src/objects/pcassay/pcassay.asn
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-- $Id: pcassay.asn 52661 2012-01-17 16:19:46Z ywang $
-- ===========================================================================
--
-- PUBLIC DOMAIN NOTICE
-- National Center for Biotechnology Information
--
-- This software/database is a "United States Government Work" under the
-- terms of the United States Copyright Act. It was written as part of
-- the author's official duties as a United States Government employee and
-- thus cannot be copyrighted. This software/database is freely available
-- to the public for use. The National Library of Medicine and the U.S.
-- Government have not placed any restriction on its use or reproduction.
--
-- Although all reasonable efforts have been taken to ensure the accuracy
-- and reliability of the software and data, the NLM and the U.S.
-- Government do not and cannot warrant the performance or results that
-- may be obtained by using this software or data. The NLM and the U.S.
-- Government disclaim all warranties, express or implied, including
-- warranties of performance, merchantability or fitness for any particular
-- purpose.
--
-- Please cite the author in any work or product based on this material.
--
-- ===========================================================================
--
-- Authors: NCBI Structure Group
--
-- File Description:
-- ASN.1 definitions for PubChem biological assay data database
--
-- ===========================================================================
NCBI-PCAssay DEFINITIONS ::= BEGIN
IMPORTS Pub FROM NCBI-Pub
BioSource FROM NCBI-BioSource
Date, Object-id FROM NCBI-General
PC-ID, PC-Source, PC-XRefData FROM NCBI-PCSubstance;
-- EXPORTS ;
-- Container for multiple Assay Data Submissions
PC-AssayContainer ::= SEQUENCE OF PC-AssaySubmit
-- Container for Data Depositions and Assay Definitions
PC-AssaySubmit ::= SEQUENCE {
assay CHOICE { -- Assay Description or pre-existing Identifier
aid INTEGER, -- Assay Identifier
aid-source PC-Source, -- External Assay Identifier
descr PC-AssayDescription, -- Assay Description (new or updated)
aidver PC-ID -- Assay Identifier/Version (for internal use)
},
data SEQUENCE OF PC-AssayResults OPTIONAL, -- Assay Data Deposition (vector)
revoke SEQUENCE OF INTEGER OPTIONAL -- List of SID's whose data is to be suppressed
}
-- Container for multiple Assay Result Sets
-- PC-AssayResultsSet ::= SEQUENCE OF PC-AssayResults
-- Assay Results provided for a given Substance tested, with respect to the results types defined in the
-- referenced Assay Description
PC-AssayResults ::= SEQUENCE {
-- Internal/External Tracking Information
sid INTEGER, -- Tested Substance ID/Version [Either valid ID or,
-- if "sid-source" is used, this is a "0" value]
-- Note: A valid ID is greater than "0"
sid-source PC-Source OPTIONAL, -- External Identifier for this Substance
-- Note: May be used in-lieu of "sid"
-- Note: This is non-optional if "sid" is "0"
version INTEGER OPTIONAL, -- Version identifier for this AID-SID Result
-- Note: Incoming data should set this to be "0"
-- Data Annotation/Qualifier and URL to further Depositor Information
comment VisibleString OPTIONAL, -- Annotation or qualifier for this Result
-- Assay Result Data for this Sample
-- Note: Users need populate only those "tid"s, for which there is data, in any order.
outcome INTEGER { -- Assay Outcome
inactive (1), -- Substance is considered Inactive
active (2), -- Substance is considered Active
inconclusive (3), -- Substance is Inconclusive
unspecified (4), -- Substance Outcome is Unspecified
probe (5) -- Substance Outcome is Unspecified
} DEFAULT unspecified,
rank INTEGER OPTIONAL, -- Rank of Assay Outcome (for result ordering)
-- Note: Larger numbers are more active
data SEQUENCE OF PC-AssayData OPTIONAL, -- Assay Data Reported for this SID (vector)
url VisibleString OPTIONAL, -- Depositor provided URL for this Result
xref SEQUENCE OF PC-AnnotatedXRef OPTIONAL, -- annotated Cross-Reference Information
-- to be removed,
-- instead regulard TID will be generated
-- which are then annotated by xref type
date Date OPTIONAL -- Pubchem Release Date
}
-- Assay Readouts/Results for a Tested Substance
PC-AssayData ::= SEQUENCE {
tid INTEGER, -- Assay Result Field Type ID (TID)
-- Note: Result Field ID's must be greater than "0"
value CHOICE { -- Assay Result, must be the same type as defined for TID
ival INTEGER,
fval REAL,
bval BOOLEAN,
sval VisibleString
}
}
-- Assay Description provided by an Organization that describes the assay/protocol performed and defines the
-- measured end-points and parameters to be stored. An Assay Description is not a database table. You can
-- define as many Result Definitions as needed and they need not be used by all Substances tested.
