amorphys
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Table of contents:
Why amorphys?
Motivations
Core concerns
Core concepts
How is it going to work?
Editor UI
Designer UI
Experiment runner
Overview of metadata organization
Sections
A recommended way of annotation
“section” class
Formatting options
Single-file format
Multi-file format
Making a project description
Organization of “project” section
“dataset” subsection
“people” subsection
“affiliations” subsection
“fundings” subsection
“data_published_by” subsection
Core objects (obsolete)
Entity
Entity class
Types of entities
Spatial entity
Temporal entity
Signals
Programs and Routines
Relationship
How Relationship works
Pre-defined relationship keys
Spatial relationships
Temporal relationships
Relationships between signals
Defining your own relationship key(s)
Context
Context class
Classes for measurements
Date
Time
Subject-related
Age
Sex
Death
Space
Quantity
Notes on unit usages
Description of protocol control
Overview
Unitary stimulus control
StimulusState
ApparatusState
Sequence-type stimulus description
Sequencer
StimulusBlock
StimulusGeneration
Context-dependent stimulus sequence
StateMachine
MachineState
MachineStateTransition
Behavioral model for a subject
Variables and expressions
Use of variables
Use of conditions
Expressions and formatters
Use of templates
Supplementary documents
Predefined subclasses for Spatial
Subject entity
Component entity
Predefined subclasses for Temporal
Procedure
Action and Block
Phase
Specific types of actions
Predefined subclasses for Signal
Sampled and its subclasses
Event and its subclasses
State
Definition of your own entity class
Metadata structure (obsolete)
Subject description
“subjects” section
Setups
“setups” section
Setup class
Acquisition
“acquisition” section
Procedures
“procedures” section
Task/Sweep control
“tasks” section
Experimental variables
An example
Scopes
Structure of scopes
Basic properties
Subsection for description of lower scope(s)
Class reference
Specification of metadata sections
section
project
“Referrable” objects
referrable
individual
institution class
person
contributor
license
citation
Miscellaneous
dataset
credit
funding
amorphys
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Index
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Index
A
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B
|
C
|
D
|
E
|
F
|
G
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
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V
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W
|
Y
A
Acquisition (built-in class)
acquisition (built-in class)
Action (built-in class)
affiliation (contributor attribute)
affiliations (project attribute)
age (Animal attribute)
(Participant attribute)
(Subject attribute)
(Tissue attribute)
amplitude (StimulusState attribute)
Animal (built-in class)
Apparatus (built-in class)
ApparatusState (built-in class)
authors (license attribute)
B
Block (built-in class)
C
channel (StimulusGeneration attribute)
ChronicPreparation (built-in class)
citation (built-in class)
Component (built-in class)
components (Setup attribute)
condition (built-in class)
contact (person attribute)
Context (built-in class)
contributor (built-in class)
control
conversion (acquisition attribute)
credit (built-in class)
D
data (DataFile attribute)
data_published_by (project attribute)
DataFile (built-in class)
dataset (built-in class)
(project attribute)
date (Acquisition attribute)
(Action attribute)
(Block attribute)
Date (built-in class)
date (ChronicPreparation attribute)
(Phase attribute)
(Procedure attribute)
death (Animal attribute)
default (condition attribute)
description
(Acquisition attribute)
(Action attribute)
(Animal attribute)
(Apparatus attribute)
(Block attribute)
(ChronicPreparation attribute)
(Component attribute)
(Context attribute)
(Device attribute)
(Entity attribute)
(Event attribute)
(MachineState attribute)
(Material attribute)
(Part attribute)
(Participant attribute)
(Phase attribute)
(Procedure attribute)
(Program attribute)
(Sampled attribute)
(Scan attribute)
(Sequencer attribute)
(Setup attribute)
(Signal attribute)
(Space attribute)
(Spatial attribute)
(State attribute)
(StateMachine attribute)
(StimulusBlock attribute)
(Subject attribute)
(Substance attribute)
(Temporal attribute)
(Tissue attribute)
(condition attribute)
(dataset attribute)
(formatter attribute)
(project attribute)
(section attribute)
(variable attribute)
Device (built-in class)
duration (StimulusBlock attribute)
E
Entity (built-in class)
Event (built-in class)
extension (DataFile attribute)
F
firstnames (person attribute)
format (DataFile attribute)
(Date attribute)
(Time attribute)
formatter (built-in class)
frequency (StimulusState attribute)
funded_by (project attribute)
funding (built-in class)
G
generates (Device attribute)
(Routine attribute)
I
id (funding attribute)
implants (Subject attribute)
individual (built-in class)
initial (StateMachine attribute)
institution (built-in class)
K
