[This local archive copy mirrored from: http://www.ncbi.nlm.nih.gov/PubMed/spec.html; see the canonical version of the document.]
NCBI standard publisher data format
This is our standard data format for publishers to use in submitting
citation data to NCBI for processing into the MEDLINE or PubMed databases.
This is a tagged format, meaning that each part of a citation
is preceded by a <Tag> string and followed by a </Tag> string, where Tag
is some appropriate label. The first two sections list the tags used and what
information they enclose; the third gives an example. If you need further
assistance, please email us at
pubmed@ncbi.nlm.nih.gov.
Note! While we
encourage the use of this format, we do not require
it; any format that provides the same
level of detail is adequate. If you wish to use another format,
please email us and provide a sample.
This document contains:
Data Tags (R = Required, O = Optional) :
ArticleSet (R) An entire submission of the set of articles.
Each issue of a given journal must be enclosed in these tags.
Article (R) An article submission. Each article must be enclosed
in these tags.
- Journal (R) The journal submission. Each issue of a given journal
must be enclosed in these tags.
- PublisherName (R) The publisher name.
- JournalTitle (R) The standard abbreviation for the journal title.
If you do not know this abbreviation,
consult the PubMed journal browser.
- Issn (R) The ISSN of the journal.
- Volume (R) The volume name or number of this journal, including any supplement information.
- Issue (O) The issue number.
- Part (O) Supplementary issue information, e.g. an issue part.
- PubDate (R) The publication date information must be enclosed in these tags.
- Year (R) The year of publication.
- Month (O) The month of publication.
- Day (O) The day of publication.
- Season (O) The season of publication (do not use if a month is available).
- HoldDate (O) The date when the journal issue can be released to the public. Do not use this field if
you wish the journal released on the publication date, given above. If you want the issue released
immediately regardless of the publication date, you may just skip this tag.
- Year (R) The year of release.
- Month (R) The month of release.
- Day (R) The day of release.
- Replaces (O) The PubMed ID of the article that this one replaces. Do not use this tag for new articles. If a
submitted article has the same bibliographical information (journal, volume, page) as an existing article and does not
contain this tag, it will be rejected.
- ArticleTitle (R) The article title.
- SubTitle (O) The article subtitle.
- FirstPage (R) The first page that the article appears on.
- LastPage (O) The last page the article appears on.
- Language (O) The language the article is in. This should be chosen from the language codes in ISO 639 (see
below). If unspecified, EN (English) is assumed.
- AuthorList (R) The author information must be enclosed in these tags.
- Author (R) Information about a single author must begin with this tag.
- LastName (R) The Author's last name.
- FirstName (R) The Author's first name or initial.
- MiddleName (O) The Author's middle name(s) or initial(s).
- Suffix (O) The Author's suffix, if any, e.g. "Jr", "Sr", "II", "IV".
- CollectiveName (special) The name of the authoring committee or
organization. This tag is used in place of LastName, FirstName, and
MiddleName for non-individual authors. The tags for an individual author
name or a collective author must be supplied, but not both.
- Affiliation (O) The institution(s) that the Author is affiliated with. This may be given as a simple string within
the <Affiliation> </Affiliation> tags, or may be subdivided among the following tags:
- Institution (O) The institution name.
- Division (O) The division of the institution.
- StreetAddress (O) The institution's street address.
- City (O) The city where the institution resides.
- PostalCode (O) The institution's postal or zip code.
- Country (O) The country where the institution resides.
- Phone (O) The institution's telephone number.
- Fax (O) The institution's Fax number.
- Email (O) The institution's e-mail address.
- PublicationType (O) A keyword giving information about what
type of citation this is.
- FullTextURL (O) The URL to be used for accesses to the full
article's text.
- SummaryURL (O) This SummaryURL is to be used for access
to summary data (e.g. an abstract view) that does not require subscription
or payment.
Both FullTextURL and SummaryURL can either be a single URL or
can have the syntax: [list of location codes]::URL;
[list of location codes]::URL; *::DefaultURL where
[list of location codes] is one or more strings, e.g. 'uk','de','it',
'gov', etc.
- PublisherId (O) The article's unic identification line.
- Abstract (O) The article's abstract.
- Keywords (O) The article's list of author-supplied key words.
Special Characters
Characters not in the standard ASCII character set must be represented
using standard
SGML entity codes. For instance, "ç"
represents a c cedilla. "’" in the example below
is a right single-quote.
<ArticleSet>
<Article>
<Journal>
<PublisherName>AAAS</PublisherName>
<JournalTitle>SCIENCE</JournalTitle>
<Issn>9731-864X</Issn>
<Volume>271 suppl. 3</Volume>
<Issue>5</Issue>
<PubDate>
<Year>1996</Year>
<Month>Mar</Month>
<Day>3</Day>
</PubDate>
</Journal>
<ArticleTitle>The Elasticity of a Single
Supercoiled DNA Molecule</ArticleTitle>
<FirstPage>1835</FirstPage>
<LastPage>1837</LastPage>
<Language>EN</Language>
<AuthorList>
<Author>
<FirstName>Kenneth</FirstName>
<MiddleName>S.</MiddleName>
<LastName>Strick</LastName>
<Suffix>Jr.</Suffix>
<Affiliation>
Laboratoire de Biophysique de l’ADN, Institut
Pasteur, 25-28 rue du Dr Roux, Paris, 75015 France.
