476 lines
33 KiB
Groff
476 lines
33 KiB
Groff
-- $Id: pcassay.asn 282508 2011-05-11 22:47:31Z ywang $
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-- ===========================================================================
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--
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-- PUBLIC DOMAIN NOTICE
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-- National Center for Biotechnology Information
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--
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-- This software/database is a "United States Government Work" under the
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-- terms of the United States Copyright Act. It was written as part of
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-- the author's official duties as a United States Government employee and
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-- thus cannot be copyrighted. This software/database is freely available
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-- to the public for use. The National Library of Medicine and the U.S.
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-- Government have not placed any restriction on its use or reproduction.
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--
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-- Although all reasonable efforts have been taken to ensure the accuracy
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-- and reliability of the software and data, the NLM and the U.S.
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-- Government do not and cannot warrant the performance or results that
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-- may be obtained by using this software or data. The NLM and the U.S.
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-- Government disclaim all warranties, express or implied, including
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-- warranties of performance, merchantability or fitness for any particular
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-- purpose.
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--
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-- Please cite the author in any work or product based on this material.
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--
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-- ===========================================================================
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--
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-- Authors: NCBI Structure Group
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--
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-- File Description:
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-- ASN.1 definitions for PubChem biological assay data database
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--
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-- ===========================================================================
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NCBI-PCAssay DEFINITIONS ::= BEGIN
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IMPORTS Pub FROM NCBI-Pub
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BioSource FROM NCBI-BioSource
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Date, Object-id FROM NCBI-General
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PC-ID, PC-Source, PC-XRefData FROM NCBI-PCSubstance;
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-- EXPORTS ;
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-- Container for multiple Assay Data Submissions
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PC-AssayContainer ::= SEQUENCE OF PC-AssaySubmit
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-- Container for Data Depositions and Assay Definitions
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PC-AssaySubmit ::= SEQUENCE {
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assay CHOICE { -- Assay Description or pre-existing Identifier
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aid INTEGER, -- Assay Identifier
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aid-source PC-Source, -- External Assay Identifier
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descr PC-AssayDescription, -- Assay Description (new or updated)
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aidver PC-ID -- Assay Identifier/Version (for internal use)
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},
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data SEQUENCE OF PC-AssayResults OPTIONAL, -- Assay Data Deposition (vector)
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revoke SEQUENCE OF INTEGER OPTIONAL -- List of SID's whose data is to be suppressed
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}
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-- Container for multiple Assay Result Sets
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-- PC-AssayResultsSet ::= SEQUENCE OF PC-AssayResults
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-- Assay Results provided for a given Substance tested, with respect to the results types defined in the
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-- referenced Assay Description
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PC-AssayResults ::= SEQUENCE {
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-- Internal/External Tracking Information
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sid INTEGER, -- Tested Substance ID/Version [Either valid ID or,
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-- if "sid-source" is used, this is a "0" value]
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-- Note: A valid ID is greater than "0"
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sid-source PC-Source OPTIONAL, -- External Identifier for this Substance
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-- Note: May be used in-lieu of "sid"
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-- Note: This is non-optional if "sid" is "0"
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version INTEGER OPTIONAL, -- Version identifier for this AID-SID Result
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-- Note: Incoming data should set this to be "0"
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-- Data Annotation/Qualifier and URL to further Depositor Information
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comment VisibleString OPTIONAL, -- Annotation or qualifier for this Result
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-- Assay Result Data for this Sample
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-- Note: Users need populate only those "tid"s, for which there is data, in any order.
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outcome INTEGER { -- Assay Outcome
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inactive (1), -- Substance is considered Inactive
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active (2), -- Substance is considered Active
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inconclusive (3), -- Substance is Inconclusive
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unspecified (4), -- Substance Outcome is Unspecified
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probe (5) -- Substance Outcome is Unspecified
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} DEFAULT unspecified,
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rank INTEGER OPTIONAL, -- Rank of Assay Outcome (for result ordering)
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-- Note: Larger numbers are more active
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data SEQUENCE OF PC-AssayData OPTIONAL, -- Assay Data Reported for this SID (vector)
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url VisibleString OPTIONAL, -- Depositor provided URL for this Result
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xref SEQUENCE OF PC-AnnotatedXRef OPTIONAL, -- annotated Cross-Reference Information
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-- to be removed,
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-- instead regulard TID will be generated
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-- which are then annotated by xref type
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date Date OPTIONAL -- Pubchem Release Date
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}
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-- Assay Readouts/Results for a Tested Substance
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PC-AssayData ::= SEQUENCE {
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tid INTEGER, -- Assay Result Field Type ID (TID)
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-- Note: Result Field ID's must be greater than "0"
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value CHOICE { -- Assay Result, must be the same type as defined for TID
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ival INTEGER,
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fval REAL,
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bval BOOLEAN,
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sval VisibleString
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}
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}
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-- Assay Description provided by an Organization that describes the assay/protocol performed and defines the
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-- measured end-points and parameters to be stored. An Assay Description is not a database table. You can
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-- define as many Result Definitions as needed and they need not be used by all Substances tested.
