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--$Revision: 1000.1 $
--**********************************************************************
--
-- 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 completness
--
-- StringStore ::= [APPLICATION 1] IMPLICIT OCTET STRING
--
-- BigInt is really an INTEGER. It is used to warn the recieving 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 Poop, 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: 1000.1 $
--****************************************************************
--
-- 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 corressponding 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 citaions
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: 1000.1 $
--**********************************************************************
--
-- 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: 1000.1 $
--**********************************************************************
--
-- MEDLARS data definitions
-- Grigoriy Starchenko, 1997
--
--**********************************************************************
NCBI-Medlars DEFINITIONS ::=
BEGIN
EXPORTS Medlars-entry, Medlars-record;
IMPORTS PubMedId FROM NCBI-Biblio;
Medlars-entry ::= SEQUENCE { -- a MEDLARS entry
pmid PubMedId, -- All entries in PubMed must have it
muid INTEGER OPTIONAL, -- Medline(OCCS) id
recs SET OF Medlars-record -- List of Medlars records
}
Medlars-record ::= SEQUENCE {
code INTEGER, -- Unit record field type integer form
abbr VisibleString OPTIONAL, -- Unit record field type abbreviation form
data VisibleString -- Unit record data
}
END
--$Revision: 1000.1 $
--********************************************************************
--
-- 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
--$Revision: 1000.1 $
--**********************************************************************
--
-- PUBMED data definitions
--
--**********************************************************************
NCBI-PubMed DEFINITIONS ::=
BEGIN
EXPORTS Pubmed-entry, Pubmed-url;
IMPORTS PubMedId FROM NCBI-Biblio
Medline-entry FROM NCBI-Medline;
Pubmed-entry ::= SEQUENCE { -- a PubMed entry
-- PUBMED records must include the PubMedId
pmid PubMedId,
-- Medline entry information
medent Medline-entry OPTIONAL,
-- Publisher name
publisher VisibleString OPTIONAL,
-- List of URL to publisher cite
urls SET OF Pubmed-url OPTIONAL,
-- Publisher's article identifier
pubid VisibleString OPTIONAL
}
Pubmed-url ::= SEQUENCE {
location VisibleString OPTIONAL, -- Location code
url VisibleString -- Selected URL for location
}
END
--$Revision: 1000.1 $
--**********************************************************************
--
-- NCBI Sequence location and identifier elements
-- by James Ostell, 1990
--
-- Version 3.0 - 1994
--
--**********************************************************************
NCBI-Seqloc DEFINITIONS ::=
BEGIN
EXPORTS Seq-id, Seq-loc, Seq-interval, Packed-seqint, Seq-point, Packed-seqpnt,
Na-strand, Giimport-id;
IMPORTS Object-id, Int-fuzz, Dbtag, Date FROM NCBI-General
Id-pat FROM NCBI-Biblio
Feat-id FROM NCBI-Seqfeat;
--*** Sequence identifiers ********************************
--*
Seq-id ::= CHOICE {
local Object-id , -- local use
gibbsq INTEGER , -- Geninfo backbone seqid
gibbmt INTEGER , -- Geninfo backbone moltype
giim Giimport-id , -- Geninfo import id
genbank Textseq-id ,
embl Textseq-id ,
pir Textseq-id ,
swissprot Textseq-id ,
patent Patent-seq-id ,
other Textseq-id , -- catch all
general Dbtag , -- for other databases
gi INTEGER , -- GenInfo Integrated Database
ddbj Textseq-id , -- DDBJ
prf Textseq-id , -- PRF SEQDB
pdb PDB-seq-id } -- PDB sequence
Patent-seq-id ::= SEQUENCE {
seqid INTEGER , -- number of sequence in patent
cit Id-pat } -- patent citation
Textseq-id ::= SEQUENCE {
name VisibleString OPTIONAL ,
accession VisibleString OPTIONAL ,
release VisibleString OPTIONAL ,
version INTEGER OPTIONAL }
Giimport-id ::= SEQUENCE {
id INTEGER , -- the id to use here
db VisibleString OPTIONAL , -- dbase used in
release VisibleString OPTIONAL } -- the release
PDB-seq-id ::= SEQUENCE {
mol PDB-mol-id , -- the molecule name
chain INTEGER DEFAULT 32 ,-- a single ASCII character, chain id
rel Date OPTIONAL } -- release date, month and year
PDB-mol-id ::= VisibleString -- name of mol, 4 chars
--*** Sequence locations **********************************
--*
Seq-loc ::= CHOICE {
null NULL , -- not placed
empty Seq-id , -- to NULL one Seq-id in a collection
whole Seq-id , -- whole sequence
int Seq-interval , -- from to
packed-int Packed-seqint ,
pnt Seq-point ,
packed-pnt Packed-seqpnt ,
mix Seq-loc-mix ,
equiv Seq-loc-equiv , -- equivalent sets of locations
bond Seq-bond ,
feat Feat-id } -- indirect, through a Seq-feat
Seq-interval ::= SEQUENCE {
from INTEGER ,
to INTEGER ,
strand Na-strand OPTIONAL ,
id Seq-id , -- WARNING: this used to be optional
fuzz-from Int-fuzz OPTIONAL ,
fuzz-to Int-fuzz OPTIONAL }
Packed-seqint ::= SEQUENCE OF Seq-interval
Seq-point ::= SEQUENCE {
point INTEGER ,
strand Na-strand OPTIONAL ,
id Seq-id , -- WARNING: this used to be optional
fuzz Int-fuzz OPTIONAL }
Packed-seqpnt ::= SEQUENCE {
strand Na-strand OPTIONAL ,
id Seq-id ,
fuzz Int-fuzz OPTIONAL ,
points SEQUENCE OF INTEGER }
Na-strand ::= ENUMERATED { -- strand of nucleid acid
