Category Archives: Literature and Language

Sente for PDF Management on the Mac and iPad (4): Reading/Annotation in Sente and Power Note Taking ($$tagging$$) with Sente Assistant

This is the seventh post in the series Digital Workflows for Academic Research on the Mac for the Columbia Libraries Digital Humanities Center.


In my previous installments on Sente, Sente for PDF Management on the Mac and iPad (1): Capturing and Organizing PDFs, Sente for PDF Management on the Mac and iPad (2): Capturing and Organizing PDFs, Metadata, Tagging, Statuses, and Sente for PDF Management on the Mac and iPad (3): Quick Add, Zotero Workflow, and Automated (Re)searching, I demonstrated the lion-share of Sente’s powerful PDF and reference retrieval and organizational features and got you on the path to setting up your own efficient, and customized library for your academic workflow needs. Before that, in the second post, PDF Chaos? Digital Workflow Basics, I discussed some best practices for staging, splitting, OCRing and setting up your Sente library.

I’d like to thank guest contributor Daniel Wessel for his insightful and comprehensive (re)introduction to the methodology and practice of outlining in scientific writing, Using Content Outlines and Circus Ponies Notebooks for Writing Articles and Theses, which features as the sixth installment of the present Digital Workflows for Academic Research on the Mac and is also viewable on our Butler Library Blog. His contribution is especially valuable and salient to the present post, and I have written this post and planned the next one–which will cover OPML, Text, and Hierarchical Structure: Moving Data between Sente, DEVONThink, CPN, Scrivener and other applications (where I’ll show you how the annotation and reference information in your personal, intertextual archive you’ve built up can be exported–using third part scripts and apps–through OPML/ RTF, and RTFD to a host of different mind map and database applications, plus writing and outlining platforms for such content outlines etc.), also with his post in mind: not only should the three posts be thought of together, but in fact, they basically constitute the peak of the series’ aspiration; namely, helping you move from tools to streamlined processes and well thought out (traditional and hybrid) methodologies which actually allow you to translate your research into realized products: theses, articles, conference papers, and sharable presentations.

The annotation functionality of Sente is its most amazing feature, in my opinion, because it allows you to read and annotate your PDFs–save quotes, make comments, and highlight–and keep them organized and synchronized on your desktop Mac and iPad–and now iPhone (as I was writing this post the new iOS version of Sente was released) through the cloud! Sente is now a one stop solution for you to keep your literature and research at hand at all times. I will also discuss what I call “power note taking,” because Sente operates on a Rich and Plaintext model such that you can easily combine it with a custom tagging system for individual notes–not just references–and even write your individual annotations on captured text in MultiMarkdown first, thus allowing you to tag, use MM syntax, and maintain the integrity of citation keys (for cite and scan). “Power note taking” thus represents making the most of all the tools in the digital humanist tool box for optimizing its use while avoiding any of your hard work being trapped in a single application. By the end of your post I think you’ll be convinced of Sente’s note taking prowess and superiority over Zotero for multiple reasons, not least since it does not yet embed annotations in PDFs, still requires the use of an external editor, and doesn’t take advantage of the simulated book that the iPad and iPhone afford.

The Centrality of Note Taking in Academic Thinking and Research

Note taking is one of the most important and fundamental practices in academic research. Not only does it help you to record, capture, and the collect ideas of others, but the benefits of dialectical thinking truly spring from annotating texts while reading them. The practice and habit of annotation for the majority of academic readers–whether on a separate sheet of paper, sticky notes, subject notebooks, in margins of a book, or in an index-card system of cross-references like Luhmann’s infamous and innovative Zettelkasten, ends up being one’s personal archive of thought and the wellspring for creative intellectual endeavors on the page. Thus note taking is not merely something we do to index and keep track of the ideas of others, but it is an important, deep-seated practice for most academic researchers that ought to be systematized as a kind of extended memory that will serve a lifetime of intellectual work.

Indeed, Luhmann, as the Taking Note Blog points out,

described his system as his secondary memory (Zweitgedächtnis), alter ego, or his reading memory or (Lesegedächtnis). Luhmann’s notecard system is different from that of others because of the way he organized the information, intending it not just for the next paper or the next book, as most other researchers did, but for a life-time of working and publishing. He thus rejected the mere alphabetical organisation of the material just as much as the systematic arrangement in accordance with fixed categories, like that of the Dewey Decimal System, for instance. Instead, he opted for an approach that was “thematically unlimited,” or is limited only insofar as it limits itself.

While there is an app that attempts to replicate the paper Zettelkasten system digitally, there is no doubt that annotation practices have a wide range of complexity and idiosyncrasy such that Zettelkasten wouldn’t work for everyone anyway, and furthermore that they all have varying degrees of adaptability in new media contexts. In any case, most mainstream annotation and reading practices have been made newly complicated on several levels by the realities of and challenges to traditional reading and writing practices in academia and our society–between digital and analog, screen and page, biological and artificial intelligence, political-economic and liberal-arts/humanistic valuations, and a panapoloy of apps, devices, and interfaces. But understanding the dynamics of what is possible with the hybridized nature of the print and print-like form with technology such as iPads, iPhones, Macs and Web 2.0 when applied to evolving traditional, “philologocentric” (if I may) annotation techniques is an advance for the digital humanities in the right direction.

Not only that, but it is really about how the scholar and researcher link together, conceive of, and think about information. Text, in its jump to the cooler hybridized media forms, is still fundamentally hot as a practice, though the text straddles the two domains, and the speed and increased access to text across media means an inherent blending and evolution of hot and cool (I use the McLuhan language playfully, but there is an obvious truth to it. See this and this too, by David Bobbitt on Teaching McLuhan–“…we misconstrue McLuhan’s “hot” versus “cool” distinction when we try to force these terms into static definitions,” for more).

Screen Shot 2014-05-29 at 12.15.21 PM

Bridging this is still of key importance.

In fact, it seems this was the motivation behind Ted Nelson’s Xanadu, now released fully after 54 years, which has been thought of as one of the key experiments in hypertext that was a parallel conceptual driver of the world wide web, though Nelson doesn’t quite see it that way. Nelson himself characterized Xanadu as “proposing an entire form of literature where links do not break as versions change; where documents may be closely compared side by side and closely annotated; where it is possible to see the origins of every quotation; and in which there is a valid copyright system– a literary, legal and business arrangement– for frictionless, non-negotiated quotation at any time and in any amount.” 

Xanadu Screenshot

Moerover, Nelson’s Xanadu vision approximates my own aims here in Digital Workflows with PDFs. As the Xandau concept states:

We foresaw in 1960 that all document work would migrate to the interactive computer screen, so we could write in new ways– – paper enforces sequence– we could escape that! – paper documents can’t be connected– we could escape that! – this means a different form of writing – this means a different form of publishing – this means a different document format, to send people and to archive. We screwed up in the 1980s, and missed our chance to be world wide hypertext (the Web got that niche). However, we can still compete with PDF, which simulates paper, by showing text connections.

While I think PDF is the future and the now, Lehmann’s Zettelkasten and Nelson’s Xandau are harbingers of what is already now possible in a well-thought-out workflow using a suite of professional apps, devices, and good practices.

A key part of that, is thinking through a system of note taking and annotation that allows us to efficiently bridge the gap between digital and analog worlds without wasting time and throwing out traditional best practices of reading and annotation with the “bath water.” How do we translate these traditional modes of reading and annotation from this Changing Practices to the realities of the cloud, multiple devices, and a deluge of electronic practices and receptacles of information? Information Deluge What is(n’t) digital humanities (and why it matters)?

Credit: Digital Humanities Manifesto 2.0

Credit: Digital Humanities Manifesto 2.0

I want to think about this in a bit more depth, and in terms of the Digital Humanities. In the first post, Introducing Digital Workflows for Academic Research on the Mac I wrote that in the world of Web 2.0, there are tools and apps galore, vast databases of digitized books, articles, shared information, websites, etc. The collection and review of information involves vastly greater quantities of text and also new kinds of media and other crucial information available through the internet which offer incredibly expanded possibilities for research. However, the repository of history and the human sciences not only still predominantly exists on paper and in the library stacks–how many times have you had to scan something in the Digital Humanities Center? raise your hands–but the reality of contemporary research involves a mixture of digital and analog materials and hybridized practices not all of which are equal: a confusing complex in which we–the biological and rational creatures–must work between machines and digital media and yet still adhere to the rightly rigorous demands of linear information presentation and scholastic conventions in the production of papers, articles, and dissertations.

In other words, when it comes to how we think with text (read and work with text) we are talking about an ancient and basic part of the scientific process (note taking and annotation), and thus we are really talking not only talking about how to adapt, but also how to evolve a key and long standing scholarly practice of textual work which inherently involves negotiating convergent practices.  Indeed, this is essentially what Presner and Schnapp argue in the Digital Humanities Manifesto 2.0–in an oft cited passage:

Digital Humanities is not a unified field but an array of convergent practices that explore a universe in which: a) print is no longer the exclusive or the normative medium in which knowledge is produced and/or disseminated; instead, print finds itself absorbed into new, multimedia configurations; and b) digital tools, techniques, and media have altered the production and dissemination of knowledge in the arts, human and social sciences. The Digital Humanities seeks to play an inaugural role with respect to a world in which, no longer the sole producers, stewards, and disseminators of knowledge or culture, universities are called upon to shape natively digital models of scholarly discourse for the newly emergent public spheres of the present era (the www, the blogosphere, digital libraries, etc.), to model excellence and innovation in these domains, and to facilitate the formation of networks of knowledge production, exchange, and dissemination that are, at once, global and local.

What I propose here in the Sente workflow for annotation really goes to the core of negotiating these convergent practices. While some utterly ill-conceived and poorly thoughtout news bites out there (like this piece in the New Republic) continute to herald the collapse of the humanities because no one supposedly reads books anymore in print (to be specific, the author somehow thinks that print qua paper is fundamentally different from print qua screen: “only wealthy institutions will be able to afford the luxury of faculty devoted to studying written and printed text…The change isn’t necessarily an evil to be decried but simply reflects how most people now generate and read narratives and textthey do it on digitally based multimedia platforms”), others trumpet the use of iPads and digital forms of print–and electronic annotation, as a fundamental revolution as if it has nothing to do with its analog counterpart, clearly missing the point. As expensive as iPads and iPhones may be, they are now “market center” and as popular as the newspaper used to be. I support a reasoned, populist approach to turning the idea of the exclusivity of the humanities (and contorted unsound evaluative categories of evaluating humanistic inquiry) on its head, come on folks!

The other problem is that there is a legitimate claim in the digital humantnies that in these convergent practices print and print like articles no longer constitute the only form of scholarship. Many contemporary professional scholars are not exclusively generating the ‘linear’ outputs–in other words, many people in academia are now producing unprintable digital scholarship. (Though for me, any idea will have to be communicable and sharable in some sort of linguistic way that resembles print, gasp!– language–at some point, or else consists of a (hermetic) futurism/avant-garde). The question is how does this kind of workflow change or work with this reality of new forms of scholarship? The question is well put because if non-printable scholarship is the real trajectory of the Digital Humanities, it could be argued that print-enabling energies should be spent on a more minimalist-coding based workflow approach that–I wager–will also help prepare scholars for more coding and data driven forms of scholarship that diverge from the written page.


