src/objects/biblio/biblio.asn
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--$Revision: 48194 $
--****************************************************************
--
-- NCBI Bibliographic data elements
-- by James Ostell, 1990
--
-- Taken from the American National Standard for
-- Bibliographic References
-- ANSI Z39.29-1977
-- Version 3.0 - June 1994
-- PubMedId added in 1996
-- ArticleIds and eprint elements added in 1999
--
--****************************************************************
NCBI-Biblio DEFINITIONS ::=
BEGIN
EXPORTS Cit-art, Cit-jour, Cit-book, Cit-pat, Cit-let, Id-pat, Cit-gen,
Cit-proc, Cit-sub, Title, Author, PubMedId, DOI;
IMPORTS Person-id, Date, Dbtag FROM NCBI-General;
-- Article Ids
ArticleId ::= CHOICE { -- can be many ids for an article
pubmed PubMedId , -- see types below
medline MedlineUID ,
doi DOI ,
pii PII ,
pmcid PmcID ,
pmcpid PmcPid ,
pmpid PmPid ,
other Dbtag } -- generic catch all
PubMedId ::= INTEGER -- Id from the PubMed database at NCBI
MedlineUID ::= INTEGER -- Id from MEDLINE
DOI ::= VisibleString -- Document Object Identifier
PII ::= VisibleString -- Controlled Publisher Identifier
PmcID ::= INTEGER -- PubMed Central Id
PmcPid ::= VisibleString -- Publisher Id supplied to PubMed Central
PmPid ::= VisibleString -- Publisher Id supplied to PubMed
ArticleIdSet ::= SET OF ArticleId
-- Status Dates
PubStatus ::= INTEGER { -- points of publication
received (1) , -- date manuscript received for review
accepted (2) , -- accepted for publication
epublish (3) , -- published electronically by publisher
ppublish (4) , -- published in print by publisher
revised (5) , -- article revised by publisher/author
pmc (6) , -- article first appeared in PubMed Central
pmcr (7) , -- article revision in PubMed Central
pubmed (8) , -- article citation first appeared in PubMed
pubmedr (9) , -- article citation revision in PubMed
aheadofprint (10), -- epublish, but will be followed by print
premedline (11), -- date into PreMedline status
medline (12), -- date made a MEDLINE record
other (255) }
PubStatusDate ::= SEQUENCE { -- done as a structure so fields can be added
pubstatus PubStatus ,
date Date } -- time may be added later
PubStatusDateSet ::= SET OF PubStatusDate
-- Citation Types
Cit-art ::= SEQUENCE { -- article in journal or book
title Title OPTIONAL , -- title of paper (ANSI requires)
authors Auth-list OPTIONAL , -- authors (ANSI requires)
from CHOICE { -- journal or book
journal Cit-jour ,
book Cit-book ,
proc Cit-proc } ,
ids ArticleIdSet OPTIONAL } -- lots of ids
Cit-jour ::= SEQUENCE { -- Journal citation
title Title , -- title of journal
imp Imprint }
Cit-book ::= SEQUENCE { -- Book citation
title Title , -- Title of book
coll Title OPTIONAL , -- part of a collection
authors Auth-list, -- authors
imp Imprint }
Cit-proc ::= SEQUENCE { -- Meeting proceedings
book Cit-book , -- citation to meeting
meet Meeting } -- time and location of meeting
-- Patent number and date-issue were made optional in 1997 to
-- support patent applications being issued from the USPTO
-- Semantically a Cit-pat must have either a patent number or
-- an application number (or both) to be valid
Cit-pat ::= SEQUENCE { -- patent citation
title VisibleString ,
authors Auth-list, -- author/inventor
country VisibleString , -- Patent Document Country
doc-type VisibleString , -- Patent Document Type
number VisibleString OPTIONAL, -- Patent Document Number
date-issue Date OPTIONAL, -- Patent Issue/Pub Date
class SEQUENCE OF VisibleString OPTIONAL , -- Patent Doc Class Code
app-number VisibleString OPTIONAL , -- Patent Doc Appl Number
app-date Date OPTIONAL , -- Patent Appl File Date
applicants Auth-list OPTIONAL , -- Applicants
assignees Auth-list OPTIONAL , -- Assignees
priority SEQUENCE OF Patent-priority OPTIONAL , -- Priorities
abstract VisibleString OPTIONAL } -- abstract of patent
Patent-priority ::= SEQUENCE {
country VisibleString , -- Patent country code
number VisibleString , -- number assigned in that country
date Date } -- date of application
Id-pat ::= SEQUENCE { -- just to identify a patent
country VisibleString , -- Patent Document Country
id CHOICE {
number VisibleString , -- Patent Document Number
app-number VisibleString } , -- Patent Doc Appl Number
