A New #WordPress plugin for #SCIENCE!

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…and other research too.

I have a work­ing first release of a plu­gin to link to research in a ScienceSeeker friendly way in a WordPress blog. It will only work with self-hosted WordPress installs, it will not work on WordPress​.com blogs.

The way it works is you enter the ID(s) of the thing(s) you want to include then, when you save the draft, the web­site pro­duces a format­ted cita­tion that it will auto­mat­ic­ally append to the con­tent of your post. It will also add a META tag to the head of the page. This will give a way to tell sites like alt​met​ric​.com what paper(s) your blog post is about.

Editing in WordPress

Editing Screen. Click to embiggen.

Citation output

The out­put. Click to largify.


It’s primar­ily built to work with DOIs, because that’s what we use most at AoB Blog. You can type in a DOI as 10.1093/aob/mct168 or http://​dx​.doi​.org/​1​0​.​1​0​9​3​/​a​o​b​/​m​c​t​168 and when the site saves it will get bulked out to the longer ver­sion. You can enter more than one entry, so stick­ing 10.1093/aob/mcp121, 10.1093/aob/mcs287, 10.1093/aob/mcq238 should work too.

Once the ref­er­ence is parsed, it appears as a cita­tion. When you have this cita­tion, you can edit it in this box. You might need to do that if the pars­ing breaks. It’s pos­sible some DOIs will give inform­a­tion in a dif­fer­ent way to most. Currently the plu­gin works with stand­ard DOIs and figshare’s DOIs. It’s very pos­sible there are some other sites that have their own stand­ards so, if you find one, let me know.

To clear the ref­er­ences and cita­tions on a post, delete all the ref­er­ences and save. The plu­gin will wipe the cita­tion box.

You can add arXiv ref­er­ences. I’ve set it so you copy and paste a URL from arXiv to the box to give http://​arxiv​.org/​a​b​s​/​1​3​0​6​.​5​148. If there’s demand it should be pos­sible to send any nine char­ac­ter ref­er­ence with a dot in the middle to the arXiv mod­ule. I’ve spot­ted a bug in the arXiv mod­ule put­ting together the screen shotes (look at the author name). I think I’ve fixed this.

It’s not so good for the Social Sciences and Humanities. Here mono­graphs are still import­ant research out­puts, which means ISBNs. These are more of a prob­lem. You enter them as a straight run of ten or thir­teen char­ac­ters. The only place I’ve found giv­ing inform­a­tion from ISBNs in a friendly format is Google Books. But from here I can only get Title, Authors and Publisher. I can­not get Publisher Location from the data.

For DOIs and arXiv papers it’s obvi­ous to link through to the paper. Books tend not to have a recog­nis­able home page. I’ve linked through to Google Books because that’s where the data comes from. But it’s pos­sible that LibraryThing or the Amazons would be bet­ter places to link to.

This sys­tem doesn’t handle book chapters yet, unless they have a DOI. Lying in bed I thought it could be handled as Chapter Authors::Chapter Title::Page Start::Page End::ISBN and any­thing with a double colon gets passed to a book chapter mod­ule for format­ting. I’m not sure if this is use­ful, or if it’s get­ting to stage where typ­ing the ref­er­ence in is more effort than it’s worth.

At the moment the link is on the iden­ti­fier, because that’s the way Research Blogging and ScienceSeeker work. Alan Cann has sug­ges­ted mak­ing the whole ref­er­ence click­able. I’m not sure if this is a good idea or not. It’s a big­ger click­able tar­get, and CSS styl­ing makes the present­a­tion a mat­ter for whoever’s site it is.

The plu­gin doesn’t work for Research Blogging yet. Research Blogging needs ref­er­ences asso­ci­ated with a sub­ject. The first way I’d writ­ten this meant that sub­jects would have to be hard­wired in. Now I think it should be pos­sible to tweak the plu­gin to add Research Blogging top­ics on a post-by-post basis, but not (yet) on a citation-by-citation basis. This would work for most people cit­ing just one paper in Research Blogging posts, but some people cite mul­tiple papers in one post. The way I’m think­ing would label all cita­tions in one post as being the same topic.

Finally, like me, it doesn’t fail grace­fully. I’ve spent quite a while get­ting the damn thing to work. Deliberately break­ing it, so I can make it fail nicely, hasn’t enthused me yet.