</Affiliation>
</Author>
<Author>
<FirstName>J.-F.</FirstName>
<LastName>Allemand</LastName>
<Affiliation>
<Institution> Laboratoire de Physique
Statistique de l’ENS, </Institution>
<StreetAddress>24 rue Lhomond</StreetAddress>
<City>Paris</City>
<PostalCode>75015</PostalCode>
<Country>France</Country>
</Affiliation>
</Author>
</AuthorList>
<PublicationType>JOURNAL ARTICLE</PublicationType>
<FullTextURL>
http://www.oup.co.uk/nar/Volume_24/Issue_02/5c0194_gml.abs.html
</FullTextURL>
<SummaryURL>
uk,fr,sp,it,de,nd,no::http://www.oup.co.uk/nar;
jp::http://www.nar.com/nar;
*::http://www.nar.com/nar
</SummaryURL>
<PublisherId>sc271_5_1835</PublisherId>
<Abstract>
Single linear DNA molecules were bound at multiple sites at
one extremity to a treated glass cover slip and at the other
to a magnetic bead. The DNA was therefore torsionally
constrained. A magnetic field was used to rotate the beads
and thus to coil and pull the DNA. The stretching force was
determined by analysis of the Brownian fluctuations of
the bead. Here, the elastic behavior of individual &lgr;
DNA molecules over- and underwound by up to 500 turns was
studied. A sharp transition was discovered from a low to
a high extension state at a force of ∼0.45 piconewtons
for underwound molecules and at a force of ∼
3 piconewtons for overwound ones. These transitions,
probably reflecting the formation of alternative structures
in stretched coiled DNA molecules, might be relevant for
DNA transcription and replication.
</Abstract>
<Keywords>
magnetic field;DNA transcription;Elasticity
</Keywords>
</Article>
</ArticleSet>
The following is a subset of the ISO 639 standard for language codes.
CODE LANGUAGE
---- --------
DA Danish
DE German
EN English
EL Greek
ES Spanish
FR French
IT Italian
IW Hebrew
JA Japanese
NL Dutch
NO Norwegian
RU Russian
SV Swedish
ZH Chinese
<!DOCTYPE ArticleSet [
<!-- ncbi.dtd; NCBI PubMed DTD Version 1.5, September 29, 1997 -->
<!ENTITY % ISOlat1 PUBLIC "ISO 8879-1986//ENTITIES Added Latin 1//EN">
%ISOlat1;
<!ENTITY % ISOlat2 PUBLIC "ISO 8879-1986//ENTITIES Added Latin 2//EN">
%ISOlat2;
<!ENTITY % ISOnum PUBLIC "ISO 8879-1986//ENTITIES Numeric and Special Graphic//EN">
%ISOnum;
<!ENTITY % ISOpub PUBLIC "ISO 8879-1986//ENTITIES Publishing//EN">
%ISOpub;
<!ENTITY % ISOgrk1 PUBLIC "ISO 8879-1986//ENTITIES Greek Letters//EN">
%ISOgrk1;
<!ENTITY % ISOgrk2 PUBLIC "ISO 8879-1986//ENTITIES Monotoniko Greek//EN">
%ISOgrk2;
<!ENTITY % ISOgrk3 PUBLIC "ISO 8879-1986//ENTITIES Greek Symbols//EN">
%ISOgrk3;
<!ENTITY % ISOtech PUBLIC "ISO 8879-1986//ENTITIES General Technical//EN">
%ISOtech;
<!ENTITY % ISOdia PUBLIC "ISO 8879-1986//ENTITIES Diacritical Marks//EN">
%ISOdia;
<!ENTITY % ISOamso PUBLIC "ISO 8879-1986//ENTITIES Added Math Symbols: Ordinary//EN">
%ISOamso;
<!ENTITY % ISOamsb PUBLIC "ISO 8879-1986//ENTITIES Added Math Symbols: Binary Operators//EN">
%ISOamsb;
<!ENTITY % ISOamsr PUBLIC "ISO 8879-1986//ENTITIES Added Math Symbols: Relations//EN">
%ISOamsr;
<!ENTITY % ISOamsn PUBLIC "ISO 8879-1986//ENTITIES Added Math Symbols: Negated Relations//EN">
%ISOamsn;
<!ENTITY % ISOamsa PUBLIC "ISO 8879-1986//ENTITIES Added Math Symbols: Arrow Relations//EN">
