Glossary, abbreviations and acronyms

AAI

Now renamed Life Science Authentication and Authorisation Infrastructure. Centrally controlled access to online resources, see LS-AAI.

AARC

Authentication and Authorisation for Research and Collaboration: a project led by GÉANT the pan-European research and education network that interconnects Europe’s National Research and Education Networks. 

Artificial Intelliegence. 
“The science and engineering of making intelligent machines.” (John McCarthy).
Often involving Machine Learning but the two are not synonymous. 

BBMRI

Biobanking and Biomolecular Resources Research Infrastructure: an ESFRI BMS Research Infrastructure which aims to increase efficacy and excellence of European biomedical research by facilitating access to quality-defined human health and disease-relevant biological resources.

BBMRI-ERIC: BBMRI European Research Infrastructure Consortium: bring together all the main players from the biobank field.

BD2K

Big Data to Knowledge: National Institute of Health (NIH) initiative established to enable biomedical research as a digital research enterprise, to facilitate discovery and support new knowledge, and to maximize community engagement.

BEIS

Dept of Business, Energy and Industrial Strategy (UK Gov.)

BioExcel

Centre of Excellence for provision of support to academic and industrial researchers in the use of high -performance computing (HPC) and high-throughput computing (HTC) in biomolecular research.

Bioinformatics

The collection, storage, and analysis of biological data using computers. It is an interdisciplinary subject and involves knowledge of programming, database design and statistics as well as biology. Bioinformatics techniques are often used to analyse genomes and proteomes, and to create three-dimensional models of biomolecules.

BioMedBridges

A joint project of twelve biomedical sciences research infrastructures on the ESFRI roadmap, completed in February 2016.

BYOD

Bring Your Own Data: A workshop that brings together data owners, domain experts (most often biologists and chemists) and FAIR data experts (and their trainees) working on selected data set(s). biologists and chemists) and FAIR data experts (and their trainees) working on selected data set(s).

CA

Collaboration Agreement: A legal document that established the ELIXIR Node and outlines the relationship with the ELIXIR Hub.

CDR

Core Data Resources European data resources that are of fundamental importance to research in the life sciences and are committed to the long term preservation of data. Coordinated by the Data Platform

Cloud computing

An online pool of shared computing resources where you can access and store data and use programs (Google Drive and Microsoft Office 365 are examples of cloud services). Unlike owning your own hardware, you can quickly adjust cloud services to your needs and only pay for what you use.

CMM(I)

Capability Maturity Model (Interrogation)

COG

Collaboration agreement Oversight Group. A group established to oversee the relationship between the ELIXIR Hub and each Node.

Commissioned Service (Also known as Implementation Study) 
This is a funding mechanism whereby ELIXIR arranges a contract to complete work setout in the Programme 

CORBEL

Coordinated Research Infrastructures Building Enduring Life-science Services'. It is a project that aims to align and coordinate the work of the European biomedical research infrastructures. See that aims to align and coordinate the work of the European biomedical research infrastructures. See and sustained framework of shared services between the ESFRI BMS RIs.

CTMM

The Center for Translational Molecular Medicine. A Dutch-based public-private partnership dedicated to the development of technologies in molecular medicine. (See TraIT below)

CWL

Common Workflow Language (see GitHub)

An approach for making multiple, related data sources available. The analysis tool 'visits' each data set and returns only the output. Raw data does not move (national borders), access is controlled (AAI), avoids Federated databases (YAD; Yet Another Database) 

DAVID

Database for Annotation, Visualisation and Integrated Discovery. A comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of gene.

DISSCO

Distributed System of Scientific Collections - the RI that joins natural history museums together

DOI

Digital Object Identifier, is a unique alphanumeric string assigned by a registration agency to identify content and provide a persistent link to its location. (eg. A publisher assigns a DOI when an article is published and made available electronically)

The Darwin Tree of Life project aims to sequence the genomes of all 70,000 species of eukaryotic organisms in Britain and Ireland.

DTL

The Dutch Techcentre for Life Sciences (DTL) is a public-private partnership of more than 50 life science organisations in the Netherlands. The majority of Dutch universities and university medical centres are DTL partners and a growing number of companies are joining the organisation.

Earth Biogenone Project

The Earth BioGenome Project (EBP), a moonshot for biology, aims to sequence, catalog and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of ten years.

European infrastructure for translational medicine: an ESFRI Research Infrastructure that brings together resources and services for research communities to translate scientific discoveries into benefits for patients.

EATRIS European Research Infrastructure Consortium: accelerate the translation of biomedical discoveries into patient benefit.

