1--$Revision: 542897 $
2--**********************************************************************
3--
4--  NCBI Taxonomy Server
5--  by James Ostell, 1995
6--  Version 1.0 - July 1995
7--
8--**********************************************************************
9
10
11
12NCBI-Taxon1 DEFINITIONS ::=
13BEGIN
14
15IMPORTS Org-ref FROM NCBI-Organism;
16
17                          -- Requests to the Taxon server
18Taxon1-req ::= CHOICE {
19	init		NULL,		-- initialize the server
20	findname	VisibleString,	-- find orgnames match string
21	getdesignator 	VisibleString,	-- find designator
22	getunique     	VisibleString,	-- get taxid for unique name
23	getidbyorg    	Org-ref,	-- get taxid matches orgref
24	getorgnames   	INTEGER,	-- get all organism names
25	getcde		NULL,		-- get name classes
26	getranks	NULL,		-- get ranks
27	getdivs		NULL,		-- get divisions
28	getgcs		NULL,		-- get gencodes
29	getlineage      INTEGER,        -- get lineage for org
30	getchildren	INTEGER,	-- get children
31	getbyid		INTEGER,  	-- get Org-ref by TaxonID
32	lookup		Org-ref,  	-- lookup by data
33	getorgmod	Taxon1-info,  	-- lookup for OrgMod
34	fini    	NULL,    	-- close the server
35	id4gi		INTEGER,  	-- get taxid by gi
36	taxachildren	INTEGER,	-- get children
37	taxalineage     INTEGER,        -- get extended lineage for org
38        maxtaxid        NULL,           -- get max taxid
39        getproptypes    NULL,           -- get property types
40        getorgprop      Taxon1-info,    -- get properties for organism
41        searchname      Taxon1-info,    -- fancy search (token set, wild card)
42        dumpnames4class INTEGER,        -- all names of certain name class
43        getdomain       VisibleString}  -- get domain description and values
44
45Taxon1-resp ::= CHOICE {
46	error		Taxon1-error,	-- sent on any error
47	init    	NULL,		-- sent by successful initiation
48	findname	SET OF Taxon1-name,
49	getdesignator	INTEGER,
50	getunique	INTEGER,
51	getidbyorg	INTEGER,
52	getorgnames	SET OF Taxon1-name,
53	getcde		SET OF Taxon1-info,
54	getranks	SET OF Taxon1-info,
55	getdivs		SET OF Taxon1-info,
56	getgcs		SET OF Taxon1-info,
57	getlineage	SET OF Taxon1-info,
58	getchildren	SET OF Taxon1-info,
59	getbyid 	Taxon1-data,
60	lookup  	Taxon1-data,
61	getorgmod	SET OF Taxon1-info,
62	fini    	NULL,
63	id4gi           INTEGER,
64	taxabyid	Taxon2-data,
65	taxachildren	SEQUENCE OF Taxon1-name,
66	taxalineage	SEQUENCE OF Taxon1-name,
67        maxtaxid        INTEGER,
68	getproptypes    SET OF Taxon1-info,
69        getorgprop      SET OF Taxon1-info,
70        searchname      SET OF Taxon1-name,
71        dumpnames4class SET OF Taxon1-name,
72        getdomain       SEQUENCE OF Taxon1-info} -- [0]:id,nof_fields,name, [1..nof_fields]:field_no,val_type,field_name, [:nof_fields]:val_id,int_val or str_len(-1 for null),str_val
73
74Taxon1-info ::= SEQUENCE {
75	ival1	INTEGER,
76	ival2	INTEGER,
77	sval	VisibleString OPTIONAL}
78
79Taxon1-name ::= SEQUENCE {
80	taxid	INTEGER,
81	cde	INTEGER,
82	oname	VisibleString OPTIONAL,
83	uname	VisibleString OPTIONAL }
84
85Taxon1-error ::= SEQUENCE {
86	level ENUMERATED {
87		none (0) ,    -- not an error, just a message
88		info (1) ,    -- informational error
89		warn (2) ,
90		error (3) ,
91		fatal (4) } ,
92	msg VisibleString OPTIONAL }
93
94Taxon1-data ::= SEQUENCE {
95	org Org-ref OPTIONAL,    -- Org-ref with Org-name and db filled in
96	div VisibleString ,  -- GenBank division
97	embl-code VisibleString OPTIONAL,     -- 2 letter EMBL code
98	is-species-level BOOLEAN }   -- species level or below
99
100Taxon2-data ::= SEQUENCE {
101	org Org-ref OPTIONAL,    -- Org-ref with Org-name and db filled in
102	blast-name SEQUENCE OF VisibleString OPTIONAL,  -- inherited blast name
103	is-uncultured BOOLEAN ,     -- belongs to environmental bin
104	is-species-level BOOLEAN }   -- species level or below
105
106END
107
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111