The more coding-based adherents of DH support this excellent technology stack called Sustainable Authorship in Plain Text Using Pandoc and Markdown which is solid combination of already-made graphic interfaces, script libraries and coding for the creation of “linear” print and print-like forms. This approach’s most “consumer” component would be Zotero, which it combines with Pandoc and Markdown. But simplicity is its key appeal (it is an app, a package and coding)–though it is strikingly scholastic (and terminal-text based) and may feel for the outsider and like learning Latin. Its adherents believe the learning for it is extremely efficient, and that its open and interoperable approach is equatable to the learning curves associated with a stack of apps with higher pay off at the end. My point is that in many ways this coding based approach to the DH is almost as “hot” as the analog practices that preceded it, and that annotation gets to the heart of where “convergent” practices can not only intersect but combine a Sustainable Authorship in Plaintext Approach with great applications and graphical interfaces for different functions and processes (also on amazing interactive devices like iPads and iPhones). I hope that you will see by the end of this article that there is a great advantage to extending and hybridizing this sort of stack within a Sente workflow and seeing how a Plaintext-Pandoc-Markdown (MultiMarkdown approach) can evolve within a WYSIWYG consumer tablet-smartphone-laptop setting, in this case involving a fairly normative, but powerful and serious platform that allows non-coders the ability to do serious work: reaching a market of coders, pre-coders, non-coders, professional and amateur scholars across the spectrum of possibility. Sente Library on iPadThe note-taking and later OPML-Plaintext hybrid workflow I propose here also does allow users to break free from apps that black box their work because the data is ultimately fungible as text (no data islands–provided one has understanding of how the file formats and processes work together), while on the other hand allowing one to move between and in and out of good, professional applications such as Sente, Scrivener, and DEVONthink which thus additionally allow intelligent users a great deal more power and flexibility–a dynamism which only increases exponentially when combined with the more coding based Markdown-Pandoc workflow. Scrivener and DEVONthink now offer full support for Markdown and MultiMarkdown and one can easily migrate plaintext fruitfully between these various applications.

Analog Annotation and Reading 

Sessa 1578 Dante Commentary with Renaissance Reader's Annotations. Credit:

Sessa 1578 Dante Commentary with Renaissance Reader’s Annotations. Credit:

Now that we’ve established that bridging and evolving textual practices between the hot and cool media and practices is really an important function of the digital humanities, there is a great deal of value to figuring out how to do traditional annotations, like making marginal and keyword annotations in texts; to make them actually work out in the digital medium by thinking about how it has been done since time immemorial.

In fact, my feeling on this is that the convergence of digital tools and traditional practices actually improves the traditional organization and doing of research in the analog mode in many myriad ways. Let’s take this example, a page from Dante Alighieri’s Convivio that I have annotated for my dissertation, which exemplifies the highly personal and individual “hot” medium analog experience of textual scholarship and reading in terms of “annotating” and an old school version what we now call #tagging. It also exemplifies its limitations in comparison to what computers can do.

Annotated Book

Alighieri, Dante. 1993. Convivio. Ed. Giorgio Inglese. Milano: Rizzoli

Having spent a lot of time with academics, this is more or less a classic example of how many scholars read books (some I know keep their annotations separate, but in that case would somewhat mirror their response to the text outside of it but still with it). What can we say about the defects of analog annotating?

  1. The analog annotations are locked in analog practices. When you make annotations directly on the pages, you have to have an external apparatus or filling system or cards, or index to your own highlights and quotes.
  2. The analog annotations are not searchable.
  3. Underlines are not actual records of quoted material. Underlines are ambiguous as to the meaning of the underlined text.
  4. The tags and keywords (keywords and words, as in my example, like “princes” are effectively tags) that go next to analog quotations are often times something you forget unless you immediately pair it with an explanation and commentary in a notecard or separate sheet of paper.
  5. There is little physical space for elongated commentary in marginal spaces which makes it really difficult to really comment there meaningfully whilst thinking and reading. Hence the popularity of speaking of “marginalized” literature as a metaphor for something sidelined next to a dominant and canonical text/authority. (Medievalists in the house: think scripture, Glossa Ordinaria, Corpus Iuris Canonici, Latin auctores, etc. etc.)
  6. If you have annotated a whole book, with marginal notes, underlined key quotes, and marginal keywords, some of which are cross-references, when you are working on a larger project, these analog annotations and cross-references are unable to speak to each other. Here we go to Ted Nelson’s Xanadu vision and Lehmann’s analog solution. Cross-referencing is literally like “See above p. whatever” cross referencing–hated because they are easy to break in publishing (when pagination gets off or material added or adapted)–but when we marginally annotate we hardly ever do this. Wikilinks and hyperlinks, or digital references would be great! This is why indexes were so important for evolved pre-digital print culture.
  7. When it’s intertextual, i.e. between ideas or facts or proper nouns in other works, authors or texts, if we wanted to make use of these marginal annotations, we’d really need to start manually re-hashing all of them and quickly assembling an outline before we forget why they are important, or what exactly the intertext is.

When this is migrated to the digital medium, it offers multiple improvements. The rest of this post will address how Sente and Sente assistant help us evolve all of this!

Annotations in Sente for Mac

I’ll demonstrate the annotations in the iOS Sente below, but let’s get started in the desktop Sente. If you’d like to see any of this in action, you can check out the official video on the website of Third Street Software or Dan LaSota’s Youtube video. To annotate a pdf attachment simply open the attachment by double clicking it in the library window. You can also access the attachment pane by clicking the reference and pressing command + option + G (⌘+ ⌥+ G).   In the attachment pane, above the displayed PDF file, you will note two icons (below).  annotationicons The “A” stands for text annotation, while the square frame allows you to take snapshot annotations (think about taking a snapshot picture of an image or portion of the PDF itself) by drawing the frame around the portion you wish to record. I’ll detail the snapshot function below. For now, let’s just examine the text annotation functions  (this should be active by default): all you have to do is click and highlight the text, which will bring up the annotation panel selector. Click Annotate Tis the question, highlight, comment, or quote? Obviously you can copy if you want to put the quote on the clipboard immediately. I think highlighting and commenting can serve a function, but my preference is to use the “quote” function almost all the time. This is because the highlight function merely highlights the text (like underlining it is only of momentary cognitive-reading value, being active in reading or marking something is important) , and the comment function makes a blank note. This will be more apparent when you try it out. 2014-05-16_15-49-08Generally, though, the quote function is the best because as you are reading you can highlight salient quotes, you can select whatever color you’d like, and when you press the “quote” button, Sente will automatically snag the exact text into the notes panel, and add it to a running list of notes associated with the particular PDF in the reference. This is alas, the “notes” tab within the reference editor. 2014-06-05_14-38-42 In the example, pictured here (above), I’ve taken several annotations to exemplify this feature. A few things to “note”:

  1. The default “quote” function will snag the selected text, highlight it on the PDF, and Sente, as circled above, will also place a sticky note icon (similar to Acrobat’s note icon) right next to your annotated text.
  2. Sente will generate the note title from the first sentence of the text you highlight.  I highly recommend that you title your note based on a summary or key point of the cited text–this will serve you greatly later when you start exporting your notes for content outlines.
  3. 2014-06-05_14-01-30The quoted text will appear under the title and a “comment” field will be left blank. Some people may want to simply quote the text and leave the comment field blank, others (and different people in different circumstances) will want to immediately comment. Below I’ll explain why I have so many phrases in $$tag$$ marks, but for now, the salient point is that I think it’s important to always put your comments in immediately. This function is great because traditional scholarship is reading and responding to ideas, and Sente’s quote/comment annotation function allows you to collect ideas and immediately capture your own responses.
  4. Moreover, tying your comments to the reference and with the quoted text and page number–besides obviously assisting in the beauty of dialectical thinking–allows you to avoid the sin of plagiarism! In his post on Content Outlines, Daniel wrote about how important it is that an “information unit… be tagged with the source. This requirement is crucial to correctly refer to the source when you write the text. Otherwise you can (and likely will) be found out as plagiarist (give Google a few years more). And whether deliberate or not, that time-bomb will impede or even destroy your career.”  Using Sente’s annotation feature to free associate and think with your quoted texts allows you to streamline and bridge your research and bibliographical practices and bridge them with your writing and poetic practices, while making sure you always remember where you had an idea and whose idea it is attributable to, and what page you found it on. 
  5. As you see in the example, Sente will put the page number of the place where your quote is from in the PDF directly into the page number field in the note. This alone deserves a small discussion.

Page numbers–do it write!

I mentioned this in a previous post cursorily, and it has just come up again recently in the Sente forums: the issue of correct pagination. I participated extensively in that discussion already, so what I say here will be a brief distillation of that and I’ll leave it to you to think about. Depending on the PDF you are annotating, page 1 may very well be page xi of Latin front matter. Depending on the number of blank pages before the main text starts and the number of Roman Numeral pages of front matter (intro, preface, TOC etc.), likewise, page 20 of the PDF document could, in fact, be actual page 3 (or whatever) of the Arabic number pagination in the printed text of which the PDF is a facsimile. This divergence is a complicated part of the hybridization of textual scholarship between media and is very very difficult to automate software to read it correctly. The good news is that the newest version of iOS Sente has vastly improved automating it, but it’s still your responsibility to manually correct, if necessary. I suggest doing it first along with making the annotation. It would be hell to fix later.

Therefore: thou shalt always make sure when you add an annotation that the pagination matches the published official pagination and would withstand bibliographic scrutiny.

Sente does not always do it automatically–but does so much better than Zotero, for example. I say do it “write,” because the purpose of marking and saving quotations, especially those we have comments on, is imperative for effectively citing and remembering where you found your text and for avoiding plagiarism in future writing projects. If you don’t do it right the first time, you may end up with an embarrassing error later. This is a key piece of metadata–especially when you run cite and scan routines for formatting footnotes, citations, and bibliographies. If the page number is wrong (John Doe 2014@12) and it should actually be (John Doe 2014@xi), you will end up with an erroneous note.

Color coding?

Sente allows you to color your citations according to the standard panel of colors (below). I have mixed feelings about color coding. Drosophiliac has some thoughts about color coding in his post on An Academic Notetaking Workflow. I’ve tinkered with an adaptation of his ideas for color coding, below, but I think it will be more appealing to other people as I personally have tried this and decided that it was more distracting than helpful. I know some people are obsessed with color coding and will love this sort of scheme, and perhaps I’ll try it out again sometime.