unknown (0) ,
plus (1) ,
minus (2) ,
both (3) , -- in forward orientation
both-rev (4) , -- in reverse orientation
other (255) }
Seq-bond ::= SEQUENCE { -- bond between residues
a Seq-point , -- connection to a least one residue
b Seq-point OPTIONAL } -- other end may not be available
Seq-loc-mix ::= SEQUENCE OF Seq-loc -- this will hold anything
Seq-loc-equiv ::= SET OF Seq-loc -- for a set of equivalent locations
END
--$Revision: 1000.1 $
--**********************************************************************
--
-- NCBI Sequence Alignment elements
-- by James Ostell, 1990
--
--**********************************************************************
NCBI-Seqalign DEFINITIONS ::=
BEGIN
EXPORTS Seq-align, Score, Score-set, Seq-align-set;
IMPORTS Seq-id, Seq-loc , Na-strand FROM NCBI-Seqloc
Object-id FROM NCBI-General;
--*** Sequence Alignment ********************************
--*
Seq-align-set ::= SET OF Seq-align
Seq-align ::= SEQUENCE {
type ENUMERATED {
not-set (0) ,
global (1) ,
diags (2) , -- unbroken, but not ordered, diagonals
partial (3) , -- mapping pieces together
disc (4) , -- discontinuous alignment
other (255) } ,
dim INTEGER OPTIONAL , -- dimensionality
score SET OF Score OPTIONAL , -- for whole alignment
segs CHOICE { -- alignment data
dendiag SEQUENCE OF Dense-diag ,
denseg Dense-seg ,
std SEQUENCE OF Std-seg ,
packed Packed-seg ,
disc Seq-align-set } ,
bounds SET OF Seq-loc OPTIONAL } -- regions of sequence over which align
-- was computed
Dense-diag ::= SEQUENCE { -- for (multiway) diagonals
dim INTEGER DEFAULT 2 , -- dimensionality
ids SEQUENCE OF Seq-id , -- sequences in order
starts SEQUENCE OF INTEGER , -- start OFFSETS in ids order
len INTEGER , -- len of aligned segments
strands SEQUENCE OF Na-strand OPTIONAL ,
scores SET OF Score OPTIONAL }
-- Dense-seg: the densist packing for sequence alignments only.
-- a start of -1 indicates a gap for that sequence of
-- length lens.
--
-- id=100 AAGGCCTTTTAGAGATGATGATGATGATGA
-- id=200 AAGGCCTTTTAG.......GATGATGATGA
-- id=300 ....CCTTTTAGAGATGATGAT....ATGA
--
-- dim = 3, numseg = 6, ids = { 100, 200, 300 }
-- starts = { 0,0,-1, 4,4,0, 12,-1,8, 19,12,15, 22,15,-1, 26,19,18 }
-- lens = { 4, 8, 7, 3, 4, 4 }
--
Dense-seg ::= SEQUENCE { -- for (multiway) global or partial alignments
dim INTEGER DEFAULT 2 , -- dimensionality
numseg INTEGER , -- number of segments here
ids SEQUENCE OF Seq-id , -- sequences in order
starts SEQUENCE OF INTEGER , -- start OFFSETS in ids order within segs
lens SEQUENCE OF INTEGER , -- lengths in ids order within segs
strands SEQUENCE OF Na-strand OPTIONAL ,
scores SEQUENCE OF Score OPTIONAL } -- score for each seg
Packed-seg ::= SEQUENCE { -- for (multiway) global or partial alignments
dim INTEGER DEFAULT 2 , -- dimensionality
numseg INTEGER , -- number of segments here
ids SEQUENCE OF Seq-id , -- sequences in order
starts SEQUENCE OF INTEGER , -- start OFFSETS in ids order for whole alignment
present OCTET STRING , -- Boolean if each sequence present or absent in
-- each segment
lens SEQUENCE OF INTEGER , -- length of each segment
strands SEQUENCE OF Na-strand OPTIONAL ,
scores SEQUENCE OF Score OPTIONAL } -- score for each segment
Std-seg ::= SEQUENCE {
dim INTEGER DEFAULT 2 , -- dimensionality
ids SEQUENCE OF Seq-id OPTIONAL ,
loc SEQUENCE OF Seq-loc ,
scores SET OF Score OPTIONAL }
-- use of Score is discouraged for external ASN.1 specifications
Score ::= SEQUENCE {
id Object-id OPTIONAL ,
value CHOICE {
real REAL ,
int INTEGER } }
-- use of Score-set is encouraged for external ASN.1 specifications
Score-set ::= SET OF Score
END
--$Revision: 1000.1 $
--*********************************************************************
--
-- 1990 - J.Ostell
-- Version 3.0 - June 1994
--
--*********************************************************************
--*********************************************************************
--
-- EMBL specific data
-- This block of specifications was developed by Reiner Fuchs of EMBL
-- Updated by J.Ostell, 1994
--
--*********************************************************************
EMBL-General DEFINITIONS ::=
BEGIN
EXPORTS EMBL-dbname, EMBL-xref, EMBL-block;
IMPORTS Date, Object-id FROM NCBI-General;
EMBL-dbname ::= CHOICE {
code ENUMERATED {
embl(0),
genbank(1),
ddbj(2),
geninfo(3),
medline(4),
swissprot(5),
pir(6),
pdb(7),
epd(8),
ecd(9),
tfd(10),
flybase(11),
prosite(12),
enzyme(13),
mim(14),
ecoseq(15),
hiv(16) ,
other (255) } ,
name VisibleString }
EMBL-xref ::= SEQUENCE {
dbname EMBL-dbname,
id SEQUENCE OF Object-id }
EMBL-block ::= SEQUENCE {
class ENUMERATED {
not-set(0),
standard(1),
unannotated(2),
other(255) } DEFAULT standard,
div ENUMERATED {
fun(0),
inv(1),
mam(2),
org(3),
phg(4),
pln(5),
pri(6),
pro(7),
rod(8),
syn(9),
una(10),
vrl(11),
vrt(12),
pat(13),
est(14),
sts(15),
other (255) } OPTIONAL,
creation-date Date,
update-date Date,
extra-acc SEQUENCE OF VisibleString OPTIONAL,
keywords SEQUENCE OF VisibleString OPTIONAL,
xref SEQUENCE OF EMBL-xref OPTIONAL }
END
--*********************************************************************
--
-- SWISSPROT specific data
-- This block of specifications was developed by Mark Cavanaugh of
-- NCBI working with Amos Bairoch of SWISSPROT
--
