NCBI Book DTD and NCBI Collection DTD Tag Library version 2.2

<ext-link>

External Link

Definition

Link to an external file, such as MEDLINE, GenBank, etc.

Remarks

Unlike the base DTD Suite, the NCBI Book DTD’s and the NCBI Collection DTD’s content model for this element includes graphical elements for use in instances where, for example, an onscreen arrow serves as the link to a picture or database.

Use the standard XLink attributes to provide a live link to the external source.

The ext-link-type attribute can be used to give an indication of the type of resource to which the external link points. While the DTD does not constrain the values of this attribute, and ordinary text is acceptable, the suggested values include:

ec

Enzyme nomenclature. See http://www.chem.qmw.ac.uk/iubmb/enzyme/

gen

GenBank identifier

genpept

Translated protein-encoding sequence database

highwire

HighWire Press intrajournal

medline

MEDLINE or PubMed identifier

pdb

Protein data bank. See http://www.rcsb.org/pdb/

pgr

Plant gene register. See http://www.tarweed.com/pgr/

pir

Protein Information Resource. See http://pir.georgetown.edu

pirdb

Protein Information Resource. See http://pir.georgetown.edu

pmc

Used to link between articles in PubMed Central (access is PMID)

sprot

Swiss-Prot. See http://www.ebi.ac.uk/swissprot/

aoi

Astronomical Object Identifier

doi

Digital Object Identifier

ftp

File transfer protocol

uri

Website or web service

cdd

Conserved Domain Database

email

An email address

entrez-gene

Entrez Gene

hmh

Human-Mouse Homology Maps

mgi

Mouse Genome Informatics

omim

Online Mendelian Inheritance in Man

pubmed

PubMed Central

sgd

Saacharomyces Genome Database

snp

Single Nucleotide Polymorphism

wbase

Wormbase

Attributes

ext-link-type Type of External Link
id Identifier
qualifier Qualifier
taxonomic-id Taxonomic Identifier
xlink:actuate Actuating the Link
xlink:href Href (Linking Mechanism)
xlink:role Role of the Link
xlink:show Showing the Link
xlink:title Title of the Link
xlink:type Type of Link
xmlns:xlink XLink Namespace Declaration

Related Elements

The <self-uri> element is used when a book (or book component) is available in multiple forms, for example as a means of indicating the online version of a print book. Conversely, a URI that indicates a different book or any other kind of external reference is usually tagged with the <ext-link> element. The element <uri>, although allowed everywhere <ext-link> is used, is more typically part of an address, information concerning a contributor, or part of a reference citation. Loosely put, an external link <ext-link> is intended to act as a link; a URI <uri> makes no promises but identifies a URI, such as a URL, when it is present in the text of an address or a citation; and self-uri points to another form of the same book (or book component).

The address element <email> is allowed as part of a paragraph as well as inside an address. There are two ways to treat an email address in text: as and <email> element or as and <ext-link> element. If both a textual phrase (“the Moody Institute’s email address”) and a mailto URL are required, the <ext-link> element should be used.

The elements used in an address include the address class elements: <addr-line>, <country>, <fax>, <institution>, and <phone> and the address linking class elements: <email>, <ext-link>, <multi-link>, and <uri>.

Model Information

Content Model

<!ELEMENT  ext-link     (#PCDATA %ext-link-elements;)*               >

Description

Any combination of:

This element may be contained in:

<address> Address/Contact Information; <aff> Affiliation; <alt-title> Alternate Title; <array> Array (Simple Tabular Array); <article-title> Article Title; <attrib> Attribution; <bold> Bold; <book-meta> Book Metadata; <book-part-meta> Book Part Metadata; <book-title> Book Title; <chem-struct> Chemical Structure (Display); <chem-struct-wrapper> Chemical Structure Wrapper; <citation> Citation; <collab> Collaborative (Group) Author; <collection-member> Collection Member; <collection-name> Collection Name; <comment> Comment in a Citation; <contrib> Contributor; <contrib-group> Contributor Group; <copyright-statement> Copyright Statement; <corresp> Correspondence Information; <def-head> Definition List: Definition Head; <disp-formula> Formula, Display; <fig> Figure; <fig-group> Figure Group; <graphic> Graphic; <inline-supplementary-material> Inline Supplementary Material; <italic> Italic; <media> Media Object; <meta-name> Metadata Data Name for Custom Metadata; <meta-value> Metadata Data Value for Custom Metadata; <monospace> Monospace Text (Typewriter Text); <multi-link> Multi-Link; <named-content> Named Special (Subject) Content; <overline> Overline; <p> Paragraph; <preformat> Preformatted Text; <publisher-loc> Publisher’s Location; <related-article> Related Article Information; <related-object> Related Object Information; <sc> Small Caps; <source> Source; <strike> Strike Through; <sub> Subscript; <subtitle> Subtitle; <sup> Superscript; <supplementary-material> Supplementary Material; <table-wrap> Table Wrapper; <table-wrap-group> Table Wrapper Group; <td> Table Data Cell (XHTML table model); <term> Definition List: Term; <term-head> Definition List: Term Head; <th> Table Header Cell (XHTML table model); <title> Title; <trans-source> Translated Source; <trans-subtitle> Translated Subtitle; <trans-title> Translated Title; <underline> Underline

Tagged Example


...
<p>In the mid-1990s, the GenBank database became part of 
the International Nucleotide Sequence Database Collaboration 
with the EMBL database (<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" 
ext-link-type="uri" xlink:href="http://www.ebi.ac.uk/">European 
Bioinformatics Institute</ext-link>, Hinxton, United Kingdom) 
and the Genome Sequence Database (GSDB; LANL, Los Alamos, NM). 
Subsequently, the GSDB was removed from the Collaboration (by 
the National Center for Genome Resources, Santa Fe, NM), and 
<ext-link xmlns:xlink="http://www.w3.org/1999/xlink" 
ext-link-type="uri" xlink:href="http://www.ddbj.nig.ac.jp/">DDBJ</ext-link> 
(Mishima, Japan) joined the group. ...</p>
...

Module

common.ent

NCBI Book DTD and NCBI Collection DTD Tag Library version 2.2

Version of October 13, 2006