Bookshelf - PowerPoint Presentation

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BookshelfLeafing through XMLNLM Journal Article Tag Suite Conference 2010Martin Latterner and Marilu HoeppnerNational Center for Biotechnology InformationNational Library of Medicine

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NLM

BOOK

DTD

v2.3Slide3

NLM Collection Catalog

PubMed

Abstracts

Electronic Literature Archive

Books, Monographs, Reports

Journals

Other publication formats

Book chapters, Monographs, Reports

Books in

PubMed

Non-PubMed Books

User guides, Documentation

Journal articles

PMC Journals

PubMed

Central

Bookshelf

Entrez

L

iterature

R

esourcesSlide4

Features of the Book DTDBooks and journals within PubMed CentralBookshelf WorkflowsIntegration of information between databasesSlide5

ModificationsAllowed icon as a child of exlnk.Allowed pre as a child of entry.Allowed glossary as a child of chapter.Added type: ppt.Added attributes id and BID to <foot>.Added attribute id to <p>.

Added <title>, child of <bibsect>.Added <bb>, <

gf

> and <

figgrp

> as children of <

linkgrp

>.

Added <email> as child of <

txtstyle

>.

Added <

pdf

> as child of <glossary>.

Added <figgrp1> as child of <entry>.

…

NCBI Book DTD 1.0

Based on ISO 12083 Article DTDSlide6

March 2003

v1.0

December 2004

v2.0

November 2005

v2.1

BOOKSHELF XML DATA

NCBI BOOK DTDSlide7

Book DTDof theNLM Journal Article Tag SuiteSlide8

Designed to capture the semantic elements of the content, not forme.g. bibliographic metadataSlide9

<front> <div type="titlepage

" level="1" id="2001902bddd00001"> <booktitle>

<

ils

style="strong">CONFLICT OF INTEREST IN MEDICAL RESEARCH</

ils

>

</

booktitle

>

<

bookauthor

>

<bookauthor.name>Committee on Conflict of Interest in Medical Research</bookauthor.name>

<bookauthor.info>Board on Health Sciences Policy</bookauthor.info>

<bookauthor.info>INSTITUTE OF MEDICINE <

ils

style="

smallcap

">

<

ils

style="emphasis"> OF THE NATIONAL ACADEMIES</

ils> </ils

> </bookauthor.info> </bookauthor> <publication.stmt> <p style="center">

<publisher> <publisher.name>THE NATIONAL ACADEMIES PRESS</publisher.name> <publisher.address><state>Washington, D.C.</state></publisher.address> </publisher>

</p> </publication.stmt> <page number="ii" id="2001902bppp00002"/> </div>

<div type="copyrightpage" level="1" id="2001902bddd00002"> <publication.stmt> <p style="normal"> <publisher>

<publisher.name><ils style="strong">THE NATIONAL ACADEMIES PRESS</ils></publisher.name> <publisher.address> <street><

ils style="strong">500 Fifth Street, N.W.</ils></street> <state><ils style="strong">Washington, DC</ils

></state> <postcode><ils style="strong">20001</ils></postcode> </publisher.address>

</publisher> </p> </publication.stmt> <publication.stmt>

<p style="flindent">ISBN <isbn

>978-0-309-13188-9</isbn> (hardcover)</p>

</publication.stmt> <copyright>Copyright <

copyright.year>2009</copyright.year

> by the <copyright.holder>National Academy of Sciences</copyright.holder>. All rights reserved.</copyright> <printinfo> <print>Printed in the United States of America</print> </

printinfo> </div></front>Slide10

<book-meta> <book-title-group> <book-title>Conflict of Interest in Medical Research</book-title>

</book-title-group> <contrib-group

>

<

contrib

contrib

-type="author">

<

collab

>Institute of Medicine (US) Committee on Conflict of Interest in Medical

Research, Education, and Practice</

collab

>

</

contrib

>

</

contrib

-group>

<publisher>

<publisher-name>National Academies Press (US)</publisher-name>

<publisher-loc>Washington (DC)</publisher-loc> </publisher> <isbn>978-0-309-13188-9</

isbn> <pub-date pub-type="ppub"> <year>2009</year> </pub-date> <permissions>

<copyright-statement>Copyright &copy; 2009, National Academy of Sciences</copyright-statement> <copyright-year>2009</copyright-year> </permissions></book-meta>Slide11

More granular text descriptions are handled at attribute levele.g. preface, foreword<sec sec-type=“preface”>Slide12
Slide13