--*********************************************************************
SP-General DEFINITIONS ::=
BEGIN
EXPORTS SP-block;
IMPORTS Date, Dbtag FROM NCBI-General
Seq-id FROM NCBI-Seqloc;
SP-block ::= SEQUENCE { -- SWISSPROT specific descriptions
class ENUMERATED {
not-set (0) ,
standard (1) , -- conforms to all SWISSPROT checks
prelim (2) , -- only seq and biblio checked
other (255) } ,
extra-acc SET OF VisibleString OPTIONAL , -- old SWISSPROT ids
imeth BOOLEAN DEFAULT FALSE , -- seq known to start with Met
plasnm SET OF VisibleString OPTIONAL, -- plasmid names carrying gene
seqref SET OF Seq-id OPTIONAL, -- xref to other sequences
dbref SET OF Dbtag OPTIONAL , -- xref to non-sequence dbases
keywords SET OF VisibleString OPTIONAL , -- keywords
created Date OPTIONAL , -- creation date
sequpd Date OPTIONAL , -- sequence update
annotupd Date OPTIONAL } -- annotation update
END
--*********************************************************************
--
-- PIR specific data
-- This block of specifications was developed by Jim Ostell of
-- NCBI
--
--*********************************************************************
PIR-General DEFINITIONS ::=
BEGIN
EXPORTS PIR-block;
IMPORTS Seq-id FROM NCBI-Seqloc;
PIR-block ::= SEQUENCE { -- PIR specific descriptions
had-punct BOOLEAN OPTIONAL , -- had punctuation in sequence ?
host VisibleString OPTIONAL ,
source VisibleString OPTIONAL , -- source line
summary VisibleString OPTIONAL ,
genetic VisibleString OPTIONAL ,
includes VisibleString OPTIONAL ,
placement VisibleString OPTIONAL ,
superfamily VisibleString OPTIONAL ,
keywords SEQUENCE OF VisibleString OPTIONAL ,
cross-reference VisibleString OPTIONAL ,
date VisibleString OPTIONAL ,
seq-raw VisibleString OPTIONAL , -- seq with punctuation
seqref SET OF Seq-id OPTIONAL } -- xref to other sequences
END
--*********************************************************************
--
-- GenBank specific data
-- This block of specifications was developed by Jim Ostell of
-- NCBI
--
--*********************************************************************
GenBank-General DEFINITIONS ::=
BEGIN
EXPORTS GB-block;
IMPORTS Date FROM NCBI-General;
GB-block ::= SEQUENCE { -- GenBank specific descriptions
extra-accessions SEQUENCE OF VisibleString OPTIONAL ,
source VisibleString OPTIONAL , -- source line
keywords SEQUENCE OF VisibleString OPTIONAL ,
origin VisibleString OPTIONAL,
date VisibleString OPTIONAL , -- OBSOLETE old form Entry Date
entry-date Date OPTIONAL , -- replaces date
div VisibleString OPTIONAL , -- GenBank division
taxonomy VisibleString OPTIONAL } -- continuation line of organism
END
--**********************************************************************
-- PRF specific definition
-- PRF is a protein sequence database crated and maintained by
-- Protein Research Foundation, Minoo-city, Osaka, Japan.
--
-- Written by A.Ogiwara, Inst.Chem.Res. (Dr.Kanehisa's Lab),
-- Kyoto Univ., Japan
--
--**********************************************************************
PRF-General DEFINITIONS ::=
BEGIN
EXPORTS PRF-block;
PRF-block ::= SEQUENCE {
extra-src PRF-ExtraSrc OPTIONAL,
keywords SEQUENCE OF VisibleString OPTIONAL
}
PRF-ExtraSrc ::= SEQUENCE {
host VisibleString OPTIONAL,
part VisibleString OPTIONAL,
state VisibleString OPTIONAL,
strain VisibleString OPTIONAL,
taxon VisibleString OPTIONAL
}
END
--*********************************************************************
--
-- PDB specific data
-- This block of specifications was developed by Jim Ostell and
-- Steve Bryant of NCBI
--
--*********************************************************************
PDB-General DEFINITIONS ::=
BEGIN
EXPORTS PDB-block;
IMPORTS Date FROM NCBI-General;
PDB-block ::= SEQUENCE { -- PDB specific descriptions
deposition Date , -- deposition date month,year
class VisibleString ,
compound SEQUENCE OF VisibleString ,
source SEQUENCE OF VisibleString ,
exp-method VisibleString OPTIONAL , -- present if NOT X-ray diffraction
replace PDB-replace OPTIONAL } -- replacement history
PDB-replace ::= SEQUENCE {
date Date ,
ids SEQUENCE OF VisibleString } -- entry ids replace by this one
END
--$Revision: 1000.1 $
--**********************************************************************
--
-- NCBI Sequence Feature elements
-- by James Ostell, 1990
-- Version 3.0 - June 1994
--
--**********************************************************************
NCBI-Seqfeat DEFINITIONS ::=
BEGIN
EXPORTS Seq-feat, Feat-id, Genetic-code;
IMPORTS Gene-ref FROM NCBI-Gene
Prot-ref FROM NCBI-Protein
Org-ref FROM NCBI-Organism
BioSource FROM NCBI-BioSource
RNA-ref FROM NCBI-RNA
Seq-loc, Giimport-id FROM NCBI-Seqloc
Pubdesc, Numbering, Heterogen FROM NCBI-Sequence
Rsite-ref FROM NCBI-Rsite
Txinit FROM NCBI-TxInit
Pub-set FROM NCBI-Pub
Object-id, Dbtag, User-object FROM NCBI-General;
--*** Feature identifiers ********************************
--*
Feat-id ::= CHOICE {
gibb INTEGER , -- geninfo backbone
giim Giimport-id , -- geninfo import
local Object-id , -- for local software use
general Dbtag } -- for use by various databases
--*** Seq-feat *******************************************
--* sequence feature generalization
Seq-feat ::= SEQUENCE {
id Feat-id OPTIONAL ,
data SeqFeatData , -- the specific data
partial BOOLEAN OPTIONAL , -- incomplete in some way?
