Tag Archives: software systems

How to retrieve ancient text data from Perseus

10 Wednesday Apr 2013

Posted by in Classics resources, Digital Classics, Greek Classics, Latin Classics, Software & Tools

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In my last post I was describing problems with the URL schema not being entirely predictable, and therefore computable from body of text to body of text (e.g. from Livy to Caesar). That is the way the URLs are formed, what constitutes a ‘body of text’, and what you might expect to see returned in a request and how that varies with each textual work.

Update: Schema will now include a ‘urn’ attribute

Warning: this is a long and somewhat technical post about using the Perseus CTS API to fetch classical texts as XML data

This stuff is important for software developers and “digital classicists” (that is, classicists who work with computer-information systems for analysing information about the classical world).

On the Digital Classics mailing list, some helpful hints managed to emerge to my queries. The first is, the Perseus XML interface I was using (it’s the one that’s behind the helpful “XML” button at the bottom of each passage in the HTML version that you typically use with your web browser) is probably on its last legs.

CTS Overview

The more up-to-date (but still in beta) version is Perseus CTS; where “CTS” stands for Canonical Text Services. CTS is built on work done by the Homer Multitext Project.

CTS appears to have three main functional components:

  • A catalogue service (actually called “getCapabilities”)
  • A reference validation and exploration service
  • A service that retrieves text

Some commentary on its limitations

What it is missing, is a search service. The catalogue is huge. It has listed in it every available Greek and Roman text in the Perseus database and includes details of all editions and translation of each text. It’s available here http://www.perseus.tufts.edu/hopper/CTS?request=GetCapabilities and I’m not actually linking that URL because don’t click on it just yet. It’s 2.1 MB of XML. Your browser may not like especially like it. Mine only manages to load it properly half the time.

When you do manage to download it and save it on your local disk (highly recommended), you’ll see it’s a pretty comprehensive catalogue of the data. Unordered. With no links to the texts in either the reference validation or text retrieval services, and nothing obvious as a field that gives you the unique identifier needed.

What the references are constructed from

The reference validation service assumes you know the reference you want to validate (and discover the sub-components of). But you need that first-level peek into the initial reference. Perseus uses Thesaurus Linguae Graecae referencing system for Greek texts, and the Packard Humanities Institute PHI Latin Texts system for Latin texts. These both principally organise their respective corpora around authors, assigning each their own index number. Thus, Homer is ‘tlg0012′ and Livy ‘phi0914′.

The references are formatted into a type of reference called a URN.

How to create the references

Now I’m going to tell you how to construct a functional reference ID for the CTS system.

First thing, load the catalogue URL into your browser. I’m not going to link it but cut and paste this one into your browser: http://www.perseus.tufts.edu/hopper/CTS?request=GetCapabilities – if you know how to use Wget or Curl use that instead.

Save the file to a convenient location on your disk. I called mine “CTS.xml”.

Open the file in a text editor. Notepad won’t cut it. Word most certainly will not (it’s not even a text editor!). One the Mac, I recommend BBEdit. [Update: it's been pointed out on the mailing list that Oxygen XML editor is an ideal tool. I use this tool at work and have it on my Mac at home. An Academic licence is $99, a full one nearly $500. Unless you do extensive work in XML I would not recommend to buy it. Probably on Windows by default Internet Explorer is the default program for an XML file. It, or Safari on the Mac, will suffice to read the document. Google's Chrome also works pretty well. Browsers will also "pretty print" the XML to make it easier to view.]

Use your editor’s search capability to find the author you want.

The ‘textgroup’ (normally the author) identifies the first level

You’ll find that the author’s work is contained in an XML element called “textgroup”. Here’s the text group for Livy, along with the groupname element identifying it:

<textgroup projid="latinLit:phi0914">
  <groupname xml:lang="en">Titus Livius (Livy)</groupname>
  ... (thousands of lines omitted)
</textgroup>

Pay careful attention to the ‘projid’ attribute of the textgroup. This helps form the root of the URN used to identify the text in Perseus. The URN always starts with ‘urn:cts:’. Add the projid to that, like this:

urn:cts:latinLit:phi0914

Check it in the reference validation service

That’s all texts/editions/translations by/of Livy in the Perseus database. Here’s a link to the reference validation service: http://www.perseus.tufts.edu/hopper/CTS?request=GetValidReff&urn=urn:cts:latinLit:phi0914. If you open that link, you’ll see, in XML, a list of all the available URNs for every version and edition and translation of Livy in the database. But unfortunately, no descriptive information what each version edition or translation is!