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-- Assay Descriptions can be modified on both description text and Result Definitions after initial submission
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-- as desired, and such udpates will be tracked in PubChem
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PC-AssayDescription ::= SEQUENCE {
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-- Internal/External Tracking Information
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aid PC-ID, -- Assay Description ID/Version [Either valid ID
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-- or, if "aid-source" is used, a "0" dummy value]
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-- Note: Version is for internal use (only?)
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-- Note: A valid ID is greater than "0"
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aid-source PC-Source OPTIONAL, -- External Identifier for this Assay Description
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-- Note: May be used in-lieu of "aid"
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-- Note: This is non-optional if "aid" ID is "0"
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-- Assay Description Information
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name VisibleString, -- Short Assay Name (for display purposes)
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description SEQUENCE OF VisibleString OPTIONAL, -- Description of Assay
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protocol SEQUENCE OF VisibleString OPTIONAL, -- Procedure used to generate results
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comment SEQUENCE OF VisibleString OPTIONAL, -- Comments or additional information
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xref SEQUENCE OF PC-AnnotatedXRef OPTIONAL, -- Annotated Cross-Reference Information
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-- Allowed Assay Result Types
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results SEQUENCE OF PC-ResultType OPTIONAL, -- Result Definitions (vector)
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-- Additional Information
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pub SEQUENCE OF Pub OPTIONAL, -- Depositor provided publications for this assay
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revision INTEGER OPTIONAL, -- Revision identifier for textual description
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target SEQUENCE OF PC-AssayTargetInfo OPTIONAL, -- Target information
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activity-outcome-method INTEGER { -- Assay Outcome Qualifier
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other (0), -- All Other Type
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screening (1), -- Primary Screen Assay
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confirmatory (2), -- Confirmatory Assay
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summary (3) -- Probe Summary Assay
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} OPTIONAL,
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dr SEQUENCE OF PC-AssayDRAttr OPTIONAL, -- Dose-Response Attribution
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substance-type INTEGER{
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small-molecule (1),
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nucleotide (2),
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other (255)
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} OPTIONAL, -- to distinguish the type of substance used in the screening
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-- Grant and project category information
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grant-number SEQUENCE OF VisibleString OPTIONAL, -- grant proposal number
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-- required for 'MLSCN' & 'MLPCN' projects
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project-category INTEGER{
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mlscn (1),
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mlpcn (2),
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mlscn-ap (3),
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mlpcn-ap (4),
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journal-article (5), -- to be deprecated
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assay-vendor (6),
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literature-extracted (7),
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literature-author (8),
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literature-publisher (9),
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rnaigi (10),
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other (255)
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} OPTIONAL, -- to distinguish projects funded through MLSCN, MLPCN or other
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-- mlscn: assay depositions from MLSCN screen center
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-- mlpcn: assay depositions from MLPCN screen center
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-- mlscn-ap: assay depositions from MLSCN assay provider
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-- mlpcn-ap: assay depositions from MLPCN assay provider
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-- required for 'MLSCN' & 'MLPCN' projects
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-- journal-article: to be deprecated; replaced by option 7,8 & 9 to better characterize data from literature
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-- literature-extracted: data from literature, extracted by curators
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-- literature-author: data from literature, submitted by author of articles
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-- literature-publisher: data from literature, submitted by journals/publishers
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-- rnaigi: RNAi screenings from RNAi Global Initiative
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-- annotation to indicate whether an assay is a panel, e.g. containing multiple components, or belongs to a group
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is-panel BOOLEAN OPTIONAL, -- annotation for panel assay, e.g. to indicate that this assay
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-- contains multiple members/components.
