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Glossary

Acronyms and Abbreviations
AMT

Dose amount

BOV

Between Occasion Variability (synonym for IOV - Inter-occasion variability)

CORR

Correlation

COV

Covariance

CTS

Clinical Trial Simulation

CWRES

Conditional Weighted Residual

DDMoRe

Drug Disease Model Resources

DoW

Description of Work

DV

Dependent Variable

EFPIA

European Federation of Pharmaceutical Industries and Associations

EMA

European Medicines Agency

EPS

Epsilon - Residual Unexplained Variability random effect

ETA

Empirical Bayes prediction of the inter-individual random effect in a PK or PD parameter

FDA

Food and Drug Administration

FIS

Framework Integration Service

ID

Individual

IDV

Independent variable

II

Inter-dose Interval

IMI

Innovative Medicines Initiative

IMI-JU

Innovative Medicines Initiative Joint Undertaking

IOF

Interoperability framework

IPRED

Individual Prediction

IWRES

Individual Weighted Residual

MDL

MDL is the Model Description Language (formerly MCL - Model Coding Language) the human writable and human readable language designed to describe pharmacometric models.

MDL-IDE

Modelling Definition Language Integrated Development Environment

MDV

Missing Dependent Variable

MIF

Mango Integration Framework

MOG

Modelling Object Group

NONMEM

NONLinear Mixed Effects Modelling (see Names)

OBS

Observed (value or data)

PD

Pharmacodynamic

PharmML

Pharmacometrics Markup Language

PK

Pharmacokinetic

PK/PD

Pharmacokinetic - Pharmacodynamic modelling

PRED

Population Prediction

PROV-O

Provenance Ontology

PsN

Perl Speaks NONMEM
http://psn.sourceforge.net

RDF

Resource Description Framework

RUV

Residual Unexplained Variability

sd

Standard Deviation

SE

Standard Error

SEE

Stand-alone Execution Environment

SO

Standard Output

TEL

Task Execution Language.
The working name within the DDMoRe project for the ddmore R package used to perform tasks with MDL and define pharmacometric workflow.

TES

Task Execution Server

var

Variance

VPC

Visual Predictive Check

WP

Work Package

WRES

Weighted Residual

XML

Extensible Markup Language

Definitions and System Names
Annotation

A description attached to a model or element of a model: see RDF triple.

Bootstrap

Bootstrap is a tool for calculating bias, standard errors and confidence intervals of parameter estimates. It does so by generating a set of new datasets by sampling individuals with replacement from the original dataset, and fitting the model to each new dataset

Connector

A piece of software which enables modelling software to communicate with the interoperability framework

Converter

A piece of software which enables translation across languages (e.g. mdl to pharmML

End-User

A specific user role with privileges to manage only his/her own jobs queues, etc.

Extensible Markup Language (XML)

An open standard for exchanging structured documents and data over the internet that was introduced by the World Wide Web Consortium (W3C).

Interoperability

DDMoRe project is to provide the capability to define the model once and then use it across a variety of target software tools. We call this “Interoperability”.

MDL

MDL is the Model Description Language (formerly MCL - Model Coding Language) the human writable and human readable language designed to describe pharmacometric models.

MDL-IDE

Modelling Definition Language Integrated Development Environment

Metadata

Metadata (metacontent) is defined as data providing information about one or more aspects of the data, such as:

  • Means of creation of the data,
  • Purpose of the data,
  • Time and date of creation,
  • Creator or author of data,
  • Placement on a computer network where the data was created,
  • Standards used
MLXTRAN

The language used to define models that are executed with Monolix.

Monolix

A software for the analysis of nonlinear mixed effects models

NM-TRAN

The language used to define models that are executed with NONMEM.

NONMEM

NONLinear Mixed Effects Modelling (see Names)

Ontology

An organization of some knowledge domain that is hierarchical and contains all the relevant entities and their relations.
An ontology is used to define the relationships and objects that are used to define the RDF Triples that describe the data, models and results with a Pharmacometrics Workflow

Pharmacometric Workflow

Tracking the evolution of a model and associated inferences from initial model to final model, capturing metadata and annotations that will facilitate creation of a run record, audit log, QC and reproducibility of all steps within the workflow. Each step in the Pharmacometric workflow may consist of a Task Workflow which defines the procedural steps required to perform a sequence of tasks for a given model.

PharmML

XML based exchange format for encoding of non-linear mixed effect models, trial design and modelling steps used in pharmacometrics. URL: pharmml.org

R

R is a free software environment for statistical computing and graphics.
https://www.r-project.org/

RDF Triple

An RDF Triple is a statement which relates one object to another. It is composed of three parts:
the subject - the entity we are describing
a predication - the relationship
the object - the description

DDMoRe uses RDF triples to describe models held within the repository, for example:
“MODEL-000034765” “has author” “Lena Friberg”

Repository

Another stated aim of the DDMoRe project is to provide a library platform for pre-competitive sharing of models - disease models, drug models etc. We call this library the “Repository”.

Standard Output (SO)

Tool-independent exchange format intended for storage of results in standardised form, enabling effective data exchange within complex workflows as well as to support the user in assessing, reviewing and reporting a modelling step.

Task Execution Service (TES)

Performs job-management within the Interoperability Framework.

Task Workflow

A sequence of tasks and procedural steps which can be captured in a scriptable language, like R, facilitating reproducibility of the outputs for a given set of inputs.

WinBUGS

Windows implementation of the BUGS (Bayesian Inference Using Gibbs Sampling) project, concerned with flexible software for the Bayesian analysis of complex statistical models using Markov chain Monte Carlo (MCMC) methods.
http://www.mrc-bsu.cam.ac.uk/bugs/winbugs/contents.shtml