  • Red – Summary
  • Orange – Important Methodological or Theoretical Information
  • Yellow – Key Information (historical/factual/topical)
  • Green – References (to other background info, papers, specific citations to follow up on)
  • Cyan – Hypotheses and interpretations
  • Magenta – Intertexts, connections to other texts, conntections to my own projects/ideas, questions for further research

You can choose whatever you want, but should probably stick to the deafault color palette above and consistently retain labels.

Snapshot and Image Annotations

In Sente, you can also take “snapshot” annotations. This is especially helpful if you want to capture an image or or a table or figure in a PDF, for example, that does not at all translate into OCR, and is hence not really annotatable based on the document’s OCR information. 2014-06-10_11-24-10 For example, say you want to note and comment on an Image, or simply want to use it later and remix it. Just click the Square box in the annotation panel. Draw a box around the object, and click “Snapshot.” 2014-06-10_11-24-35 The “snapshot” now appears as an individual note in the notes pane. There’s nothing more to it.

Sente for iPad and iPhone: Setup and Interface Sente in AppStore

The exciting news is that while writing this post I had the opportunity to beta test the new version of Sente, which has now been expanded to work on iOS generally–to put it on your iPhone and/or iPad– get it in the App Store. Here I will quickly walk you through the features, which should be familiar to you from what I’ve already said about desktop Sente. Generally, the new Sente iOS interface offers seamless synchronization and functionality with your synchronized libraries. I tend to read just as much on my iPhone as I do on my iPad, and I’m just thrilled that everything now syncs on my phone too.  (In fact, there’s something of a phone device zombie-ism around, we are all walking around constantly glued to our devices, especially iPhones and Androids. Perhaps the addiction to devices is not a good thing, but I’ll leave you to be the judge of that). First things first. When you install a library, it will download from your cloud account. IMG_0082 The next box will ask you to decided to download all or download attachments ad hoc: IMG_0083 What you choose here should really depend on how big your iPad storage is. I invested in a 128gb capacity iPad, so I could automatically download all my attachments, but on my iPhone, which is limited to 16gb, I do download on demand, also because I have data service on the iPhone, but not on the iPad. The Sente Library screen will now pop up and your references will be installed from the cloud. IMG_0085 I won’t try to explicate this because I have already gone over the functions, such as Smart Collections, Ratings, Status etc. in the previous posts. It should just be noted that you can navigate your library that way as well as via your Quick Tag ontologies from the Desktop Sente in the iOS version too once everything has synchronized. Once your references have synchronized (and if you chose automatic sync with a very large library, you may need to give it some good time to sync), you can access your references by Pressing on the file folder icon –here “25 References in Library”– and it will open the list.

iOS Sente: Downloading Attachments

If you’ve chosen not to download automatically, you need to press the triangle button on your reference, or navigate to the “File” tab and select to download the reference from the cloud sync. IMG_0385 iOS Sente: Reference Pane

Here I will show you reference editor interface first, and later the reading and annotation interface. By way of example here is a reference with an attachment I read and annotated for this post. I’ve downloaded the attachment, so let’s get started by familiarizing ourselves with the  reference pane. iOS Sente Reference 1 There are four menus you can access here. “Reference” is the initial window, and is basically the iOS equivalent of the reference editor in the desktop version. Pressing “edit” will allow you to modify and correct the metadata of your reference, as usual. Likewise, you see that whatever statuses you setup in your library have synced here too, and you can also assign a rating.  Pressing “Tags” will allow you to add or modify tags to your reference. iOS Sente Tags Pressing the “File” menu will display the auto link options for the reference, iOS Sente Reference File Tab Here, for example, clicking the “Google Scholar” Autolink, will open the iOS Sente browser (for the record, I won’t discuss it here but you can also do target browsing and file downloading in the iOS Sente browser in a way that is similar to the desktop version). Here we see the “Google Scholar” page of similar articles. Clicking on any of the entries will allow you to enter targeted browsing mode and save new references and PDFs. IMG_0115 In any case, as I was saying before, besides the auto links, you can also open the attachment from within the reference pane: pressing “open file” will open the PDF in Sente’s reading interface. iOS Sente Reading Interface 1 You can also access the reading interface of an attachment by pressing on the icon of the PDF in the library pane, provided it’s already been downloaded. As you see, I’ve already annotated this some, but how does the digital annotation and reading work?

Sente for iPad and iPhone: Reading and Annotation

Once we tap the PDF attachment, we enter the reading mode on the iPad–which will be intuitive for almost everyone who has used a tablet at this point. You will see thumbnail previews of specific pages on the bottom of the screen. To move ahead within the document you can tap forward pages on the thumbnails, or swipe from right to left with your fingers to move between pages like turing pages of a book. Moreover, the orientation will change on the iPad and iPhone depending on whether your are holding the device vertically or horizontally. You can also zoom in a quite crisp resolution to specific sides or parts of the PDF within the Sente reader depending on what’s comfortable for your own eyes. So reading down the page I find a quote I’d like to remember. iOS Sente makes this a piece of cake. IMG_0060 Using either a stylus of choice, or my finger, I simply highlight the text i’d like (dragging the two selector dots around the text) and the annotation menu comes up. It includes the same options that the desktop version does. In this case the quote actually wraps into the next column (this is not a problem on other non-column set PDFS) setting, so to capture the whole sentence or paragraph I copy the rest of the portion on the next column first, then press quote on the selected text and go back in and am ready to paste it in my reference. IMG_0062 Note that the actual page 82 matches the page number printed in the digital text. You will always want to make sure the page numbers match. I discussed this already, and the new iOS version of Sente has made some great improvements in this arena, but as a good practice, as with all metadata, it is worth making sure it’s right the first time. Reading through the text I can zoom in close to the text easily, Sente puts a little icon next to my highlighted text, there is no pixelation: IMG_0066Here is what that annotation looks like in the annotation editor: IMG_0065 On the iPhone:IMG_0352 Serious Sente annotators will want a durable bluetooth keyboard/case combo. I use this Belkin case keyboard combo with my iPad air. It’s about $100, but why not get the most of your iPad investment? 71HxxcRO26L._SL1500_   I think having the keyboard option handy makes taking annotations on the train or bus a breeze. There are a myriad of styli out there, I don’t think it matters which one you pick, but I personally like one that feels like a real pen or pencil. The physical feedback or at least nostalgia for the traditional reading and writing practice feels really really good as an iPad (which inadvertently weights about as much as a slim scholarly hardback) digital humanist. There’s just something about holding the stylus and reading the text like an old book that I like, call it philology I guess.

Browsing Bookmarks and Annotations

Once I’ve annotated everything, I can browse my annotations and bookmarks. Click the Book icon at the top of the window in reading mode: IMG_0100 Here we can see the pages I’ve bookmarked. Press the plus button to add a new bookmark, and “edit” to edit them. IMG_0099 Going back to the reference pane, you can also view your notes and access them from the “notes” tab–and again–this time on my iPhone, not iPad. The joy, everything is synchronized! iPhone Notes Pane Otherwise, Sente’s iOS interface really allows you a lot of flexibility in browsing your documents, quotes, comments, annotations and highlights. You can view everything as a gallery of thumbnails. Sente iOS Gallery Annotations The Book icon will open a tab that contains tabs. The bookmarks and annotation tabs will take you back to your individual annotations or bookmarked pages embedded in the PDF through the Sente browser. But I like the outline tab as well because it translates and enhances the traditional table of contents function. If your PDF has the table of contents metadata built in Sente will allow you to navigate the document (book, really) by the outline TOC. IMG_0113

Searching in iOS Sente 

Another great function is the OCR search functionality. The Search Icon, with magnifying glass was added in an update 6.81 after I took the above screen shots, but was really present the whole time as well in the previous version and in the initial 6.8 iOS release via the action menu (I only mention it to make sure there’s not confusion about why it was missing in some of the other screen shots). iOS Sente Search Organizing Creativity This function is really great and enhances the reading and note taking functionality of the traditional linear printed text when translated into OCR text and made fungible on the iPad device. You suddenly have something that works like an enhanced e-text. If you want, for example, to read and annotate based on certain keywords, or tag pages based on those keywords, bookmark based on key words, Sente’s got you covered here too.  As you can see Sente will find all the instances of the search string, and allow you to navigate to the pages where it is found. It will also, as in the example (above) highlight them, in this case, the instances of “Sente” in Daniel Wessel’s book Organizing Creativity.  Obviously, other PDF readers and software have this function too, but the complex of functions under one roof, here geared towards the nuts and bolts of academic research and reference management is the key and crowning part here, and the ability of searching the PDF for OCRed text that allows you to dynamically to create and manage your own archive of metadata that pairs with your own research database.

Emailing Notes and Attachments in iOS Sente 

By this point you’re probably thinking “this is great, but how do I manage and organize all these individual citations?” You can enter your annotations in the reference pane and can always opt to send them to yourself. IMG_0383 Once you make your choice, press send and Sente will automate the process and open a new email for your in apple mail.

Power Note Taking with Sente Assistant

But what about making use of your many annotations as a personal archive? How to deploy them and find particular annotations? Since Sente still doesn’t yet allow you to tag individual notes, but only references, the Sente community has created it’s own solution to this. Many of you have by now noticed the many $$tagged$$ strings I put into my individual comments. I put them there as the digital equivalents of keyword or sticky tags or marginal key words in the margins of texts. This allows me, using the tag characters $$string string$$ along with Sente Assistant to start generating a tag index within my Sente library. Screen Shot 2014-05-23 at 11.20.56 AM In my opinion, Sente Assistant is perhaps one of the crowning examples of what kinds of practical things can occur from a determined user group dedicated to finding solutions to creating more functionality in already great software. Sente assistant is an amazing commercial-free companion application to Sente written by M. Roberts and inspired by Dana Leighton’s script, which I will discuss in the post on OPML–where I will continue showing you other applications of how to move reference and note information out of Sente into other applications as part of a complete workflow. No doubt some of these features are things I’m sure Sente’s development team are going to natively include in future releases of the software, but for now, Sente Assistant’s features add significantly to the already amazing functionalities of the iOS and OS X Mavericks suite.

Running Sente Assistant on your synchronized Sente libraries, all your notes and references become instantly accessible as a personal archive. The Sente Assistant allows you to:

  • Browse your Sente notes, sorted by their correct position on the source page
  • Perform keyword, wildcard, or tag searches of your notes
  • Search the references you select in Sente, or across all notes in your Library
  • Generate an index of all tagged notes
  • Identify duplicate references in your library
  • Save your filtered notes or search results in a single RTF, HTML, PDF, ODT, DOC, DOCX, or TXT file
  • Customize the presentation of your notes in the Assistant

Download Sente Assistant (the thread for the application is found here). The most recent version is .68, and can be downloaded here. Once you download the package, click to unzip it, and navigate to the folder. I recommend reading the entire “Read Me,” though I will repeat some of the things here. To install the Assistant, unzip the file and place the entire Sente Assistant folder inside your Applications folder. All the pieces needed by the Assistant are contained within this one folder. To use Sente Assistant drag it to your applications folder. Sente Assistant Folder I’d also drag the Sente Assistant app into your dock bar, so you can easily click on it. Now, once that is done, you need to click the Icon “Sente Assistant”–which also is an application in the task manager called “Visual Works”, open Safari, and navigate to


You will want to make a bookmark for this in your browser.

