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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 . . .
                                                              JANUARY–MARCH 2011   •   VOLUME 65 NUMBER 1




   California Agriculture
                                                                                                                             APRIL–JUNE 2011   •   VOLUME 65 NUMBER 2




                                                              California Agriculture
                                                          Growing bigger, better:
                                                          Artisan olive oil comes of age
                                                                                                                                                                                                     (the University
                                                                                       California Agriculture
                                                                                                                                                     JULY–SEPTEMBER 2011   •   VOLUME 65 NUMBER 3



                                                                                                                                                                                                     of California’s
                                                                                                                                                                                                     peer-reviewed
                                                                                                    Food as
                                                                                                    medicine                                                                                         journal of
                                                                                                                                                                                                     agriculture, and
                                                                                                                                                                                                     natural and
University of California   |   Peer-reviewed Research and News in Agricultural, Natural and Human Resources




                                                                                                     Down on the farm:


                                                                                                                                                                                                     human
                                                                                                     Agritourism on the rise
                                                                                                             Also: Free trade, constructed wetlands,
                                                                                                                               Can what we eat help cure what ails us?
                                                                                                                   rice nitrogen, smart sprayers, almond irrigation




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




                                                                                       University of California   |   Peer-reviewed Research and News in Agricultural, Natural and Human Resources
                                                                                                                                                                                                     research) . . .
. . . 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?
We need a multi-tasking tool to
create content that is


                       ?

                    Discoverable
                      Accessible
                    Actively linked
Flexible -- rendered across platforms and devices
            Visible in the scholarly world
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

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Xml what is it and why do we care?

  • 1. XML: What is it and why do we care? California Agriculture University of California Agriculture and Natural Resources Communication Services and Internet Technology
  • 2. Or how a mild-mannered journal . . . JANUARY–MARCH 2011 • VOLUME 65 NUMBER 1 California Agriculture APRIL–JUNE 2011 • VOLUME 65 NUMBER 2 California Agriculture Growing bigger, better: Artisan olive oil comes of age (the University California Agriculture JULY–SEPTEMBER 2011 • VOLUME 65 NUMBER 3 of California’s peer-reviewed Food as medicine journal of agriculture, and natural and University of California | Peer-reviewed Research and News in Agricultural, Natural and Human Resources Down on the farm: human Agritourism on the rise Also: Free trade, constructed wetlands, Can what we eat help cure what ails us? rice nitrogen, smart sprayers, almond irrigation resources University of California | Peer-reviewed Research and News in Agricultural, Natural and Human Resources University of California | Peer-reviewed Research and News in Agricultural, Natural and Human Resources research) . . .
  • 3. . . . can have superpowers on the Web* *especially the semantic Web
  • 4. Readers today are problem solvers Tunisia, January 2011
  • 5. They seek relevant information,
  • 7. and find a solution. .
  • 8. 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
  • 9. Information wants to be free* ... Information wants to be expensive* *Stewart Brand, Hackers Convention 1984
  • 10. 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 . . .
  • 11. At the same time, faculty authors need “impact” as shown by "metrics" in both the the popular
  • 12. and scholarly worlds. Luckily the Web helps us do both.
  • 13. 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
  • 14. Our content is free in another way now . . . it is no longer restricted to a container
  • 15. 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
  • 16. But with so many formats and devices -- and readers with different devices -- how can we do this?
  • 17. We need a multi-tasking tool to create content that is ? Discoverable Accessible Actively linked Flexible -- rendered across platforms and devices Visible in the scholarly world
  • 18. 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>
  • 19. Transforms to HTML on the Web
  • 21. 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.
  • 22. 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>
  • 23. 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
  • 24. 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.
  • 25. 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)
  • 26. 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.
  • 27. 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.
  • 28. 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
  • 29. 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
  • 30. 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.
  • 31. We now deliver XML directly to databases. They display it as soon as we signal new content.
  • 32. One favorable result: Greater visibility for faculty authors June ‘11: Impact factor for 2010 doubled to .92
  • 33. . . . and continued upward
  • 34. . . . with a favorable long-term trend.
  • 35. We are charting and analyzing popular metrics
  • 36. 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/
  • 37. Making your content discoverable to readers and internet databases, aggregators, browsers . . . whether in Ghana . . . Or Iowa