1. EBI is an Outstation of the European Molecular Biology Laboratory. Tutorial 5: ChEBI - On-line Submission and Curation

2. ChEBI – On-line submission and curationJanuary 15, 20162 What is ChEBI? Chemical Entities of Biological Interest Freely available Focused on ‘small’ chemical entities (no proteins or nucleic acids) Illustrated dictionary of chemical nomenclature Provides chemical ontology High quality, manual curation Public release: First Monday of every month (latest release: 22,000 manually curated entries; 620,000 total entries). Data made available via Public web application Flat-file binary table dumps Oracle table dumps Generic SQL table dumps MDL SD file export Query via Web services Access ChEBI at http://www.ebi.ac.uk/chebi/

3. ChEBI – On-line submission and curationJanuary 15, 20163 ChEBI entry view (i)

4. ChEBI – On-line submission and curationJanuary 15, 20164 ChEBI entry view (ii)

5. ChEBI – On-line submission and curationJanuary 15, 20165 ChEBI entry view (iii)

6. ChEBI – On-line submission and curationJanuary 15, 20166 ChEBI entry view (iv)

7. ChEBI – On-line submission and curationJanuary 15, 20167 The submission tool Web-based software utility to enable direct user submissions Needed to alleviate backlog of user requests An invitation to the community to participate in the growth and development of ChEBI Secure (submitter registration required) Simple stepwise procedure Instant generation of ChEBI ID and inclusion in next monthly public release Access at https://www.ebi.ac.uk/chebi/submissions/ or via ChEBI home pagehttps://www.ebi.ac.uk/chebi/submissions/

8. ChEBI – On-line submission and curationJanuary 15, 20168 Submission validations Built-in integrity checker will check for: Uniqueness of name Uniqueness of chemical structure Correctness of ontology relationships No non-allowed cycles Relationships only between entities of relevant types Correctness of xref format CAS Registry Number DrugBank KEGG LIGAND/DRUG/GLYCAN Lipid Maps

9. ChEBI – On-line submission and curationJanuary 15, 20169 Login page

10. ChEBI – On-line submission and curationJanuary 15, 201610 Submission Step 1 (i)

11. ChEBI – On-line submission and curationJanuary 15, 201611 Submission Step 1(ii)

12. ChEBI – On-line submission and curationJanuary 15, 201612 Submission Step 2

13. ChEBI – On-line submission and curationJanuary 15, 201613 Submission Step 3

14. ChEBI – On-line submission and curationJanuary 15, 201614 Submission Step 4(i)

15. ChEBI – On-line submission and curationJanuary 15, 201615 Submission Step 4(ii)

16. ChEBI – On-line submission and curationJanuary 15, 201616 Submission preview(i)

17. ChEBI – On-line submission and curationJanuary 15, 201617 Submission preview(ii)

18. ChEBI – On-line submission and curationJanuary 15, 201618 Submission confirmation

19. ChEBI – On-line submission and curationJanuary 15, 201619 ChEBI submissions Feb 2009 – Sep 2010 (Data as at September 9th 2010)

20. ChEBI – On-line submission and curationJanuary 15, 201620 ChEBI submitters Reactome Gene Ontology Consortium RSC Journals Rutgers Univ. Cornell Univ. Carleton Univ. Stanford Univ. SIB IntAct Rhea Array Express Manchester Centre for Integrative Systems Biology EML Research, Heidelberg Dept of Genetics, Cambridge Univ.

21. ChEBI – On-line submission and curationJanuary 15, 201621 Submission tool - Future plans Bulk submissions (by invitation only) - imminent Modifications to existing ChEBI entries - ???

22. ChEBI – On-line submission and curationJanuary 15, 201622 The ChEBI team Curators Marcus Ennis Steve Turner Zara Josephs Nico Adams Gareth Owen Developers Paula de Matos (team coordinator) Janna Hastings Adriano Dekker Kenneth Haug Group Leader Christoph Steinbeck ChEBI is funded by the European Commission under SLING, contract number 226073 within the Research Infrastructure Action of the FP7 “Capacities Specific” Programme. www.ebi.ac.uk/chebi