Book and Collection Tag Library version 3.0

<ext-link>

External Link

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

Remarks

Unlike the base Suite, the Book Tag Set’s and the Collection Tag Set’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 Tag Set 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

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

pmcid

PubMed Central identifier

pmid

PubMed identifier

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

pmid

PubMed Central Identifier

sgd

Saacharomyces Genome Database

snp

Single Nucleotide Polymorphism

wbase

Wormbase

Attributes

ext-link-type Type of External Link
id Identifier
qualifier Qualifier
specific-use Specific Use
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

<self-uri> is used when an article is available in multiple forms, for example, as a means of indicating the online version of a print article. Conversely, a URI that indicates a different article or any other kind of external reference is usually tagged with <ext-link>. <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 article.

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>.

Content Model

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

Expanded Content Model

(#PCDATA | bold | italic | monospace | overline | overline-start | overline-end | roman | sans-serif | sc | strike | underline | underline-start | underline-end | alternatives | inline-graphic | private-char | graphic | media | named-content | styled-content | sub | sup)*

Description

Any combination of:

This element may be contained in:

<address>, <aff>, <alt-title>, <array>, <article-title>, <attrib>, <bold>, <book-meta>, <book-part-meta>, <book-title>, <chapter-title>, <chem-struct>, <chem-struct-wrap>, <collab>, <collection-member>, <collection-name>, <comment>, <contrib>, <contrib-group>, <copyright-statement>, <corresp>, <def-head>, <disp-formula>, <disp-formula-group>, <element-citation>, <fig>, <fig-group>, <funding-statement>, <graphic>, <inline-supplementary-material>, <italic>, <license-p>, <media>, <meta-value>, <mixed-citation>, <monospace>, <multi-link>, <named-content>, <overline>, <p>, <part-title>, <preformat>, <product>, <publisher-loc>, <related-article>, <related-object>, <roman>, <sans-serif>, <sc>, <source>, <strike>, <styled-content>, <sub>, <subtitle>, <sup>, <supplementary-material>, <table-wrap>, <table-wrap-group>, <td>, <term>, <term-head>, <th>, <title>, <trans-source>, <trans-subtitle>, <trans-title>, <underline>

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

common3.ent

Book and Collection Tag Library version 3.0

Version of November 2008