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-- A panel assay can be one assay reporting readouts for
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-- many targets, or reporting readouts for different
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-- cell lines, or different organisms
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-- examples such as bioassay containing kinase profiling data
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-- or bioassay containing cytoxicity data for multiple cell lines
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-- or bioassay containing screening data from different stages,
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-- such as primary screening, follow ups
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assay-group SEQUENCE OF VisibleString OPTIONAL, -- annotation for assay gruop information, e.g. this
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-- assay belongs to a group of assay associated by
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-- a unique name, e.g. the value assigned to 'assay-group',
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-- assays belonging to this group can be
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-- retrieved using this unique name
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-- it is depositor's responsibility to make the name
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-- distinct if necessary
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-- this can be used as the mechanism to specify 'related bioassays'
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-- before hand so it is not necessary to update the descriptions of
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-- related assays when new group member submitted to PubChem
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panel-info PC-AssayPanel OPTIONAL, -- for 'panel' type of bioassay only
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-- store assay panel member information
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is-mlp-late-stage BOOLEAN OPTIONAL, -- verification for 'late-stage-data' deposition
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categorized-comment SEQUENCE OF PC-CategorizedComment OPTIONAL
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-- to report categorized description/comment by associating with a category title
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}
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-- Description for Panel Assay
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-- Describe general information about the panel, and link to information for each panel member
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PC-AssayPanel ::= SEQUENCE {
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name VisibleString, -- short name for the panel, such as 'Kinase Profiling'
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descr VisibleString OPTIONAL, -- short description of this panel
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member SEQUENCE OF PC-AssayPanelMember OPTIONAL -- store panel member information
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}
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-- Specific information about each panel member(or component), such as target, cell line name, cross-reference ...
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PC-AssayPanelMember ::= SEQUENCE {
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mid INTEGER, -- ID for panel member
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-- if a kinase panel with 300 kinases, ID will range from 1 to 300
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-- TIDs of the same panel member to be grouped based on panel member ID
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name VisibleString OPTIONAL, -- short name for this panel member
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description VisibleString OPTIONAL, -- description about specifics of this panel member
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-- such as about cell line, or target information
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protocol SEQUENCE OF VisibleString OPTIONAL, -- Specific procedure used to generate results for the panel member
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comment SEQUENCE OF VisibleString OPTIONAL, -- Comments or additional information
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target SEQUENCE OF PC-AssayTargetInfo OPTIONAL, -- often provided for profiling assays across protein families
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xref SEQUENCE OF PC-AnnotatedXRef OPTIONAL, -- annotated Cross-Reference Information
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activity-outcome-method INTEGER { -- Assay Outcome Qualifier
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other (0), -- All Other Type
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screening (1), -- Primary Screen Assay
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confirmatory (2), -- Confirmatory Assay
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summary (3) -- Probe Summary Assay
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} OPTIONAL,
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dr SEQUENCE OF PC-AssayDRAttr OPTIONAL, -- Dose-Response Attribution within the panel member
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categorized-comment SEQUENCE OF PC-CategorizedComment OPTIONAL
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-- to report categorized description/comment by associating with a category title
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}
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-- Definition for Categorized description/comment
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-- This field is added to provide flexibility for depositors to present textual description/comments in a desirable way
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-- and to facilitate information validation by the depositor and data exchange with PubChem
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PC-CategorizedComment ::= SEQUENCE {
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title VisibleString, -- title for the description/comment
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comment SEQUENCE OF VisibleString -- description/comment content
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}
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-- Assay Dose-response attribute information used to define a set of readouts
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-- as being part of a dose-response curve (for curve plotting/analysis)
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PC-AssayDRAttr ::=SEQUENCE {
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id INTEGER, -- Unique dose-response test set identifier
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-- Note: A valid ID is greater than "0"
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descr VisibleString OPTIONAL, -- Dose-Response Curve Description (used as curve title)
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dn VisibleString OPTIONAL, -- Dose Axis Description (used as axis name)
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rn VisibleString OPTIONAL, -- Response Axis Description (used as axis name)
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type INTEGER {
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experimental (0), -- dose-response data points measured directly by experiment
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calculated (1) -- dose-response data points derived from fitted curve
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} OPTIONAL
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}
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-- Molecular target information provides by organization describes the functionality of the target,
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-- facilitates the linking between PubChem bioassays, and the linking between target molecule to other NCBI resources
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PC-AssayTargetInfo ::= SEQUENCE {
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name VisibleString, -- Molecular name of target
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mol-id INTEGER, -- NCBI database identifier of the target molecule
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molecule-type INTEGER { -- Assay Target Type
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protein (1), -- mol-id: NCBI Protein GI
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dna (2), -- mol-id: NCBI Nucleotide GI
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rna (3), -- mol-id: NCBI Nucleotide GI