You can down­load it from my Dropbox at https://​www​.drop​box​.com/​s​/​k​b​0​w​0​2​j​r​3​4​a​g​r​2​v​/​r​e​s​e​a​r​c​h​l​i​n​k​s​.​zip. You install it by going to your plu­gin menu and upload­ing the zip file. You make sure you upload it to your test site, because this is still beta soft­ware. I think this will be com­pat­ible with the final ver­sion, but I’m not will­ing to guar­an­tee. If you have installed the pre­vi­ous ver­sion, this ver­sion is utterly incom­pat­ible and using the two at the same time will break access to your blog in a very emphatic way. This is why I test on a desktop server.

I’ll be test­ing this shortly, in par­tic­u­lar the way it handles COinS. There may be a simple and eleg­ant way of adding COinS to ref­er­ences, but I don’t know what it is.

WordPress shortcodes for DOIs and other research links

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I’ve writ­ten a plu­gin for WordPress that adds short­codes to link to research. To use it you’ll need a self-installed WordPress blog. A blog at word​press​.com won’t be able to use it.

[doi id=“10.1093/aob/mct148”]link text[/doi] links the link text to http://​dx​.doi​.org/​1​0​.​1​0​9​3​/​a​o​b​/​m​c​t​148 It also does a few more things.

If there are research codes used, the blog checks to see if it has cita­tions stored for them. If it does then it out­puts a References sec­tion at the end of the post. It’s not in this post, because I’m not actu­ally using the short­code in this post.

If there isn’t a cita­tion stored, the blog will go through each DOI and make one. It’s designed to make cita­tions com­pat­ible with the ScienceSeeker web­site. If you’re a sci­ence blog­ger then you would do well to sign up to this.

It solves a prob­lem with alt­met­rics too.

At AoB Blog we post about vari­ous papers, usu­ally from Annals of Botany or AoB PLANTS. If people like what they see and tweet a link to the post, the post gets credit for the link, but the ori­ginal paper doesn’t. It wasn’t the ori­ginal paper tweeted, it was the post. I’ve talked with people at OUP and Altmetric​.com and the answer we settled on was to add a meta tag in the header.

<meta name=“DCTERMS.isBasedOn” scheme=“DCTERMS.URI” content=“http://dx.doi.org/10.1093/aob/mct148”/>

This gives a way to con­nect a post to the paper it’s com­ment­ing on. It only works from the second time a page is loaded, but the first is usu­ally a pre­view by the author, so that’s not critical.

Not everything people want to link to has a DOI. What do you do if you have a mix of DOI and http:// links and you want to use them in the same ref­er­ence sec­tion? There is a url shortcode.

[url id=“http://aobblog.com/2013/08/brachypodium-is-not-arabidopsis/” author=“Chaffey, N.” date=“2013” title=“Brachypodium is NOT Arabidopsis(!)” website=“AoB Blog”]

…will out­put a cita­tion in a sim­ilar style to the DOI cita­tion, with a ‘date accessed’ note added, set to whenever you first run the short­code. If you don’t spe­cify a pub­lic­a­tion date then it sets this year. If you don’t spe­cify an author then it is set to ‘Unknown’.

You can down­load the code from Dropbox and install it, or have a laugh the at code. The code is not sleek, because I wanted to see what was hap­pen­ing each step of the way. As a warn­ing, I don’t know if this is secure code or not. That’s not likely to be a big prob­lem if it’s just you on your site, but it’s an issue if you have a multi-author blog.

Also it doesn’t handle a few other things yet. There is a space for an [arxiv] short­code. I haven’t added this yet because arxiv out­puts metadata in a dif­fer­ent way to dx​.doi​.org. Despite hav­ing DOIs, Figshare doesn’t work with it either. I don’t know why Figshare out their DOIs in a dif­fer­ent way, because I haven’t spoken to them yet. There’s prob­ably a good reason, so that might mean mak­ing a [fig­share] short­code to handle those links.

At the moment the code is up for dis­cus­sion. Once I’ve under­stood this page and added arxiv and fig­share sup­port then I’ll see about adding it to the WordPress plu­gin repository.

Download the plu­gin as a zip file

Update: Thanks to Stack Overflow I now know how to get data for an ISBN, so an [isbn] short­code will be pos­sible too.

Mick Aston

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Mick Aston was prob­ably the best-known archae­olo­gist in the UK. I’d also go so far as to say that he was the most influ­en­tial archae­olo­gist of the last 25 years.

Mick Aston

Mick Aston (centre). Photo by Wessex Archaeology.