We still need the catalogue file. Go back to the catalogue file.

The ‘work’ identifies the next level of reference

Search for a book. In my case, let’s look for “Book 1″ of Livy. You’ll see the catalogue file is unordered. The version I looked at, Livy books started at Book 11 (what? The one of the missing books is miraculously in the Perseus database I hear you say? Unfortunately, it’s just the periocha of book 11). The unordered nature of the database make it especially annoying: you have to search, and you can’t browse.

Anyway the entry for Book 1 looks something like this:

<textgroup projid="latinLit:phi0914">
  <groupname xml:lang="en">Titus Livius (Livy)</groupname>
  <!-- ... (thousands of lines omitted) -->
  <work projid="latinLit:phi0011" xml:lang="lat">
    <title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">
    The History of Rome, Book 1</title>
 <!-- ... (thousands of lines omitted) -->
</work></textgroup>

See how the Book is contained in an XML element called “work”? Note the “projid” element of the work. In this case, we don’t need the “latinLit:” part, the interesting part of the id is the “phi0011″: that’s the ID for Book 1 of Livy. We add it to the URN we’ve been constructing as follows:

urn:cts:latinLit:phi0914.phi0011

The ‘edition’ and/or ‘translation’ identifies a specific version of the work

While that’s supposed to be valid reference to Livy’s book 1, Perseus contains at least two Latin editions of the text and three English translations. These are listed inside the “work” element in either “edition” or “translation” elements, like so (for brevity I have omitted some lines that give data about the citation system of the edition):

<work projid="latinLit:phi0011" xml:lang="lat">
  <title xmlns="http://purl.org/dc/elements/1.1/" xml:lang="en">
   The History of Rome, Book 1</title>
  <edition projid="latinLit:perseus-lat1">
    <label xml:lang="en">The History of Rome, Book 1</label>
    <description xmlns="" xml:lang="en">Titi Livi ab urbe condita libri 
     editionem priman curavit Guilelmus Weissenborn editio altera auam
     curavit Mauritius Mueller Pars I. Libri I-X. Editio Stereotypica.
     Titus Livius. W. Weissenborn. H. J. M&amp;#252;ller. Leipzig. 
     Teubner. 1898. 1.
    </description>
    <!-- some lines omitted -->         
  </edition>
  <translation projid="latinLit:perseus-eng1">
    <label xml:lang="en">The History of Rome, Book 1</label>
    <description xmlns="" xml:lang="en">Livy. Books I and II With An
     English Translation. Cambridge. Cambridge, Mass., Harvard 
     University Press; London, William Heinemann, Ltd. 1919.
    </description>
    <!-- some lines omitted -->         
  </translation>
  <edition projid="latinLit:perseus-lat2">
    <label xml:lang="en">The History of Rome, Book 1</label>
    <description xmlns="" xml:lang="en">Livy. Books I and II With An
     English Translation. Cambridge. Cambridge, Mass., Harvard 
     University Press; London, William Heinemann, Ltd. 1919.
    </description>
    <!-- some lines omitted -->         
  </edition>
  <edition projid="latinLit:perseus-lat3">
    <label xml:lang="en">The History of Rome, Book 1</label>
    <description xmlns="" xml:lang="en">Livy. Ab urbe condita. Robert
     Seymour Conway. Charles Flamstead Walters. Oxford. Oxford 
     University Press. 1914. 1.</description>
    <!-- some lines omitted -->         
    <memberof collection="Perseus:collection:Greco-Roman"></memberof>
  </edition>
  <translation projid="latinLit:perseus-eng2">
    <label xml:lang="en">The History of Rome, Book 1</label>
    <description xmlns="" xml:lang="en">Livy. History of Rome by Titus
     Livius, the first eight Books. literally translated, with notes 
     and illustrations, by. D. Spillan. York Street, Covent Garden,
     London. Henry G. Bohn. John Child and son, printers. 1857. 1.
    </description>
    <!-- some lines omitted -->         
  </translation>
  <translation projid="latinLit:perseus-eng3">
    <label xml:lang="en">The History of Rome, Book 1</label>
    <description xmlns="" xml:lang="en">Perseus:bib:oclc,2311635, Livy.
     History of Rome. English. Translation by. Rev. Canon Roberts. New
     York, New York. E. P. Dutton and Co. 1912. 1. Livy. History of 
     Rome. English Translation. Rev. Canon Roberts. New York, New York.
     E.P. Dutton and Co. 1912. 2.</description>
    <!-- some lines omitted -->         
  </translation>
</work>