except BOOLEAN OPTIONAL , -- something funny about this?
comment VisibleString OPTIONAL ,
product Seq-loc OPTIONAL , -- product of process
location Seq-loc , -- feature made from
qual SEQUENCE OF Gb-qual OPTIONAL , -- qualifiers
title VisibleString OPTIONAL , -- for user defined label
ext User-object OPTIONAL , -- user defined structure extension
cit Pub-set OPTIONAL , -- citations for this feature
exp-ev ENUMERATED { -- evidence for existence of feature
experimental (1) , -- any reasonable experimental check
not-experimental (2) } OPTIONAL , -- similarity, pattern, etc
xref SET OF SeqFeatXref OPTIONAL , -- cite other relevant features
dbxref SET OF Dbtag OPTIONAL , -- support for xref to other databases
pseudo BOOLEAN OPTIONAL , -- annotated on pseudogene?
except-text VisibleString OPTIONAL } -- explain if except=TRUE
SeqFeatData ::= CHOICE {
gene Gene-ref ,
org Org-ref ,
cdregion Cdregion ,
prot Prot-ref ,
rna RNA-ref ,
pub Pubdesc , -- publication applies to this seq
seq Seq-loc , -- to annotate origin from another seq
imp Imp-feat ,
region VisibleString, -- named region (globin locus)
comment NULL , -- just a comment
bond ENUMERATED {
disulfide (1) ,
thiolester (2) ,
xlink (3) ,
thioether (4) ,
other (255) } ,
site ENUMERATED {
active (1) ,
binding (2) ,
cleavage (3) ,
inhibit (4) ,
modified (5),
glycosylation (6) ,
myristoylation (7) ,
mutagenized (8) ,
metal-binding (9) ,
phosphorylation (10) ,
acetylation (11) ,
amidation (12) ,
methylation (13) ,
hydroxylation (14) ,
sulfatation (15) ,
oxidative-deamination (16) ,
pyrrolidone-carboxylic-acid (17) ,
gamma-carboxyglutamic-acid (18) ,
blocked (19) ,
lipid-binding (20) ,
np-binding (21) ,
dna-binding (22) ,
signal-peptide (23) ,
transit-peptide (24) ,
transmembrane-region (25) ,
other (255) } ,
rsite Rsite-ref , -- restriction site (for maps really)
user User-object , -- user defined structure
txinit Txinit , -- transcription initiation
num Numbering , -- a numbering system
psec-str ENUMERATED { -- protein secondary structure
helix (1) , -- any helix
sheet (2) , -- beta sheet
turn (3) } , -- beta or gamma turn
non-std-residue VisibleString , -- non-standard residue here in seq
het Heterogen , -- cofactor, prosthetic grp, etc, bound to seq
biosrc BioSource }
SeqFeatXref ::= SEQUENCE { -- both optional because can have one or both
id Feat-id OPTIONAL , -- the feature copied
data SeqFeatData OPTIONAL } -- the specific data
--*** CdRegion ***********************************************
--*
--* Instructions to translate from a nucleic acid to a peptide
--* conflict means it's supposed to translate but doesn't
--*
Cdregion ::= SEQUENCE {
orf BOOLEAN OPTIONAL , -- just an ORF ?
frame ENUMERATED {
not-set (0) , -- not set, code uses one
one (1) ,
two (2) ,
three (3) } DEFAULT not-set , -- reading frame
conflict BOOLEAN OPTIONAL , -- conflict
gaps INTEGER OPTIONAL , -- number of gaps on conflict/except
mismatch INTEGER OPTIONAL , -- number of mismatches on above
code Genetic-code OPTIONAL , -- genetic code used
code-break SEQUENCE OF Code-break OPTIONAL , -- individual exceptions
stops INTEGER OPTIONAL } -- number of stop codons on above
-- each code is 64 cells long, in the order where
-- T=0,C=1,A=2,G=3, TTT=0, TTC=1, TCA=4, etc
-- NOTE: this order does NOT corresspond to a Seq-data
-- encoding. It is "natural" to codon usage instead.
-- the value in each cell is the AA coded for
-- start= AA coded only if first in peptide
-- in start array, if codon is not a legitimate start
-- codon, that cell will have the "gap" symbol for
-- that alphabet. Otherwise it will have the AA
-- encoded when that codon is used at the start.