The reason is Time Team, an archae­olo­gical series on Channel 4. If Sky at Night is Astronomy then Time Team when Mick Aston was in it was archae­ology. Its suc­cess massively expan­ded the uptake of archae­ology by stu­dents. Mick Aston’s idea was respons­ible sup­port­ing an incal­cul­able num­ber of jobs in uni­ver­sity depart­ments. It’s easy to over­look was an aston­ish­ing idea Time Team was.

The tra­di­tional doc­u­ment­ary places the aca­demic speaker at the author­ity speak­ing Truth. A recent example is Rise of the Continents, where Mantle Plumes are presen­ted as unques­tioned fact as noted in the post at The Theatre of Reason. A com­mon grumble is that sci­ence is a pro­cess not a body of fact, so how do you show pro­cess? Mick Aston reckoned you could pro­duce a usable brief eval­u­ation of an archae­olo­gical site in three days and this became Time Team. A cam­era crew fol­lowed an archae­olo­gical team as they dug for three days.

Below I’ve embed­ded the epis­ode from Blaenavon, which I hope 4oDDocumentaries have made widely access­ible.* You could make a drink­ing game from the num­ber of times someone says they don’t know some­thing. To steal a line from Paul Bahn: it’s not about find­ing things, it’s about find­ing things out.

As a meas­ure of impact, I offer another series, Bonekickers. Bonekickers was an attempt by the Life on Mars team to pro­duce a drama around an archae­ology unit. It was laughed out of the sched­ules because Time Team had demon­strated to a large chunk of the UK pop­u­la­tion how archae­ology worked. To be fair Bonekickers was pretty awful in its own right, but it’s thanks to the impact of Time Team that it became truly ris­ible. Can you ima­gine that hap­pen­ing with any other aca­demic discipline?

Mick Aston’s influ­ence meant that he became a ste­reo­type of an archae­olo­gist in his own time. That could sound snide, but rather it’s a meas­ure of how loved by the pub­lic he was.

He also had the poten­tial to keep innov­at­ing. After leav­ing Time Team, he’d been work­ing with Timothy Taylor on Dig Village. In some ways he was in the twi­light of his career, but he still could have shone for many years like the even­ing star.

Photo Time Team in Salisbury by Wessex Archaeology. This image licensed under a Creative Commons by-nc-sa licence.

*I’m not optim­istic that it’s vis­ible bey­ond the UK. You can search for Time Team on YouTube, but embed­ding those videos isn’t sens­ible. Uploading a pro­gramme whole­sale, breach­ing the copy­right isn’t neg­ated by say­ing “No infringe­ment of copy­right is inten­ded”. These videos will be com­ing down sooner or later. My per­sonal favour­ite epis­ode is prob­ably Llygadwy / Celtic Spring, but that’s not so typ­ical of the series.

Want a happy holiday? Pray for an Arctic blast Telegraph tells numerate readers.

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Dr Arnall’s hap­pi­ness for­mula is: O + (N x S) + Cpm/T + He. Put more simply, a numer­ical value for being out­doors (O) was added to nature (N) mul­ti­plied by social inter­ac­tion (S), added to child­hood sum­mer memor­ies and pos­it­ive thoughts (Cpm) divided by tem­per­at­ure (T), and added to hol­i­day excite­ment (He).

So explains the Daily Telegraph. When divid­ing a smal­ler denom­in­ator gives a big­ger num­ber. 1/10 is a big­ger num­ber than 1/100 des­pite 100 being big­ger than 10. When T approaches zero Cpm/T approaches infin­ity. Dr Arnall is we will be hap­pi­est when T = 0. That’s a sum­mer where the tem­per­at­ure hits freez­ing point if you’re meas­ur­ing in Centigrade,* when you’ll be infin­itely happy. If you’re meas­ur­ing in Fahrenheit you’ll be euphoric when the tem­per­at­ure reaches the equi­val­ent of –18ºC.

What’s pain­ful to read is that he doesn’t seem to under­stand his own for­mula. He’s quoted as say­ing: “June has also seen some warm weather after the cold spring, with people hop­ing more warm spells are ahead,” without warn­ing that in his fantasy this warm weather would be less pleas­ing than cold and drizzle.

*Anders Celsius ori­gin­ally set his scale the other way round, so that boil­ing point was 0º and water froze at 100º. Despite this, I strongly doubt Dr Arnall would he happy if someone tripped and spilled the con­tents of a boil­ing kettle over him.