Now, assuming we’re after the Teubner edition of the text (the first one), we can use that edition’s ‘projId’ attribute as before, and stripping the ‘latinLit’ from it and adding it to the URN we’ve been building up, we get:

urn:cts:latinLit:phi0914.phi0011.perseus-lat1

This is the complete reference to the Weissenborn & Mueller edition of Livy’s Book 1 published by Teubner.

Check it in the reference service

We can hit up the reference validation service with that URN as follows: http://www.perseus.tufts.edu/hopper/CTS?request=GetValidReff&urn=urn:cts:latinLit:phi0914.phi0011.perseus-lat1 – you will see a complete collection of URNs for the distinct parts of Book 1 in the Teubner edition of the text.

URNs for specific passages

This URN is all of the preface that’s found at the start of Book 1:

urn:cts:latinLit:phi0914.phi0011.perseus-lat1:pr

This URN is all of Chapter 1 of Book 1 (not including the preface):

urn:cts:latinLit:phi0914.phi0011.perseus-lat1:1

You can also get parts of chapters, here is 1.4.2:

urn:cts:latinLit:phi0914.phi0011.perseus-lat1:4.2

Fetch the text chunk you want

These arguments are passed to the ‘urn’ parameter of text retrieval service of Perseus like this: http://www.perseus.tufts.edu/hopper/CTS?request=GetPassage&urn=urn:cts:latinLit:phi0914.phi0011.perseus-lat1:pr (that’s the preface).

Anatomy of the URN format used by Perseus

    urn:cts:latinLit:phi0914.phi0011.perseus-lat1:4.2
    {1}:{2}:   {3}  :   {4} . {5}   .  {6}       :{7}
  • {1} It’s a urn. This part is fixed.
  • {2} The urn is part of the ‘cts’ namespace. This part is fixed.
  • {3} The Latin Literature namespace. Would be ‘greekLit’ for Greek texts, and possibly other values.
  • {4} The textgroup’s identifier. It’s normally either the TLG or PHI author index value. In the catalogue it’s contained in the ‘projid’ attribute of the ‘textgroup’ element, stripped of the namespace.
  • {5} The work’s identifier. This may map to an author’s title or to an individual book in a larger collection of texts. This also apparently comes from either TLG or PHI indices (I’ve not verified this fact for sure). In the catalogue it’s contained in the ‘projid’ attribute of the ‘work’ element, stripped of the namespace.
  • {6} The edition of the work. This may also be a translation. This is a Perseus-specific value. In the catalogue it’s contained in the ‘projid’ attribute of the ‘edition’ or ‘translation’ element, stripped of the namespace.
  • {7} The text reference. This will be specific to the work and edition you are referencing. You can find out a simple unadorned list of what’s available by querying the reference validation service with the URN up to this point at the argument.

Note how the textgroup, work and edition use dots for separators but otherwise the data element delimiter is a colon.

Commentary

There are still problems:

  • You cannot get all of book 1 in a single hit (at least for Livy).
  • If you want book 2, you have to repeat this process (it’s phi0012)
    • So, Chapter 1 of book 2 of the Teubner text looks like this URN: urn:cts:latinLit:phi0914.phi0012.perseus-lat1:1
    • Repeat and rinse for other books/editions
  • Entirely different authors and works may have different results or slightly different algorithms for building URNs.
  • The catalogue elements ‘textgroup’, ‘work’, ‘edition’ and ‘translation’ should each have a child element, ‘urn’, that builds this URN for you, so that such explanations as I’ve attempted are unnecessary.
  • The reference checking service needs to include a modicum of descriptive information about the URNs that are returned.
  • There needs to be a search service that stitches all this together.

