The MetaSaurus project, a metabolomics story
Objectives
Build a knowledge model suitable for metabolomic studies based on published ontologies, thesauri and controlled vocabularies
Design a methodology for building a knowledge model for a scientific community from this use case
Exploit and enrich the INRAE thesaurus with concepts from this knowledge model
The MetaSaurus project, which extends over a period of 18 months, therefore proposes to bring together knowledge engineering experts from the INRAE institute and data science experts in the field of metabolomics with the objectives of 1) developing a "pivotal model", adapted to metabolomic studies; 2) selecting methodologies of interest for the construction of "pivotal model(s)" in science; 3) sharing this experience with other scientific communities wishing to engage in a similar approach.
Tasks and agenda
MetaSaurus is an INRAE project, funded by the INRAE-DipSO annual program.
The project is planned to start in June 2022 for a duration of 18 months. The funding obtained to the DipSO will allow the recruitment of two interships in 2023 (one intership on the methodology part in knowledge engineering and one intership on the implementation part of the "pivotal model" in metabolomics as well as part of the funding of the first year seminar (MetaboHUB co-financing).
This project is an opportunity for INRAE Metabolomics community to contribute and enriching The INRAE Thesaurus
Partners
MetaboHUB is the French National Facility in Metabolomics & Fluxomics created in 2013 in the framework of the Program Investment for the Future launched by the French Ministry of Research and Higher Education and the National Agency for Science (ANR). MetaboHUB aims at providing state-of-the-art tools, services and support in metabolomics and fluxomics to academic research teams and industrial partners in the fields of nutrition, health, agriculture and biotechnology.
TRANSFORM, one of the 14 INRAE Research Divisions, aims to position INRAE as a major international player in the circular bioeconomy by focusing its activity on the concepts, technologies and innovations needed to meet the societal and environmental challenges of today and tomorrow. TRANSFORM acts for the development of circular and sustainable systems. Its research is put at the service of the economy of the resources and the reduction of waste. In the food processing field, TRANSFORM develops research on the construction of the multifaceted aspects of food quality.
DipSO is INRAE’s directorate for open science. It contributes to the development and implementation of the institute's open science policy, to opening research and its results and to the evolution of e-infrastructures. DipSO offers a range of services available to help INRAE and its corps of scientists and professionals in their efforts for open and participative science.
CATI PROSODIE promotes, accompanies and enhances the FAIR implementation of data and code management and sharing for the purposes of reuse and reproducibility of science.
Bibliography
Monica Chagoyen, Florencio Pazos, Tools for the functional interpretation of metabolomic experiments, Briefings in Bioinformatics, Volume 14, Issue 6, November 2013, Pages 737–744, 10.1093/bib/bbs055
Alice Cambiaghi, Manuela Ferrario, Marco Masseroli, Analysis of metabolomic data: tools, current strategies and future challenges for omics data integration, Briefings in Bioinformatics, Volume 18, Issue 3, May 2017, Pages 498–510, 10.1093/bib/bbw031
Mélanie Pétéra, Cecile Cabasson, Blandine Comte, Christophe Duperier, Olivier Filangi, et al.. A project-scale map of metadata to improve future data management. Analytics 2022, Sep 2022, Nantes, France. hal-03776494
Atsushi Fukushima, Mikiko Takahashi, Hideki Nagasaki, Yusuke Aono, Makoto Kobayashi, Miyako Kusano, Kazuki Saito, Norio Kobayashi, Masanori Arita, Development of RIKEN Plant Metabolome MetaDatabase, Plant and Cell Physiology, Volume 63, Issue 3, March 2022, Pages 433–440, 10.1093/pcp/pcab173
