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--$Revision: 1.12 $********************************************
--
-- entrez2.asn
-- Version 1
--
-- API to Entrez Engine (1999)
-- Retrieval of sequence done through ID1 module
-- Also, SeqId queries
-- Retrieval of PubMed records through PubMed module
-- Retrieval of Structures through PubStruct module
-- Retrieval of Genomes through Genomes module
--
--***************************************************************
NCBI-Entrez2 DEFINITIONS ::=
BEGIN
--**************************************
-- Entrez2 common elements
--**************************************
Entrez2-dt ::= INTEGER -- a date/time stamp
Entrez2-db-id ::= VisibleString -- database name
Entrez2-field-id ::= VisibleString -- field name
Entrez2-link-id ::= VisibleString -- link name
Entrez2-id-list ::= SEQUENCE { -- list of record UIDs
db Entrez2-db-id , -- the database
num INTEGER , -- number of uids
uids OCTET STRING OPTIONAL } -- coded uids
--****************************************
-- The structured form of the boolean is the same in a request or
-- return so that it easy to modify a query. This means some
-- fields are only considered in a return value, like counts
-- by term. They are ignored in a request.
-- The structured boolean supports specific boolean components,
-- an unparsed string in query syntax, and UID lists as
-- elements of a boolean. This makes it possible to submit
-- a single string, a fully structured query, or a mixture.
-- The UID list feature means one can also perform refinements
-- on UID lists from links, neighbors, or other operations.
-- UID list query now returns a history key for subsequent use.
--*****************************************
Entrez2-boolean-exp ::= SEQUENCE {
db Entrez2-db-id , -- database for this query
exp SEQUENCE OF Entrez2-boolean-element , -- the Boolean
limits Entrez2-limits OPTIONAL } -- date bounds
Entrez2-boolean-element ::= CHOICE {
str VisibleString , -- unparsed query string
op Entrez2-operator , -- logical operator
term Entrez2-boolean-term , -- fielded term
ids Entrez2-id-list , -- list of UIDs - returns history key in reply
key VisibleString } -- history key for uploaded UID list or other query
--*****************************************
-- the term is both sent and received as parts of
-- queries and replies. The attributes can be filled in
-- by either, but may be ignored by one or the other. Flags are
-- shown if a real value is only of use in the query (Q), only
-- in the reply (R), or used in both (B)
-- do-not-explode and do-not-translate are only active set by
-- by the query. However, they retain those settings in the
-- return value so they can be resent with a new query
--******************************************
Entrez2-boolean-term ::= SEQUENCE {
field Entrez2-field-id , -- B
term VisibleString , -- B
term-count INTEGER OPTIONAL, -- R count of records with term
do-not-explode BOOLEAN DEFAULT FALSE, -- Q do not explode term
do-not-translate BOOLEAN DEFAULT FALSE} -- Q do not use synonyms
Entrez2-operator ::= INTEGER {
and (1) ,
or (2) ,
butnot (3) ,
range (4) ,
left-paren (5) ,
right-paren (6) }
--***************************************
-- Entrez2 Request types
--***************************************
--****************************************
-- The basic request wrapper leaves space for a version which
-- allow the server to support older clients
-- The tool parameter allows us to log the client types for
-- debugging and tuning
-- The cookie is a session ID returned by the first Entrez2-reply
--****************************************
Entrez2-request ::= SEQUENCE { -- a standard request
request E2Request , -- the actual request
version INTEGER , -- ASN1 spec version
tool VisibleString OPTIONAL , -- tool making request
cookie VisibleString OPTIONAL , -- history session cookie
use-history BOOLEAN DEFAULT FALSE } -- request should use history
E2Request ::= CHOICE { -- request types
get-info NULL , -- ask for info block
eval-boolean Entrez2-eval-boolean , -- Boolean lookup
get-docsum Entrez2-id-list , -- get the DocSums
get-term-pos Entrez2-term-query, -- get position in term list
get-term-list Entrez2-term-pos , -- get Term list by position
get-term-hierarchy Entrez2-hier-query, -- get a hierarchy from a term
get-links Entrez2-get-links , -- get specific links from a UID list
get-linked Entrez2-get-links , -- get subset of UID list which has links
get-link-counts Entrez2-id } -- get all links from one UID
--****************************************
-- When evaluating a boolean query the counts of hits is always
-- returned.