I hope someone can find this of use.

Creating academic documents without Microsoft Word

28 Tuesday Aug 2012

Posted by in Academia, Software & Tools

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Anyone who knows me, or reads this blog will know all about my absolute disdain for Microsoft software; both in terms of operating systems (i.e. Windows) and especially their “productivity” tools like Word, Excel and Powerpoint (well, Excel, if you need a spreadsheet, is a fairly good program, but its being ruined by its ‘Officization’). If there is a God, I believe there is a special place in hell reserved for the designers and developers of Outlook especially.

In regards to authoring academic works, I’ve written on multiple occasions previously about various tools and software process for scholarly research, and especially, on not using Word in the writing process for my PhD.

I’m very pleased to report I’ve been able to eliminate almost entirely Microsoft Word from this process. I still have to send chapter drafts to my supervisor in RTF format, which can be opened in Word. My graduate school “milestone” documents (which I must complete at regular intervals to show progress) also come in Word flavour only. But from the mainline of my PhD chapters; Word is now officially gone.

To guide my research process I use a program called Papers. This is highly recommended for all scholars. To write the document drafts, I use Scrivener. Scrivener allows you to write in short sections, which it terms “Scrivenings”. These can be reduced to an index card view on the front of which you can put a short summary, and engage in some drag and drop rearranging of your argument or writing. All that process I have documented in this prior post.

What is different is that inside Scrivener I am writing in the MultiMarkdown format. This is a ‘plain text’ style mark up format that allows you to use a plain text editor, if you need to. It is an extension of John Gruber’s original Markdown language (a markup language that I am using to write this blog post in).

MultiMarkdown is pretty neat and allows you to insert markup in a document in such a way that keeps it pretty readable. It also allows you to export to multiple target output formats, the most common being HTML and PDF. To show you just how trivial and easy it is, here’s an example of a Latin quote and translation;

    >*Has tantas viri virtutes ingentia vitia aequabant: 
    inhumana crudelitas perfidia plus quam Punica, nihil 
    veri nihil sancti, nullus deum metus nullum ius 
    iurandum nulla religio* (21.4.9)

    >These great qualities of the man were equalled by his 
    unnatural vices: his inhuman barbarity, his treachery 
    far worse than Punic, he had nothing of truth, nothing 
    of sanctity, he lacked in fear of the gods, had no 
    lawful oaths, and no religious feeling.

(BTW It was also stonkingly trivial to put that code sample into this post.)

As you can see, a single “>” at the start of a paragraph indicates the paragraph is a quote. Text inside a pair of asterisks ( * … * ) is made italic. Two asterisks ( ** … ** ) is bold. In HTML the output of that, in the standard stylesheet of this blog would be;

Has tantas viri virtutes ingentia vitia aequabant: inhumana crudelitas perfidia plus quam Punica, nihil veri nihil sancti, nullus deum metus nullum ius iurandum nulla religio (21.4.9)

These great qualities of the man were equalled by his unnatural vices: his inhuman barbarity, his treachery far worse than Punic, he had nothing of truth, nothing of sanctity, he lacked in fear of the gods, had no lawful oaths, and no religious feeling.

From there in Scrivener, I can export this text to RTF format, for my supervisor and others who insist on broken formats, or for “production” purposes, into LaTeX format. Latex is a proper typesetting markup format that gives you fine control over all sorts of options, and allows output to PDF. The PDF looks absolutely a ton better than anything that Word and its ilk can produce. It has the advantage of being editable in a plain text editor – many common editors such as Textmate or BBEdit have Latex plugins. However the best bet I found was to install the Mac Latex package – this is absolutely free (not just as in beer) and comes with a great Tex/Latex editor called TeXShop. There are also other great Latex editors around.