keywords (dataset attribute)
L
lastname (person attribute)
layout (Setup attribute)
license (Animal attribute)
(Participant attribute)
(Subject attribute)
(Tissue attribute)
(built-in class)
(dataset attribute)
LineScan (built-in class)
M
MachineState (built-in class)
MachineStateTransition (built-in class)
manipulations (ChronicPreparation attribute)
Material (built-in class)
MEA (built-in class)
mode (StimulusState attribute)
model (Apparatus attribute)
(Device attribute)
monitors (Device attribute)
N
name (citation attribute)
(dataset attribute)
(individual attribute)
(institution attribute)
(license attribute)
(person attribute)
(referrable attribute)
O
offset (StimulusState attribute)
order (Block attribute)
(Phase attribute)
(procedures attribute)
origin (Tissue attribute)
output (StimulusBlock attribute)
P
Part (built-in class)
Participant (built-in class)
parts (Animal attribute)
(Apparatus attribute)
(Component attribute)
(Device attribute)
(Material attribute)
(Part attribute)
(Participant attribute)
(Spatial attribute)
(Subject attribute)
(Substance attribute)
(Tissue attribute)
people (project attribute)
person (built-in class)
Phase (built-in class)
phases (procedures attribute)
precision (Quantity attribute)
Procedure (built-in class)
procedures (Block attribute)
(Phase attribute)
(built-in class)
Program (built-in class)
programs (acquisition attribute)
project (built-in class)
properties (State attribute)
protocol (Routine attribute)
provided_to (funding attribute)
pulse (StimulusState attribute)
Q
quality (Event attribute)
(Sampled attribute)
(Scan attribute)
(Signal attribute)
(State attribute)
Quantity (built-in class)
R
range (Sampled attribute)
(Scan attribute)
(Signal attribute)
reads (Routine attribute)
reference (Acquisition attribute)
(Action attribute)
(Animal attribute)
(Apparatus attribute)
(Block attribute)
(ChronicPreparation attribute)
(Component attribute)
(Context attribute)
(Device attribute)
(Entity attribute)
(Event attribute)
(Material attribute)
(Part attribute)
(Participant attribute)
(Phase attribute)
(Procedure attribute)
(Program attribute)
(Sampled attribute)
(Scan attribute)
(Setup attribute)
(Signal attribute)
(Spatial attribute)
(State attribute)
(Subject attribute)
(Substance attribute)
(Temporal attribute)
(Tissue attribute)
reference_type (citation attribute)
references (dataset attribute)
referrable (built-in class)
role (Event attribute)
(Sampled attribute)
(Scan attribute)
(Signal attribute)
(State attribute)
roles (contributor attribute)
Routine (built-in class)
routines (Program attribute)
runs (Device attribute)
S
Sampled (built-in class)
scale (Space attribute)
Scan (built-in class)
section (built-in class)
sequence (Sequencer attribute)
sequencer (Acquisition attribute)
Sequencer (built-in class)
setup (Acquisition attribute)
(Action attribute)
(Block attribute)
Setup (built-in class)
setup (ChronicPreparation attribute)
(Phase attribute)
(Procedure attribute)
setups (built-in class)
sex (Animal attribute)
sexuality (Participant attribute)
shape (Space attribute)
Signal (built-in class)
signals (acquisition attribute)
size (Scan attribute)
source (funding attribute)
(MachineStateTransition attribute)
Space (built-in class)
Spatial (built-in class)
State (built-in class)
state (StimulusGeneration attribute)
StateMachine (built-in class)
states (StateMachine attribute)
StimulusBlock (built-in class)
StimulusGeneration (built-in class)
StimulusState (built-in class)
stores (Routine attribute)
subject
Subject (built-in class)
subjects (built-in class)
Substance (built-in class)
supplier (Apparatus attribute)
(Component attribute)
(Device attribute)
(Material attribute)
(Part attribute)
(Program attribute)
(Substance attribute)
switch (condition attribute)
T
target (MachineStateTransition attribute)
tasks (built-in class)
Temporal (built-in class)
Time (built-in class)
timeout (MachineState attribute)
Tissue (built-in class)
transitions (MachineState attribute)
type (Acquisition attribute)
(Action attribute)
(Animal attribute)
(Apparatus attribute)
(Block attribute)
(ChronicPreparation attribute)
(Component attribute)
(Context attribute)
(Device attribute)
(Entity attribute)
(Event attribute)
(Material attribute)
(Part attribute)
(Participant attribute)
(Phase attribute)
(Procedure attribute)
(Program attribute)
(Quantity attribute)
(Sampled attribute)
(Scan attribute)
(Sequencer attribute)
(Setup attribute)
(Signal attribute)
(Spatial attribute)
(State attribute)
(StateMachine attribute)
(Subject attribute)
(Substance attribute)
(Temporal attribute)
(Tissue attribute)
U
unit (Quantity attribute)
(Space attribute)
uri (citation attribute)
(individual attribute)
(institution attribute)
(license attribute)
(person attribute)
(referrable attribute)
V
value (Date attribute)
(Quantity attribute)
(Time attribute)
values (Event attribute)
(State attribute)
variable (built-in class)
Video (built-in class)
Volume (built-in class)
W
where (formatter attribute)
Y
year (license attribute)