path: root/asn/asnpub.all

--$Revision: 6.3 $
--**********************************************************************
--
--  NCBI General Data elements
--  by James Ostell, 1990
--  Version 3.0 - June 1994
--
--**********************************************************************

NCBI-General DEFINITIONS ::=
BEGIN

EXPORTS Date, Person-id, Object-id, Dbtag, Int-fuzz, User-object;

-- StringStore is really a VisibleString.  It is used to define very
--   long strings which may need to be stored by the receiving program
--   in special structures, such as a ByteStore, but it's just a hint.
--   AsnTool stores StringStores in ByteStore structures.
-- OCTET STRINGs are also stored in ByteStores by AsnTool
-- 
-- typedef struct bsunit {             /* for building multiline strings */
   -- Nlm_Handle str;            /* the string piece */
   -- Nlm_Int2 len_avail,
       -- len;
   -- struct bsunit PNTR next; }       /* the next one */
-- Nlm_BSUnit, PNTR Nlm_BSUnitPtr;
-- 
-- typedef struct bytestore {
   -- Nlm_Int4 seekptr,       /* current position */
      -- totlen,             /* total stored data length in bytes */
      -- chain_offset;       /* offset in ByteStore of first byte in curchain */
   -- Nlm_BSUnitPtr chain,       /* chain of elements */
      -- curchain;           /* the BSUnit containing seekptr */
-- } Nlm_ByteStore, PNTR Nlm_ByteStorePtr;
--
-- AsnTool incorporates this as a primitive type, so the definition
--   is here just for completeness
-- 
--  StringStore ::= [APPLICATION 1] IMPLICIT OCTET STRING
--

-- BigInt is really an INTEGER. It is used to warn the receiving code to expect
--   a value bigger than Int4 (actually Int8). It will be stored in DataVal.bigintvalue
--
--   Like StringStore, AsnTool incorporates it as a primitive. The definition would be:
--   BigInt ::= [APPLICATION 2] IMPLICIT INTEGER
--

-- Date is used to replace the (overly complex) UTCTtime, GeneralizedTime
--  of ASN.1
--  It stores only a date
--

Date ::= CHOICE {
    str VisibleString ,        -- for those unparsed dates
    std Date-std }             -- use this if you can

Date-std ::= SEQUENCE {        -- NOTE: this is NOT a unix tm struct
    year INTEGER ,             -- full year (including 1900)
    month INTEGER OPTIONAL ,   -- month (1-12)
    day INTEGER OPTIONAL ,     -- day of month (1-31)
    season VisibleString OPTIONAL ,  -- for "spring", "may-june", etc
    hour INTEGER OPTIONAL ,    -- hour of day (0-23)
    minute INTEGER OPTIONAL ,  -- minute of hour (0-59)
    second INTEGER OPTIONAL }  -- second of minute (0-59)

-- Dbtag is generalized for tagging
-- eg. { "Social Security", str "023-79-8841" }
-- or  { "member", id 8882224 }

Dbtag ::= SEQUENCE {
    db VisibleString ,          -- name of database or system
    tag Object-id }         -- appropriate tag

-- Object-id can tag or name anything
--

Object-id ::= CHOICE {
    id INTEGER ,
    str VisibleString }

-- Person-id is to define a std element for people
--

Person-id ::= CHOICE {
    dbtag Dbtag ,               -- any defined database tag
    name Name-std ,             -- structured name
    ml VisibleString ,          -- MEDLINE name (semi-structured)
                                --    eg. "Jones RM"
    str VisibleString }         -- unstructured name

Name-std ::= SEQUENCE { -- Structured names
    last VisibleString ,
    first VisibleString OPTIONAL ,
    middle VisibleString OPTIONAL ,
    full VisibleString OPTIONAL ,    -- full name eg. "J. John Smith, Esq"
    initials VisibleString OPTIONAL,  -- first + middle initials
    suffix VisibleString OPTIONAL ,   -- Jr, Sr, III
    title VisibleString OPTIONAL }    -- Dr., Sister, etc

--**** Int-fuzz **********************************************
--*
--*   uncertainties in integer values

Int-fuzz ::= CHOICE {
    p-m INTEGER ,                    -- plus or minus fixed amount
    range SEQUENCE {                 -- max to min
        max INTEGER ,
        min INTEGER } ,
    pct INTEGER ,                    -- % plus or minus (x10) 0-1000
    lim ENUMERATED {                 -- some limit value
        unk (0) ,                    -- unknown
        gt (1) ,                     -- greater than
        lt (2) ,                     -- less than
        tr (3) ,                     -- space to right of position
        tl (4) ,                     -- space to left of position
        circle (5) ,                 -- artificial break at origin of circle
        other (255) } ,              -- something else
    alt SET OF INTEGER }             -- set of alternatives for the integer


--**** User-object **********************************************
--*
--*   a general object for a user defined structured data item
--*    used by Seq-feat and Seq-descr

User-object ::= SEQUENCE {
    class VisibleString OPTIONAL ,   -- endeavor which designed this object
    type Object-id ,                 -- type of object within class
    data SEQUENCE OF User-field }    -- the object itself

User-field ::= SEQUENCE {
    label Object-id ,                -- field label
    num INTEGER OPTIONAL ,           -- required for strs, ints, reals, oss
    data CHOICE {                    -- field contents
        str VisibleString ,
        int INTEGER ,
        real REAL ,
        bool BOOLEAN ,
        os OCTET STRING ,
        object User-object ,         -- for using other definitions
        strs SEQUENCE OF VisibleString ,
        ints SEQUENCE OF INTEGER ,
        reals SEQUENCE OF REAL ,
        oss SEQUENCE OF OCTET STRING ,
        fields SEQUENCE OF User-field ,
        objects SEQUENCE OF User-object } }