Latex is often used in Mathematics and Physical Sciences because it how fantastic control over the typesetting of complex equations; something that Word fails abysmally at. It is less common in the Humanities, but not absolutely unknown. However it might seem complex and daunting to people not used to the idea of separating editing and markup from output formats or manipulating computer code in plain text editors. It is most definitely not a WYSIWYG editing system. It looks like the following;

    \begin{quote}\SingleSpace \emph{
    Has tantas viri virtutes ingentia vitia aequabant: 
    inhumana crudelitas perfidia plus quam Punica, nihil 
    veri nihil sancti, nullus deum metus nullum ius 
    iurandum nulla religio} (21.4.9)

    These great qualities of the man were equalled by his 
    unnatural vices: his inhuman barbarity, his treachery 
    far worse than Punic, he had nothing of truth, nothing 
    of sanctity, he lacked in fear of the gods, had no 
    lawful oaths, and no religious feeling.
    \end{quote}

Well actually I tell a little lie here. This is effectively what happens. What I really do, in my document preamble, is define a command called latinquote — like this;

    % quotes Latin test in italic (emph), 
    % then the reference, a blank line, 
    % and then the translation. in \SingleSpace.
    \newcommand{\latinquote}[3] {
        \begin{quote}\SingleSpace \emph{#1} #2

        #3
        \end{quote}
    }

And then in my document, I use the command as follows, supplying it with the three arguments specified as #1 #2 and #3 above;

    \latinquote{
    Has tantas viri virtutes ingentia vitia aequabant: 
    inhumana crudelitas perfidia plus quam Punica, nihil 
    veri nihil sancti, nullus deum metus nullum ius 
    iurandum nulla religio}
    {(21.4.9)}
    {These great qualities of the man were equaled by his 
    unnatural vices: his inhuman barbarity, his treachery 
    far worse than Punic, he had nothing of truth, nothing 
    of sanctity, he lacked in fear of the gods, had no 
    lawful oaths, and no religious feeling.}

But for an old code warrior like me, that’s just fine! Using custom commands like that, if I want to redefine how my Latin quotes are output, I can do it in a single place (in the command definition) and every quote now transforms itself to the defined style next time I generate the PDF. I can also edit and write my project also on my iPad, using the Logitec iPad keyboard/case thing I got. The editor I use on the iPad understands MultiMarkdown and it syncs to Scrivener via text files on Dropbox. I can also edit the Latex directly (but there is only one program on the iPad that will generate the PDF from the Latex file and I’m not sure I want to use it). Additionally, I can check in my Latex files to an SVN or GIT repository for safe keeping and versioning!

I’ve still got a few wrinkles to iron out of my system yet;

  • MultiMarkdown’s referencing system is a bit rubbish (you put the references at the end of the MultiMarkdown document, which is clunky). For the time being I am still using Scrivener’s built in footnote insertion tooling. This converts just fine (in fact, great) to Latex’s footnotes but I’d like to keep to a pure “text only” system if possible.

  • Exporting to RTF through MultiMarkdown from Scrivener doesn’t make attractive RTF files. I may in the future stick to straight Latex and use the latex2rtf converter to get RTF.

  • MultiMarkdown doesn’t produce the cleanest of Latex. I have to spend a bit of time stripping the complexity off the generated Latex. I will have to investigate how to control this process from the outset in MultiMarkdown (specifically, in the MultiMarkdown installation that Scrivener uses).

  • After it goes through the compilation to MultiMarkdown format into Latex, I have to locate all the latin quotes (for example) and re-apply the use of the \latinquote command. This can be tedious; I need to automate it.

  • I need to develop a custom Latex .sty that embodies the various layout parameters that’s expected by my Graduate School (they are pretty basic).

  • I have to work out a good path to integrating Papers, Scrivener, MultiMarkdown with the BibTex referencing system that’s commonly used in Latex.

However it’s great to be free from having to use Microsoft Word clunkiness (now if only they can kill it off at work …).

Electronic Tools for Scholarship – my personal approach

27 Friday Jan 2012

Posted by in Academia, Classical history, Digital Classics, Personal, Software & Tools

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I have written before on the issue of software tools to better aid scholarly research (also known as: writing your PhD), not just on this blog, but also on my technical blog let x=x. This post is spurred by a brief conversation I had this afternoon with postgrad classicists about organising their electronic information, and hopefully will tie together some of those threads.

TL;DR – scroll down to the conclusion.