ArticleBook

<abbrev-journal-title>

<article>

<article-categories>

<article-id>

<article-meta>

<conf-acronym>

<conference>

<conf-num>

<conf-theme>

<floats-group>

<front>

<front-stub>

<issue-sponsor>

<journal-meta>

<journal-subtitle>

<journal-title>

<journal-title-group>

<response>

<series-text>

<series-title>

<string-conf>

<sub-article>

<unstructured-

kwd

-group>

<x>

<alternate-form><area><book><book-front><book-meta><book-part>

<book-part-categories><book-part-meta><book-title><book-title-group>

<collection><collection-id><collection-list><collection-member><collection-meta>

<collection-name><map><map-group><multi-link>

DTD v3.0

ElementsSlide14

<map-group>XML<map-group id="my-map-id"> <graphic xlink:href="

img-uri"/>

<map

map

-name="my-map">

<area map-shape="

rect

" map-

coords

="1,1,51,76"

xlink:href

="uri1"/>

<area map-shape="

rect

" map-

coords

="54,4,94,74"

xlink:href

="ur2"/>

</map>

</map-group>

X

HTML

<

img

src="img-uri" usemap="#my-map-id"/>

<map id="my-map-id" name="my-map"> <area href="uri1" shape="rect

" coords="1,1,51,76"/> <area href="uri2" shape="rect

" coords="54,4,94,74"/></map>Slide15

<multi-link>XML<multi-link> <term>IDDM2</term> <ext-link ext-link-type="url

" xlink:href="LINK1">Bookshelf</ext-link>

<ext-link ext-link-type="

url

"

xlink:href

="LINK2">PubMed Central</ext-link>

…

</multi-link>Slide16

ArticleBook

abbrev-type

article-type

response-type

alternate-form-type

book-id

book-part-number

book-part-type

graphic-type (obsolete)

indexed

map-alt

map-

coords

map-name

map-shape

primary

qualifier

taxonomic-id

DTD v3.0

AttributesSlide17

Books & Journals in PubMed CentralSlide18

Source ConversionThird-party vendor services: Tagging rules for journals can be applied to book content, especially, for lower level document objects. Citations Figures Tables

In-house conversion: For content submitted in external DTDs, code reuse of PMC journal modules for handling: Dates

Strings

CALS to XHTML table conversionSlide19

Data Processing and IngestSoftware to lookup PubMed IDs in citations<pub-id pub-id-type=”pmid”>Imaging resizing software and

validation checks for graphics and supplementary data files such as PDFLoading code for the extraction of key information, such as dates, subject categories, etcSlide20

CHOP-IT-UPSlide21

Output FormatsHTMLUses base XSLT Article rendering rules for conversion of XML to HTML; book-specific overwrites or modificationsPDFUses XSL-FO base code for articles; book-specific overwrites or modifications Slide22

Advantages of using a Shared Tag SetShare XSLT modules during ingest, conversion processes, and renderingUse similar database infrastructureEnables closer integration for a variety of processes, such as PubMed submission and

indexingSlide23

Bookshelf WorkflowsSlide24

Submission of Content to BookshelfPDF or WordXML in NLM Book DTDXML in external DTDsWord authoring followed by conversion to XML (in-house

)Slide25

<book>

Submitted

Files

PDF

Word

XML (External DTD)

NLM Book DTD XML

Third-party vendor

or

In-house Converters

Requirements

Pass validation

Pass

stylecheck

Slide26

<book-part>

PMC

<

book-part>

<

book-part>

<

book-part>

CMS

<

book>

CHOP-IT-UPSlide27
Slide28

NCBI

Word converter

XML

Instant HTML Preview

Publish to

Bookshelf

Microsoft Word

document

Word Authoring Followed by Conversion to XMLSlide29

StylecheckerCheck business rulesGoal: one set of rendering rules for uniform source XML data2 Checkpoints

Whole book (modified article stylechecker)

Individual book-part (article

stylechecker

)Slide30

Integrating Content from Different Databases Slide31
Slide32

<!DOCTYPE sec SYSTEM "book.dtd"><sec><title/><sec id="molgen.tables" >

<title/><p content-type="

molecular_genetics

"><italic>Information in the

Molecular Genetics and OMIM tables may differ from that elsewhere

in the

GeneReview

: tables may contain

more recent information. &#x02014;</italic>ED.</p>

<table-wrap id="

pkd-ar.molgen.TA

" position="anchor">

<caption>

<p>Table A. Polycystic Kidney Disease,

Autosomal

Recessive:

Genes and Databases</p>

</caption>

<table>

<

tbody

>

<

tr

><th

>Gene Symbol</th><th>Chromosomal Locus</th>

<th>Protein Name</th><

th>Locus Specific</th><th>HGMD</th>

</tr>Data in the JATS Book DTD Delivered from External Database

<?get-external-xml molgen.tables?>Processing Instruction in Source XMLSlide33

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