Genetic-code ::= SET OF CHOICE {
name VisibleString , -- name of a code
id INTEGER , -- id in dbase
ncbieaa VisibleString , -- indexed to IUPAC extended
ncbi8aa OCTET STRING , -- indexed to NCBI8aa
ncbistdaa OCTET STRING , -- indexed to NCBIstdaa
sncbieaa VisibleString , -- start, indexed to IUPAC extended
sncbi8aa OCTET STRING , -- start, indexed to NCBI8aa
sncbistdaa OCTET STRING } -- start, indexed to NCBIstdaa
Code-break ::= SEQUENCE { -- specific codon exceptions
loc Seq-loc , -- location of exception
aa CHOICE { -- the amino acid
ncbieaa INTEGER , -- ASCII value of NCBIeaa code
ncbi8aa INTEGER , -- NCBI8aa code
ncbistdaa INTEGER } } -- NCBIstdaa code
Genetic-code-table ::= SET OF Genetic-code -- table of genetic codes
--*** Import ***********************************************
--*
--* Features imported from other databases
--*
Imp-feat ::= SEQUENCE {
key VisibleString ,
loc VisibleString OPTIONAL , -- original location string
descr VisibleString OPTIONAL } -- text description
Gb-qual ::= SEQUENCE {
qual VisibleString ,
val VisibleString }
END
--**********************************************************************
--
-- NCBI Restriction Sites
-- by James Ostell, 1990
-- version 0.8
--
--**********************************************************************
NCBI-Rsite DEFINITIONS ::=
BEGIN
EXPORTS Rsite-ref;
IMPORTS Dbtag FROM NCBI-General;
Rsite-ref ::= CHOICE {
str VisibleString , -- may be unparsable
db Dbtag } -- pointer to a restriction site database
END
--**********************************************************************
--
-- NCBI RNAs
-- by James Ostell, 1990
-- version 0.8
--
--**********************************************************************
NCBI-RNA DEFINITIONS ::=
BEGIN
EXPORTS RNA-ref, Trna-ext;
IMPORTS Seq-loc FROM NCBI-Seqloc;
--*** rnas ***********************************************
--*
--* various rnas
--*
-- minimal RNA sequence
RNA-ref ::= SEQUENCE {
type ENUMERATED { -- type of RNA feature
unknown (0) ,
premsg (1) ,
mRNA (2) ,
tRNA (3) ,
rRNA (4) ,
snRNA (5) ,
scRNA (6) ,
other (255) } ,
pseudo BOOLEAN OPTIONAL ,
ext CHOICE {
name VisibleString , -- for naming "other" type
tRNA Trna-ext } OPTIONAL } -- for tRNAs
Trna-ext ::= SEQUENCE { -- tRNA feature extensions
aa CHOICE { -- aa this carries
iupacaa INTEGER ,
ncbieaa INTEGER ,
ncbi8aa INTEGER ,
ncbistdaa INTEGER } OPTIONAL ,
codon SET OF INTEGER OPTIONAL , -- codon(s) as in Genetic-code
anticodon Seq-loc OPTIONAL } -- location of anticodon
END
--**********************************************************************
--
-- NCBI Genes
-- by James Ostell, 1990
-- version 0.8
--
--**********************************************************************
NCBI-Gene DEFINITIONS ::=
BEGIN
EXPORTS Gene-ref;
IMPORTS Dbtag FROM NCBI-General;
--*** Gene ***********************************************
--*
--* reference to a gene
--*
Gene-ref ::= SEQUENCE {
locus VisibleString OPTIONAL , -- Official gene symbol
allele VisibleString OPTIONAL , -- Official allele designation
desc VisibleString OPTIONAL , -- descriptive name
maploc VisibleString OPTIONAL , -- descriptive map location
pseudo BOOLEAN DEFAULT FALSE , -- pseudogene
db SET OF Dbtag OPTIONAL , -- ids in other dbases
syn SET OF VisibleString OPTIONAL } -- synonyms for locus
END
--**********************************************************************
--
-- NCBI Organism
-- by James Ostell, 1994
-- version 3.0
--
--**********************************************************************
NCBI-Organism DEFINITIONS ::=
BEGIN
EXPORTS Org-ref;
IMPORTS Dbtag FROM NCBI-General;
--*** Org-ref ***********************************************
--*
--* Reference to an organism
--* defines only the organism.. lower levels of detail for biological
--* molecules are provided by the Source object
--*
Org-ref ::= SEQUENCE {
taxname VisibleString OPTIONAL , -- preferred formal name
common VisibleString OPTIONAL , -- common name
mod SET OF VisibleString OPTIONAL , -- unstructured modifiers
db SET OF Dbtag OPTIONAL , -- ids in taxonomic or culture dbases
syn SET OF VisibleString OPTIONAL , -- synonyms for taxname or common
orgname OrgName OPTIONAL }
OrgName ::= SEQUENCE {
name CHOICE {
binomial BinomialOrgName , -- genus/species type name
virus VisibleString , -- virus names are different
hybrid MultiOrgName , -- hybrid between organisms
namedhybrid BinomialOrgName , -- some hybrids have genus x species name
partial PartialOrgName } OPTIONAL , -- when genus not known
attrib VisibleString OPTIONAL , -- attribution of name
mod SEQUENCE OF OrgMod OPTIONAL ,
lineage VisibleString OPTIONAL , -- lineage with semicolon separators
gcode INTEGER OPTIONAL , -- genetic code (see CdRegion)
mgcode INTEGER OPTIONAL , -- mitochondrial genetic code
div VisibleString OPTIONAL } -- GenBank division code
OrgMod ::= SEQUENCE {
subtype INTEGER {
strain (2) ,
substrain (3) ,
type (4) ,
subtype (5) ,
variety (6) ,
serotype (7) ,
serogroup (8) ,
serovar (9) ,
cultivar (10) ,
pathovar (11) ,
chemovar (12) ,
biovar (13) ,
biotype (14) ,
group (15) ,
subgroup (16) ,
isolate (17) ,
common (18) ,
acronym (19) ,
dosage (20) , -- chromosome dosage of hybrid
nat-host (21) , -- natural host of this specimen
sub-species (22) ,
specimen-voucher (23) ,
authority (24) ,
forma (25) ,
forma-specialis (26) ,
ecotype (27) ,
synonym (28) ,
anamorph (29) ,
teleomorph (30) ,
breed (31) ,
old-lineage (253) ,
old-name (254) ,
other (255) } , -- ASN5: old-name (254) will be added to next spec
subname VisibleString ,
attrib VisibleString OPTIONAL } -- attribution/source of name
BinomialOrgName ::= SEQUENCE {
genus VisibleString , -- required
