Saturday, October 25, 2014

Citations get HOT

The Public Library of Science research section, PLOSLabs ( has announced some very interesting news about the work that they are doing on citations, which they are calling "Rich Citations".

Citations are the ultimate "linked data" of academia, linking new work with related works. The problem is that the link is human-readable only and has to be interpreted by a person to understand what the link means. PLOS Labs have been working to make those citations machine-expressive, even though they don't natively provide the information needed for a full computational analysis.

Given what one does have in a normal machine-readable document with citations, they are able to pull out an impressive amount of information:
  • What section the citation is found in. There is some difference in meaning whether a citation is found in the "Background" section of an article, or in the "Methodology" section. This gives only a hint to the meaning of the citation, but it's more than no information at all.
  • How often a resource is cited in the article. This could give some weight to its importance to the topic of the article.
  • What resources are cited together. Whenever a sentence ends with "[3][7][9]", you at least know that those three resources equally support what is being affirmed. That creates a bond between those resources.
  • ... and more
As an open access publisher, they also want to be able to take users as directly as possible to the cited resources. For PLOS publications, they can create a direct link. For other resources, they make use of the DOI to provide links. Where possible, they reveal the license of cited resources, so that readers can know which resources are open access and which are pay-walled.

This is just a beginning, and their demo site, appropriately named "alpha," uses their rich citations on a segment of the PLOS papers. They also have an API that developers can experiment with.

I was fortunate to be able to spend a day recently at their Citation Hackathon where groups hacked on ongoing aspects of this work. Lots of ideas floated around, including adding abstracts to the citations so a reader could learn more about a resource before retrieving it. Abstracts also would add search terms for those resources not held in the PLOS database. I participated in a discussion about coordinating Wikidata citations and bibliographies with the PLOS data.

Being able to datamine the relationships inherent in the act of citation is a way to help make visible and actionable what has long been the rule in academic research, which is to clearly indicate upon whose shoulders you are standing. This research is very exciting, and although the PLOS resources will primarily be journal articles, there are also books in their collection of citations. The idea of connecting those to libraries, and eventually connecting books to each other through citations and bibliographies, opens up some interesting research possibilities.

Sunday, October 19, 2014 - where it works

In the many talks about, it seems that one topic that isn't covered, or isn't covered sufficiently, is "where do you do it?" That is, where does it fit into your data flow? I'm going to give a simple, typical example. Your actual situation may vary, but I think this will help you figure out your own case.

The typical situation is that you have a database with your data. Searches go against that database, the results are extracted, a program formats these results into a web page, and the page is sent to the screen. Let's say that your database has data about authors, titles and dates. These are stored in your database in a way that you know which is which. A search is done, and let's say that the results of the search are:
author:  Williams, R
title: History of the industrial sewing machine
date: 1996
This is where you are in your data flow:

The next thing that happens (and remember, I'm speaking very generally) is that the results then are fed into a program that formats them into HTML, probably within a template that has all your headers, footers, sidebars and branding and sends the data to the browser. The flow now looks like

Let's say that you will display this as a citation, that looks like:
Williams, R. History of the industrial sewing machine. 1996.
Without any fancy formatting, the HTML for this is:
<p>Williams, R. History of the industrial sewing machine. 1996.</p>
Now we can see the problem that is designed to fix. You started with an author, a title and date, but what you are showing to the world is a string of characters are that undifferentiated. You have lost all the information about what these represent. To a machine, this is just another of many bazillions of paragraphs on the web. Even if you format your data like this:
<p>Author: Williams, R.</p>
<p>Title:  Williams, R. History of the industrial sewing machine</p>
<p>Date: 1996</p>
What a machine sees is:
<p>blah: blah</p>
<p>blah: blah</p>
<p>blah: blah</p>  
What we want is for the program that is is formatting the HTML to also include some metadata from that retains the meaning of the data you are putting on the screen. So rather than just putting HTML formatting, it will add formatting from has metadata elements for many different types of data. Using our example, let's say that this is a book, and here's how you could mark that up in
<div vocab="">
<div   typeof="Book">
    <span property="author">Williams, R.</span> <span property="name">History of the industrial sewing machine</span>. <span property="datePublished">1996</span>.
Again, this is a very simple example, but when we test this code in the Google Rich Snippet tool, we can see that even this very simple example has added rich information that a search engine can make use of:
To see a more complex example, this is what Dan Scott and I have done to enrich the files of the Bryn Mawr Classical Reviews.

The review as seen in a browser (includes markup)

The review as seen by a tool that reads the structured data.

From these you can see a couple of things. The first is that the markup does not change how your pages look to a user viewing your data in a browser. The second is that hidden behind that simple page is a wealth of rich information that was not visible before.

Now you are probably wondering: well, what's that going to do for me? Who will use it? At the moment, the users of this data are the search engines, and they use the data to display all of that additional information that you see under a link:

In this snippet, the information about stars, ratings, type of film and audience comes from schema. org mark-up on the page.

Because the data is there, many of us think that other users and uses will evolve. The reverse of that is that, of course, if the information isn't there then those as yet undeveloped possibilities cannot happen.

Wednesday, October 01, 2014

This is what sexism looks like

[Note to readers: sick and tired of it all, I am going to report these "incidents" publicly because I just can't hack it anymore.]

I was in a meeting yesterday about RDF and application profiles, in which I made some comments, and was told by the co-chair: "we don't have time for that now", and the meeting went on.

Today, a man who was not in the meeting but who listened to the audio sent an email that said:
"I agree with Karen, if I correctly understood her point, that this is "dangerous territory".  On the call, that discussion was postponed for a later date, but I look forward to having that discussion as soon as possible because I think it is fundamental."
And he went on to talk about the issue, how important it is, and at one point referred to it as "The requirement is that a constraint language not replace (or "hijack") the original semantics of properties used in the data."

The co-chair (I am the other co-chair, although reconsidering, as you may imagine) replied:
"The requirement of not hijacking existing formal specification languages for expressing constraints that rely on different semantics has not been raised yet."
"Has not been raised?!" The email quoting me stated that I had raised it the very day before. But an important issue is "not raised" until a man brings it up. This in spite of the fact that the email quoting me made it clear that my statement during the meeting had indeed raised this issue.

Later, this co-chair posted a link to a W3C document in an email to me (on list) and stated:
"I'm going on holidays so won't have time to explain you, but I could, in theory (I've been trained to understand that formal stuff, a while ago)"
That is so f*cking condescending. This happened after I quoted from W3C documents to support my argument, and I believe I had a good point.

So, in case you haven't experienced it, or haven't recognized it happening around you, this is what sexism looks like. It looks like dismissing what women say, but taking the same argument seriously if a man says it, and it looks like purposely demeaning a woman by suggesting that she can't understand things without the help of a man.

I can't tell you how many times I have been subjected to this kind of behavior, and I'm sure that some of you know how weary I am of not being treated as an equal no matter how equal I really am.

Quiet no more, friends. Quiet no more.

(I want to thank everyone who has given me support and acknowledgment, either publicly or privately. It makes a huge difference.) 

Some links about "'Splaining"