233 lines
6.4 KiB
Groff
233 lines
6.4 KiB
Groff
--$Revision: 6.0 $
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--*********************************************************************
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--
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-- 1990 - J.Ostell
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-- Version 3.0 - June 1994
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--
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--*********************************************************************
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--*********************************************************************
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--
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-- EMBL specific data
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-- This block of specifications was developed by Reiner Fuchs of EMBL
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-- Updated by J.Ostell, 1994
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--
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--*********************************************************************
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EMBL-General DEFINITIONS ::=
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BEGIN
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EXPORTS EMBL-dbname, EMBL-xref, EMBL-block;
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IMPORTS Date, Object-id FROM NCBI-General;
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EMBL-dbname ::= CHOICE {
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code ENUMERATED {
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embl(0),
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genbank(1),
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ddbj(2),
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geninfo(3),
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medline(4),
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swissprot(5),
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pir(6),
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pdb(7),
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epd(8),
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ecd(9),
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tfd(10),
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flybase(11),
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prosite(12),
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enzyme(13),
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mim(14),
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ecoseq(15),
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hiv(16) ,
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other (255) } ,
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name VisibleString }
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EMBL-xref ::= SEQUENCE {
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dbname EMBL-dbname,
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id SEQUENCE OF Object-id }
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EMBL-block ::= SEQUENCE {
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class ENUMERATED {
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not-set(0),
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standard(1),
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unannotated(2),
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other(255) } DEFAULT standard,
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div ENUMERATED {
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fun(0),
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inv(1),
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mam(2),
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org(3),
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phg(4),
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pln(5),
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pri(6),
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pro(7),
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rod(8),
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syn(9),
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una(10),
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vrl(11),
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vrt(12),
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pat(13),
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est(14),
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sts(15),
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other (255) } OPTIONAL,
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creation-date Date,
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update-date Date,
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extra-acc SEQUENCE OF VisibleString OPTIONAL,
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keywords SEQUENCE OF VisibleString OPTIONAL,
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xref SEQUENCE OF EMBL-xref OPTIONAL }
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END
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--*********************************************************************
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--
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-- SWISSPROT specific data
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-- This block of specifications was developed by Mark Cavanaugh of
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-- NCBI working with Amos Bairoch of SWISSPROT
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--
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--*********************************************************************
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SP-General DEFINITIONS ::=
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BEGIN
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EXPORTS SP-block;
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IMPORTS Date, Dbtag FROM NCBI-General
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Seq-id FROM NCBI-Seqloc;
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SP-block ::= SEQUENCE { -- SWISSPROT specific descriptions
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class ENUMERATED {
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not-set (0) ,
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standard (1) , -- conforms to all SWISSPROT checks
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prelim (2) , -- only seq and biblio checked
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other (255) } ,
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extra-acc SET OF VisibleString OPTIONAL , -- old SWISSPROT ids
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imeth BOOLEAN DEFAULT FALSE , -- seq known to start with Met
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plasnm SET OF VisibleString OPTIONAL, -- plasmid names carrying gene
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seqref SET OF Seq-id OPTIONAL, -- xref to other sequences
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dbref SET OF Dbtag OPTIONAL , -- xref to non-sequence dbases
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keywords SET OF VisibleString OPTIONAL , -- keywords
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created Date OPTIONAL , -- creation date
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sequpd Date OPTIONAL , -- sequence update
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annotupd Date OPTIONAL } -- annotation update
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END
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--*********************************************************************
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--
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-- PIR specific data
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-- This block of specifications was developed by Jim Ostell of
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-- NCBI
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--
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--*********************************************************************
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PIR-General DEFINITIONS ::=
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BEGIN
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EXPORTS PIR-block;
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IMPORTS Seq-id FROM NCBI-Seqloc;
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PIR-block ::= SEQUENCE { -- PIR specific descriptions
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had-punct BOOLEAN OPTIONAL , -- had punctuation in sequence ?
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host VisibleString OPTIONAL ,
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source VisibleString OPTIONAL , -- source line
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summary VisibleString OPTIONAL ,
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genetic VisibleString OPTIONAL ,
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includes VisibleString OPTIONAL ,
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placement VisibleString OPTIONAL ,
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superfamily VisibleString OPTIONAL ,
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keywords SEQUENCE OF VisibleString OPTIONAL ,
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cross-reference VisibleString OPTIONAL ,
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date VisibleString OPTIONAL ,
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seq-raw VisibleString OPTIONAL , -- seq with punctuation
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seqref SET OF Seq-id OPTIONAL } -- xref to other sequences
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END
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--*********************************************************************
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--
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-- GenBank specific data
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-- This block of specifications was developed by Jim Ostell of
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-- NCBI
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--
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--*********************************************************************
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GenBank-General DEFINITIONS ::=
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BEGIN
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EXPORTS GB-block;
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IMPORTS Date FROM NCBI-General;
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GB-block ::= SEQUENCE { -- GenBank specific descriptions
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extra-accessions SEQUENCE OF VisibleString OPTIONAL ,
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source VisibleString OPTIONAL , -- source line
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keywords SEQUENCE OF VisibleString OPTIONAL ,
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origin VisibleString OPTIONAL,
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date VisibleString OPTIONAL , -- OBSOLETE old form Entry Date
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entry-date Date OPTIONAL , -- replaces date
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div VisibleString OPTIONAL , -- GenBank division
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taxonomy VisibleString OPTIONAL } -- continuation line of organism
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END
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--**********************************************************************
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-- PRF specific definition
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-- PRF is a protein sequence database crated and maintained by
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-- Protein Research Foundation, Minoo-city, Osaka, Japan.
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--
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-- Written by A.Ogiwara, Inst.Chem.Res. (Dr.Kanehisa's Lab),
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-- Kyoto Univ., Japan
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--
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--**********************************************************************
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PRF-General DEFINITIONS ::=
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BEGIN
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EXPORTS PRF-block;
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PRF-block ::= SEQUENCE {
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extra-src PRF-ExtraSrc OPTIONAL,
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keywords SEQUENCE OF VisibleString OPTIONAL
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}
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PRF-ExtraSrc ::= SEQUENCE {
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host VisibleString OPTIONAL,
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part VisibleString OPTIONAL,
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state VisibleString OPTIONAL,
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strain VisibleString OPTIONAL,
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taxon VisibleString OPTIONAL
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}
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END
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--*********************************************************************
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--
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-- PDB specific data
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-- This block of specifications was developed by Jim Ostell and
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-- Steve Bryant of NCBI
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--
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--*********************************************************************
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PDB-General DEFINITIONS ::=
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BEGIN
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EXPORTS PDB-block;
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IMPORTS Date FROM NCBI-General;
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PDB-block ::= SEQUENCE { -- PDB specific descriptions
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deposition Date , -- deposition date month,year
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class VisibleString ,
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compound SEQUENCE OF VisibleString ,
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source SEQUENCE OF VisibleString ,
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exp-method VisibleString OPTIONAL , -- present if NOT X-ray diffraction
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replace PDB-replace OPTIONAL } -- replacement history
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PDB-replace ::= SEQUENCE {
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date Date ,
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ids SEQUENCE OF VisibleString } -- entry ids replace by this one
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END
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