-- Assay Descriptions can be modified on both description text and Result Definitions after initial submission
-- as desired, and such udpates will be tracked in PubChem
PC-AssayDescription ::= SEQUENCE {
-- Internal/External Tracking Information
aid PC-ID, -- Assay Description ID/Version [Either valid ID
-- or, if "aid-source" is used, a "0" dummy value]
-- Note: Version is for internal use (only?)
-- Note: A valid ID is greater than "0"
aid-source PC-Source OPTIONAL, -- External Identifier for this Assay Description
-- Note: May be used in-lieu of "aid"
-- Note: This is non-optional if "aid" ID is "0"
-- Assay Description Information
name VisibleString, -- Short Assay Name (for display purposes)
description SEQUENCE OF VisibleString OPTIONAL, -- Description of Assay
protocol SEQUENCE OF VisibleString OPTIONAL, -- Procedure used to generate results
comment SEQUENCE OF VisibleString OPTIONAL, -- Comments or additional information
xref SEQUENCE OF PC-AnnotatedXRef OPTIONAL, -- Annotated Cross-Reference Information
-- Allowed Assay Result Types
results SEQUENCE OF PC-ResultType OPTIONAL, -- Result Definitions (vector)
-- Additional Information
pub SEQUENCE OF Pub OPTIONAL, -- Depositor provided publications for this assay
revision INTEGER OPTIONAL, -- Revision identifier for textual description
target SEQUENCE OF PC-AssayTargetInfo OPTIONAL, -- Target information
activity-outcome-method INTEGER { -- Assay Outcome Qualifier
other (0), -- All Other Type
screening (1), -- Primary Screen Assay
confirmatory (2), -- Confirmatory Assay
summary (3) -- Probe Summary Assay
} OPTIONAL,
dr SEQUENCE OF PC-AssayDRAttr OPTIONAL, -- Dose-Response Attribution
substance-type INTEGER{
small-molecule (1),
nucleotide (2),
other (255)
} OPTIONAL, -- to distinguish the type of substance used in the screening
-- Grant and project category information
grant-number SEQUENCE OF VisibleString OPTIONAL, -- grant proposal number
-- required for 'MLSCN' & 'MLPCN' projects
project-category INTEGER{
mlscn (1),
mlpcn (2),
mlscn-ap (3),
mlpcn-ap (4),
journal-article (5), -- to be deprecated
assay-vendor (6),
literature-extracted (7),
literature-author (8),
literature-publisher (9),
rnaigi (10),
other (255)
} OPTIONAL, -- to distinguish projects funded through MLSCN, MLPCN or other
-- mlscn: assay depositions from MLSCN screen center
-- mlpcn: assay depositions from MLPCN screen center
-- mlscn-ap: assay depositions from MLSCN assay provider
-- mlpcn-ap: assay depositions from MLPCN assay provider
-- required for 'MLSCN' & 'MLPCN' projects
-- journal-article: to be deprecated; replaced by option 7,8 & 9 to better characterize data from literature
-- literature-extracted: data from literature, extracted by curators
-- literature-author: data from literature, submitted by author of articles
-- literature-publisher: data from literature, submitted by journals/publishers
-- rnaigi: RNAi screenings from RNAi Global Initiative
-- annotation to indicate whether an assay is a panel, e.g. containing multiple components, or belongs to a group
is-panel BOOLEAN OPTIONAL, -- annotation for panel assay, e.g. to indicate that this assay
-- contains multiple members/components.
