University of Glasgow

Roderic Page

![ipad_iphone.gif](http://lh3.ggpht.com/_Gct8lVAxKqQ/THw7Le_ZgII/AAAAAAAAAu4/ijqYE-khl18/ipad_iphone.gif?imgmax=800){border="0"
width="200" align="right"}Continuing the series of posts about reading
scientific articles on the iPad, here are some quick notes on perhaps
the most polished app I\'ve seen, [Papers for
iPad](http://mekentosj.com/papers/ipad/). As with earlier posts on the
[Nature](http://iphylo.blogspot.com/2010/08/viewing-scientific-articles-on-ipad.html)
and
[PLoS](http://iphylo.blogspot.com/2010/08/viewing-scientific-articles-on-ipad_24.html)
apps, I\'m not writing an in-depth review - rather I\'m interested in
the basic interface design.  
  
Papers is available for the [Mac](http://mekentosj.com/papers/), as well
as the [iPhone](http://mekentosj.com/papers/iphone/) and iPad. Unlike
social bibliographic apps such as Zotero and Mendeley, Papers lacks a
web client. Instead, all your PDFs are held on your Mac, which can be
wirelessly synced with Papers on the iPad or iPhone.  
  
**Navigation popover**  
  
Papers makes extensive of use of the split view, in which the screen is
split into two panes, the left-hand split becoming a popover when you
hold the iPad in porrtait orientation. Almost all of the functionality
of the iPhone version is crammed into the left-hand split. The popover
displays the main interface categories (library, help, collections that
you\'ve put PDFs into), collections of documents, metadata for
individual papers (which you can edit), as well as search results from a
wide range of databases:  
  

::: {style="text-align:center;"}
![papers.jpg](http://lh5.ggpht.com/_Gct8lVAxKqQ/THw-lgHy0iI/AAAAAAAAAvA/gH39Rf4HM_4/papers.jpg?imgmax=800){border="0"
width="400"}
:::

  
Some of these features you encounter as you drill down, say from library
to list of papers, to details about a document, others you can access by
clicking on the tab bar at the bottom.  
  
**PDF display**  
Like the PLoS app, Papers displays PDFs. It doesn\'t use a page-turning
effect, rather you swipe through the pages from left to right, with the
current page indicated below in a page control (what Sencha Touch
describe as a carousel control).  
  

::: {style="text-align:center;"}
![touch5.jpg](http://lh3.ggpht.com/_Gct8lVAxKqQ/THxC4rTsV1I/AAAAAAAAAvI/ZTF2vn62bZ8/touch5.jpg?imgmax=800){border="0"
width="400"}
:::

  
Given that the document being displayed is a PDF there is no interaction
with the images or citations, but you can add highlights and
annotations.  
  
**Summary**  
Papers is the first of the iPad apps I\'ve discussed that isn\'t limited
to a single publisher. If and article is online, or in your copy of
Papers for the Mac, then you can view it in Papers for iPad. It is the
app that I use on a day to day basis, although the PDF viewer can feel a
little clunky. I think anyone designing an application reader should
play with Papers for a while, if only to see the level of functionality
that can be embedded in the basic iPad split view.


Continuing the series of posts about reading scientific articles on the iPad, here are some quick notes on perhaps the most polished app I've seen, Papers for iPad. As with earlier posts on the Nature and PLoS apps, I'm not writing an in-depth review - rather I'm interested in the basic interface design.Papers is available for the Mac, as well as the iPhone and iPad.

Viewing scientific articles on the iPad: Papers

The ability to create PDFs for the articles
[BioStor](http://biostor.org/) extracts from the [Biodiversity Heritage
Library](http://www.biodiversitylibrary.org) has been the single most
[requested feature for
BioStor](http://biostor.uservoice.com/forums/36526-general). I\'ve taken
a while to get around to this \-- for a bunch of reasons \-- but I\'ve
finally added it today. You can get a PDF of an article by either
clicking on the PDF link on the page for an article, or by appending
\".pdf\" to the article URL (e.g.,
<http://biostor.org/reference/570.pdf>). In some ways the BioStor PDFs
are pretty basic - they contain page images, not the OCR text, so they
tend to be quite large and you can\'t search for text within the
article. But what they do have is XMP metadata.  
  
**XMP metadata**  
![7950C5D8-3299-48CF-96A0-9D02BA6F0B03.jpg](http://lh3.ggpht.com/_Gct8lVAxKqQ/S74im04xc_I/AAAAAAAAAoU/wv_LW3et2bg/7950C5D8-3299-48CF-96A0-9D02BA6F0B03.jpg?imgmax=800){border="0"
width="165" height="66" align="right"}One of the great bugbears about
organising bibliographies is the lack of embedded metadata in PDFs, in
other words [Why can\'t I manage academic papers like
MP3s?](http://www.freelancepropaganda.com/archives/MP3vPDF.pdf) (see my
[earlier
post](http://iphylo.blogspot.com/2007/05/itunes-and-citation-metadata.html)
for some background). Music files and digital photos contain embedded
metadata that store information such as song title and artist in the
case of music, or date, exposure, camera model, and GPS co-ordinates in
the case of digital images. This means software (and webs sites such as
Flickr) can automatically organise your collection of media based on
this embedded metadata.  
  