ECA

ELIXIR Consortium Agreement; an agreement between ELIXIR Hub and each Node to establish the legal basis for ELIXIR

ECCB

European Conference on Computational Biology. The main computational biology and bioinformatics conference in Europe

• 2020 (Barcelona)
• 2019 (Basel) Joint with ISMB

ECP

ELIXIR Compute Platform

EDAM

Embrace Data And Methods ontology: A simple ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM provides a set of terms with synonyms and definitions, organised into an intuitive hierarchy for convenient use.

EDD

ELIXIR Deposition Database

EDP

ELIXIR Data Platform

EGA

European Genome-phenome Archive Link

EGI

European Grid Infrastructure: A federation of 19 cloud providers aiming to create and deliver open solutions for science and research infrastructures EGI-ENGAGE: to accelerate the implementation of the Open Science Commons by expanding the capabilities, complementing community-specific capabilities.

EIP

ELIXIR Interoperability Platform link

EJP-RD

European Joint Programme for Rare Diseases

ELIXIR

European Life-Science Infrastructure 
Unusually for this field, it is not a direct accronym, it appears to have been suggested by Janet Thornton at an early stage plannign meetign in the late 1990's.  

ELIXIR IAC

ELIXIR Industry Advisory Committee, a body appointed by the ELIXIR Board to provide high-level, strategic advice and input to ELIXIR from industry.

ELIXIR Innovation & SME Programme

A series of specialised events hosted by ELIXIR Nodes for companies, in order to support Europe's industry and in particular its Small to Medium Sized Enterprises (SMEs).

ELIXIR SAB

ELIXIR Scientific Advisory Board, the body composed of independent scientists that oversee the

ELSI

Ethical Legal and Social Issues; guided in ELIXIR by a policy

EMBRIC

The European Marine Biological Research Infrastructure Cluster is designed to accelerate the pace of scientific discovery and innovation from marine Bio-Resources.

ENVRIplus

ENVRIplus is a Horizon 2020 project bringing together Environmental and Earth System Research Infrastructures, projects and networks together with technical specialist partners to create a more coherent, interdisciplinary and interoperable cluster of Environmental Research Infrastructures across Europe.

EOSC

European Open Science Cloud: a virtual environment with open and seamless services for storage, management, analysis and re-use of research data, across borders and scientific disciplines. EOSC Portal: access to the various EOSC components

ERC

European Research Council

erinha

European Research Infrastructure on Highly pathogenic Agents. The ERINHA2 project aims at building a pan-European research infrastructure to reinforce the European coordination and capacities for the study and the surveillance of highly pathogenic micro-organisms.

ESFRI

European Strategy Forum on Research Infrastructures: A strategic instrument to develop the scientific integration of Europe and to strengthen its international outreach.

ESFRI- BMS

Biological and Medical Sciences: A group of experts appointed by ESFRI to monitor the scientific requirements and needs for Research Infrastructures in their respective scientific areas

ETP

ELIXIR Tools Platform

eTRANSAFE

eTRANSAFE will develop infrastructure and policies to share toxicology data (including ‘omics) for investigational drugs in public-private partnerships.

EUDAT

European Collective Data Infrastructure

EuropePMC

Europe PubMed Central. A repository, providing access to worldwide life sciences articles, books,

ExCo

Executive Committee of a Platform, supported by a Platform Coordinator, generally 2-3 people

FAIR

An international drive to ensure data is:

• Findable (Registries, Discovery tools) 
• Accessible (Open access, API) 
• Interoperable (Standard format, ontoligical terms) 
• Re-useable (Additional data be equally available) 

FHD

Federated Human Data

GA4GH

The Global Alliance for Genomics and Health; international standards organisation formed to meet the current challenges and opportunities in genomic research and medicine.

GBIF

Global Biodiversity Information Facility: An international organisation that focuses on providing free and open access to biodiversity data. 

GDPR

General Data Protection Regulation

Gene

A locus (or region) of DNA that is responsible for creating a particular protein or a particular function. Genes carry the information that determines traits like eye colour, and are the basic units of hereditary. Humans have around 25,000 genes.

Genome

The genetic material of an organism, which consists of DNA (or RNA in RNA viruses). It contains all of an organism’s genes, and is present in every cell that has a nucleus. Each genome contains the information needed to build that organism and allow it to grow and develop.  

GOBLET

Global Organisation for Bioinformatics Learning, Education & Training

Grid

In computing, a grid is a collection of computers that is owned by multiple organisations in different locations and connected together so that users can share the combined power of the resources. It differs from cloud because cloud resources are usually run by one organisation

An open source programming framework that helps you process and store huge data sets in a distributed computing environment (like a grid). Hadoop services let you access, store and process data, and help you manage data governance and security.

H2020

H2020 IMI

Innovative Medicines Initiative, Europe's largest public-private initiative aiming to speed up the development of better and safer medicines for patients. IMI is a joint undertaking between the European Union and the pharmaceutical industry association EFPIA.