species VisibleString OPTIONAL , -- species required if subspecies used
subspecies VisibleString OPTIONAL }
MultiOrgName ::= SEQUENCE OF OrgName -- the first will be used to assign division
PartialOrgName ::= SEQUENCE OF TaxElement -- when we don't know the genus
TaxElement ::= SEQUENCE {
fixed-level INTEGER {
other (0) , -- level must be set in string
family (1) ,
order (2) ,
class (3) } ,
level VisibleString OPTIONAL ,
name VisibleString }
END
--**********************************************************************
--
-- NCBI BioSource
-- by James Ostell, 1994
-- version 3.0
--
--**********************************************************************
NCBI-BioSource DEFINITIONS ::=
BEGIN
EXPORTS BioSource;
IMPORTS Org-ref FROM NCBI-Organism;
--********************************************************************
--
-- BioSource gives the source of the biological material
-- for sequences
--
--********************************************************************
BioSource ::= SEQUENCE {
genome INTEGER { -- biological context
unknown (0) ,
genomic (1) ,
chloroplast (2) ,
chromoplast (3) ,
kinetoplast (4) ,
mitochondrion (5) ,
plastid (6) ,
macronuclear (7) ,
extrachrom (8) ,
plasmid (9) ,
transposon (10) ,
insertion-seq (11) ,
cyanelle (12) ,
proviral (13) ,
virion (14) ,
nucleomorph (15) ,
apicoplast (16) ,
leucoplast (17) ,
proplastid (18) ,
endogenous-virus (19)
} DEFAULT unknown ,
-- 4 more genome values coming
-- nucleomorph (15)
-- apicoplast (16)
-- leucoplast (17)
-- proplastid (18)
origin INTEGER {
unknown (0) ,
natural (1) , -- normal biological entity
natmut (2) , -- naturally occurring mutant
mut (3) , -- artificially mutagenized
artificial (4) , -- artificially engineered
synthetic (5) , -- purely synthetic
other (255) } DEFAULT unknown ,
org Org-ref ,
subtype SEQUENCE OF SubSource OPTIONAL ,
is-focus NULL OPTIONAL } -- to distinguish biological focus
SubSource ::= SEQUENCE {
subtype INTEGER {
chromosome (1) ,
map (2) ,
clone (3) ,
subclone (4) ,
haplotype (5) ,
genotype (6) ,
sex (7) ,
cell-line (8) ,
cell-type (9) ,
tissue-type (10) ,
clone-lib (11) ,
dev-stage (12) ,
frequency (13) ,
germline (14) ,
rearranged (15) ,
lab-host (16) ,
pop-variant (17) ,
tissue-lib (18) ,
plasmid-name (19) ,
transposon-name (20) ,
insertion-seq-name (21) ,
plastid-name (22) ,
country (23) ,
segment (24) ,
endogenous-virus-name (25) ,
other (255) } ,
name VisibleString ,
attrib VisibleString OPTIONAL } -- attribution/source of this name
END
--**********************************************************************
--
-- NCBI Protein
-- by James Ostell, 1990
-- version 0.8
--
--**********************************************************************
NCBI-Protein DEFINITIONS ::=
BEGIN
EXPORTS Prot-ref;
IMPORTS Dbtag FROM NCBI-General;
--*** Prot-ref ***********************************************
--*
--* Reference to a protein name
--*
Prot-ref ::= SEQUENCE {
name SET OF VisibleString OPTIONAL , -- protein name
desc VisibleString OPTIONAL , -- description (instead of name)
ec SET OF VisibleString OPTIONAL , -- E.C. number(s)
activity SET OF VisibleString OPTIONAL , -- activities
db SET OF Dbtag OPTIONAL , -- ids in other dbases
processed ENUMERATED { -- processing status
not-set (0) ,
preprotein (1) ,
mature (2) ,
signal-peptide (3) ,
transit-peptide (4) } DEFAULT not-set }
END
--********************************************************************
--
-- Transcription Initiation Site Feature Data Block
-- James Ostell, 1991
-- Philip Bucher, David Ghosh
-- version 1.1
--
--
--
--********************************************************************
NCBI-TxInit DEFINITIONS ::=
BEGIN
EXPORTS Txinit;
IMPORTS Gene-ref FROM NCBI-Gene
Prot-ref FROM NCBI-Protein
Org-ref FROM NCBI-Organism;
Txinit ::= SEQUENCE {
name VisibleString , -- descriptive name of initiation site
syn SEQUENCE OF VisibleString OPTIONAL , -- synonyms
gene SEQUENCE OF Gene-ref OPTIONAL , -- gene(s) transcribed
protein SEQUENCE OF Prot-ref OPTIONAL , -- protein(s) produced
rna SEQUENCE OF VisibleString OPTIONAL , -- rna(s) produced
expression VisibleString OPTIONAL , -- tissue/time of expression
txsystem ENUMERATED { -- transcription apparatus used at this site
unknown (0) ,
pol1 (1) , -- eukaryotic Pol I
pol2 (2) , -- eukaryotic Pol II
pol3 (3) , -- eukaryotic Pol III
bacterial (4) ,
viral (5) ,
rna (6) , -- RNA replicase
organelle (7) ,
other (255) } ,
txdescr VisibleString OPTIONAL , -- modifiers on txsystem
txorg Org-ref OPTIONAL , -- organism supplying transcription apparatus
mapping-precise BOOLEAN DEFAULT FALSE , -- mapping precise or approx
location-accurate BOOLEAN DEFAULT FALSE , -- does Seq-loc reflect mapping
inittype ENUMERATED {
unknown (0) ,
single (1) ,
multiple (2) ,
region (3) } OPTIONAL ,
evidence SET OF Tx-evidence OPTIONAL }
Tx-evidence ::= SEQUENCE {
exp-code ENUMERATED {
unknown (0) ,
rna-seq (1) , -- direct RNA sequencing
rna-size (2) , -- RNA length measurement
np-map (3) , -- nuclease protection mapping with homologous sequence ladder
np-size (4) , -- nuclease protected fragment length measurement
pe-seq (5) , -- dideoxy RNA sequencing
cDNA-seq (6) , -- full-length cDNA sequencing
pe-map (7) , -- primer extension mapping with homologous sequence ladder
pe-size (8) , -- primer extension product length measurement
pseudo-seq (9) , -- full-length processed pseudogene sequencing
rev-pe-map (10) , -- see NOTE (1) below
other (255) } ,
expression-system ENUMERATED {
unknown (0) ,
physiological (1) ,
in-vitro (2) ,
oocyte (3) ,
transfection (4) ,
transgenic (5) ,
other (255) } DEFAULT physiological ,
low-prec-data BOOLEAN DEFAULT FALSE ,
from-homolog BOOLEAN DEFAULT FALSE } -- experiment actually done on