-- In addition, you can request the UIDs of the hits or the
-- the parsed query in structured form (with counts by term),
-- or both.
--****************************************
Entrez2-eval-boolean ::= SEQUENCE { -- evaluate Boolean query
return-UIDs BOOLEAN DEFAULT FALSE, -- return UID list?
return-parse BOOLEAN DEFAULT FALSE, -- return parsed query?
query Entrez2-boolean-exp } -- the actual query
Entrez2-dt-filter ::= SEQUENCE {
begin-date Entrez2-dt,
end-date Entrez2-dt,
type-date Entrez2-field-id }
Entrez2-limits ::= SEQUENCE { -- date limits
filter-date Entrez2-dt-filter OPTIONAL,
max-UIDs INTEGER OPTIONAL, -- max UIDs to return in list
offset-UIDs INTEGER OPTIONAL} -- start partway into UID list
Entrez2-id ::= SEQUENCE { -- a single UID
db Entrez2-db-id ,
uid INTEGER }
Entrez2-term-query ::= SEQUENCE {
db Entrez2-db-id ,
field Entrez2-field-id ,
term VisibleString }
Entrez2-hier-query ::= SEQUENCE {
db Entrez2-db-id ,
field Entrez2-field-id ,
term VisibleString OPTIONAL , -- query with either term
txid INTEGER OPTIONAL } -- or Taxonomy ID
Entrez2-term-pos ::= SEQUENCE { -- request portions of term list
db Entrez2-db-id ,
field Entrez2-field-id ,
first-term-pos INTEGER ,
number-of-terms INTEGER OPTIONAL } -- optional for hierarchy only
Entrez2-get-links ::= SEQUENCE { -- request links of one type
uids Entrez2-id-list , -- docs to link from
linktype Entrez2-link-id , -- type of link
max-UIDS INTEGER OPTIONAL , -- maximum number of links to return
count-only BOOLEAN OPTIONAL , -- return only the counts
parents-persist BOOLEAN OPTIONAL } -- allow original uids in list
--**********************************************************
-- Replies from the Entrez server
-- all replies contain the date/time stamp when they were executed
-- to do reqular date bounded searches use this value+1 to search
-- again later instead of recording the date/time on the client machine
-- the cookie allows a simple key string to represent UID lists in the history
--**********************************************************
Entrez2-reply ::= SEQUENCE {
reply E2Reply , -- the actual reply
dt Entrez2-dt , -- date/time stamp from server
server VisibleString , -- server version info
msg VisibleString OPTIONAL , -- possibly a message to the user
key VisibleString OPTIONAL , -- history key for query
cookie VisibleString OPTIONAL } -- history session cookie
E2Reply ::= CHOICE {
error VisibleString , -- if nothing can be returned
get-info Entrez2-info , -- the database info
eval-boolean Entrez2-boolean-reply, -- result of boolean query
get-docsum Entrez2-docsum-list,
get-term-pos INTEGER, -- position of the term
get-term-list Entrez2-term-list,
get-term-hierarchy Entrez2-hier-node,
get-links Entrez2-link-set,
get-linked Entrez2-id-list,
get-link-counts Entrez2-link-count-list }
Entrez2-info ::= SEQUENCE { -- describes all the databases
db-count INTEGER , -- number of databases
build-date Entrez2-dt , -- build date of databases
db-info SEQUENCE OF Entrez2-db-info } -- info by database
Entrez2-db-info ::= SEQUENCE { -- info for one database
db-name Entrez2-db-id , -- internal name
db-menu VisibleString , -- short name for menu