A word of warning. I use an Apple Macintosh, I have done so for quite a few years and in fact I’ve just bought my 4th straight 15″ MacBook Pro and there are six Macs in the house at the moment. All software mentioned here runs on a Macintosh. Obviously some of it may be available for Windows or Linux users, or equivalents. However I don’t care. I’m discussing what works (and doesn’t) for me, and that means on a Mac.

Writing tools

Although this process is naturally later than research in a temporal sense, writing tools are so centrally important to the process of all researchers in any Humanities subject, that they have to be dealt with as a priority. You need to choose the writing tool that best suits what you need to do in the way you want to write it: research tools have to fit into that “flow” and if they don’t, you generally chuck them out rather than adapt your writing methods.

First, there is Microsoft Word. For some people. this is as far as it gets. Word is their world. I understand Word fairly well, but I also understand it’s limitations and it’s annoyances. I generally only use it when I have to.

For general research writing, I use a tool called Scrivener, from Literature and Latte. Its more tailored to people like scriptwriters or novelists, however, it’s an invaluable tool to organise your thinking. You can write small focussed chunks of text on a topic and theme, and then use things like the ‘cork board’ to organise those chunks (presented as index cards onto which you can write a summary of their contents) into something approaching a coherent argument. Then you can flip back to the ‘Scrivenings’ view, which shows you the full text of the selected items, to see what needs altering to make the argument flow properly.

Once you’re happy with your draft in Scrivener, you “compile” the document into a target format, like an .RTF document:

Compiling a document from Scrivner's cork board view

After this you can polish the document in the word processor of your choice.

I did use Apple Pages for the bulk of my M.A. Thesis. It’s a great tool. I did find it lacked a couple of features I use in Word — at the end I exported from Pages into Word format and did the final production to PDF from Word.

Probably for my PhD, at the production stage I will probably use some type of TeΧ tool, likeLaTeΧ. Suggestions welcome on this idea.

Research tools

Here’s where I gets trickier, I think. For my M.A. I tried to use Evernote to organise article PDFs I got from databases, but I found in the end, that Evernote was just not up to the mark in terms of scholarly research. It has a lot of other neat features that users like but I found it unsustainable in use, mainly because I had to search for documents in databases with my web browser and then import the PDF into Evernote, including typing out the title and author.

In the end I ditched Evernote for version 1 of a program called Papers. Version 2 is now out. Papers connects me to the academic databases (warning: has a built-in bio-science prejudice) – even using my university’s Ezproxy for free access to them – and then allows me to search the databases to my heart’s content. It then imports the PDF into your own database. So you build your research database over time, and as well as searching databases, you can search your own research collection, as below:

Searching for everyone who quotes Walsh inside my research database

It also has an iPad app that will automatically sync with the Mac program and put all the PDFs on your iPad so you can read them there. This is very, very handy. Reading PDFs off a screen is horrible. Before I got the iPad I had to print out all my articles – not good for the environment! On the iPad you can annotate the PDFs, but I don’t do this, I either take notes into a notebook the traditional way, or I type the notes into a special research document in Scrivener. But having the iPad set up on a stand next to my computer screen while I do this is a tremendous boon.

If you have PDF books, you can import them into Papers, although you may have to type-in the title and author data. Many PDFs that you download from databases have data in them in such a way that Papers can sometimes auto-determine this data for you, if you have the PDFs already on your disk, but book PDFs rarely do. Papers can also handle journal abbreviations.

If I get e-books (ePub) from my library I immediately strip the useless copy protection which prevents the document from being utilised in a sane manner, and then load them up on my iPad using Apple’s iBooks. You can annotate documents in iBooks. It also handles PDFs, but not as well as ePub. The only drawback with this method is that in iBooks you lose the “original page number” that you get in the Adobe DRM’d viewer. But I think this is a fault of the idea of citing a “page” number in a document that can reformat itself to conform with any desired display as necessary. Classicists already know the way to cite “continuously scrolling” documents! But alas, the necessary numbering system is never included in the ePub documents. So you are forced to refer back to the original to get the “proper” page reference (and this means another 24 hour borrowing of the ePub document from the “library” to get it. This stuff all proves me that proprietary DRM is anti-scholarship, as I’ve said before.