-- close homolog
-- NOTE (1) length measurement of a reverse direction primer-extension
-- product (blocked by RNA 5'end) by comparison with
-- homologous sequence ladder (J. Mol. Biol. 199, 587)
END
--$Revision: 1000.1 $
--**********************************************************************
--
-- NCBI Sequence Analysis Results (other than alignments)
-- by James Ostell, 1990
--
--**********************************************************************
NCBI-Seqres DEFINITIONS ::=
BEGIN
EXPORTS Seq-graph;
IMPORTS Seq-loc FROM NCBI-Seqloc;
--*** Sequence Graph ********************************
--*
--* for values mapped by residue or range to sequence
--*
Seq-graph ::= SEQUENCE {
title VisibleString OPTIONAL ,
comment VisibleString OPTIONAL ,
loc Seq-loc , -- region this applies to
title-x VisibleString OPTIONAL , -- title for x-axis
title-y VisibleString OPTIONAL ,
comp INTEGER OPTIONAL , -- compression (residues/value)
a REAL OPTIONAL , -- for scaling values
b REAL OPTIONAL , -- display = (a x value) + b
numval INTEGER , -- number of values in graph
graph CHOICE {
real Real-graph ,
int Int-graph ,
byte Byte-graph } }
Real-graph ::= SEQUENCE {
max REAL , -- top of graph
min REAL , -- bottom of graph
axis REAL , -- value to draw axis on
values SEQUENCE OF REAL }
Int-graph ::= SEQUENCE {
max INTEGER ,
min INTEGER ,
axis INTEGER ,
values SEQUENCE OF INTEGER }
Byte-graph ::= SEQUENCE { -- integer from 0-255
max INTEGER ,
min INTEGER ,
axis INTEGER ,
values OCTET STRING }
END
--$Revision: 1000.1 $
--**********************************************************************
--
-- NCBI Sequence Collections
-- by James Ostell, 1990
--
-- Version 3.0 - 1994
--
--**********************************************************************
NCBI-Seqset DEFINITIONS ::=
BEGIN
EXPORTS Bioseq-set, Seq-entry;
IMPORTS Bioseq, Seq-annot, Seq-descr FROM NCBI-Sequence
Object-id, Dbtag, Date FROM NCBI-General;
--*** Sequence Collections ********************************
--*
Bioseq-set ::= SEQUENCE { -- just a collection
id Object-id OPTIONAL ,
coll Dbtag OPTIONAL , -- to identify a collection
level INTEGER OPTIONAL , -- nesting level
class ENUMERATED {
not-set (0) ,
nuc-prot (1) , -- nuc acid and coded proteins
segset (2) , -- segmented sequence + parts
conset (3) , -- constructed sequence + parts
parts (4) , -- parts for 2 or 3
gibb (5) , -- geninfo backbone
gi (6) , -- geninfo
genbank (7) , -- converted genbank
pir (8) , -- converted pir
pub-set (9) , -- all the seqs from a single publication
equiv (10) , -- a set of equivalent maps or seqs
swissprot (11) , -- converted SWISSPROT
pdb-entry (12) , -- a complete PDB entry
mut-set (13) , -- set of mutations
pop-set (14) , -- population study
phy-set (15) , -- phylogenetic study
eco-set (16) , -- ecological sample study
gen-prod-set (17) , -- genomic products, chrom+mRNa+protein
other (255) } DEFAULT not-set ,
release VisibleString OPTIONAL ,
date Date OPTIONAL ,
descr Seq-descr OPTIONAL ,
seq-set SEQUENCE OF Seq-entry ,
annot SET OF Seq-annot OPTIONAL }
Seq-entry ::= CHOICE {
seq Bioseq ,
set Bioseq-set }
END
--$Revision: 1000.1 $
--**********************************************************************
--
-- NCBI Sequence elements
-- by James Ostell, 1990
-- Version 3.0 - June 1994
--
--**********************************************************************
NCBI-Sequence DEFINITIONS ::=
BEGIN
EXPORTS Bioseq, Seq-annot, Pubdesc, Seq-descr, Seqdesc, Numbering, Heterogen,
Seq-hist, GIBB-mol;
IMPORTS Date, Int-fuzz, Dbtag, Object-id, User-object FROM NCBI-General
Seq-align FROM NCBI-Seqalign
Seq-feat FROM NCBI-Seqfeat
Seq-graph FROM NCBI-Seqres
Pub-equiv FROM NCBI-Pub
Org-ref FROM NCBI-Organism
BioSource FROM NCBI-BioSource
Seq-id, Seq-loc FROM NCBI-Seqloc
GB-block FROM GenBank-General
PIR-block FROM PIR-General
EMBL-block FROM EMBL-General
SP-block FROM SP-General
PRF-block FROM PRF-General
PDB-block FROM PDB-General;
--*** Sequence ********************************
--*
Bioseq ::= SEQUENCE {
id SET OF Seq-id , -- equivalent identifiers
descr Seq-descr OPTIONAL , -- descriptors
inst Seq-inst , -- the sequence data
annot SET OF Seq-annot OPTIONAL }
--*** Descriptors *****************************
--*
Seq-descr ::= SET OF Seqdesc
Seqdesc ::= CHOICE {
mol-type GIBB-mol , -- type of molecule
modif SET OF GIBB-mod , -- modifiers
method GIBB-method , -- sequencing method
name VisibleString , -- a name for this sequence
title VisibleString , -- a title for this sequence
org Org-ref , -- if all from one organism
comment VisibleString , -- a more extensive comment
num Numbering , -- a numbering system
maploc Dbtag , -- map location of this sequence
pir PIR-block , -- PIR specific info
genbank GB-block , -- GenBank specific info
pub Pubdesc , -- a reference to the publication
region VisibleString , -- overall region (globin locus)
user User-object , -- user defined object
sp SP-block , -- SWISSPROT specific info
dbxref Dbtag , -- xref to other databases
embl EMBL-block , -- EMBL specific information
create-date Date , -- date entry first created/released
update-date Date , -- date of last update
prf PRF-block , -- PRF specific information
pdb PDB-block , -- PDB specific information
het Heterogen , -- cofactor, etc associated but not bound
source BioSource , -- source of materials, includes Org-ref
molinfo MolInfo } -- info on the molecule and techniques
--******* NOTE:
--* mol-type, modif, method, and org are consolidated and expanded
--* in Org-ref, BioSource, and MolInfo in this specification. They
--* will be removed in later specifications. Do not use them in the
--* the future. Instead expect the new structures.