Sente Assistant Interface

Remember you have to have a Sente Library active. When your library is active Sente Assistant presents you several different options for visualizing your data. Notes and summary shows you the totality of your archive, in order of reference, as dialectic of your thoughts with other authors’ texts and intertexts. Screen Shot 2014-06-12 at 1.12.35 PM You can also save all your notes into an RTF file. Screen Shot 2014-06-09 at 2.19.41 PM Tagging Individual Notes and the Sente Assistant Tag Cloud

Sente Assistant’s preferences allow you to customize the color and textual aesthetics etc. as you’d like. Here the really important thing is how to configure your tags. I offer you something that I’ve experimented with and that think works well for several purposes. 2014-06-09_13-47-39By default, the tag format uses a hash mark (e.g., #Sente), but you can make your own custom format from the “Preferences” pane. The tag pattern you set on this page is used to generate the tag index. If you use the hash mark or another single character, your tags cannot include spaces; however, if you use curly brackets or some other characters at the beginning and ending of the tag pattern, your tags can be strings that include spaces, hyphens, or other non-alphanumeric characters. For the tag markers, only non-alphanumeric characters are recognized for tags, with the exception of a few reserved characters used by the SQLite database (e.g., single quote, underscrore, percent sign, and ampersand). To save this configuration make sure Sente is closed, and then “quit” Sente Assistant. When you quit and re-open, you have to restart Safari and the Visual Works application (this is documented in the Sente Assistant) PDF manual. iPhone Notes Pane Thus the point is that using the familiar #hashtag we are all familiar with from Twitter, it is possible to tag individual notes, but I’ve tested several combinations, and I find the most reliable tagging regime here is to use $$tag tag$$ because it lets you make both one word and multiword tags that do not interfere with other characters in the system or SQLite database, and these tags do not interfere with plain text syntax that might be useful to those who routinely use Markdown and Multimarkdown to write. The result of these $$tags$$ in my notes can be seenin the list view, when you go to Sente Assistant’s “Tag Index”–accessible from a drop box menu in the interface. Screen Shot 2014-06-09 at 2.00.09 PM The plain text $$tags$$ are all indexed and hyperlinked now: Sente Assistant Tag Index When you click on the tags within the assistant, it will take you to all the references which include the tag in that library (also keep in mind since it’s plain text embedded within the reference) you can move these across libraries and keep the tags. Sente Assistant will always interpret them.

In the next section I talk about using Markdown and Multimarkdown in notes, but $$tagging$$ with dollar signs in my Sente annotations translates into beautiful tag clouds. If you employed this over hundreds or even thousands of your own comments and notes in your Sente reference and annotation database, the sky would be the limit for harnessing the power of your personal thought archive. There are ways this can be amplified using a Wiki or DEVONthink that cannot be discussed here fully, but Sente Assistant allows this tagging, tag clouding and searching not just of all notes, but of individual notes.

This is something different for now from the Ulysses III kind of tagging using Openmeta tags, see Macademic on this, and I think that ultimately if you get DEVONthink in the mix you are all set in searching metadata. Anyway, I like this kind of tagging because it combines the best of WYSIWYG interfacing, plain text scholarship stacks, and the enhancements of digital text and tablet computing.

Idea: MultiMarkdown inside individual annotations

For those of you who use MultiMarkdown, you will probably like where I’m going with this. If you’re not familiar with MultiMarkdown, it is a derivative of Markdown and facilities easy formatting for writing hassle-free with plain text. Here’s a syntax guide for the uninitiated. The custom tags feature is great because whether you want to write in an outliner, mind map, or word processor, but desire to retain non-interference with other syntaxes, like MultiMarkdown, you could use your tag custom option and make dollar sign $$abc$$ for the tags to insert in the annotations to quoted passages.

This is great because that wouldn’t interfere with either with normal (John Done 2014@page number(s)) in texts–important for Citation Keys used in Cite-Scan functions (to be discussed perhaps in a different setting) or other identifiers with brackets in exported notes that I end up using in a body paragraph. Here’s an example I made in MultiMarkdown Composer: MultiMarkDown Composer Example So if you’re not familiar with MultiMarkdown, to summarize: if I have a note with several tags in the comments, like $$tag one$$ $$economics$$ $$aristotle$$ $$food$$, and I export the notes into a text I’m writing –and they inadvertently end up in the editor or I keep them in a note or comment to remind myself of topics etc. in the tags as mental cue of whatever I want– I don’t have to worry about interference with (Author Year@ pages) citation tags from Sente, the “# “used by MultiMarkdown for headings, or even the other bracketed [^abc xyc cdefg] syntax for footnotes. In the end (as in the above example) you can annotate directly when doing the commentary on the text if you wish something like [^See (Kaye 2007@22-25)], which generates a footnote with the scan citation i’ve chosen.  It doesn’t mess up citations [#] with page number, ex. cite a fake book.[p. 43][#fake] [#fake]: (john doe 2000@44)- etc. The tags, moreover, are rendered by MM like this: \[ tag \[.

Some people might not like this, but you can easily delete the junk when you edit your paper, or simply find replace and delete all of them when ready, and at the least it will be a reminder to you that you had tagged a key piece of information there and perhaps you should make sure you don’t need to consult the tag cloud for more information there anyway. At the moment, these tags do not coincide with Openmeta tags, but if you put them into DEVONthink they should be indexed anyway.

Help, I need to take notes on a real print book!


Iris Pen Express 6 for Mac

Get a scan Pen! I personally use an older model IRISPen express 6, but have also become familiar with a newer generation Product called WorldPenScan, Made by PenPower Inc. I have not tested it, but I have used the IRISPen Express 6, and it works for me in English, Italian, and German with about 90% accuracy–meaning that if you learn to calibrate and use it correctly, as well as hold it well and not scan two lines of text you can get pretty good accuracy of OCRing text on the fly. In any case, the point is that you can and will want to scan quotes into your Sente library sometimes without having to physically scan the book and there’s no reason why you can’t do it into a blank note in Sente–this will also sync into your library.

Doing so is self-explanatory. Get a scan pen, scan the paragraph or lines: IMG_0358   In this example, I scanned a few lines from MacKinnon’s book, which needs a bit of manual correcting. Also, don’t forget to put in the proper page number, so that you don’t improperly cite it, if you end up doing so. Screen Shot 2014-06-09 at 2.09.58 PM

Daniel Wessel: Using Content Outlines and Circus Ponies Notebooks for Writing Articles and Theses


This is the sixth post in the series Digital Workflows for Academic Research on the Mac for the Columbia Libraries Digital Humanities Center. It is written by guest contributor Dr. Daniel Wessel. Daniel is a scientist at a research institute in Tuebingen, and holds a research doctorate in Psychology from the University of Tuebingen (Eberhard-Karls-Universität Tübingen), Germany. During his dissertation thesis on supporting interest and learning with mobile devices, he became interested in ways to organize creativity in art and science (including writing a thesis).  This interest turned into a blog and a freely available eBook, Organizing Creativity ( 

There is no way around it. At one point, all writers face the task of collecting and organizing all their ideas and evidence to produce a coherent written text. And academic texts usually contain a lot of complex information. Putting this information into a coherent structure can be overwhelming and seem like an insurmountable task.

However, there are different ways to facilitate this task. Scientific writing is a craft — it works by using tools on the materials you have. And the tool I highly recommend for scientific writing is a content outline.

In this text, I’ll describe content outlines, their advantages and possible disadvantages, how to create them, and using an outliner application for working with them (with Circus Ponies Notebook as example application).

Content Outlines

Content outlines are different from simple structural outlines of a text, e.g., the Introduction, Methods, Results and Discussion structure for articles, or Introduction, Main Part, Conclusion structure for essays. They are also different from to do lists (e.g., what you want to read for the text) or mere place-holders (e.g., to what you want to refer at which part of the text, like “something about x here”). 

Instead, a content outline contains all the information that is used in the final text in a flexible, self-contained structure. In other words, in a content outline, you write down everything you want to use in the text, but in short information units you can easily move around. 

Every information unit in the content outline must fulfill the following two characteristics:

  1. Independent Units: The information unit must be understood on its own. This requirement essentially means short texts, almost like bullet points on a slide, but still understandable. It allows changes in the order of the information when you create a coherent structure or narrative. You grab it and move it around and can still make sense of it.
  2. Source Information: Each information unit must be tagged with the source. This requirement is crucial to correctly refer to the source when you write the text. Otherwise you can (and likely will) be found out as plagiarist (give Google a few years more). And whether deliberate or not, that time-bomb will impede or even destroy your career.

outline_sketchThe outline itself is usually not only linear, but also hierarchical, i.e., it contains groupings of information (see sketch on the right). This mirrors the later text, as text are usually linear. But texts also contain groupings or hierarchies of information. For example, you give an overview, then go into the details. Or vice versa, you group small pieces of information into summaries. Grouping information units is crucial: Unless you aggregate information, you risk get lost in the details, of losing sight of the wood in all the trees.

In a content outline, you create this hierarchical structure by indenting information, often multiple times. This indentation gives you a visual structure and allows you to refer back to the concrete information that is the basis of, e.g., a summary. Nothing gets lost, but everything is easy to find. And it can be easily changed later on. Prior to writing you can decide in which depth (“indent level”) you want to use the information for your text.

With a content outline, you focus on getting the information down first (the bones of the text). Writing can support thinking and you should think when you externalize and collect the information in a content outline. This allows you to see which information you have available, and to group and sort it into a coherent structure. But you don’t write actual paragraphs (the “flesh” of the text). Because when you write paragraphs, the sentences stick to each other (“thus …”, “therefore …”, or merely by their implicit order). Yes, you want the text to flow from sentence to sentence, but only when you are sure that this is the order in which you want to provide the information — i.e., in the final text.

While the rough position of the material is usually determined by the structure (e.g., your analyses go into the results section, your interpretation into the discussion section), you need the flexibility to reorder information within these sections. After all, you are not putting down facts one after the other like a robot. You argue in your writing, you are writing to make a point, to show a finding, and show why it matters or should matter to the reader. As objective and as truthful as possible. But you argue, and finding that structure to organize your information into a convincing narrative is hard. Trying to create or improve this narrative when you have already written a lot of text is tedious and wastes a lot of time and effort. You have to unravel your text again and again, like Sisyphus stuck in editing hell.

Note that the information you collect in a content outline can be anything that is relevant for your text, e.g., structure information of the text (e.g., “Introduction”, “Methods”, …), summaries of studies you have read, models of theories, notes on how you conducted your studies, result tables, diagrams from analyses, notes about your interpretations of results, conclusions, etc. Nearly everything has its place somewhere in the content outline. Whether it goes into the final text is another question which you can decide later. But externalize it — and keep it flexible.

