venerdì 20 novembre 2020

Announcing... SWAT4(HC)LS 202...1

This may not come as a surprise, as there has been no communication from SWAT during the past year. 

As a matter of fact we had already planned the logistic for the SWAT4HCLS 2020, when the pandemic imposed the first lockdown across the globe. We have been thinking a bit on whether to host a physical event or not and later, as the second wave hit,  whether to host an online event.

At the end uncertainty didn't play well for us, and we have decided that is best to skip one year... and announce directly the 2021 event, that will be hosted on Leiden (NL) in December.

If you miss some SWAT community, we may still hold a 1 day virtual hackathon. If you are interested, please register your availability and ideas here:

mercoledì 30 ottobre 2019

Registrations to SWAT4HCLS 2019 are now open!

We apologies for all delays!

Registrations are open and we will soon publish the list of accepted papers.

giovedì 8 agosto 2019

Updates from SWAT4HCLS

A few updates from SWAT4HCLS:
We have confirmed our first two keynotes:
Denny Vrandecic from Google Research, and Helen Parkinson from EMBL-EBI.
Ronald Cornett is also joining us as scientific chair this year.

venerdì 28 giugno 2019

SWAT4HCLS 2019 CfP is out

CfP: SWAT4LS 2019

12th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences, 9-12th December 2019, Edinburgh, UK

For over a decade SWAT4HCLS has provided a venue where a vibrant and open community of researchers, developers, users and professionals from varied backgrounds have come together to discuss future targets, current limitations and real experiences in the use of semantic and web technologies in healthcare and life sciences.  
We invite submissions for the 2019 editions in all our topics of interest.


Full paper submission: September 9th
Posters and demo submissions: October 7th
Notification of acceptance: October 21st

Monday, December 9th: Tutorials
Tuesday, December 10th: Main Conference, Evening: Conference dinner
Wednesday, December 11th: Main Conference
Thursday, December 12th: Hackathon
Confirmed Keynotes

Tutorials and conference will take place at Heriott-Watt University, Edinburgh

Jonas Almedia, General Scientific chair
Chris Baker, Agrisemantics track chair
Andra Waagmaseter, Open Data chair
Albert Burger, local chair, 
Andrea Splandiani, M.Scott Marshall: general chair

Andrea Splendiani, Adrian Paschke, M.Scott Marshall, Paolo Romano: SWAT4HCLS committee.


Topics of interest include, but are not limited to Semantic and Web technologies designed for, and applied, in Healthcare and the Life Sciences.

Semantic technologies and their application in healthcare and life sciences
  • Knowledge representation systems in life sciences, medicine, healthcare and agriculture.
  • NLP and text mining using semantic technologies.
  • Methods and standards to improve discoverability and reusability of data repositories
  • Semantic Querying, Data validation languages, Knowledge Graphs, Rule-based systems.
  • Semantic workflow technologies and semantic web services applied in life sciences.
  • Infrastructures supporting provenance, traceability, trust and reproducibility.
  • Bridging semantics and analytics in the context of healthcare and life sciences
  • Novel approaches to utilizing existing biomedical data without sharing it, e.g. bring the analysis to the data
  • Deep learning and semantic technologies.
  • Computing on knowledge graphs
  • Data curation and cleansing pipelines and approaches

  • New biomedical ontologies
  • Open Data Integration and Interoperability
  • Data repositories, integrated knowledge bases and data catalogues
  • Gold data sets
  • Biomedical ontologies, rules and medical standards for information exchange and interoperability.

Current challenges and experiences
  • Application and impact of data standards applied in clinical practice, public health and agribusiness
  • Empirical studies and evaluation of Semantic Web tools and applications in the life science domains
  • Ethical issues, privacy and data governance in healthcare, agri, and medical data in Semantic Web
  • Studies focussing on the adoption of Semantic Technologies by knowledge workers in life sciences
  • Business models for as (semantic) data economy

New applications of semantic technologies
  • Semantic infrastructures for person-centric healthcare data ecosystems
  • Semantic approaches to data repurposing in healthcare and patient generated data
  • Use of semantics to enable translational medicine, personalized medicine and precision agriculture
  • Semantic scientific publishing in the life sciences, medicine and healthcare, public health
  • Clinical Intelligence from Electronic Health Records (EHRs), patient data and clinical trial data
  • Future directions for Semantic Web technologies in the life sciences and interdisciplinary fields. including water science, agro science, and veterinary science, biodivesrity, drug repositioning
  • Harnessing linked data for Research Assessment/Monitoring and Evaluation

Types of submission
The following types of submissions for SWAT4HCLS 2019 are invited:

Long papers: 
  • Research papers – Original research on a topic of interest to the SWAT4HCLS audience.
  • In-use papers – New applications and tool descriptions addressing a topic of interest to the SWAT4HCLS audience.

