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Workshop: Ontologies4Chem – Ontologies for chemistry
07.09.2022 @ 14:30 – 08.09.2022 @ 17:30 CEST
Ontologies are a holistic approach to semantically describe data, information and knowledge of a domain. They provide terms, relations and logic to semantically annotate and link data building knowledge graphs. The application of standard taxonomies and vocabularies from the very beginning of data generation and along research workflows in electronic lab notebooks (ELNs), software tools, and their final publication in data repositories create FAIR data straightforwardly. In Biology, Chemistry and related sciences quite a few chemical already exist to describe the molecules, their characteristics and reactions.
During this workshop we aim to bring together creators, curators and users of chemical ontologies to discuss their application in research data annotations and a general roadmap for joint efforts on future developments. Further topics will include latest developments on tools to work with ontologies, the provision of ontologies with terminology services and their integration in other services/software.
Costs: Free
Venue: Online
Duration: 2 days, 3-4 hours each
Participants: ~ 40
Aims:
- Deepen and/or establish collaboration between ontology curators and NFDI4Chem + other NFDI consortia related to chemistry
- Develop joint strategies: ontologies for research data management and beyond
- Work concretely on ontologies
- Application of ontologies in research data annotations
- Inspire service developers and data repository developers to use ontologies
- Inspire chemists to use ontologies
- Deepen liaison with other NFDI consortia
Preliminary Agenda:
Day 1 (2:30pm – ~6pm CEST)
- Welcome, Introduction Role of ontologies in NFDI and NFDI4Chem
- Introducing Ontologies4Chem
- Chemistry Ontologies, past and current developments (presented by curators, order of presentations not final)
- Stuart Chalk, IUPAC Gold Book – Compendium of Chemical Terminology
- Adnan Malik, ChEBI https://www.ebi.ac.uk/chebi/
- Egon Willighagen on CHEMINF – https://github.com/semanticchemistry/semanticchemistry
- Colin Batchelor on RSC Ontologies (RXNO, CHMO, MOP) – https://github.com/rsc-ontologies
- Charles Tapley Hoyt on ChIRO – https://github.com/chemical-roles/chemical-roles
- Chris Mungall – https://github.com/chemkg/chemrof
- Break
- Matúš Kalaš on EDAM https://github.com/edamontology/edamontology
- James Overton – OBI
- Michel Dumontier – SIO
- Alasdair Gray – Bioschemas.org
- Chemistry and other ontologies in chemistry related NFDI consortia
- Chemistry and other ontologies in NFDI4Health
- Chemistry and other ontologies in NFDI4Cat
- Break
- Current Tool developments
- Closing day one
Day 2: (2:30pm – ~5:40pm CEST)
- Community-driven Ontology Development – Best practices
- NFDI4Cat Ontology Workflow, N. Kockmann, A. Behr.
- Ontology development for Raman, NMR in NFDI4Chem, Philip Strömert
- 2022-09-08 (Bio) Schemas4Chem , Steffen Neumann
- Tools used in projects for data annotations
- Application of ontologies in ELN, TS, data repositories in NFDI4Chem, Venkata Chandrasekhar Nainala
- IUPAC FairSpec project, Bob Hanson
- The use of ontologies for the data annotation in Pubchem, Evan Bolton
- ClassyFire – automated chemical classification in application contexts, David Wishart
- Break
- Parallel Hands On Sessions (45 min)
- Hands on Ontology Curation
- Hands on Data annotation using Ontologies
- Semantification of NMR data, Philip Strömert
- Closing Discussion: NFDI Roadmap for Ontologies in chemistry and related. How to join forces.