Advantages of Content Outlines

In my experience, a content outline is the best mixture of a) having information to create a structure and think about what you want to say, and b) keeping the flexibility to actually implement the structure you come up with. 

Treating your material as information units that are understandable on their own, refer back to the source information, and can be freely reordered and grouped, essentially turns writing your text into building with Lego(TM) bricks. You can build your thesis or article with these bricks, allowing you to easily deal with the information you have and change the order until you get to a narrative that works. You can also “weigh” each stone for its quality and group them into “prefabricated” parts. 

Additionally, these are some of the advantages of externalizing all the information you need for the text in a content outline:

  • You can discover contradictions and gaps: Using content outlines allows you to see contradictions and discover gaps in your arguments. Humans have a high capability for holding contradictory thoughts. If you never thought about the two distant aspects of your text together, you might miss a contradiction. Externalizing your thoughts early prevents you from stumbling upon them when you have already written a lot of — suddenly questionable — text.
  • You are less likely to forget anything: There are a lot of things you have to consider for a good scientific text. You cannot hold everything in your mind — and if you did, there wouldn’t be much capacity for anything else.
  • You have a guide for writing: During the actual writing process, it provides you with the necessary information to write a good first draft “in one go”. You do not need to look up information or do additional analyses, which interrupts the writing flow.
  • You can focus on other things: You do not have to keep all the information or the sequence of the text in mind (virtually impossible), thus it reduces the mental effort to remember information. You can use the available resources to focus on the quality aspects of scientific writing (e.g., precision and clarity).

Once you have ordered the information in the right sequence, writing can become a breeze: The logical structure is clear to see and guides the writing process. For example, when my content outline (27k+ cells/1338 outline pages/320k words) of my dissertation was finished, I was able to write the thesis document (250 pages, 71k words) in a month.

Challenges of Content Outlines

No tool is perfect, not for every task and not for every person. There are (at least) three important caveats to consider when using content outlines:

  1. There is no guarantee that the content outline “works” until you have written the text. While you can gauge the text by “reading” the content outline — you essentially have talking points — there still is a gap between the content outline and the final text. Still, with some experience, you can learn “read” the content outline fairly well to get an idea whether it works or not.
  2. A content outlines puts a lot of work in finding the right structure before starting to write actual text. Keeping the structure flexible yet having all information available avoids editing hell … but it takes a long time until you have text to show for. It’s risky if it fails. While fewer revisions might be needed, do not underestimate the final writing task (being able to type with 10 fingers is really helpful here). Also, given that much of the writing happens “in one go”, be sure you know the requirements of the text that is expected from you. A good recommendation is to write a two page writing sample based on the content outline first and give it to your supervisor for a feedback. Identify the kind of mistakes you make and keep a reminder in sight while writing the final text.
  3. Given that you write the actual text relatively late, so there is little to share with an adviser. Whereas it contains all the information in the right sequence, a content outline is very hard for others to understand. A bit like giving someone index cards with talking points and asking them to do a presentation. It would not go well. Thus, you cannot simply give the content outline to your adviser to discuss your work. However, you can either type a short summary (the hierarchical structure of the content outlines makes this easy), or verbally discuss the structure. After all, the content outline does give you the necessary talking points. The content outline is also a good basis to create presentations for colloquiums, conference submissions, etc. After all, the information is available small information units to pick and chose from.

Creating a Content Outline

If you want to use a content outline for your text, try the following steps (and have a look at the tool suggestion in the next section):

  1. Create a structure outline first. Most texts have clear structural requirements (e.g., Introduction, Method, …). Start with this structural information, as it is the highest-level structure for the content outline. Make it stand out via highlighting, bold, etc.
  2. Collect all your information in the content outline. When writing, take care to:
    • Use short notes, not full sentences for the cell content: Avoid using “connections” like “therefore”, “thus”, “this means”, etc. They connect sentences and “glue” them together and you cannot resort them easily.
    • Use square brackets […] to add context information when needed: For example, what does “this” stand for, or “these points”? Even more important: Always make sure you keep your notes in line with the direction the author argued for! Imagine you write down points “for position x” an author has mentioned. But the author overall argues strongly “against x”. In these cases it’s important that you don’t cite the author later as arguing “for x”, even if this person conceded that there are arguments it. Authors take a very dim view on being misrepresented — for good reasons. It’s essentially quote-mining.
    • Always use tags or square brackets to denote the source information: Yes, you might never write in this characteristic style now, but the text you have to write likely has the same style requirements. And once you have written text of your own in that style, it will be very hard to differentiate between text you found and text you have written. In time you might even naturally write in that characteristic style (welcome to the community). This is particularly relevant for a PhD theses which takes years to write. Trust me on this, after a few years, you will have no idea where that information did come from. And plagiarism, intentionally or accidental, damages or ends careers.
    • Within an information unit, clearly differentiate between your own notes and cited text: Related to the previous point, use quotation marks if you mix cited text with your own notes. Alternatively, if you cite a lot and suddenly write your own notes, use something like “myNote:” or square brackets […] for your own notes.
    • Be careful if the cited text refers to another text: Authors frequently refer to other sources. If they use a verbatim quote, use something like “INQUOTE:” to make clear that it is not the authors who say this, but the people they cite. If they summarize other texts, preserve the information that this is a summary by the authors of another work. Never ever simply take their citation or summary as if you had read the cited text. If you would do this, you blindly trust the authors that their citation of the other text is correct. Even worse, when authors cite other authors, they carefully select what they cite or how they summarize a paper. You have to, as you cannot cite everything and condensing naturally reduces the amount of information. But this selection or summary might bias or misrepresent the work. So in adopting a citation other authors make, you not only take their verbatim quote or summary, you also adopt their point of view. And unless you know the original text, you have no way of knowing whether you actually agree with their take on the cited work. For a striking example in everyday life, look at a controversial topic in the news and compare it to the original sources.
    • Don’t depend on, but use, inspiration: If you get inspired and come up with good sentences or ways to explain complex issues in simple ways, by all means, write them down as well. Keeping something to write handy and write them down helps, as ideas frequently come at inopportune moments. It does not matter on which medium you capture, it all ends up in the content outline anyway. While the information units are bones, sometimes a paragraph or too can be helpful as well or treated as one unit. It’s stupid to depend on inspiration, but even more so not to use it when it presents itself. And you can always split sentences into smaller information units (and frequently, you should).
    • Create a hierarchical structure by aggregating information when needed: If possible, group information and write informative summaries above the grouped information. Don’t just name the content, summarize it in your own words. For example, instead of writing that the indented information deals with “arguments for x”, write a short summary of the arguments or reduce them to one or two words each. It will be a simplification, but putting the content in your own words will help you understand it. Later you can look at the summarized information to focus on the big picture or look at the indented information to dive into the details.
  3. Continue to collect the information until you have created the whole content outline. It might seem like a good idea to go in sections, e.g., first create a content outline for the introduction, then write the “final” text for the introduction, then create the content outline for the methods, etc. However, until you know what you want and can say, it makes little sense to write an introduction (or any other part of the text). Get the bones of the whole text before you start adding flesh — otherwise you might be creating a monster.
  4. Check the content. In particular:
    • Go through the whole content outline to ensure you have everything you need for the final text: Compare, e.g., the introduction with the conclusion to ensure that you have everything for an overarching frame. Check whether you have all the necessary analyses. All the figures, etc. pp. Look for gaps and contradictions.
    • Look at the aggregated information to make sure you know which story to tell: Yes, scientific writing must be objective and truthful, but it must also be understandable to the reader. And this requires some kind of narrative, ensuring the reader understands its importance and its findings. Create this narrative and write down a short preliminary abstract of your work. A couple of sentences, no more than half a page what your work is about. Focus on the story you tell, the information you provide. Make sure the reader understands the point of your work.
    • Re-“read” the content outline, one section after the other and make sure the information is in the right sequence: Treat it like telling someone the text. Not what it is about, but the actual content. If necessary, make notes what is important and what you need to remember while writing. Use another color for these notes. The point here is to ensure the clarity necessary to express your point when you start writing. To use an analogy, like “the more you sweat in training, the less you bleed in combat”, the more (easy) changes you make in the content outline, the less (excruciating) changes you have to make in the full text.
  5. Put the content outline next to your writing software and write down the text. The beauty of the content outline is that all information is visible and in the right order. In writing, the following things might be useful:
    • Re-read before you write: Before you write a section, check whether you still think the sequence makes sense. It will also remind you of the direction the writing will go.
    • Keep the depth in mind: While the content outline gives you guidance, you can make decisions on the fly, esp. regarding the depth you want to go into. Do you want to go further and further in the indentations (details, in depth) or stick to the surface? How much detail do you(r readers) need? As you can have summaries of summaries and so on, this gives you quite a bit of flexibility during writing. Best decide in advance how deep the text will be in different sections.
    • Keep attached to the lifeline (mostly): The content outline also serves as lifeline not to stray from your original narrative. If you have new ideas while writing, you might want to stop and think whether it makes sense to include them in your writing. The content outline shows you how the structure unfolds at the moment. Decide whether it makes sense to change it. Unless it’s a really important issue, I would normally recommend to capture the idea somewhere else and use it for another text. It might also fit into the “further studies” section of the work.
    • Mark (but don’t delete) which information units you have already used: Immediately after using it, mark the information as used. For example, by using checkboxes, striking the text through, etc. Just don’t delete it. In some cases, you realize that the text is going nowhere and want to start anew with this section. Then it’s helpful to still have the outline available. It’s also helpful to have a look at the x-ray version of the text, even if you have already added flesh, e.g., for a presentation or supervisor summary.

Using Outliner Applications

Theoretically, you could create a content outline on paper. Practically, when it comes to content outlines, digital tools shine. Digital tools give you the ability to quickly deal with a lot of information in a highly flexible manner. While you can use any program from a simple text editor to Word to MindMap Apps or the like, I would strongly suggest taking a look at an outliner

Outliners use “cells” to contain information. But unlike the cells in Excel or other spreadsheet programs, you can easily move the cells to re-arrange them. Even more practical, you create a hierarchical order by indenting cells below other cells. The indented cell becomes a child cell of the parent cell it is indented under. You can then collapse all child cells under the parent cell, leaving only the parent cell visible. This makes it easy to move the parent cell around (and with it, all not-visible child cells) until you want to expand the parent cell again to view its child cells. 

To give an example, have a look at the following video (animated gif, also as Video on YouTube):


This function is extremely useful for dealing with lots of hierarchical information — which is the basis for every article or thesis. You can collapse information as needed to see only the big picture, compare, e.g., information in the introduction with the conclusion to ensure a consistent frame, put lots of statistical detail information in child cells and summaries in the parent cells to help you make sense of the data, and much more. 

There are a lot of different outliner programs. Personally I use Circus Ponies Notebook, which — unfortunately — is only available for the Mac (and iPad). But the Wikipedia entry has a list of outliners, including ones for Windows and Linux. In selecting an outliner, make sure you can export the data and that it is stable even when containing a lot of information. 