Short papers:
  • Position papers, application notes, discovery notes,. using Semantic Web applications and tools.
  • Software demos – Present software and tools in action.

Industry talks (abstract only required):
  • Industry Application: report on industrial applications or research. (Semantic Publishers, Pharma, Healthcare, Agribusiness)
  • Data Challenge Showcase: Are you planning a Data Challenge and want to reach out to expert participants. Submit an abstract with details of your target goals, timeline and prizes.
  • Open Innovation: Are you an life science company that with more data than you can analyse and want experts to help find new insights. Submit an abstract with details of your target goals, license agreements, timeline, publication policy
  • Business Models: Business models that leverage semantically rich data (e.g. publishing companies, for-profit data providers)

Posters and Demos

Accepted workshop papers will be published in CEUR proceedings. We are working on a special issue covering selected SWAT4HCLS works from 2018 and 2019.

Instructions for authors
All submissions will be handled via the EasyChair submission system at .
All papers and posters must be in English and submitted in pdf using the LNCS format .
Submissions for long papers must be a maximum of ten pages.
Submissions for short papers must be a maximum of five pages.
Submissions for posters abstract must be a maximum of two pages.
Submissions of industry abstracts must be a maximum of two pages.
Papers will be peer-reviewed by at least three members of the Scientific Program Committee.

giovedì 30 maggio 2019

Kickstarting SWAT4(HC)LS 2019 !

Is that time of the year...
Preparations for SWAT4(HC)LS 2019 are well underway.
We have finalised a venue, that will be in Edinburgh, Dec. 9-12 and we have defined the following timeline:
  • Tutorial submissions deadline: June 15th*
  • Paper submissions: September 9th 
  • Poster submission deadline: October 7th
  • Notification of acceptance: October 21st
From now one, expect a steady flow of news as the program develops!

*write at at info  @ if interested

lunedì 12 novembre 2018

Additional tutorial on OpenEHR at SWAT4HCLS 2018

We are happy to announce that Caroline Boenisch will provide a tutorial on openEHR, that will complement our lineup on healthcare standards.

OpenEHR standardizes heterogeneous medical IT systems and the resulting dispersion of medical data in archetypes and templates. These archetypes are developed in collaboration with the international openEHR community, which consists of physicians, computer scientists and processing as well as standardization experts. The results are systems and tools that add value to decision-making support in day-to-day clinical practise and support research questions. These tools will reduce workload and improve semantic traceability. Furthermore, model-generated code and user interfaces are an area of continuous innovation in openEHR and promise to revolutionize health computing.

venerdì 2 novembre 2018

The preliminary program of SWAT4HCLS 2018 is out!

Breaking news!
The preliminary program for SWAT4HCLS 2018 is out:
(follow the link for the actual program with timing)


December 3rd Tutorial day

Data and Standards (data and standards: challenges where semantics can make an impact) 
Data science (fundamentals)
Semantics  (Semantic tools and applications)
Room ARoom BRoom C

Data and Standards
Data Science
Coffee Break

Data and Standards
Data Science
tutorial continues
tutorial continues
Lunch Break

Data and Standards
Data and Standards
Coffee Break

Data and Standards
tutorial continues


December 4th-5th Conference days

Conference day 1

Registration (opens 8.30)

Welcome, introduction. Outline of the conference and hackathon

Keynote by Philip Bourne

Selected Talks
Using semantic technologies to enhance metadata submissions to public repositories in biomedicine. Attila L. Egyedi, Martin O’Connor, Marcos Martínez-Romero, Debra Willrett, Josef Hardi, John Graybeal and Mark Musen.
Using Wikidata for semantic data modeling in education and research. Annika Jacobsen, Andra Waagmeester, Rajaram Kaliyaperumal, Greg Stupp, Lynn Schriml, Mark Thompson, Andrew I. Su and Marco Roos.  (short paper)