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gene (4), -- mol-id: NCBI Gene ID
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biosystem (5), -- mol-id: NCBI BioSystems ID
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other (255)
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} DEFAULT protein,
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organism BioSource OPTIONAL, -- Target Organism
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descr VisibleString OPTIONAL, -- Target Description (e.g., cellular functionality and location)
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comment SEQUENCE OF VisibleString OPTIONAL -- Comments or Additional Information
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}
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-- Annotated Cross-Reference (XRef) Information to allow the XRef to be qualified, as to its meaning or context
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PC-AnnotatedXRef ::= SEQUENCE {
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xref PC-XRefData, -- Cross-Reference Information
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comment VisibleString OPTIONAL, -- Annotation qualifier describing Cross-Reference meaning
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type INTEGER {
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pcit (1), -- primary PMID/citation directly associated with the current assay data
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pgene (2) -- gene encoding the protein assay target
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} OPTIONAL
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}
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-- Definition of Allowed Result Types for a given Assay
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PC-ResultType ::= SEQUENCE {
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-- Tracking or Description Information
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tid INTEGER, -- Assay Result Field Type ID (TID)
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name VisibleString, -- Result Field Name (short name for display)
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description SEQUENCE OF VisibleString OPTIONAL, -- Result Field Description
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-- Result Data Type and Validation Information
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type INTEGER { -- Result Data Type
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float (1),
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int (2),
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bool (3),
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string (4)
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},
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constraints CHOICE { -- Allowed Values, used for validating incoming data
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-- If type is "float"
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fset SEQUENCE OF REAL, -- Allowed values must be equal to one of these
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fmin REAL, -- Allowed values (x) must be [ fmin <= x ]
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fmax REAL, -- Allowed values (x) must be [ x <= fmax ]
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frange PC-RealMinMax, -- Minimum/Maximum Range [ min <= x <= max ]
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-- If type is "int"
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iset SEQUENCE OF INTEGER, -- Allowed values must be equal to one of these
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imin INTEGER, -- Allowed values (x) must be [ imin <= x ]
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imax INTEGER, -- Allowed values (x) must be [ x <= imax ]
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irange PC-IntegerMinMax, -- Minimum/Maximum Range [ min <= x <= max ]
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-- If type is "string"
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sset SEQUENCE OF VisibleString -- Allowed values must be equal to one of these
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} OPTIONAL,
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-- Unit information provides the units for the values reported for this TID. For example, if the values
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-- reported for this TID are a concentration, e.g., micro-molar, setting the unit "um" allows PubChem to
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-- know that the value, e.g., "1.3", is actually "1.3 uM". This also allows PubChem to properly report the
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-- units when displaying the reported values for this TID. If the enumerated units provided below are
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-- insufficient, you may represent the units as a string in the optional "sunit" field (see below).
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unit INTEGER { -- Units for Value
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ppt (1), -- Parts per Thousand
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ppm (2), -- Parts per Million
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ppb (3), -- Parts per Billion
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mm (4), -- milliM
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um (5), -- microM
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nm (6), -- nanoM
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pm (7), -- picoM
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fm (8), -- femtoM
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mgml (9), -- milligrams per mL
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ugml (10), -- micrograms per mL
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ngml (11), -- nanograms per mL
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pgml (12), -- picograms per mL
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fgml (13), -- femtograms per mL
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m (14), -- Molar
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percent (15), -- Percent
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ratio (16), -- Ratio
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sec (17), -- Seconds
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rsec (18), -- Reciprocal Seconds
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min (19), -- Minutes
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rmin (20), -- Reciprocal Minutes
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day (21), -- Days
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rday (22), -- Reciprocal Days
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ml-min-kg (23), -- milliliter / minute / kilogram
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l-kg (24), -- liter / kilogram
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hr-ng-ml (25), -- hour * nanogram / milliliter
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cm-sec (26), -- centimeter / second
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mg-kg (27), -- milligram / kilogram
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none (254),
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unspecified (255)
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} OPTIONAL,
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-- ATTENTION: sunit field is DEPRECATED. It is no longer
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-- supported and remains for legacy data only.
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sunit VisibleString OPTIONAL, -- Unit Type (as a String)
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-- Value Transform information qualifies the values reported for this TID. For example, if the values
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-- reported for this TID are "-Log10 GI50", you may want to consider setting
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-- the "nlog" value below. In doing so, PubChem would know that the value, e.g., "5.0"
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-- is actually "1.0e-5". If the transformation applied is not listed, you may represent
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-- this transformation as a string in the "stransform" (see below) for eventual inclusion
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-- in the enumerated transform list below.
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--
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--
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-- ATTENTION: transform field is DEPRECATED. It is no longer
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-- supported and remains for legacy data only.