![mendeley.png](http://lh5.ggpht.com/_Gct8lVAxKqQ/S74hQjsI-hI/AAAAAAAAAoM/d6zKe6zZ3Vw/mendeley.png?imgmax=800){border="0"
width="64" height="64"
align="right"}![papers.png](http://lh4.ggpht.com/_Gct8lVAxKqQ/S74hfr_zxPI/AAAAAAAAAoQ/mGKRrKKeylY/papers.png?imgmax=800){border="0"
width="64" height="64" align="right"}Wouldn\'t it be great if there was
an equivalent for PDFs of papers, whereby the PDF contains all the
relevant the bibliographic details (article title, authorship, journal,
volume, pages, etc.), and reference managing software could read this
and automatically put the PDF into whatever categories you chose (e.g.,
by author, journal, or date)? Well, at least two software programs can
do this, namely the cross-platform [Mendeley](http://www.mendeley.com),
and [Papers](http://mekentosj.com/papers/), which supports Apple\'s
Macintosh, iPhone, and iPad platforms. Both programs can read
bibliographic metadata in Adobe\'s [Extensible Metadata
Platform](http://en.wikipedia.org/wiki/Extensible_Metadata_Platform)
(XMP), which has been adopted by journals such as
[*Nature*](http://blogs.nature.com/wp/nascent/2008/12/xmp_labelling_for_nature.html),
and CrossRef has recently been experimenting in [providing services to
add XMP to
PDFs](http://www.crossref.org/CrossTech/2009/12/add_crossref_metadata_to_pdfs.html).  
  
One reason I put off adding PDFs to BioStor was the issue of simply
generating dumb PDFs for which users would then have to retype the
corresponding bibliographic metadata if they wanted to store the PDF in
a reference manager. However, given that both Papers and Mendeley
support XMP, you can simply drag the PDF on to either program and they
will extract the details for you (including a list of up to 10 taxonomic
names found in the article). Both Papers and Mendeley support the notion
of a \"watched folder\" where you can dump PDFs and they will
\"automagically\" appear in your reference manager\'s library. Hence, if
you use either program you should be able to simply download PDFs from
BioStor and add them to your library without having to retype anything
at all.  
  
**Technical details**  
This post is being written as I\'m waiting to catch a plane, so I
haven\'t time to go into all the gory details. The basic tools I used to
construct the PDfs were [FPDF](http://www.fpdf.org/) and
[ExifTool](http://www.sno.phy.queensu.ca/~phil/exiftool/), which
supports injecting
[XMP](http://www.sno.phy.queensu.ca/~phil/exiftool/TagNames/XMP.html)
into PDFs (I couldn\'t find another free tool that could insert XMP into
a PDF that didn\'t already have any XMP metadata). I store basic Dublin
Core and PRISM metadata in the PDF. The ten most common taxonomic names
found in the pages of the article are stored as subject tags.  
  
![FA644E5D-F2DE-4B00-BADD-140806C4EE00.jpg](http://lh4.ggpht.com/_Gct8lVAxKqQ/S74pHpx_kHI/AAAAAAAAAoY/T5Xbd_9mLB8/FA644E5D-F2DE-4B00-BADD-140806C4EE00.jpg?imgmax=800){border="0"
width="116" height="85" align="right"}Initially it appeared that only
Papers could extract XMP, Mendeley failed completely (somewhat
confirming my [prejudices about
Mendeley](http://iphylo.blogspot.com/2009/09/google-scholar-metadata-quality-and.html)).
However, I sent an example PDF to Mendeley support, and they helpfully
diagnosed the problem. Because XMP metadata can\'t always be trusted,
Mendeley compares title and author values in the XMP metadata with text
on the first couple of pages of the PDF. If they match, then the program
accepts the XMP metadata. Because my initial efforts as creating PDfs
just contained the BHL page images and no text, they wouldn\'t pass
Mendeley\'s tests. Hence, I added a cover page containing the basic
bibliographic metadata for the article, and now Mendeley is happy (the
program itself is growing on me, but if you\'re an Apple fanboy like me,
Papers has native look and feel, and syncing your library with your
iPhone is a killer feature). There are a few minor differences in how
Papers and Mendeley handle tags. Papers will take text in the Dublin
Core \"Subject\" tag and use those as keywords, whereas to get Mendeley
to extract tags I had to store them using the \"Keywords\" tag
(implemented using FPDF\'s `SetKeywords` function). But after a bit of
fussing I think the BioStor PDFs should play nice in both programs.  


The ability to create PDFs for the articles BioStor extracts from the Biodiversity Heritage Library has been the single most requested feature for BioStor. I've taken a while to get around to this -- for a bunch of reasons -- but I've finally added it today.

Publicaciones de Rogue Scholar

Viewing scientific articles on the iPad: Papers

BioStor gets PDFs with XMP metadata - bibliographies made easy with Mendeley and Papers