HDCs

Human Data Communities (link) 

HGTD

Human Genomics and Translational Data (link) 

HoN

ELIXIR Head of Nodes Committee, committee composed of representatives of ELIXIR Nodes and EMBL-EBI, that gives advice to the ELIXIR Board and Director in relation to ELIXIR activities and has a major role in developing and agreeing the ELIXIR scientific and technical strategy.

HPC

High Performance Computing using multiple computers to perform a task. HPC clusters divide up tasks into smaller, more manageable ones and run these concurrently across multiple computers. This allows researchers to run large, complex analyses of data that are too big for a single machine to cope with.

HTC

High Throughput Computing

Human Data and Translational Research. One of the Scientific Tiers under the 2024-28 Programme with a number of open funding calls. (See also BFSP and CMR)

Hub

The ELIXIR Hub coordinates and supports the services run by the ELIXIR Nodes and has overall responsibility for developing and delivering the ELIXIR Scientific Programme. It is based at the Wellcome Genome Campus near Cambridge, UK. See Who we are.

A cloud computing environment that uses a mix of on-premises, private cloud and third-party, public cloud services with orchestration between the two platforms. By allowing workloads to move between private and public clouds as computing needs and costs change, hybrid cloud gives businesses greater flexibility and more data deployment options

International Conference for Research Infrastructures, a biennial event that brings together stakeholders in the field of research infrastructures to discuss international cooperation.

Implementation study (aka CoS) 

ELIXIR projects intended to implement the Scientific Plan through a relatively narrow focus and short term duration (two years), funded through the budget of the ELIXIR Hub and are used to connect ELIXIR Nodes. 

INDIGO DataCloud

An H202 project, an open source data and computing platform targeted at scientific communities, deployable on multiple hardware and provisioned over hybrid, private or public, e-infrastructures.

IRDiRC

International Rare Diseases Research Consortium

ISBE

The ESFRI BMS research infrastructure on systems biology, which aims to facilitate the use of model-driven approaches to understand complex biological systems, enabling their function to be altered in a rational and predictive way.

International Society for Computational Biology: a scholarly society for advancing understanding of living systems through computation and for communicating scientific advances worldwide.

ITSoneDB

A comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences

JABBA

Just Another Bogus Bioinformatics Algorithm

Key Contributor's Update - an update on relevant actions and ELIXIR activities circulated every Friday afternoon to key members in ELIXIR.

LIMS

Laboratory Information Management System is software that allows you to effectively manage

LTS-WG

Board to consider long-term options for maintaining Core Data Resources consisting of

Machine Actionable Data Management Plan
Machine Actionable Software Management Plan

MC

patents and clinical guidelines

Member/Member State

A country in ELIXIR that has signed the ELIXIR Consortium Agreement (see How countries join). It can also mean an institution that is part of ELIXIR e.g. the University of Manchester is part of ELIXIR UK, and so is a ‘member’ of ELIXIR

Metagenomics

The study of genetic material sampled directly from the environment (rather than cultured in a laboratory). In marine metagenomics, for example, the genetic material studied is taken from samples of seawater taken directly from the sea.

Minimum Information About a Plant Phenotyping Experiment; an open, community driven project to harmonize data from plant phenotyping experiments.

MSCA

Marie Skodowska-Curie Actions. A grant making body associated with H2020

NeLS

This is NeLS portal for the administration of Norwegian e-Infrastructure for Life Sciences. NeLS is one of the packages of the ELIXIR.NO project.

NIST

National Institute for Science and Technology. Both is a physical sciences laboratory, and a non-regulatory agency of the United States Department of Commerce, to promote innovation and industrial competitiveness

Node

An institution within a country that runs that country’s ELIXIR services e.g. the Dutch Techcentre for Life Sciences (DTL) oversees the work of ELIXIR Netherlands. It is the Dutch Node. See How countries join.

OBIS

Ocean Biogeographic Information System

Observer

In ELIXIR, an Observer is a country that has not yet signed the ELIXIR Consortium Agreement (ECA), which all members have signed. It may be that the country is still working towards signing it. See How countries join.

PaaS

Platform as a Service, is a cloud computing model in which a third-party provider delivers hardware and software tools

PI

Principal Investigator

Pistoia Alliance

A not-for-profit alliance of life science companies, vendors, publishers, and academics that work together to lower barriers to innovation in R&D.

A group of scientists who coordinate ELIXIR’s activities in a particular area. There are five Platforms or areas of work within ELIXIR (Data, Tools, Interoperability, Compute and Training).

POC

Proof of Concept

Proteome

The proteins found in an organism over its entire life cycle, or in a particular cell type at a particular time under defined environmental conditions.

The study of the proteins of a particular cell, tissue or organism, often produce inventories of the protein structures produced by the same tissue under different conditions.