db-descr VisibleString , -- longer explanatory name
doc-count INTEGER , -- total number of records
field-count INTEGER , -- number of field types
fields SEQUENCE OF Entrez2-field-info,
link-count INTEGER , -- number of link types
links SEQUENCE OF Entrez2-link-info,
docsum-field-count INTEGER,
docsum-fields SEQUENCE OF Entrez2-docsum-field-info }
Entrez2-field-info ::= SEQUENCE { -- info about one field
field-name Entrez2-field-id , -- the internal name
field-menu VisibleString , -- short string suitable for menu
field-descr VisibleString , -- longer, explanatory name
term-count INTEGER , -- number of terms in field
is-date BOOLEAN OPTIONAL ,
is-numerical BOOLEAN OPTIONAL ,
single-token BOOLEAN OPTIONAL ,
hierarchy-avail BOOLEAN OPTIONAL ,
is-rangable BOOLEAN OPTIONAL ,
is-truncatable BOOLEAN OPTIONAL }
Entrez2-link-info ::= SEQUENCE { -- info about one link
link-name Entrez2-link-id ,
link-menu VisibleString ,
link-descr VisibleString ,
db-to Entrez2-db-id , -- database it links to
data-size INTEGER OPTIONAL } -- size of link data element
Entrez2-docsum-field-type ::= INTEGER {
string (1) ,
int (2) ,
float (3) ,
date-pubmed (4) }
Entrez2-docsum-field-info ::= SEQUENCE {
field-name VisibleString,
field-description VisibleString,
field-type Entrez2-docsum-field-type }
Entrez2-boolean-reply ::= SEQUENCE {
count INTEGER , -- records hit
uids Entrez2-id-list OPTIONAL, -- if uids requested
query Entrez2-boolean-exp OPTIONAL } -- if parsed query requested
Entrez2-docsum-list ::= SEQUENCE {
count INTEGER , -- number of docsums
list SEQUENCE OF Entrez2-docsum }
Entrez2-docsum ::= SEQUENCE {
uid INTEGER , -- primary uid (gi, pubmedid)
docsum-data SEQUENCE OF Entrez2-docsum-data }
Entrez2-docsum-data::= SEQUENCE {
field-name VisibleString,
field-value VisibleString }
Entrez2-term-list ::= SEQUENCE {
pos INTEGER, -- position of first term in list
num INTEGER, -- number of terms in list
list SEQUENCE OF Entrez2-term }
Entrez2-term ::= SEQUENCE {
term VisibleString ,
txid INTEGER OPTIONAL,
count INTEGER , -- count of records with this term
is-leaf-node BOOLEAN OPTIONAL } -- used for hierarchy only
Entrez2-hier-node ::= SEQUENCE { -- for hierarchical index
cannonical-form VisibleString , -- the official name
lineage-count INTEGER , -- number of strings in lineage
lineage SEQUENCE OF Entrez2-term OPTIONAL , -- strings up the lineage
child-count INTEGER , -- number of children of this node
children SEQUENCE OF Entrez2-term , -- the children
is-ambiguous BOOLEAN OPTIONAL } -- used for hierarchy only
--*******************************************
-- Links are returned in sets also using OCTET STRINGS
--*******************************************
Entrez2-link-set ::= SEQUENCE { -- set of links
ids Entrez2-id-list ,
data-size INTEGER OPTIONAL , -- size of data elements
data OCTET STRING OPTIONAL } -- coded scores
Entrez2-link-count-list ::= SEQUENCE { -- all links from 1 uid
link-type-count INTEGER , -- number of types of links
links SEQUENCE OF Entrez2-link-count }
Entrez2-link-count ::= SEQUENCE { -- link count of one type
link-type Entrez2-link-id ,
link-count INTEGER }
END
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