-- A panel assay can be one assay reporting readouts for
-- many targets, or reporting readouts for different
-- cell lines, or different organisms
-- examples such as bioassay containing kinase profiling data
-- or bioassay containing cytoxicity data for multiple cell lines
-- or bioassay containing screening data from different stages,
-- such as primary screening, follow ups
assay-group SEQUENCE OF VisibleString OPTIONAL, -- annotation for assay gruop information, e.g. this
-- assay belongs to a group of assay associated by
-- a unique name, e.g. the value assigned to 'assay-group',
-- assays belonging to this group can be
-- retrieved using this unique name
-- it is depositor's responsibility to make the name
-- distinct if necessary
-- this can be used as the mechanism to specify 'related bioassays'
-- before hand so it is not necessary to update the descriptions of
-- related assays when new group member submitted to PubChem
panel-info PC-AssayPanel OPTIONAL, -- for 'panel' type of bioassay only
-- store assay panel member information
is-mlp-late-stage BOOLEAN OPTIONAL, -- verification for 'late-stage-data' deposition
categorized-comment SEQUENCE OF PC-CategorizedComment OPTIONAL
-- to report categorized description/comment by associating with a category title
}
-- Description for Panel Assay
-- Describe general information about the panel, and link to information for each panel member
PC-AssayPanel ::= SEQUENCE {
name VisibleString, -- short name for the panel, such as 'Kinase Profiling'
descr VisibleString OPTIONAL, -- short description of this panel
member SEQUENCE OF PC-AssayPanelMember OPTIONAL -- store panel member information
}
-- Specific information about each panel member(or component), such as target, cell line name, cross-reference ...
PC-AssayPanelMember ::= SEQUENCE {
mid INTEGER, -- ID for panel member
-- if a kinase panel with 300 kinases, ID will range from 1 to 300
-- TIDs of the same panel member to be grouped based on panel member ID
name VisibleString OPTIONAL, -- short name for this panel member
description VisibleString OPTIONAL, -- description about specifics of this panel member
-- such as about cell line, or target information
protocol SEQUENCE OF VisibleString OPTIONAL, -- Specific procedure used to generate results for the panel member
comment SEQUENCE OF VisibleString OPTIONAL, -- Comments or additional information
target SEQUENCE OF PC-AssayTargetInfo OPTIONAL, -- often provided for profiling assays across protein families
xref SEQUENCE OF PC-AnnotatedXRef OPTIONAL, -- annotated Cross-Reference Information
activity-outcome-method INTEGER { -- Assay Outcome Qualifier
other (0), -- All Other Type
screening (1), -- Primary Screen Assay
confirmatory (2), -- Confirmatory Assay
summary (3) -- Probe Summary Assay
} OPTIONAL,
dr SEQUENCE OF PC-AssayDRAttr OPTIONAL, -- Dose-Response Attribution within the panel member
categorized-comment SEQUENCE OF PC-CategorizedComment OPTIONAL
-- to report categorized description/comment by associating with a category title
}
-- Definition for Categorized description/comment
-- This field is added to provide flexibility for depositors to present textual description/comments in a desirable way
-- and to facilitate information validation by the depositor and data exchange with PubChem
PC-CategorizedComment ::= SEQUENCE {
title VisibleString, -- title for the description/comment
comment SEQUENCE OF VisibleString -- description/comment content
}
-- Assay Dose-response attribute information used to define a set of readouts
-- as being part of a dose-response curve (for curve plotting/analysis)
PC-AssayDRAttr ::=SEQUENCE {
id INTEGER, -- Unique dose-response test set identifier
-- Note: A valid ID is greater than "0"
descr VisibleString OPTIONAL, -- Dose-Response Curve Description (used as curve title)
dn VisibleString OPTIONAL, -- Dose Axis Description (used as axis name)
rn VisibleString OPTIONAL, -- Response Axis Description (used as axis name)
type INTEGER {
experimental (0), -- dose-response data points measured directly by experiment