For an example of a good outliner, let’s look at Circus Ponies Notebook and why it works well for creating content outlines.

Outliner Example: Circus Ponies Notebook

Circus Ponies Notebook is an app for Mac OS X and the iPad (see figure below). I strongly recommend using the Mac version and not the iPad version. The Mac version is snappy and a joy to use. The iPad version is nice when you want to have your outline available, but a bit sluggish for actual work.

cpn4 As the name suggests, Circus Ponies Notebook (CPN) uses a notebook metaphor. The concept of a notebook is intuitively familiar and provides multiple ways to structure information. You can use different notebooks for different topics, and use dividers and different pages within a notebook. On each page you can write your information in outlines. 

For an article, using a single page to collect and sort all the information is probably best. For a thesis, at least in the beginning it can be helpful to use multiple pages (one for each major section, and perhaps other pages to plan studies and analyses). 

To facilitate work, CPN provides a lot of useful functionality.

  • Cells: Cells, the Lego(TM) bricks of your writing, can be assigned with priorities, stickies, keywords (= tags), and much more. They can easily be rearranged by clicking on the gray circle on the left of the cell (triangle if it’s a parent cell containing child cells) and dragging and dropping them.
  • Cell content: Cells can handle almost any data. You can directly write text in a cell — and you will likely do this a lot. Using text allows you to easily search for it. But you can also add files like Word or Pages documents, Excel files, PowerPoint presentations, videos, sound files, images, scripts, data files, etc. pp. If CPN recognizes the file, it shows, e.g. the image itself or the first page of a PDF file. If CPN does not recognize the file, it still imports it and shows you an icon of the file. Double click it and it opens in the respective application. I would not use CPN as document storage, but inserting the necessary images, statistical analyses, etc. and being able to easily move them around? Highly useful.
  • Different copy and paste options: You can paste text with and without formatting. You can also paste text as outline. Any paragraph break will start a new outliner cell. Note that if you copy and paste cells, depending on the copy and paste method you chose, keywords you have assigned to a cell will either be preserved or lost! Check the “Edit”, “Copy” and “Paste” options.
  • Navigation: There’s a content tab on the left, a Forward/Back Button similar to a browser in the toolbar, tabs can be assigned to dividers or pages, stickies (the red one in the picture) can used as bookmarks for pages or specific cells, and much more.
  • Multidex: CPN automatically creates an index of all used words, capitalized words, Numbers, Symbols, Internet Addresses, Highlighting, Keywords (= tags assigned to cells), stickers, attachments (= files, incl. images, added to the notebook), and more. Highly useful if you search for something.
  • Export as rtfd, Word, etc.: Given that CPN is not that widely used, you might need to get your outline in a different format if you want to share it. You can export the outline as webpage, rtfd, doc, and much more. Look at the export options, esp. the “Expand all Items before exporting” option. CPN can export what is current visible in your outline (e.g., collapsed cells will not be exported/printed), or expand all before exporting. Both have their uses, be sure you get what you want.

Looking at these features in context of content outlines, you can see why this program is so incredibly useful:

  • Cell hierarchy to deal with the content information: As written above, you can indent cells to order the information hierarchically and expand/collapse as needed.
  • Pasting Text as Outline to quickly import and reorder information: If you want to restructure a document, simply copy and paste it as outline. If you want to remove the formatting, copy and paste with match style first, then cut everything and paste it again as outline (on the page, not in a cell). Given that paragraph starts a new cell, you have the text neatly separated in cells by paragraph. This separation allows you to reorder the paragraphs quickly, create parent cells with summaries of the paragraph’s content, etc. You can split a cell into two by pressing ctr + RETURN. The cell is split at the cursor position. Very useful to split imported text into smaller units.
  • Keywords for source information: As you can assign keywords to cells, it’s very useful to use keywords for the source information. For example, if you use authorname_year (or authorname_authorname_year, etc.) to name and refer to your literature, you can use this as a tag. Want to know where the information in the cell is from? Display the keywords (cmd + k) and the information is there. Note that:
    • Length of source names: Using a short reference like authorname_year does not waste much screen space (you can manually change the width of the keyword margin). Use a, b, c, etc. for multiple works by the same author(s) in the same year.
    • Assigning Keywords/Tags: To assign keywords, write the author information, highlight it, and right-click on the highlighted text and chose “Assign as Keyword”. You can then click on any cell (gray circle/triangle) in the notebook to highlight the whole cell and right-click on the cell to select “Keywords”, “Add” and select the keyword. Even better, you can select multiple cells to assign the selected keyword to all these cells. If you enter a lot of information from the same source, it can help to create a new page, enter the information there, then select all cells and assign the keyword in one go.
    • Keywords for own notes: If you want to use keywords for your own notes as well (to ensure that you remember that these are your thoughts), consider using something like “0 your_name”. The keywords are sorted alphabetically and given that you probably assign this keyword a lot, it saves lots of scrolling. Personally, I do not tag my own thoughts — any cell without keyword (or source information in the text itself) is hopefully(?!) by me.
    • Keywords can vanish when using copy & paste: However, be careful when you copy and paste cells. Depending on the copy & paste option (CPN has several), keywords are either preserved or get removed. Check after pasting that the keyword is still there.
    • Keywords and Multidex: If you want to know where you have used which source, have a look at the Multidex. The keywords have a page there. Essentially an outliner page that lets you display this information as child cells of the used keywords.
  • Text formatting (when needed): You can easily change the font (notebook wide default with the Inspector, in the cell with cmd + t). However, best use one font only. Formatting should signal which information is important, not look “nice“. Bold, italics and text colors (via cmd + shift + c) can be helpful. Personally, I use orange as color for general reminders which information must be in which section and what must be clear to the reader after reading the section. I use red for personal notes to make it stand out within a lot of cited text.
  • Highlighted cells (to indicate their indent level): Given that you can indent the cells quickly and easily, it’s sometimes difficult to see which cells belong to which parent cells, or to see the indent level on which the cell is. Personally, I use cell highlighting for the highest levels. For example, in an article, cells with the structure information (Introduction, Methods, Results, Discussion) would be highlighted green (next indent levels would be blue, yellow, orange, red, purple — it’s the way I sorted my crayons as a child and the sequence makes sense to me). Using cell highlighting can provide useful visual information about the structure.
  • flexible_checkingCheckboxes during writing: You can easily assign checkboxes to the cells (select all, right-click on the cell, “Add a Status Checkbox”). These checkboxes are invaluable when writing. Mark which information you have used immediately after you have used it. If you are interrupted or stop for a while, you can quickly pick up where you left. Note that there is a setting in the CPN Preferences (cmd + ,) under the “Action Items” tab: “Change an item’s status to “completed” when all of its children are completed” I recommend deactivating this option. It allows you to tick off the checkboxes independent of the hierarchical structure the cells are in (see figure on the right). Otherwise, checking a parent cell will check all child cells, and when you checking the last child cell, the parent cell will be ticked off as well.


Caveats when using Circus Ponies Notebook

If you use CPN, there are (at least) two caveats you should know about.

  1. Keep old versions of backups: Doing Backups — early, often, saved on another medium, and stored in a safe location — is good advice in any case. With CPN, make sure to keep the old backups. CPN only loads the page you want to display, so if there ever is an error in saving the file, you might not immediately notice it, but only when you open that page. In case you cannot open a page anymore, you can then go back to prior versions (don’t use Mac’s Time Machine for it, if the disk is full, old backups will be overwritten).
  2. Careful with the search and replace function: The search and replace function (cmd + f) does not show you the settings unless you click on the magnifying glass. As search and replace uses or does not use case, and can relate to the page or the whole notebook, have a look at the search settings before you search and replace. Otherwise, you might affect more (or less) than you want. BTW, be especially careful when you import text and want to replace hyphenation by using search and replace. If the text contains numbers with negative values, the search and replace might replace the minus sign too. And in contrast to words with missing hyphenation this is much harder to spot while the consequences are much, much worse.

Final Recommendation

This was a short introduction to content outlines. Two final words of advice. 

First, tools do not work for everyone and tools are not a silver bullet. I (and others) find content outlines very useful, but they will not work for everyone and for every task. Also, CPN, no matter how powerful it is as an outliner, will not work for everyone. Try out whether it works for you, there’s a free 30 day trial version available. If it does not work for you, look for a different solution. And keep in mind that even the best tools cannot replace effort and persistence, they can only help you to to augment it. 

Second, if it works for you, consider using content outlines as long-term storage for your notes, not only for writing one particular text. Just imagine notebooks dealing with different subtopics, each containing pages with outlines of notes about the domain you work in. And all the cells include the source information as part of the outline cells — which are preserved when you copy these cells into an outline for another paper. You essentially have a box of sorted Lego(TM) bricks to work with. With the hierarchical structure of these outlines containing groupings of information units, you even have prefabricated parts which you can copy and paste into a new outline for a new text. In contrast to copying from a finished text, you only copy the bones, allowing you to add new flesh to it and thus avoiding verbatim self-plagiarism. Creating these Topic Notebooks can be extremely useful for long term work with a topic. 

In this text, I did not go into the details of how a text must be structured, as this depends on the particular discipline. It should work for any discipline which requires a written text, i.e. all. But if you want to know how the actual text must look like, ask your supervisor for an exceptionally well-written work. It might be hard to abstract from it, but it might give you an idea about the characteristic style that is required. If you want to have a short look at an actual content outline, you can see the first few hundred cells of my dissertation thesis outline on YouTube

I hope using a content outline can help you putting the complex information, which is the basis of your text, into a coherent structure. Without being overwhelmed by it. 

If you have questions, suggestions, and/or ideas, I’d like to hear them. Drop me a line. You can also contact me on my blog at

Sente for PDF Management on the Mac and iPad (1): Capturing and Organizing PDFs

This post will focus on the business of capturing, categorizing, and organizing your PDFs in a coherent library using Sente for Mac.

Sente Loading Screen

If you followed my last post, PDF Chaos? Digital Workflow Basics, I discussed the chaos that can ensue without establishing a coherent filing system for PDF documents–and illustrated it with a chaotic demo library. I then walked through some “do’s and dont’s” of filenaming, splitting, and OCRing PDFs in a library staging inbox. Here we will start to  transform this disorganized library, and you will see how you can simplify and organize your PDF Chaos while also exploring how Sente can help you with the rest of your Academic Workflow.

So for the first post (of several) on Sente, I will focus chiefly on setting up libraries and introducing Sente’s key features. I assume you will have read my first post, Introducing Digital Workflows for Academic Research, and latest post where I give some basic principles for workflows with PDFs.

 Subsequent posts will explore:

  1. Annotation and notetaking on PDFs, including tagging, and also annotating with your iPad on the go.
  2. Sente’s automated research and document collecting capabilities; smart collections; bibliographic formatting; and other selected advanced functions.
  3. How to make use of Sente Assistant and some amazing free Apple Scripts to integrate the power of OPML into your workflow so that you can move your Sente annotations into Devonthink Pro Office, Scrivener, and other software, for writing.