--*
--***************************
--********************************************************************
--
-- MolInfo gives information on the
-- classification of the type and quality of the sequence
--
-- WARNING: this will replace GIBB-mol, GIBB-mod, GIBB-method
--
--********************************************************************
MolInfo ::= SEQUENCE {
biomol INTEGER {
unknown (0) ,
genomic (1) ,
pre-RNA (2) , -- precursor RNA of any sort really
mRNA (3) ,
rRNA (4) ,
tRNA (5) ,
snRNA (6) ,
scRNA (7) ,
peptide (8) ,
other-genetic (9) , -- other genetic material
genomic-mRNA (10) , -- reported a mix of genomic and cdna sequence
cRNA (11) , -- viral RNA genome copy intermediate
other (255) } DEFAULT unknown ,
tech INTEGER {
unknown (0) ,
standard (1) , -- standard sequencing
est (2) , -- Expressed Sequence Tag
sts (3) , -- Sequence Tagged Site
survey (4) , -- one-pass genomic sequence
genemap (5) , -- from genetic mapping techniques
physmap (6) , -- from physical mapping techniques
derived (7) , -- derived from other data, not a primary entity
concept-trans (8) , -- conceptual translation
seq-pept (9) , -- peptide was sequenced
both (10) , -- concept transl. w/ partial pept. seq.
seq-pept-overlap (11) , -- sequenced peptide, ordered by overlap
seq-pept-homol (12) , -- sequenced peptide, ordered by homology
concept-trans-a (13) , -- conceptual transl. supplied by author
htgs-1 (14) , -- unordered High Throughput sequence contig
htgs-2 (15) , -- ordered High Throughput sequence contig
htgs-3 (16) , -- finished High Throughput sequence
fli-cdna (17) , -- full length insert cDNA
htgs-0 (18) , -- single genomic reads for coordination
htc (19) , -- high throughput cDNA
other (255) } -- use Source.techexp
DEFAULT unknown ,
techexp VisibleString OPTIONAL , -- explanation if tech not enough
completeness INTEGER {
unknown (0) ,
complete (1) , -- complete biological entity
partial (2) , -- partial but no details given
no-left (3), -- missing 5' or NH3 end
no-right (4) , -- missing 3' or COOH end
no-ends (5) , -- missing both ends
other (255) } DEFAULT unknown }
GIBB-mol ::= ENUMERATED { -- type of molecule represented
unknown (0) ,
genomic (1) ,
pre-mRNA (2) , -- precursor RNA of any sort really
mRNA (3) ,
rRNA (4) ,
tRNA (5) ,
snRNA (6) ,
scRNA (7) ,
peptide (8) ,
other-genetic (9) , -- other genetic material
genomic-mRNA (10) , -- reported a mix of genomic and cdna sequence
other (255) }
GIBB-mod ::= ENUMERATED { -- GenInfo Backbone modifiers
dna (0) ,
rna (1) ,
extrachrom (2) ,
plasmid (3) ,
mitochondrial (4) ,
chloroplast (5) ,
kinetoplast (6) ,
cyanelle (7) ,
synthetic (8) ,
recombinant (9) ,
partial (10) ,
complete (11) ,
mutagen (12) , -- subject of mutagenesis ?
natmut (13) , -- natural mutant ?
transposon (14) ,
insertion-seq (15) ,
no-left (16) , -- missing left end (5' for na, NH2 for aa)
no-right (17) , -- missing right end (3' or COOH)
macronuclear (18) ,
proviral (19) ,
est (20) , -- expressed sequence tag
sts (21) , -- sequence tagged site
survey (22) , -- one pass survey sequence
chromoplast (23) ,
genemap (24) , -- is a genetic map
restmap (25) , -- is an ordered restriction map
physmap (26) , -- is a physical map (not ordered restriction map)
other (255) }
GIBB-method ::= ENUMERATED { -- sequencing methods
concept-trans (1) , -- conceptual translation
seq-pept (2) , -- peptide was sequenced
both (3) , -- concept transl. w/ partial pept. seq.
seq-pept-overlap (4) , -- sequenced peptide, ordered by overlap
seq-pept-homol (5) , -- sequenced peptide, ordered by homology
concept-trans-a (6) , -- conceptual transl. supplied by author
other (255) }
Numbering ::= CHOICE { -- any display numbering system
cont Num-cont , -- continuous numbering