Thanasis Vergoulis presents ELIXIR, an intergovernmental organisation aiming to coordinate, integrate and sustain bioinformatic resources across Europe | OSFair2017 Workshop Workshop title: Open Science as a service: tools for research communities Workshop overview: The aim of this workshop is to work with research communities especially interested/relevant to open science publishing paradigms: publishing of literature, datasets, methods, and experiments for reproducibility and transparent assessment of science. This will be an interactive session with communities presenting their requirements and current tooling to identify overlaps, better and cost-effective solutions. When: DAY 2 - PARALLEL SESSION 3

1. THE ELIXIR VIEW OF
OPEN SCIENCE
Thanasis Vergoulis
"Athena" RC, Greece

2. OUTLOOK
➤ ELIXIR is an intergovernmental organisation aiming to
coordinate, integrate and sustain bioinformatic resources
across Europe
➤ Founded in 2014 & partly funded by EC (RI - Horizon2020)
➤ 22 countries-members
➤ 180+ research organisations
➤ Coordinator: EMBL’s EBI
➤ Researchers across whole Europe
to take advantage of the outcomes.
datasets tools comp. services interoperability training

3. SCIENTIFIC PROCESS
Observation
Theory
Experiment
(in silico)
Publication
perform comp.
analysis on new
dataset
or
perform new comp.
analysis on old
dataset
…
journals are
preferable
Articles
Tools
Datasets

4. SCHOLARLY COMMUNICATION PRACTICES
Tools
- Perl, Python, R; also Web apps (PHP)
- Many open source (github)
- Workflows (Galaxy, Taverna)
Articles
- OA very usual - promotion by prestigious journals
- Supplementary data (tables, figures, text)
- MEDLINE / PubMed (open PMC)
Datasets
- Files, databases; interlinking (usually w/o
using standards)
- Mandatory for reproducibility
- Versioning is important in many cases
bio.tools (https://bio.tools/)
- Tools registry (>6100 tools)
- Free content (CC BY-SA 4.0)
- Connection with publications
- Use EDAM for descriptions
- Incorporation of tool
benchmarking & service
monitoring

5. SCHOLARLY COMMUNICATION DESIDERATA
➤ Handling multiple dataset versions
➤ Need for indicative qualitative measures
➤ Vast amount of articles published annually
➤ Publish or perish?
➤ A large portion of them is problematic or erroneous
➤ Counting citations is not enough
➤ Many interesting quality aspects
➤ Visit BiP! finder poster for details!

6. More info: https://www.elixir-europe.org/
vergoulis@imis.athena-innovation.gr