Weekly Brief, 31 July 2023

This week's highlights

Upload your ELIXIR All Hands 2023 slides and posters!

Please remember to upload your slides or posters presented during ELIXIR All Hands 2023 on the F1000 ELIXIR Gateway

Artificial Intelligence for Science - new publication with ELIXIR authors' contributions

A recently published book, Artificial Intelligence for Science, features three chapters with ELIXIR authors:

• Chapter 22: A Roadmap for Defining Machine Learning Standards in Life Sciences
  Fotis Psomopoulos, Carole Goble, Leyla Jael Castro, Jennifer Harrow, and Silvio C. E. Tosatto
• Chapter 27: Schema.org for Scientific Data
  Alasdair Gray, Leyla J. Castro, Nick Juty, and Carole Goble
• Chapter 33: FAIR: Making Data AI-Ready
  Susanna-Assunta Sansone, Philippe Rocca-Serra, Mark Wilkinson, and Lee Harland

Check these chapters on Google book

Recommended reads

lesSDRF Is More: Maximizing The Value Of Proteomics Data Through Streamlined Metadata Annotation

An ELIXIR Implementation study

Sharing data and resources has revolutionized life sciences. However, the lack of comprehensive metadata remains a significant challenge to unlocking the full potential of publicly shared data. This study investigated metadata annotations in proteomics data sets from the PRIDE database, and identified major gaps in metadata provision. To bridge this gap, the authors created a user-friendly, ontology-based Streamlit application, named lesSDRF, that guides users through the annotation process using SDRF. lesSDRF aims to encourage researchers to provide more detailed metadata annotations, leading to greater insights and scientific advances in proteomics.

Read more

A comparison of approaches to accessing existing biological and chemical relational databases via SPARQL

An ELIXIR-CZ paper

There is a growing need for database systems and databases stored in them to be interoperable with each other. One of the possible solutions to address this issue is to use systems based on Semantic Web technologies, namely on the Resource Description Framework (RDF) to express data and on the SPARQL query language to retrieve the data. Converting a relational database into the RDF form and storing it in a native RDF database system may not be desirable in many cases. This review compares different RDB-to-RDF mapping systems with a primary focus on those that can be used free of charge. It shows that these systems represent a viable method providing sufficient performance.

Read more

Updates from Nodes

VHP4Safety/EOSC Kubernetes Workshop

23-24 August 2023 | Hybrid - Maastricht, The Netherlands

ELIXIR-NL will host the virtual platform for animal-free risk evaluation in toxicology supported by EOSC-Life. This workshop would discuss how support groups like SURF (NL), EOSC, and the ELIXIR Compute Platform can support such developments, and develop plans to collaborate.

More information and registration

Updates from Communities

Reminder: Call for new ELIXIR Single Cell Omics Community co-lead

Deadline: 7 August 2023

The ELIXIR Single Cell Omics Community is looking for one new co-lead to join the Community leadership team (Eija Korpelainen & Naveed Ishaque). Candidates should submit a short statement of their background and what they believe they will bring to the role.

A big thank you to Paulo Czarnewski for his work as a co-lead and we wish him all the best as he moves to a new role.

For any questions or nominations, please contact clare.garrard [at] elixir-europe.org (Clare Garrard)

More information

Register for the Galaxy Community meeting

4-6 October 2023 | Hybrid - Freiburg, Germany
Registration deadline: 18 September (in person) | 3 October (online)

The Galaxy Community will hold its F2F/hybrid Meeting in October. The meeting is integrated into the European Galaxy Days. The meeting will include presentations, workshops and participant engagement.

More information and registration

Reminder: Register for the Biodiversity Community F2F & Implementation Study meeting

13-15 September 2023 | Hybrid - Barcelona, Spain
Registration deadline: 17 August (in person) | 12 September (online)

The Biodiversity Community will hold its F2F/hybrid meeting in September. The meeting is held back to back with the emerging Microbiome Community (hosting one joint session) and links the Community F2F with an Implementation Study meeting. There will be time for updates, presentations, progress reports and discussions. A part of the meeting will be dedicated to the 2024-2028 Scientific Programme and the Community's possible role and activities.

Register now

Reminder: Register for the Emerging Microbiome/Marine Metagenomics Community meeting

12-13 September 2023 | Hybrid - Barcelona, Spain
Registration deadline: 17 August (in person) | 12 September (online)

The Emerging Microbiome/Marine Metagenomics Community will hold its F2F/hybrid Meeting in September. The meeting is held back to back with the Biodiversity Community and focuses on the final touches of the Community white paper and first ideas for upcoming Community activities. There will be time for updates, presentations, progress reports and discussions. A part of the meeting will be dedicated to the 2024-2028 Scientific Programme and the Community's possible role and activities.

Register now

Updates from Focus Groups

EOSC Symposium 2023: ELIXIR Travel Grant Now Open

Deadline: 7 August 2023

Applications are now open for the ELIXIR travel grant funded attendance of EOSC Symposium 2023. Please submit your travel grant application via SurveyMonkey

Please note that the official registration deadline for the EOSC Symposium event is today.

RDA Plenary 21: ELIXIR Travel Grant Now Open

Deadline: 7 August 2023

Applications are now open for the ELIXIR travel grant funded attendance of RDA Plenary 21, 23-26 October 2023. Please submit your travel grant application via SurveyMonkey.

Please further note the official registration deadline for the RDA Plenary 21 event is 20 October 2023.

Further information on ELIXIR Travel Grant Scheme

Updates from other initatives

Open call: Support for the implementation of SARS-CoV-2 data hubs at national and regional levels

Deadline: 1 September 2023

The BY-COVID project has an open call for proposals to support the implementation of additional SARS-CoV-2 data hubs to increase the flow of viral sequence data into the European Nucleotide Archive (ENA), in line with open science principles.

More information

Upcoming ELIXIR events & webinars

ELIXIR Training Courses & Webinars

The ELIXIR TeSS portal has a variety of interesting events and courses organised by the ELIXIR Nodes. For more, visit TeSS portal

ELIXIR Events and Conferences

Emerging Microbiome/Marine Metagenomics Community meeting
12-13 September 2023 | Hybrid - Barcelona, Spain

Biodiversity Community F2F & Implementation Study meeting
13-15 September 2023 | Hybrid - Barcelona, Spain

BioHackathon Europe 2023
30 October - 3 November 2023 | Barcelona, Spain

Job vacancies

All vacancies are also published on the ELIXIR website (also including those from industry). If you need our help communicating your new open positions, you can submit a job advertisement and it will automatically appear on our newsletters. Go to our vacancy page to submit a job
 

Semantic Web Architect

UK CEH

Auxiliary RESEARCHER (M/F) in the area of Bioinformatics/Data Science

Centro de Ciencias do Mar (CCMAR)

Bioinformatician in Cancer Genomics

Institute for Research in Biomedicine (IRB Barcelona)

Python Developer

CRG

Researcher-expert Federated Health Data infrastructures

Hasselt University