Alternatives in this area are Mendeley and Zotero. I signed up to a Mendeley account but I’ve not really used it as I stuck with Papers. Zotero claims that “It lives right where you do your work—in the web browser itself”, the only fly in that ointment is I don’t actually do much of my work in a web browser. I mean, wikipedia is still not an acceptable source, right? Plus with Papers I don’t have to search JSTOR and then go to Project Muse and enter the same search in there too. I can just search once right in Papers and make sure I’ve got both JSTOR and Project Muse and any other relevant databases selected. I can also review the articles before deciding to import them or not right in the one program.

Citation managers

I have also used Endnote (my University gives me a free licence) to manage my modern citations and their bibliography. However, the problem for Classicists with Endnote, and this goes for all citation managers, is that they assume you have only one referencing style. In other words, when you have to manage your ancient sources separately, and possibly cite them differently, as you generally do in Classics, a citation manager can get in the way, enormously. Also I find that many people can’t cope with the complexity of making a custom citation and bibliographical style especially if the one they need isn’t available as a default in their citation manager of choice. Although I could, being a professional computer programmer, and an anal-retentive taxonomic organiser, so much of this stuff doesn’t scare me as much, but I can’t bring myself to recommend it to anyone.

Papers 2 added citation features, which brings a great integration to your research database and your citations and bibliography. However they are fairly primitive at the moment, and geared towards science users and therefore not useful to Humanities scholars (especially Classicists without our multiple citation formats). I’m kind-of ambivalent about this. For me, Papers’ number one feature is research article search and database management, so I hope they don’t screw that over to compete with specialised citation managers like Endnote. I can cope managing this stuff manually, for the moment.

What I do use with Papers, though, is it’s ability to just “drag and drop” entries from it into an open document and it will paste the entry as in a Bibliographic entry. This is just plain text so it can be adjusted as required. I then tend to manually manage my citations (we currently use a hybrid system of MLA format in footnotes, not inline MLA).

Dragging and dropping a Bibliographic entry from Papers into Scrivener

Conclusion

I tend to live in Scrivener and Papers. I write mostly with Scrivener. I sync my article PDFs in Papers for the Mac across to iOS Papers on my iPad so I can read them on-the-go and without printing them all out. I read ePub in iBooks, and I don’t use electronic annotations very much – preferring to use a notepad and pencil, or just type my notes straight into the “Research” section in my Scrivener document. Citation managers I avoid, but I do love the drag-and-drop bibliographic entry function in Papers.

Comments, clarifications, suggestions, flames, all welcome.

Humanities use of ‘fuzzy’ data

01 Thursday Dec 2011

Posted by in Archaeology, Digital Classics, Humanties, Science & Tech, Software & Tools

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A neat summary of the sort of problem that often arises in the interface between the sciences and the humanities.

How do we balance supporting novice spatial users alongside experts? Or, is geospatial analysis necessarily GIS?:

By focusing simply on technology training, there is the danger that, as well as being seen as irrelevant, too difficult or simply just boring for users (academics or students), the data gets overlooked or is made to fit a ‘system’ of analysis. For example, one problem of using GIS in humanities is the issue of ‘fuzzy’ data. This isn’t just a case of the system failing to cope with fuzziness: it also betrays an underlying assumption that data can, and should be, disambiguated and clear. For humanists, however, the questions driving research are often precisely those that look to nuance or complicate the material. We like messy results. Humanists need worry less about producing an accurate and/or truthful representation and more about how maps can be used as entry points to explore the data—this is seeing maps as   part of the investigative process rather than as an end in and of themselves.

(Via PELAGIOS)

The Pelagios Graph Explorer: An information superhighway for the ancient world

13 Sunday Nov 2011

Posted by in Archaeology, Classical history, Classics resources, Digital Classics, Science & Tech, Software & Tools

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The Pelagios Graph Explorer: An information superhighway for the ancient world:

Just as the settlements around the Ancient Mediterranean would seem disconnected without the sea to join them, so online ancient world resources have been separated, until now. Meaning “of the sea”, Pelagios has brought this world together using the principles of Linked Open Geodata. The Pelagios Graph Explorer allows students, researchers and the general public to discover the cities of antiquity and explore the rich interconnections between them.

(Via PELAGIOS)