END

--$Revision: 6.2 $
--****************************************************************
--
--  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;

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


--$Revision: 6.0 $
--**********************************************************************
--
--  MEDLINE data definitions
--  James Ostell, 1990
--
--  enhanced in 1996 to support PubMed records as well by simply adding
--    the PubMedId and making MedlineId optional
--
--**********************************************************************

NCBI-Medline DEFINITIONS ::=
BEGIN

EXPORTS Medline-entry, Medline-si;

IMPORTS Cit-art, PubMedId FROM NCBI-Biblio
        Date FROM NCBI-General;

                                -- a MEDLINE or PubMed entry
Medline-entry ::= SEQUENCE {
    uid INTEGER OPTIONAL ,      -- MEDLINE UID, sometimes not yet available if from PubMed
    em Date ,                   -- Entry Month
    cit Cit-art ,               -- article citation
    abstract VisibleString OPTIONAL ,
    mesh SET OF Medline-mesh OPTIONAL ,
    substance SET OF Medline-rn OPTIONAL ,
    xref SET OF Medline-si OPTIONAL ,
    idnum SET OF VisibleString OPTIONAL ,  -- ID Number (grants, contracts)
    gene SET OF VisibleString OPTIONAL ,
    pmid PubMedId OPTIONAL ,               -- MEDLINE records may include the PubMedId
    pub-type SET OF VisibleString OPTIONAL, -- may show publication types (review, etc)
    mlfield SET OF Medline-field OPTIONAL ,  -- additional Medline field types
    status INTEGER {
	publisher (1) ,      -- record as supplied by publisher
        premedline (2) ,     -- premedline record
        medline (3) } DEFAULT medline }  -- regular medline record

Medline-mesh ::= SEQUENCE {
    mp BOOLEAN DEFAULT FALSE ,       -- TRUE if main point (*)
    term VisibleString ,                   -- the MeSH term
    qual SET OF Medline-qual OPTIONAL }    -- qualifiers

Medline-qual ::= SEQUENCE {
    mp BOOLEAN DEFAULT FALSE ,       -- TRUE if main point
    subh VisibleString }             -- the subheading

Medline-rn ::= SEQUENCE {       -- medline substance records
    type ENUMERATED {           -- type of record
        nameonly (0) ,
        cas (1) ,               -- CAS number
        ec (2) } ,              -- EC number
    cit VisibleString OPTIONAL ,  -- CAS or EC number if present
    name VisibleString }          -- name (always present)

Medline-si ::= SEQUENCE {       -- medline cross reference records
    type ENUMERATED {           -- type of xref
        ddbj (1) ,              -- DNA Data Bank of Japan
        carbbank (2) ,          -- Carbohydrate Structure Database
        embl (3) ,              -- EMBL Data Library
        hdb (4) ,               -- Hybridoma Data Bank
        genbank (5) ,           -- GenBank
        hgml (6) ,              -- Human Gene Map Library
        mim (7) ,               -- Mendelian Inheritance in Man
        msd (8) ,               -- Microbial Strains Database
        pdb (9) ,               -- Protein Data Bank (Brookhaven)
        pir (10) ,              -- Protein Identification Resource
        prfseqdb (11) ,         -- Protein Research Foundation (Japan)
        psd (12) ,              -- Protein Sequence Database (Japan)
        swissprot (13) ,        -- SwissProt
        gdb (14) } ,            -- Genome Data Base
    cit VisibleString OPTIONAL }    -- the citation/accession number

Medline-field ::= SEQUENCE {
    type INTEGER {              -- Keyed type
	other (0) ,             -- look in line code
	comment (1) ,           -- comment line
        erratum (2) } ,         -- retracted, corrected, etc
    str VisibleString ,         -- the text
    ids SEQUENCE OF DocRef OPTIONAL }  -- pointers relevant to this text

DocRef ::= SEQUENCE {           -- reference to a document
    type INTEGER {
        medline (1) ,
        pubmed (2) ,
        ncbigi (3) } ,
    uid INTEGER }

END

--$Revision: 6.0 $
--********************************************************************
--
--  Publication common set
--  James Ostell, 1990
--
--  This is the base class definitions for Publications of all sorts
--
--  support for PubMedId added in 1996
--********************************************************************

NCBI-Pub DEFINITIONS ::=
BEGIN

EXPORTS Pub, Pub-set, Pub-equiv;

IMPORTS Medline-entry FROM NCBI-Medline
        Cit-art, Cit-jour, Cit-book, Cit-proc, Cit-pat, Id-pat, Cit-gen,
        Cit-let, Cit-sub, PubMedId FROM NCBI-Biblio;

Pub ::= CHOICE {
    gen Cit-gen ,        -- general or generic unparsed
    sub Cit-sub ,        -- submission
    medline Medline-entry ,
    muid INTEGER ,       -- medline uid
    article Cit-art ,
    journal Cit-jour ,
    book Cit-book ,
    proc Cit-proc ,      -- proceedings of a meeting
    patent Cit-pat ,
    pat-id Id-pat ,      -- identify a patent
    man Cit-let ,        -- manuscript, thesis, or letter
    equiv Pub-equiv,     -- to cite a variety of ways
	pmid PubMedId }      -- PubMedId

Pub-equiv ::= SET OF Pub   -- equivalent identifiers for same citation

Pub-set ::= CHOICE {
    pub SET OF Pub ,
    medline SET OF Medline-entry ,
    article SET OF Cit-art ,
    journal SET OF Cit-jour ,
    book SET OF Cit-book ,
    proc SET OF Cit-proc ,      -- proceedings of a meeting
    patent SET OF Cit-pat }

END