But, why Sente?

Some people will argue that it is not worth paying for Sente when there is other software like Mendeley, for example, which does similar things for free. This is a complex issue,  which is not as simple as free or unfree–and similar can hide substantial difference. Since it cannot be discussed appropriately here, I will post a separate, companion piece on this issue, as it also offers the opportunity to discuss some key considerations about privacy and academic work, the pros and cons of paid versus unpaid software, and a more holistic view of the various trade-offs–including functionalities like social networking–that users should consider in selecting the core application component of their Digital Workflow among software like Sente, Papers, Mendeley, Zotero, and others.

For now, let’s just say it’s my opinion that Sente really shines over software like Zotero, for example, which does not offer an integrated cloud-based synchronization system for large PDF libraries and bibliographies along with a professional solution for serious annotation and idea collection during the review and thinking phase of your research. Again, with Devonthink, OPML scripts, and Sente Assistant, I’ll show you how you can use, search, tag, organize and analyze your collected quotes and comments from reading your PDFs, and even how to drop them into outlining software and use them as fungible material for your writing and production phase of work, but Sente itself is amazing as a one stop-shop tool. Sente’s versatility is what makes it so effective for maintaining control in the research process, leaving you ready to mold and create the research product you want, and is why I have chosen it as my staple workflow application.

In fact, according to President of Third Street Software, Inc. and Sente creator, Michael Cinkosky–with whom I’ve had the pleasure of discussing Sente and his long term goals for its development in some detail in preparing this and future posts–the name “Sente” derives from Japanese:

the name “Sente” is a Japanese term from the ancient game of Go. A player is said to have sente when they are controlling the direction of the game through the force of their moves. The other player is said to have gote (go-tay) because they have little choice but to respond passively to the player with sente. My goal with Sente was to help people feel more in control of their literature research and less like they were simply struggling to keep up.

As he elaborates, this vision of control drove the development of the software’s various features to where it is today:

My primary goal when I launched this company was to make it easier for people involved in research to acquire, organize and keep abreast of the literature most relevant to their research. I had already spent many years building software systems in support of scientific research (mostly biology) but I regularly heard complaints from users about how hard it was for them to stay current with the literature. All of the reference managers at the time were focused on formatting bibliographies, not on facilitating literature discovery and organization. I asked people what tools they were using to stay current with the literature, but they never had any. Programs like EndNote were (accurately, I think) seen as formatting tools, but not research tools.

So that is the main problem we have been focused on. For the first couple of years, we did not even do bibliography formatting, but people obviously want their reference manager to format bibliographies, so we eventually added this capability. But our primary focus was, and remains, on search, acquisition, organization, understanding, etc. Thus, we have devoted significant effort to features like: hierarchical tagging (what we call QuickTags); the ability to automatically capture quotations when highlighting text in a PDF; and transparent sync that lets you have your library up-to-date at all times, across all your Macs and iPads (and, soon, iPhones). We understand that people involved in academic research never really stop thinking about their research and they want to know they are not missing anything important in their field, and that once they find something, they don’t want to lose it. Our vision for Sente is that it be integral to the day-to-day activities of becoming, and remaining, an expert in each user’s chosen area of study.

I also asked Michael about how he sees Sente in relation to “free” tools like Mendeley, especially with regards to privacy and monetization, and he was kind enough to give me some details of his vision for the future of Sente. As I already said, I will discuss these issues in a later post.

Download Sente

Now, if you’re new to Sente, head on over to Third Street Software and download it, if not you might already know the basics covered here. The free license allows you a limited library, but the $59.99 academic license is completely worth it, giving you unlimited libraries and as much cloud synchronization space you need. If you’re not convinced, use the free version until you are.

Considerations before we begin

Sente is a powerful piece of software that includes many functions. The next few posts are merely designed to demonstrate what you can do with it in some elementary ways, but I insist that–as with anything else worthwhile–if you like what you see in trying it here, you will need to eventually spend some time reading the Sente manual, especially in regards to its more complex cite and scan features, the use and modification of citation styles, the integration of Sente with Microsoft Word, Scrivener, and Mellel, setting up autolinks etc. I realize that many people might balk at this initially because learning new software can often interfere with our work and involves an investment of precious time. But the truth is that Sente is such an amazing program because it combines several functions and processes that used to belong to multiple applications, streamlines them, and as such is worth spending some time (beyond reading these posts) to learn to use properly if you like what you see.

Capture and Organization

Sente’s first amazing feature is its easy interface for capturing PDFs and organizing them, which I focus on in this post, leaving aside its research collection functionalities for later.

Before we start bringing in our PDFs, let’s set it up. I argued previously that it is really important to have a consistent system of filing. David Allen reccomends an A-Z file, and I agree. Basically, I think every Sente library (which can be set up as a local or synced library) should be set-up with the Chicago Author-Date (or APA) system in mind–and I mean this conceptually: Sente will allow you to format your actual citations and bibliography in all of the standard styles, and thousands of others. All I mean is that we will set up the library so that when you add a PDF to Sente, it will be re-named, added to the library bundle, deleted in its previous location, and given a new name based on its Author-Date-Title.

Here is a demo library, DigitalWorkflows, I’ve made for this series.

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For now, I will let the user explore the greater interface. Let’s go immediately to “Library Setup,” and “Attachment Handling.”

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“Attachment Handling” is where you set up your library. “Attachment” handling because Sente is going to allow you to create a reference in your library and attach the document to that reference.

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While there is a separate panel of Sente Preferences, the library settings are mainly here. I reccommend the following settings (as pictured above)–but the good thing is that no matter what you choose for your file names and filing system, even if you have a thousand items and attachments, Sente will automatically re-name and re-file everything for you to fit your needs and whim, even if you change your mind later.

As I indicated, I model mine on the Chicago Manual of Style Author-Date model, which is very similar to APA bibliographic model, and in any case, makes perfect rational sense:  a folder for every Author (Last Name, fore name),  a folder for the Year/Date of works, and a folder for individual Titles (which is a good policy, especially if an author has more than one book or article published in the same year).

With Sente, when the file gets added to a library with this setup, the PDF is automatically renamed too. When we press apply, as the Sente box here shows, the software will now set up this structure for your library, and henceforth automatically move the files to the bundle, rename them, and delete the old files. Again, I advise selecting “file/renaming” instead of making a copy, because it makes little sense to have multiple versions of PDF files loose on your system outside of the library–unless under special circumstances.

Go ahead, press apply. Once you hit apply, you will receive a notification explaining your choice:

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Now, you may be wondering what “inside the library bundle” means. Where will Sente put my stuff? Sente stores files inside a closed library as a Sente library file, aka “bundle” (with a “.sente6lib” file extension), but don’t worry, that doesn’t mean you can’t access it. In fact, it just means that it keeps things filed for you automatically. The bundle is like a package containing all the references, attachments, and other information that comprises your entire library. Thus each library file is a bundle in this set up, and while you can set up libraries without bundles, this is not recommended, because it presents a hazard for breaking libraries and opens the door to losing data and inconsistencies. I make a master library for all my documents, and make new libraries including those and other files–or merely import Zotero or Endnote bibliographies as libraries–for different projects or with specific products in mind.

I want to show what things actually look like in your library bundle, so that you understand the rationality of the organizing principle Sente operates on, and so that you see concretely what the above pictured configuration looks like under the hood.

Library Bundle

To access the library bundle, navigate to the folder in which you keep the Sente library file (.sente6lib file), and right clicking “show package contents.” Here is what my “DigitalWorkflows.sente6lib” bundle looks lke. What we see is our author date framework, later we will index this structure to our Macintosh finder and spotlight, and DevonThink, but now just note that while Sente gives you a beautiful interface to experience your files and use them, it is also ordering them and keeping them safe as data not proprietarily locked in its system.

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So, now that we have our library set up, have made the settings to our liking, and understand the concept behind the library bundle, let’s add our PDFs.

Adding PDFs to Sente Libraries from your PDF inbox

So remembering our messy PDF inbox, let’s one by one add the files.  Remember the article I mentioned in the last post? Namely, 724707_1.pdf? Screen-Shot-2014-04-08-at-3.26.19-PM

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To add this file, simply drag it from the folder into the Library.  Sente will then then open up a “citation lookup” box.

Citation Lookup

Now since we OCRed the PDF before, everything in it is searchable, highlightable. This makes that essential part of the workflow worthwhile. Sente goes the rest of the way: simply highlight the title of the article, and right click (which we Mac users means control click). You now get a choice of citation look up.

Sente gives you two options, one is to automatically search for the selected text on Google Scholar, Google Books, Library of Congress, or WorldCat; the second option will allow you to copy the text and will then automatically open a search box in the selected catalog or database and let you manually paste it to search for it there.  I choose Google scholar for now:

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Once I highlight the title, control click it, and select “Google Scholar,” Sente now opens its targeted citation lookup mode. Voilà, here’s our reference!

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Screen Shot 2014-04-16 at 1.21.19 PMOn the right hand side, we see a reference box with targets. Upon clicking the target that matches, Sente pulls up the reference editor, which will allow us to edit the reference before adding it to the Library.

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An aside on precise and imprecise metadata 

Now, people should understand here that Sente merely gives you access to a wide variety of options for importing “metadata” about your document. I’ve found in my experience that Google metadata tends to be inconsistent and sometimes prone to errors in precision, because it seems that they build the metadata (I assume) often by scanning title and catalog pages, and having an algorithm make somewhat accurate guesses based on large pools of data about which pieces of information, that is–type of publication, author name, editor name, press, etc.– belong to the appropriate fields. Though it is almost always better to select Worldcat (OCLC) or an official academic library catalog for importing metadata, since Google is so pervasive I wanted to show that while it does work, it exemplifies some pitfalls that you should always look out for when adding metadata period.

Thou shalt always make sure your metadata is accurate the first time, and save hours and embarrassment later

Just as I have put so much emphasis on coherent filing, so too, we must put emphasis on precise metadata–not least because with every file you add, correct metadata will ensure you can actually simply just find things in your library. Depending on the database you import your information from, you will sometimes not populate your fields completely accurately. If you do not check to make sure that it looks good the first time, and that the data is correct, you will have to spend hours later correcting it all when you go to make your official bibliography, and use the cite and scan functions. In the worst case scenario, your bibliography will have embarrassing errors later if you have to use it but don’t have time to fix it when you do notice.

In other words, we still will need (and this is often the case, because full automation is somewhat of an absurd idea), to exercise rational intelligence in populating the fields. Sente does populate the fields correctly in so far as the data input to begin with in the originating database is correct.

As a general rule, Worldcat and academic libraries, like Stanford and University of Wisconsin work quite well within Sente. You can also target from Columbia’s CLIO, which I’ll show in a later post. The point is that since you want to treat this like your real, legitimate library–because it is as real and legitimate as a paper library–you want the information to match up as much as possible the first time.

