2. The current status
• WormBase release WS260 has over 6000
Molecule records
– Nearly 5000 are from chemical databases.
– 300 are from publications.
– (1000 have both).
3. Sources of data
Database Full Name
CTD Comparative Toxicogenomics Database
ChEBI Chemical Entities of Biological Interest
ChemIDplus ChemIDplus Lite
KEGG COMPOUND
NLM_MeSH Medical Subject Headings
SMID-DB Small Molecule Identifier Database
4. Sources of data
• 273 publications
–Manually curated
• Journal scanning.
• Other curators e.g. molecules from large scale
gene expression datasets.
• Authors e.g. Michael Witting has curated data
from 40 papers covering many datasets.
6. Future Goals 1
• Integration of quantitative data.
– Table: genotype, larval stage, growth conditions,
metabolite, concentration, analysis method.
• Representation of reactions and pathways.
• Assign WormBase identifiers (WBID) to all
metabolites in C. elegans.
7. Future Goals 2
• “Market Place” for reference curation
standards.
– Smoother exchange between labs.
– Gold standard for methods/protocols.
• Revise the WormBase model.
– Is the metabolite commercially available?
– Flag whether drug or endogenous metabolite.
• Community driven curation.
8. WormJam
A discussion group for the C. elegans metabolism,
metabolic network reconstruction and metabolomics
communities to facilitate community-based
development of shared resources to address global
challenges.
• Created end of April following GENiE workshop in
Cambridge, UK.
• GENiE Workshop: Extending the consensus
representation of C. elegans metabolism.
– Correspondence article in review in Nature Biotechnology
wormjam@googlegroups.com
9. Annotation Jamboree
• 9th & 10th November, 2017 Helmholtz Centrum
Muenchen.
• Goals
– Gap filling of metabolic pathways.
– Annotation of new enzymes.
– Align European standards with WormBase and wider
community
• Organisers: Olivia Casanueva, Michael Witting,
Janna Hastings & Christoph Kaleta.
Find out how to download the whole set. Work in progress
Will make file available on FTP and will be available in wormmine. Elegans or not?
Slurped in external database (mainly CDT), synched with chebi. One off 5 years ago.
Manually curated. Papers identified.
To ask karen: how did you get the data from these databases?
Is it right that they have been manually curated, Karen?
Write some more stuff.
Can authors send papers?No. Curators? Yes (Wen, large scale gene expression).
Identify papers by journal scanning.
Witting curated about 40 papers – covering all sorts of datasets.
Annotate this with funky arrows and explanations etc. inchi key = international chemical identifier – describe what this is. Standard way to encode molecular information and to facilitate the search for such information in databases and on the webTodo: expand diagram and add it. Overview taken from chebi
Representation of metabolic reactions and pathways. For data analysis it is important to have the link between metabolites, enzymes/proteins and genes and having an overall picture of metabolism. Working towards consensus model (next jamboree) and this model will be deposited somewhere (maybe BiGG – knowledgebase of genome-scale metabolic network reconstructions (bigg.ucsd.edu). Be good if wormbase could take this over.
Student in M’s lab. Will state that these goals have been made in collaboration with the wormjam community.
WBIDs for all metabolites. Student helping in the Witting lab Central place for reference standards – smoother exchange between labs. And not note if the metabolite is commercially available or from a specific lab.
Market place? Knowledgebase? Repository?
Community to work more with chebi.
Exchange with ChEBI already in place. We can liase with chebi. Expand on this (read up on the wormjam list).
I will look at the wiki page you’ve written Karen to get up to speed with the proposed new model changes.