calculated (1) -- dose-response data points derived from fitted curve
} OPTIONAL
}
-- Molecular target information provides by organization describes the functionality of the target,
-- facilitates the linking between PubChem bioassays, and the linking between target molecule to other NCBI resources
PC-AssayTargetInfo ::= SEQUENCE {
name VisibleString, -- Molecular name of target
mol-id INTEGER, -- NCBI database identifier of the target molecule
molecule-type INTEGER { -- Assay Target Type
protein (1), -- mol-id: NCBI Protein GI
dna (2), -- mol-id: NCBI Nucleotide GI
rna (3), -- mol-id: NCBI Nucleotide GI
gene (4), -- mol-id: NCBI Gene ID
biosystem (5), -- mol-id: NCBI BioSystems ID
other (255)
} DEFAULT protein,
organism BioSource OPTIONAL, -- Target Organism
descr VisibleString OPTIONAL, -- Target Description (e.g., cellular functionality and location)
comment SEQUENCE OF VisibleString OPTIONAL -- Comments or Additional Information
}
-- Annotated Cross-Reference (XRef) Information to allow the XRef to be qualified, as to its meaning or context
PC-AnnotatedXRef ::= SEQUENCE {
xref PC-XRefData, -- Cross-Reference Information
comment VisibleString OPTIONAL, -- Annotation qualifier describing Cross-Reference meaning
type INTEGER {
pcit (1), -- primary PMID/citation directly associated with the current assay data
pgene (2) -- gene encoding the protein assay target
} OPTIONAL
}
-- Definition of Allowed Result Types for a given Assay
PC-ResultType ::= SEQUENCE {
-- Tracking or Description Information
tid INTEGER, -- Assay Result Field Type ID (TID)
name VisibleString, -- Result Field Name (short name for display)
description SEQUENCE OF VisibleString OPTIONAL, -- Result Field Description
-- Result Data Type and Validation Information
type INTEGER { -- Result Data Type
float (1),
int (2),
bool (3),
string (4)
},
constraints CHOICE { -- Allowed Values, used for validating incoming data
-- If type is "float"
fset SEQUENCE OF REAL, -- Allowed values must be equal to one of these
fmin REAL, -- Allowed values (x) must be [ fmin <= x ]
fmax REAL, -- Allowed values (x) must be [ x <= fmax ]
frange PC-RealMinMax, -- Minimum/Maximum Range [ min <= x <= max ]
-- If type is "int"
iset SEQUENCE OF INTEGER, -- Allowed values must be equal to one of these
imin INTEGER, -- Allowed values (x) must be [ imin <= x ]
imax INTEGER, -- Allowed values (x) must be [ x <= imax ]
irange PC-IntegerMinMax, -- Minimum/Maximum Range [ min <= x <= max ]
-- If type is "string"
sset SEQUENCE OF VisibleString -- Allowed values must be equal to one of these
} OPTIONAL,
-- Unit information provides the units for the values reported for this TID. For example, if the values
-- reported for this TID are a concentration, e.g., micro-molar, setting the unit "um" allows PubChem to
-- know that the value, e.g., "1.3", is actually "1.3 uM". This also allows PubChem to properly report the
-- units when displaying the reported values for this TID. If the enumerated units provided below are
-- insufficient, you may represent the units as a string in the optional "sunit" field (see below).
unit INTEGER { -- Units for Value
ppt (1), -- Parts per Thousand
ppm (2), -- Parts per Million
ppb (3), -- Parts per Billion
mm (4), -- milliM
um (5), -- microM
nm (6), -- nanoM
pm (7), -- picoM
fm (8), -- femtoM
mgml (9), -- milligrams per mL
ugml (10), -- micrograms per mL
ngml (11), -- nanograms per mL
pgml (12), -- picograms per mL
fgml (13), -- femtograms per mL
m (14), -- Molar
percent (15), -- Percent
ratio (16), -- Ratio
sec (17), -- Seconds
rsec (18), -- Reciprocal Seconds
min (19), -- Minutes
rmin (20), -- Reciprocal Minutes
day (21), -- Days
rday (22), -- Reciprocal Days
ml-min-kg (23), -- milliliter / minute / kilogram
l-kg (24), -- liter / kilogram
hr-ng-ml (25), -- hour * nanogram / milliliter
cm-sec (26), -- centimeter / second
mg-kg (27), -- milligram / kilogram
none (254),
unspecified (255)
} OPTIONAL,
-- ATTENTION: sunit field is DEPRECATED. It is no longer
-- supported and remains for legacy data only.