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transform INTEGER { -- Value Type Details
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linear (1), -- Linear Scale (x)
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ln (2), -- Natural Log Scale (ln x)
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log (3), -- Log Base 10 Scale (log10 x)
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reciprocal (4), -- Reciprocal Scale (1/x)
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negative (5), -- Negative Linear Scale (-x)
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nlog (6), -- Negative Log Base 10 Scale (-log10 x)
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nln (7) -- Negative Natural Log Scane (-ln x)
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} OPTIONAL,
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-- ATTENTION: stransform field is DEPRECATED. It is no longer
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-- supported and remains for legacy data only.
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stransform VisibleString OPTIONAL, -- Value Transform Type (as a String)
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tc PC-ConcentrationAttr OPTIONAL, -- Tested concentration attribute
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ac BOOLEAN OPTIONAL, -- if true, indicates that this TID field
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-- provides active concentration summary by
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-- reporting the concentration which produces
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-- 50% of the maximum possible biological response
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-- such as IC50, EC50, AC50, GI50 etc.
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-- or by reporting constant parameters such as Ki,
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-- that based on which the activity outcome in this assay is called
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panel-info PC-AssayPanelTestResult OPTIONAL, -- needed for panel assay only
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-- each panel member may have a number of TID columns reported
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-- such TIDs are grouped by panel member ID, see PC-AssayPanelMemberInfo
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annot INTEGER {
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pmid (1), -- PubMed ID
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mmdb (2), -- MMDB ID
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url (3), -- indicate TID data is a url that provides supplementary information
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protein-gi (4), -- GenBank General ID (GI) for a Protein
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nucleotide-gi (5), -- GenBank General ID (GI) for a Nucleotide
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taxonomy (6), -- Taxonomy ID for an Organism
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mim(7), -- MIM, Mendelian Inheritance in Man, ID
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gene(8), -- Entrez Gene ID
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probe(9), -- Entrez Probe ID
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aid (10), -- PubChem BioAssay ID, may be used in 'Summary' assay
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sid (11), -- PubChem Substance ID, may be used in 'Summary' assay
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cid (12), -- PubChem Compound ID
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protein-target-gi (13), -- GenBank General ID (GI) for a Protein target
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biosystems-target-id (14), -- NCBI BioSystems ID
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target-name (15), -- target name
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target-descr (16), -- brief target description
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target-tax-id (17), -- NCBI Taxonomy ID for target molecule
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gene-target-id (18), -- NCBI Gene ID for a gene target
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dna-nucleotide-target-gi (19), -- GenBank General ID (GI) for a DNA Nucleotide target
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rna-nucleotide-target-gi (20) -- GenBank General ID (GI) for a RNA Nucleotide target
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} OPTIONAL -- treat substance associated cross-reference as regular TID
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-- web servers would make a link
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-- to the corresponding record in Entrez databases
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-- treat substance associated target information as regular TID
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-- for example, for RNAi screening data, each 'substance' may
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-- correspond to a specific gene target
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}
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PC-AssayPanelTestResult ::= SEQUENCE {
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mid INTEGER, -- panel member ID, see PC-AssayPanelMemberInfo
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-- track association between a group of TIDs and panel member
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|
readout-annot INTEGER {
|
|
regular (1), -- to indicate this TID column is a regular readout
|
|
outcome (2), -- to indicate this TID column is "outcome" of the particular panel member
|
|
score(3), -- to indicate this TID column reports activity score of the particular panel member
|
|
-- to be used for neighboring assays
|
|
ac (4) -- to indicate this TID column is "active concentration"
|
|
-- 'outcome' and 'ac' type of TID are to be used for data analysis
|
|
-- across members of panel
|
|
-- or across multiple assays including other panel assays
|
|
} DEFAULT regular
|
|
|
|
}
|
|
|
|
--The concentration attribute is to indicate that the readout under this test result field is biological concentration-response data, the attribute provides the value and unit of the tested concentration
|
|
PC-ConcentrationAttr ::= SEQUENCE {
|
|
concentration REAL,
|
|
unit INTEGER { -- Units for Concentration
|
|
|
|
um (5) -- microM
|
|
},
|
|
dr-id INTEGER OPTIONAL -- Dose-Response Attribution ID (if applicable)
|
|
}
|
|
|
|
|
|
-- Mininum and Maximum Constraints on an Integer Value (used for validating incoming data)
|
|
PC-IntegerMinMax ::= SEQUENCE {
|
|
min INTEGER, -- Minimum Value Allowed
|
|
max INTEGER -- Maximum Value Allowed
|
|
}
|
|
|
|
|
|
-- Mininum and Maximum Constraints on a Real Value (used for validating incoming data)
|
|
PC-RealMinMax ::= SEQUENCE {
|
|
min REAL, -- Minimum Value Allowed
|
|
max REAL -- Maximum Value Allowed
|
|
}
|
|
|
|
|
|
END
|