Checking your entry

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Screen Shot 2014-04-16 at 1.24.22 PMLook at this example, does anything look off? First of all, in the original import of metadata, it says “conference proceedings.” In many ways, conference proceedings will function like journal articles, but I prefer in this case, based on the information available to me, to classify this as a journal article. Always check and make sure it’s the correct sort of publication, sometimes it is not, or will require you to decide long term if you care about making the difference between the books and conference proceedings category, or the difference between certain proceedings and stand-alone articles which proceed from said conference proceedings. My advice is merely to be consistent. Moreover, note that Google scholar has populated “7247, 724707” in the pages field. This is clearly not the pages, but is the volume data information for this database publication! (If you click “add new reference” in a hurry, you just added something you’ll need to correct later, or will inconveniently discover as an error). We now discover the origins and rationale of 724707_1.pdf as a file name.

Here I not only correct the data, but take the opportunity to add the DOI (digital object identifier), and also check to make sure there is nothing out of place. If the item is an edited volume with one or more editors qua authors (i.e. the volume’s editor is the primary citable contributor) , you can change the names to “editor” by clicking the drop down box, and then click the editor category, selecting “make editor primary contributor role.”

In the “preview” window, which I have set up to preview the citation according to my custom Chicago 16 Author Date bibliographic format rules–a slightly modified Chicago 15 AD–we see what the citation would look like in a bibliography. Once I fix things and click the edit button again, the updated citation will appear in the preview. Everything seems in place. Once we click “add reference,” we now see our document added to our library, and the PDF is readable in the reading window. If you use Sente on a synchronized iPad, this will automatically synchronize.

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Stay tuned on the next post on Sente, and in the meantime get started with your new library!

Database Trial: Numerique Premium


We are currently trialing a new database of French e-books, Numérique Premium, through April 12, 2014. The collection contains nearly 850 full-text titles in a variety of fields, including history, religion, philosophy, politics, literature/literary theory, film, and architecture. Publishers include:  Belles Lettres, Canadian Scholars Press, CNRS éditions, ENS éditions, Gallimard,Flammarion, Nouveau Monde, Picard, Presses universitaires de McGill, Association française pour la recherche en histoire du cinéma, Association des Professeurs d’Histoire-Géographie, Société des études robespierristes, Fondation Napoléon, Fondation Charles de Gaulle, Institut Napoléon…

This resource is currently only available on-campus until April 12, 2014. Please send any comments or questions to Meredith Levin, Western European Humanities Librarian, at

Bonne Lecture!!!

PHI Latin Texts–now online

Cicero palimpsest, 5th century For years, the best collection of searchable texts from Latin antiquity was the Packard Humanities Institute PHI CD-ROM #5.3, available in the Digital Humanities Center in 305 Butler.  Getting these texts available online was the Holy Grail of digital classics research.

But now the Grail is at hand, as the Latin texts from PHI 3.5 are now online.  Approximately 350 authors, representing almost all classical literary texts up to 200 CE (with a handful of later authors) are now readable and searchable online.

Bookmark this URL for easy access:
or do a TITLE search in CLIO for Classical Latin Texts.
For further information, please contact:
Karen Green
Ancient & Medieval History and Religion Librarian
Karen Green

Medieval Studies: Finding Secondary Sources Online

There are several resources online for identifying secondary literature: articles, books, dissertations, etc.  It is prudent to take advantage of all of these resources for a given topic, rather than relying on a single resource to provide all possible results.
Chained library, Hereford Cathedral
International Medieval Bibliography Online
Bibliography de Civilisation Médiévale
The International Medieval Bibliography (IMB) and the Bibliography de Civilisation Médiévale (BCM) index articles and monographs, respectively.  They are cross-searchable from a single interface.  The IMB covers all aspects of medieval studies within the date range of 400 to 1500 for the entire continent of Europe,  and for the Christian Middle East and North Africa, indexing articles beginning in 1967.  The BCM indexes monographs in the same areas, beginning in 1957.
Iter: Gateway to the Middle Ages and Renaissance
The Iter Bibliography indexes a wide range of journals and essay collections in all scholarly disciplines for the period 400 to 1700.  The main page of the Iter Gateway offers a wide variety of bibliographical tools and e-books of interest to those studying the late medieval and early modern periods.
Feminae: Medieval Women and Gender Index
A free resource that indexes journal articles, book reviews, and essay collections on the topic of women, gender, and sexuality for Europe and the Christian Middle East and North Africa in the years from 450 to 1500.
JSTOR provides full-text PDFs of over 1000 journals in over 60 disciplines.  Coverage of each title begins with volume 1 and continues to a rolling wall of approximately five years ago.  As a result, JSTOR is not a good resource for current scholarship.  Searching in JSTOR is best suited for very specific events, places, or people.
ProQuest Digital Dissertations
The bibliographies of dissertations are extremely useful.  This database allows searching of titles and abstracts for nearly every American dissertation since 1861.  Dissertations deposited since 1995 may well be available in PDF format.  Foreign dissertations may be requested via Interlibrary Loan from the Center for Research Libraries.

 For more information on any of these resources, on supplementing these with print resources, or on research in medieval studies generally, please contact:

Karen Green
Karen Green
Ancient & Medieval History and Religion Librarian


Medieval Studies: Finding Primary Sources Online

Augustine, De civitate Dei, S. XV; Columbia RBML Plimpton ms 47, f. 20vThe Libraries subscribe to a wide number of resources that provide access to Latin texts of the Middle Ages.  Here are some you might find useful (this is a selection, not a comprehensive list).
You can bookmark the URLs below for use from any location: 

Patrologia Latina: the full-text database
An electronic edition of the 200+ volumes of Migne’s Patrologia Latina, containing writings of the Fathers of the Church and other churchmen.  Authors range from Tertullian (†220) to Pope Innocent III (†1216).  In Latin.

Library of Latin Texts
Beginning with the authors contained in the Corpus Christianorum (both Series Latina and Continuatio Medievalis), and expanded to include those of Roman antiquity as well as the post-medieval Church, the LLT contains texts from the beginning of Latin literature (Livius Andronicus, 240 BC) through to the Second Vatican Council (1962-1965).  In Latin.

Acta Sanctoruma: the full-text database
The catalogue of Christian saints, from the first martyr through the counter-Reformation, with texts presented in chronological order by feast day.  In Latin.

Monumenta Germaniae Historica (MGH)
A selection of texts tracing the history of Germany from its Frankish beginnings through the late middle ages, from the MGH’s five divisions: Scriptores, Leges, Diplomata, Epistolae, and Antiquitates.  In Latin. 

The full electronic MGH, without an English-language interface, may be found here.

Medieval Travel Writing
A collection of medieval manuscripts dating from the 13th to the 16th centuries, featuring accounts of journeys to the Holy Land, India and China.  In Latin, French, German, Italian, and Spanish, with supporting materials in English.

Medieval Family Life
Full-color images of the original medieval manuscripts that comprise these letter collections of the Paston, Cely, Plumpton, Stonor, and Armbrugh families, along with full-text searchable transcripts from printed editions.  In 15th-century English, with supporting materials in modern English.

Medieval and Early Modern Sources Online
Digitized editions of texts concerning economic, political, legal, and ecclesiastical history (e.g. treasury accounts, chronicles, papal registers). Most are from England, Ireland, and Scotland.  Primarily in Latin.

For information on additional full-text resources, assistance in navigating these databases, or general reference assistance, please contact:

Karen Green
Karen Green
Ancient & Medieval History and Religion Librarian

HathiTrust: A Shared Digital Repository

HathiTrustColumbia is a member of the HathiTrust Digital Library, a vast repository of nearly 9 million volumes, 2.5 million of which are full-text searchable.  Though international in scope, The HathiTrust collection is especially useful for magazines & journals published before 1924, US government documents, and multi-volume works.

Login for the most complete search options, which include:

  • ability to search standard catalog records or across the full-text of the collection
  • single (?) and multiple letter truncation (*)
  • simple Boolean searching
  • keyword in context (full-text only) displays in the ascii text (though not in the PDFs)
  • ability to create private (or public) collections and search only within that content
  • ability to search public collections created by others

The interface offers a variety of views: page, scroll, flip, thumbnails, ascii text; and supports PDFs downloads of selected pages or the entire document.

Here are a just a few HathiTrust journals that are indexed in the Readers Guide Retrospective, but not currently available online from other sources: The Survey, The Delineator, Ladies Home Journal, Forum, The Independent, Good Housekeeping.

Due to the complexity of serials cataloging, there are sometimes multiple records in the HathiTrust catalog for the same journal.  CLIO also includes links to HathiTrust content, either as separate records, or as links in the sidebar in catalog records for paper subscriptions.  If you don’t find the years you are looking for in CLIO, be sure to search the HathiTrust collection separately.  Because they are based on deposited collections, some of these journal runs are currently incomplete, but as the HathiTrust collection grows, these gaps should be filled. 

Image from Frank Leslie's Ladies Magazine

In May 2011, The HathiTrust Research Center was formed to support "computational access for nonprofit and educational users to published works in the public domain stored within HathiTrust." 

If you any have questions about accessing, searching, or downloading material in the HathiTrust Digital Library, or in any other collection, please let us know.



Columbia has recently acquired the online version of Germanistik

This index lists books, essays, and articles published from 1960 to the present on German language and literature, including theater, media, and cultural history.  The entries for the first ten years have fairly basic search terms ("Shakespeare and English drama in German popular journals, 171701759, for example is only listed under the author and Shakespeare), but beginning in 1979, more detailed keywords (in German only) are provided.  This is much more complete for German material than the MLA, though of course, the MLA has older material.

The instructions are available in both English and German, and the searching is fairly straight forward, though there isn’t a lot of information provided about the search terms; "Type of publication" is one option, but there doesn’t seem to be a list of the types the reader can search.  The only one I have found that works is "Buch" (there is nothing for "Artikel", and no articles I found had a type listed), and that only works for recent publications–the oldest book I found about Goethe searching for "Buch" was published in 1996.  So it seems that the best way to search is the simplist–author (called Name), and title.  Keyword only searches what we would recognize as subject headings.

Unfortunately, the source doesn’t have elinks, so the reader will have to look the journal up in CLIO.  These journals are often abbreviated, but putting the cursor over the abbreviated title will show the complete title and citation. 

Google Books adds EPUB Downloading Format


Youth Many books published before 1925 can now be downloaded from Google Books in the EPUB format, an excellent format for reading on iPhones, iPod Touches, iPads, and other mobile devices.

Here are some of our favorite EPUB readers:

  • iPhone, iPod Touch, or iPad: Stanza  (free from the app store)
  • Android Phones:  Aldiko
  • Blackberry: BePub
  • PDAs and other mobile devices Mobipocket

Wikipedia has useful list of EPUB readers.   Do you have a favorite?  Please comment with your favorite reader.

Google Books - Youth


Search Google Books from your mobile device, and click the EPUB download option. 

If you are searching Google Books from a desktop, save the link to the book and email it to yourself.  When you click on the link, Stanza and other readers will save and open the text.