names and dates. It's confusing that the full stop in Word regex syntax stands for a full stop, whereas in OOo it stands for any character, while in Word a question mark stands for any character and in OOo it means zero or one of the preceding character.

In short, regular expressions are so powerful that it is a very good idea to practise on test documents and compare the results carefully with the original before trying them out on a live piece. But they may well change your life.

As with many things, this has apparently changed in Word 2007 – but that is a matter for another column.


What is this file?
http://extensions.pndesign.cz/

RAR, SIT, CDR... A special case of three-letter abbreviations, and one that plagues technical editors, is the file extension. Authors are endlessly inventive at submitting files in peculiar formats, and the first question you need to answer is "What program did they use to generate that?" This page answers that quickly and neatly. The site is lightweight and simple to navigate.

I should note in passing that while Wikipedia is always something of a lottery, documenting the peculiar programs that can be used to open peculiar files is one of its strengths.


Abbreviations for editors
http://www.nactem.ac.uk/software/acromine/

Anyone with experience of lists of abbreviations and acronyms will have spotted that they're seldom up to date and often contain abbreviations and acronyms which, from a cursory internet search, seem to exist only in lists, rather than out in the wild. So an abbreviation list that is somehow automatically generated from current material would be extremely welcome.

AcroMine has been around for a few years but you may not have seen it before. The idea is to take all of PubMed and look for word sequences that regularly co-occur with expressions in brackets that match.

But how well does it work across disciplines? My first attempt was a term used in nuclear magnetic resonance spectroscopy: INEPT. AcroMine correctly identifies this as "insensitive nuclei enhanced by polarization transfer". AcroMine offers 22 hits for "MMR"; the most common is, surprisingly, not the vaccine against measles, mumps, and rubella but "mismatch repair". AcroMine even correctly offers "Large Hadron Collider" as an expansion for "LHC", demonstrating that these days PubMed is a resource for scientific, technical, and medical editors of all disciplines.


Online biochemical and chemical nomenclature
http://www.chem.qmul.ac.uk/iupac/

This website may look old-fashioned, but it will still be invaluable when the likes of Facebook are a distant memory. Here on a single page are many of the recommendations of the International Union of Biochemistry and Molecular Biology (IUBMB) and those recommendations of the International Union of Pure and Applied Chemistry (IUPAC) that are particularly relevant to editors working in the life sciences.


Blog update
http://scienceblogs.com/notrocketscience/
http://www.badscience.net/
http://david-crystal.blogspot.com/

Many journal publishers (BMJ, OUP, NPG, RSC, ACS) are using blogging to promote their own articles, but I thought it would be more interesting to look at some contrasting blogs from the very different worlds of science and medicine.

Ed Yong's Not Exactly Rocket Science concentrates on readable accounts for non-experts of peer-reviewed published material. Readers outside the UK might be unfamiliar with Ben Goldacre's Bad Science, which is both a column in The Guardian and a rather longer and more-often updated blog covering how the media reports medicine. It is a sobering but immensely entertaining read.

Lastly and most relevantly for people whose job is working with language, David Crystal, scourge of prescriptivists, has a blog about how language actually works which is well worth following and learning from. An excellent comment on style guides is worth repeating in full:
Style guides should be explaining to people what English allows us to say and write, and pointing out the strengths and weaknesses of different usages in different contexts. Blanket bans are a nonsense.


Physics and physical chemistry
http://old.iupac.org/publications/books/gbook/

The International Union of Pure and Applied Physics (IUPAP) doesn't put its recommendations online, but IUPAC's Green Book, which is based in part on the recommendations of IUPAP and also on ISO 31 (now superseded by ISO 80000-3:2006, which costs only CHF 96), is online as a PDF of its second edition, and the third edition will appear online soon.

It's an indispensable vade mecum for editing equations and the kind of mathematical expressions that one sees in running scientific text and was immensely useful throughout my doctorate and my years as a technical editor.


Colin Batchelor
batchelorc@rsc.org

Thanks to Richard Hurley


Something to contribute?
Please send interesting or useful links to Paola de Castro (paola.decastro@iss.it). Sites in European languages other than English are also of interest (but please provide a short review in English); any that relate to areas of science other than biology and medicine will be very welcome.