doc-type VisibleString OPTIONAL } -- Patent Doc Type
Cit-let ::= SEQUENCE { -- letter, thesis, or manuscript
cit Cit-book , -- same fields as a book
man-id VisibleString OPTIONAL , -- Manuscript identifier
type ENUMERATED {
manuscript (1) ,
letter (2) ,
thesis (3) } OPTIONAL }
-- NOTE: this is just to cite a
-- direct data submission, see NCBI-Submit
-- for the form of a sequence submission
Cit-sub ::= SEQUENCE { -- citation for a direct submission
authors Auth-list , -- not necessarily authors of the paper
imp Imprint OPTIONAL , -- this only used to get date.. will go
medium ENUMERATED { -- medium of submission
paper (1) ,
tape (2) ,
floppy (3) ,
email (4) ,
other (255) } OPTIONAL ,
date Date OPTIONAL , -- replaces imp, will become required
descr VisibleString OPTIONAL } -- description of changes for public view
Cit-gen ::= SEQUENCE { -- NOT from ANSI, this is a catchall
cit VisibleString OPTIONAL , -- anything, not parsable
authors Auth-list OPTIONAL ,
muid INTEGER OPTIONAL , -- medline uid
journal Title OPTIONAL ,
volume VisibleString OPTIONAL ,
issue VisibleString OPTIONAL ,
pages VisibleString OPTIONAL ,
date Date OPTIONAL ,
serial-number INTEGER OPTIONAL , -- for GenBank style references
title VisibleString OPTIONAL , -- eg. cit="unpublished",title="title"
pmid PubMedId OPTIONAL } -- PubMed Id
-- Authorship Group
Auth-list ::= SEQUENCE {
names CHOICE {
std SEQUENCE OF Author , -- full citations
ml SEQUENCE OF VisibleString , -- MEDLINE, semi-structured
str SEQUENCE OF VisibleString } , -- free for all
affil Affil OPTIONAL } -- author affiliation
Author ::= SEQUENCE {
name Person-id , -- Author, Primary or Secondary
level ENUMERATED {
primary (1),
secondary (2) } OPTIONAL ,
role ENUMERATED { -- Author Role Indicator
compiler (1),
editor (2),
patent-assignee (3),
translator (4) } OPTIONAL ,
affil Affil OPTIONAL ,
is-corr BOOLEAN OPTIONAL } -- TRUE if corresponding author
Affil ::= CHOICE {
str VisibleString , -- unparsed string
std SEQUENCE { -- std representation
affil VisibleString OPTIONAL , -- Author Affiliation, Name
div VisibleString OPTIONAL , -- Author Affiliation, Division
city VisibleString OPTIONAL , -- Author Affiliation, City
sub VisibleString OPTIONAL , -- Author Affiliation, County Sub
country VisibleString OPTIONAL , -- Author Affiliation, Country
street VisibleString OPTIONAL , -- street address, not ANSI
email VisibleString OPTIONAL ,
fax VisibleString OPTIONAL ,
phone VisibleString OPTIONAL ,
postal-code VisibleString OPTIONAL }}
-- Title Group
-- Valid for = A = Analytic (Cit-art)
-- J = Journals (Cit-jour)
-- B = Book (Cit-book)
-- Valid for:
Title ::= SET OF CHOICE {
name VisibleString , -- Title, Anal,Coll,Mono AJB
tsub VisibleString , -- Title, Subordinate A B
trans VisibleString , -- Title, Translated AJB
jta VisibleString , -- Title, Abbreviated J
iso-jta VisibleString , -- specifically ISO jta J
ml-jta VisibleString , -- specifically MEDLINE jta J
coden VisibleString , -- a coden J
issn VisibleString , -- ISSN J
abr VisibleString , -- Title, Abbreviated B
isbn VisibleString } -- ISBN B
Imprint ::= SEQUENCE { -- Imprint group
date Date , -- date of publication
volume VisibleString OPTIONAL ,
issue VisibleString OPTIONAL ,
pages VisibleString OPTIONAL ,
section VisibleString OPTIONAL ,
pub Affil OPTIONAL, -- publisher, required for book
cprt Date OPTIONAL, -- copyright date, " " "
part-sup VisibleString OPTIONAL , -- part/sup of volume
language VisibleString DEFAULT "ENG" , -- put here for simplicity
prepub ENUMERATED { -- for prepublication citations
submitted (1) , -- submitted, not accepted
in-press (2) , -- accepted, not published
other (255) } OPTIONAL ,
part-supi VisibleString OPTIONAL , -- part/sup on issue
retract CitRetract OPTIONAL , -- retraction info
pubstatus PubStatus OPTIONAL , -- current status of this publication
history PubStatusDateSet OPTIONAL } -- dates for this record
CitRetract ::= SEQUENCE {
type ENUMERATED { -- retraction of an entry
retracted (1) , -- this citation retracted
notice (2) , -- this citation is a retraction notice
in-error (3) , -- an erratum was published about this
erratum (4) } , -- this is a published erratum
exp VisibleString OPTIONAL } -- citation and/or explanation
Meeting ::= SEQUENCE {
number VisibleString ,
date Date ,
place Affil OPTIONAL }
END