RD-Connect

An integrated platform connecting databases, registries, biobanks and clinical bioinformaticians for rare disease research

RDA

The Research Data Alliance, a global initiative which aims to accelerate and facilitate research data sharing and exchange.

RDM /
RDM Toolkit

RDDS

Reference Data Distribution Service

RDF

Resource Description Framework

RFP

Request For Proposal; a document that solicits a proposal (eg Implementation Study) as part of a competitive bidding process

RI

Research Infrastructure; A network of facilities, databases and services used by the science community to conduct research. By combining these resources then the research becomes more effective because data and expertise can be pooled.

RIAs

Research and Innovation Actions – most H2020 we take part in will be RIAs or CSAs

RIR

Recommended Interoperability Resources. Services that supports description, reporting, annotation, sustainability and provision of biological data, coordinated by the Interoperability Platform

RItrain

Research Infrastructures Training Programme, funded by BBMIR to develop a competency profile and curriculum for distributed RI operators and managers. (nb. Pronounced "Rye Train" rather than "Retrain") 

SaaS

Software as a service is a software distribution model in which a third-party provider hosts applications and makes them available to customers over the Internet.

SAB

Scientific Advisory Board, an independent body, made up of leading experts from around the world, provinding scientific advice. (eg ELIXIR SAB) 

Schema

A database schema represents the logical configuration of all or part of a relational database. It can exist both as a visual representation and as a set of formulas known as integrity constraints that govern a database, expressed in a data definition language, such as SQL.
Schema.org: a community activity to create, maintain, and promote schemas

SDP

Service Delivery Plan. A contractual agreement between ELIXIR and each Node setting the roles and responsibilities of the Node.

The process of discovering the order of nucelotides in DNA or RNA, or the order of amino acids in a protein. There are four types of nucleotides in DNA. Each gene is made up of a sequence of nucleotides.

Different meanings in different contexts, it is both used as a synonym of "infrastructure" as well as a "process" or established way of doing things

• Node Services: LifeScience tools and resources from each Node 
• Commissioned Service: Activities funded by ELIXIR to implement the current Programme

SIB

Swiss Institute of Bioinformatics

Solve-RD

Project to deliver diagnostic tests for most rare diseases by 2020, funded by Horizon 2020 research and innovation programme

SOP

Standard Operating Procedure. A set of step-by-step instructions compiled by an organization to help workers carry out complex routine operations.

STFC

Science and Technology Facilities Council

STRIDES

Science and Technology Research Infrastructure for Discovery, Experimentation, and Sustainability, an initiative to provide biomedical researchers access to advanced, cost-effective computational infrastructure, tools and services.

A computer that has more computational capacity than a general-purpose computer. Supercomputers split large tasks into smaller tasks and work on all the sub-tasks at once (parallel processing). Grids and HPC clusters are examples of supercomputers.

SWC/DC

Software and Data Carpentry

TeCG (TeC) 

ELIXIR Technical Coordinators Group, the body composed of technical representatives of each of the ELIXIR Nodes who will ensure ELIXIR-wide knowledge exchange on the ELIXIR technical strategy. 

TES

Task Execution Service. Executing the tasks within a CWL workflow (see also WES)

TeSS

Training e-Support System A portal to collect, disseminate and organise information about bioinformatics training from ELIXIR Nodes and various third-party providers

TIaaS

Training Infrastructure as a Service (eg. Galaxy TIaaS) 

TraIT

The CTMM Translational Research IT (TraIT) project is developing and implementing a long-lasting IT infrastructure for translational research projects in the Netherlands

TrCG (TrC)

ELIXIR Training Coordinators Group, the body composed of training representatives of each of ELIXIR Node. 

TRS

Tool Registry Service; An API enabling an interoperable library of genomic analysis tools, under GA4GH. 

Tryggve

A Nordic project established by NeIC and ELIXIR Nodes of DK, FI, NO and SE to provide infrastructure for cross-border collaboration on sensitive biomedical data. The project develops and connects secure platforms at the participating nodes. link

Use Case

Within ELIXIR, these are collaborations between ELIXIR and life scientists in a particular domain (e.g. rare disease). They give feedback on the services developed by ELIXIR Platforms and ensure that the services match the scientists’ needs. These are now refered to as Communities 

WES

Workflow Execution Service. Coordinating specified workflows using CWL. (See also TES)

WGC

Wellcome Genome Campus (formerly Wellcome Trust Genome Campus WTGC) including the EBI, Sanger Institute, Conference Centre, Hinxton Hall etc

WP

Work Package; A group of related tasks within a project.

WTSI

Wellcome Trust Sanger Institute (part of the Wellcome Genome Campus with around 800 of nearly 3,000 people working here.)