Coffee break

Selected talks
The Story of an Experiment: A Provenance-based Semantic Approach towards Research Reproducibility. Sheeba Samuel, Kathrin Groeneveld, Frank Taubert, Daniel Walther, Tom Kache, Teresa Langenstück, Birgitta König-Ries, Martin Buecker and Christoph Biskup. 
DSAP: Data Sharing Agreement Privacy Ontology. Mingyuan Li and Reza Samavi. 
FP12 Full paper (6) Kody Moodley, Amrapali Zaveri, Chunlei Wu and Michel Dumontier. A model for capturing provenance of assertions about chemical substances
Increasing the nanopublication recall with a BridgeDb Identifier Mapping Service. Egon Willighagen. (short paper) 

Lunch break (12.30- 13.30)

Keynote by Medha Devare

Selected talks
Design of a framework to support reuse of Open Data about agriculture. Alec Gordon, Mohammad Sadnan Al Manir, Brandon Smith, Amir Hossein Rezaie and Christopher Baker. 
TBD (Short Talk)
Ontology-Driven Metadata Enrichment for Genomic Datasets. Anna Bernasconi, Arif Canakoglu, Andrea Colombo and Stefano Ceri. 

Lightning poster presentations

Poster and demo session, Coffee break

Panel discussion (Agrisemantics)
Social dinner (conference end at 18.00)

Conference day 2

Registration (opens at 8.30)

Recap from the previous day


Selected Talks
Sparklis over PEGASE Knowledge Graph: A New Tool for Pharmacovigilance. Carlos Bobed, Laura Douze, Sébastien Ferré and Romaric Marcilly. 
Allotrope Data Format – Semantic Data Management in Life Sciences. Heiner Oberkampf, Helge Krieg, Christian Senger, Thomas Weber and Wolfgang Colsman. (Industry report)
Architecture for the harmonization of clinical cohort data in the IMI EMIF projectRudi Verbeeck, Luiza Gabriel and Michel van Speybroeck. (Industry report)

Coffee break

Selected talks
A Distributed Analytics Platform to Execute FHIR based Phenotyping Algorithms. Md. Rezaul Karim, Binh-Phi Nguyen, Lukas Zimmermann, Toralf Kirsten, Matthias Löbe, Frank Meineke, Holger Stenzhorn, Oliver Kohlbacher, Stefan Decker and Oya Beyan. 
A Semantic Data Integration Methodology for Translational Neurodegenerative Disease Research. Sumit Madan, Maksims Fiosins, Stefan Bonn and Juliane Fluck. 
Cooperation of bio-ontologies for the classification of genetic intellectual disabilities : a diseasome approach. Gabin Personeni, Marie-Dominique Devignes, Malika Smail-Tabbone, Philippe Jonveaux, Céline Bonnet and Adrien Coulet.
Progress Towards an Ontology Mapping Service. Industry (38) Ian Harrow, Martin Romacker, Andrea Splendiani, Peter Woollard, Tom Plasterer, Rainer Winnenburg, Scott Markel, Siddharth Mehta, Chris Piddington, Yasmin Alam-Faruque, Rama Balakrishnan, Jane Lomax, Jane Reed, Christian Senger, Jabe Wilson, Filip Pattyn, Ernesto Jimenez-Ruiz and Simon Jupp.  (Industry report)

Lunch break (12.30-13.30)

Keynote by Dean Allemang

Selected talks
Evaluation of Knowledge Graph Embedding Approaches for Drug-Drug Interaction Prediction using Linked Open Data. Remzi Çelebi, Erkan Yaşar, Hüseyin Uyar, Özgür Gümüş, Oguz Dikenelli and Michel Dumontier.  
Vec2SPARQL: integrating SPARQL queries and knowledge graph embeddings. Maxat Kulmanov, Senay Kafkas, Andreas Karwath, Alexander Malic, Georgios V Gkoutos, Michel Dumontier and Robert Hoehndorf.  

Poster and demo session, Coffee break

Selected talks
Data2Services: enabling automated conversion of data to services.Vincent Emonet, Amrapali Zaveri, Alexander Malix, Andreea Grigoriu and Michel Dumontier. 
Getting the best of Linked Data and Property Graphs: rdf2neo and the KnetMiner Use Case. Marco Brandizi, Ajit Singh and Keywan Hassani-Pak.

Panel discussion
(ends at 17.30)

December 6th Hackathon day

Feel free to add your idea to the hackathon brainstorming doc!