Sansone, SA., Rocca-Serra, P., Field, D. et al. Toward interoperable bioscience data. Nat Genet 44, 121–126 (2012). 10.1038/ng.1054
ISA Model and Serialization Specifications - https://isa-specs.readthedocs.io
Metabolomics Workbench mwTab file format specification Version 1.5 - mwTab_specification.pdf
Metabolomics Workbench Mwtab’s documentation - https://mwtab.readthedocs.io
Sud, M. et al. Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. Nucleic Acids Res. 44, D463–D470 (2016) 10.1093/nar/gkv1042
MassBank Record Format 2.6.0 – MassBank Consortium (May 13, 2022) - MassBankRecordFormat.md
Semantic Metabolomics from S. Neumann - RDF MassBank Resource Module
Bino, RJ et al. Potential of metabolomics as a functional genomics tool, Trends in Plant Science, Volume 9, Issue 9, 2004, Pages 418-425, ISSN 1360-1385, 10.1016/j.tplants.2004.07.004
Fiehn, O., Robertson, D., Griffin, J. et al. The metabolomics standards initiative (MSI). Metabolomics 3, 175–178 (2007). 10.1007/s11306-007-0070-6
MSI Board Members:. The Metabolomics Standards Initiative. Nat Biotechnol 25, 846–848 (2007). 10.1038/nbt0807-846b
Sumner LW,et al. Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI). Metabolomics. 2007 10.1007/s11306-007-0082-2
Salek, R.M. et al. COordination of Standards in MetabOlomicS (COSMOS): facilitating integrated metabolomics data access. Metabolomics (2015). 10.1007/s11306-015-0810-y
Schober D., et al. NmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data Ana.Chem. (2018) 10.1021/acs.analchem.7b02795
Salek RM, Haug K, Steinbeck C. Dissemination of metabolomics results: role of MetaboLights and COSMOS. Gigascience. (2013) 10.1186/2047-217X-2-8
Goodacre, R. Water, water, every where, but rarely any drop to drink. Metabolomics 10, 5–7 (2014) 10.1007/s11306-013-0618-6
Spicer RA, Salek R, Steinbeck C. A decade after the metabolomics standards initiative it's time for a revision. Sci Data. (2017) 10.1038/sdata.2017.138
Viant, M.R. et al. Use cases, best practice and reporting standards for metabolomics in regulatory toxicology. Nat Commun 10, 3041 (2019) 10.1038/s41467-019-10900-y
The Standard Metabolic Reporting Structures working group. Summary recommendations for standardization and reporting of metabolic analyses. Nat Biotechnol 23, 833–838 (2005) 10.1038/nbt0705-833
Jenkins H, Hardy N, Beckmann M, Draper J, Smith AR, Taylor J, Fiehn O, Goodacre R, Bino RJ, Hall R, Kopka J, Lane GA, Lange BM, Liu JR, Mendes P, Nikolau BJ, Oliver SG, Paton NW, Rhee S, Roessner-Tunali U, Saito K, Smedsgaard J, Sumner LW, Wang T, Walsh S, Wurtele ES, Kell DB. A proposed framework for the description of plant metabolomics experiments and their results. Nat Biotechnol. (2004) 10.1038/nbt1041
Sansone, SA., Schober, D., Atherton, H.J. et al. Metabolomics standards initiative: ontology working group work in progress. Metabolomics 3, 249–256 (2007). 10.1007/s11306-007-0069-z
Buendia P et al. Ontology-based metabolomics data integration with quality control. Bioanalysis. 2019 Jun;11(12):1139-1155. Epub 2019 Jun 10. Erratum in: Bioanalysis. 2020 Feb;12(3):205 10.4155/bio-2018-0303
Jupp S. et al. (2015) A new Ontology Lookup Service at EMBL-EBI. In: Malone, J. et al. (eds.) Proceedings of SWAT4LS International Conference 2015 - www.ebi.ac.uk/ols
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14. 10.1093/nar/gkr469 - bioportal.bioontology.org
Strömert, Philip, Hunold, Johannes, Castro, André, Neumann, Steffen and Koepler, Oliver. "Ontologies4Chem: the landscape of ontologies in chemistry" Pure and Applied Chemistry, vol. 94, no. 6, 2022, pp. 605-622 10.1515/pac-2021-2007
Kenneth Haug, et al, MetaboLights: a resource evolving in response to the needs of its scientific community, Nucleic Acids Research, Volume 48, Issue D1, 08 January 2020, Pages D440–D444, 10.1093/nar/gkz1019