XML: What is it and why do we care?

California Agriculture University of California Agriculture and Natural Resources Communication Services and Internet Technology

Or how a mild-mannered journal . . .

(the University of California’s peer-reviewed journal of agriculture, and natural and human resources research) . . .

University of California | Peer-reviewed Research and News in Agricultural, Natural and Human Resources

Growing bigger, better:Artisan olive oil comes of age

California AgricultureJANUARY–MARCH 2011 • VOLUME 65 NUMBER 1

University of California | Peer-reviewed Research and News in Agricultural, Natural and Human Resources

Down on the farm: Agritourism on the rise

Also: Free trade, constructed wetlands, rice nitrogen, smart sprayers, almond irrigation

California AgricultureA P R I L – J U N E 2 0 1 1 • V O L U M E 6 5 N U M B E R 2

University of California | Peer-reviewed Research and News in Agricultural, Natural and Human Resources

Food as medicine

Can what we eat help cure what ails us?

California AgricultureJULY–SEPTEMBER 2011 • VOLUME 65 NUMBER 3

. . . can have superpowers on the Web*

*especially the semantic Web

Readers today are problem solvers

Tunisia, January 2011

They seek relevant information,

repurpose and recombine it . . .

and find a solution. .

Readers will go to great lengths to get the information they need.

As government tried to block protests, the people went from

YouTube, to Facebook, to Twitter

Information wants to be free* . . .

Information wants to be expensive*

*Stewart Brand, Hackers Convention 1984

The tension will not go away Readers expect more – discoverable,

accessible content that can be viewed on the "container of choice" – iPhone, Android, Kindle,

iPad, laptop . . .

At the same time, faculty authors need “impact”

as shown by "metrics" in both the the popular

and scholarly worlds. Luckily the Web helps us do both.

As land-grant universities, we have

• quality content, • some of the best science in the world, and • a long tradition of open-access information, both print and Web

Our content is free in another way now . . . it is no longer

restricted to a container

Once we have the content in digital form, we can render it in various chunks and containers

–books, ebooks, PDFs, blogs, websites, journals, ezines, even good old print

page turners, presence on databases

But with so many formats and devices -- and readers with

different devices -- how can we do this?

?

Discoverable Accessible

Actively linked Flexible -- rendered across platforms and devices

Visible in the scholarly world

We need a multi-tasking tool to create content that is

XML = “extensible markup language”

•  a language for documents containing structured information;

•  Including both content and markers, tags identifying what role that content plays.

•  For example:

<title>Huckleberry Finn</title> <author>Mark Twain</author>

Transforms to HTML on the Web

XML metadata behind it

Active links on the Web

•  References •  Adam KL. Community Supported Agriculture 2006. Fayetteville, AR:ATTRA-National Sustainable

Agriculture Information Service. www.attra.org/attra-pub/PDF/csa.pdf •  Altieri MA. Agroecology: The Science of Sustainable Agriculture 1995. Boulder, CO:Westview Pr. 448p. •  Anderson-Wilk M. Does community-supported agriculture support conservation?. J Soil Water Conserv.

2007. 62(6):126-7A. •  DeLind LB. Ferguson AE. Is this a women's movement? The relationship of gender to community-

supported agriculture in Michigan. Hum Organ. 1999. 58(2):190-200. •  Feenstra G. CSAs: The consumer-farmer connection. Cal Ag. 1994. 48(5):8- DOI: 10.3733/ca.v048n05p8

[CrossRef] •  Flora CB. Bregendahl C. The role of collaborative community supported agriculture: Lessons from Iowa.

Leopold Ctr Prog Rep. 2007. 16:44-7. •  Galt RE. Counting and mapping community-supported agriculture in the United States and California:

Contributions from critical cartography/GIS. ACME: Int E-J Crit Geogr. 2011. 10(2):131-62. •  Hinrichs CC. Embeddedness and local food systems: Notes on two types of direct agricultural market. J

Rural Stud. 2000. 16(3):295-303. DOI: 10.1016/S0743-0167(99)00063-7 [CrossRef] •  Klonsky K. Siebert J. Organic agricultural production in California. California Agriculture: Dimensions and

Issues 2004. Berkeley, CA:Giannini Foundation. p. 241-56.

XML tagging for one reference •  <ref id="R8"><nlm-citation citation-type="journal"> •  <person-group person-group-type="author"> •  <name><surname>Hinrichs</surname> •  <given-names>CC</given-names></name></person-group> •  <article-title>Embeddedness and local food systems: Notes on two

types of direct agricultural market</article-title> •  <source>J Rural Stud</source> •  <year>2000</year> •  <volume>16</volume> •  <issue>3</issue> •  <fpage>295</fpage><lpage>303</lpage> •  <pub-id pub-id-type="doi">10.1016/S0743-0167(99)00063-7</pub-

id> •  </nlm-citation></ref>

Why is XML so useful?

•  Machine readable •  Flat file – no style •  Talks to relational databases – backbone

of semantic Web •  A standard for that can be recognized by

eReaders and mobile devices, databases and platforms – and poured into different containers

What “flavor” of XML ?

•  There are different kinds of XML. •  Each is a DTD or document type

definition, a set of rules defining content and structure.

For maximum functionality: NLM DTD *

•  Established in 2003 by the National Library of Medicine, the world’s largest biomedical library

•  Designed for content posted to Pub Med Central – a digital archive of biomedical and life sciences journal literature.

•  Provides free access to full text of articles

* Known also as Journal Article Tag Suite (JATS)

Now the de facto international standard of scholarly publication

It is popular among aggregators, and house style for Atypon and Allen Press, recommended by HighWire and Public Library of Science.

Flavor?

•  Each “flavor” OF XML includes elements, attributes, and entities, and defines relationships among them.

•  There are code checkers on line that enable you to test your code for – proper structure (Is there an end tag for every

start tag?) and – conformation to the standard.

Functionality -- most important

•  XML enables content to be channeled into myriad formats and devices: web sites, digital edition on laptop, application for smartphone, reading devices, eReaders, YouTube or Podcast if video or audio files.

•  It enables content to be indexed by scholarly databases including Thomson ISI Web of Science

Another option: XML metadata + PDF

•  PDFs are true visual representations of how text is meant to look

•  PDFs are easy to read because they retain formatting

•  They include vector graphics that scale cleanly in any device

California Agriculture has posted full text in XML and PDF format back to our first issue

in 1946.

Beginning in July 2011: California Agriculture went electronic version of record.

We now deliver XML directly to databases. They display it as soon as we signal new content.

One favorable result: Greater visibility for faculty authors June ‘11: Impact factor for 2010 doubled to .92

. . . and continued upward

. . . with a favorable long-term trend.

We are charting and analyzing popular metrics

Steps to XML

1. Hire a web editor (someone familiar with XML flavors, transforms, and CSS).

2. Get a friendly, helpful IT programmer to build a database, create transforms and calls

3. Hire vendor to digitize your backfile (our vendor is Aptara) 4. Learn to maintain and update your site with editorial staff and

designers.

Check out helpful websites: JATS-Con 2011 PPTs and some videos go to:

http://www.ncbi.nlm.nih.gov/books/NBK57252/ NLM DTD and PubMed Central code checker http://www.ncbi.nlm.nih.gov/pmc/pub/validation/

Making your content discoverable to readers and internet databases, aggregators, browsers . . .

whether in Ghana . . . Or Iowa