sunit VisibleString OPTIONAL, -- Unit Type (as a String)
-- Value Transform information qualifies the values reported for this TID. For example, if the values
-- reported for this TID are "-Log10 GI50", you may want to consider setting
-- the "nlog" value below. In doing so, PubChem would know that the value, e.g., "5.0"
-- is actually "1.0e-5". If the transformation applied is not listed, you may represent
-- this transformation as a string in the "stransform" (see below) for eventual inclusion
-- in the enumerated transform list below.
--
--
-- ATTENTION: transform field is DEPRECATED. It is no longer
-- supported and remains for legacy data only.
transform INTEGER { -- Value Type Details
linear (1), -- Linear Scale (x)
ln (2), -- Natural Log Scale (ln x)
log (3), -- Log Base 10 Scale (log10 x)
reciprocal (4), -- Reciprocal Scale (1/x)
negative (5), -- Negative Linear Scale (-x)
nlog (6), -- Negative Log Base 10 Scale (-log10 x)
nln (7) -- Negative Natural Log Scane (-ln x)
} OPTIONAL,
-- ATTENTION: stransform field is DEPRECATED. It is no longer
-- supported and remains for legacy data only.
stransform VisibleString OPTIONAL, -- Value Transform Type (as a String)
tc PC-ConcentrationAttr OPTIONAL, -- Tested concentration attribute
ac BOOLEAN OPTIONAL, -- if true, indicates that this TID field
-- provides active concentration summary by
-- reporting the concentration which produces
-- 50% of the maximum possible biological response
-- such as IC50, EC50, AC50, GI50 etc.
-- or by reporting constant parameters such as Ki,
-- that based on which the activity outcome in this assay is called
panel-info PC-AssayPanelTestResult OPTIONAL, -- needed for panel assay only
-- each panel member may have a number of TID columns reported
-- such TIDs are grouped by panel member ID, see PC-AssayPanelMemberInfo
annot INTEGER {
pmid (1), -- PubMed ID
mmdb (2), -- MMDB ID
url (3), -- indicate TID data is a url that provides supplementary information
protein-gi (4), -- GenBank General ID (GI) for a Protein
nucleotide-gi (5), -- GenBank General ID (GI) for a Nucleotide
taxonomy (6), -- Taxonomy ID for an Organism
mim(7), -- MIM, Mendelian Inheritance in Man, ID
gene(8), -- Entrez Gene ID
probe(9), -- Entrez Probe ID
aid (10), -- PubChem BioAssay ID, may be used in 'Summary' assay
sid (11), -- PubChem Substance ID, may be used in 'Summary' assay
cid (12), -- PubChem Compound ID
protein-target-gi (13), -- GenBank General ID (GI) for a Protein target
biosystems-target-id (14), -- NCBI BioSystems ID
target-name (15), -- target name
target-descr (16), -- brief target description
target-tax-id (17), -- NCBI Taxonomy ID for target molecule
gene-target-id (18), -- NCBI Gene ID for a gene target
dna-nucleotide-target-gi (19), -- GenBank General ID (GI) for a DNA Nucleotide target
rna-nucleotide-target-gi (20) -- GenBank General ID (GI) for a RNA Nucleotide target
} OPTIONAL -- treat substance associated cross-reference as regular TID
-- web servers would make a link
-- to the corresponding record in Entrez databases
-- treat substance associated target information as regular TID
-- for example, for RNAi screening data, each 'substance' may
-- correspond to a specific gene target
}
PC-AssayPanelTestResult ::= SEQUENCE {
mid INTEGER, -- panel member ID, see PC-AssayPanelMemberInfo
-- track association between a group of TIDs and panel member
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