%ISOamsa;
<!ENTITY % ISOamsc PUBLIC "ISO 8879-1986//ENTITIES Added Math Symbols: Delimiters//EN">
%ISOamsc;
<!ENTITY % ISObox PUBLIC "ISO 8879-1986//ENTITIES Box and Line Drawing//EN">
%ISObox;
<!ENTITY % ISOcyr1 PUBLIC "ISO 8879-1986//ENTITIES Russian Cyrillic//EN">
%ISOcyr1;
<!ENTITY % ISOcyr2 PUBLIC "ISO 8879-1986//ENTITIES Non-Russian Cyrillic//EN">
%ISOcyr2;
<!ENTITY % data "(#PCDATA | e1 | e2 | e3 | e4 | e5 | e6
| e7 | e8 | e9 | sup | inf)*">
<!-- This is the top level element -->
<!ELEMENT ArticleSet - - ( Article+)>
<!ELEMENT Article - - ( Journal, Replaces?, ArticleTitle, FirstPage,
LastPage?, Language?, AuthorList?,
PublicationType?, FullTextURL?, SummaryURL?,
PublisherId?, Abstract?, Keywords? )>
<!ELEMENT Journal - - ( PublisherName, JournalTitle, Issn,
Volume, Issue?, Part?, PubDate,
HoldDate? )>
<!ELEMENT PublisherName - - (#PCDATA)>
<!ELEMENT JournalTitle - - (#PCDATA)>
<!ELEMENT Issn - - (#PCDATA)>
<!ELEMENT Volume - - (#PCDATA)>
<!ELEMENT Issue - - (#PCDATA)>
<!ELEMENT Part - - (#PCDATA)>
<!ELEMENT PubDate - - ( year, month?, day?, season? )>
<!ELEMENT Year - - (#PCDATA)>
<!ELEMENT Month - - (#PCDATA)>
<!ELEMENT Day - - (#PCDATA)>
<!ELEMENT Season - - (#PCDATA)>
<!-- End of PubDate group -->
<!ELEMENT HoldDate - - ( Year, Month, Day )>
<!-- End of Journal group -->
<!ELEMENT Replaces - - (#PCDATA)>
<!ELEMENT ArticleTitle - - (#PCDATA, SubTitle? )>
<!ELEMENT SubTitle - - (#PCDATA)>
<!-- End of ArticleTitle group -->
<!ELEMENT FirstPage - - (#PCDATA)>
<!ELEMENT LastPage - - (#PCDATA)>
<!ELEMENT Language - - (#PCDATA)>
<!ELEMENT AuthorList - - ( Author+ )>
<!ELEMENT Author - - ( (FirstName, MiddleName?, LastName, Suffix?) |
CollectiveName),
Affiliation? )>
<!ELEMENT FirstName - - (#PCDATA)>
<!ELEMENT MiddleName - - (#PCDATA)>
<!ELEMENT LastName - - (#PCDATA)>
<!ELEMENT CollectiveName - - (#PCDATA)>
<!ELEMENT Suffix - - (#PCDATA)>
<!ELEMENT Affiliation - - ( #PCDATA | ( Institution?, Division?,
StreetAddress?, ( City | PostalCode | Country )*,
Phone?, Fax?, Email? )>
<!ELEMENT Institution - - (#PCDATA)>
<!ELEMENT Division - - (#PCDATA)>
<!ELEMENT City - - (#PCDATA)>
<!ELEMENT Country - - (#PCDATA)>
<!ELEMENT StreetAddress - - (#PCDATA)>
<!ELEMENT PostalCode - - (#PCDATA)>
<!ELEMENT Phone - - (#PCDATA)>
<!ELEMENT Fax - - (#PCDATA)>
<!ELEMENT Email - - (#PCDATA)>
<!-- End of Affiliation group -->
<!-- End of Author group -->
<!-- End of AuthorList group -->
<!ELEMENT PublicationType - - (#PCDATA)>
<!ELEMENT FullTextURL - - (#PCDATA)>
<!ELEMENT SummaryURL - - (#PCDATA)>
<!ELEMENT PublisherId - - (#PCDATA)>
<!ELEMENT Abstract - - (%data;)+>
<!ELEMENT Keywords - - (%data;)+>
<!-- End of Article group -->
<!-- End of ArticleSet group -->
<!-- Commonly used formatting elements -->
<!ELEMENT e1 - - (%data;)*>
<!ELEMENT e2 - - (%data;)*>
<!ELEMENT e3 - - (%data;)*>
<!ELEMENT e4 - - (%data;)*>
<!ELEMENT e5 - - (%data;)*>
<!ELEMENT e6 - - (%data;)*>
<!ELEMENT e7 - - (%data;)*>
<!ELEMENT e8 - - (%data;)*>
<!ELEMENT e9 - - (%data;)*>
<!ELEMENT sup - - (%data;)*>
<!ELEMENT sub - - (%data;)*>
<!ELEMENT inf - - (%data;)*>
]>
Credits: Brandon Brylawski,
Alexander Levitsky
Last Modified: September 29, 1997