LABORATORY INFORMATICS
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relevant to the life sciences sector. ChEBI includes information about the function, or role, of the compound in its biological context. Importantly, many external resources link to ChEBI due to its careful curation, the availability of a stable identifier for each entry, and its ontology which can be combined with other ontologies to enable reasoning, Leach suggested. Additionally, EMBL-EBI provides a
resource known as UniChem, which allows scientists to link chemical structures across different databases. This includes external resources that may not be focused on small molecules, but which contain some small-molecule information. This capability relies upon the ability to unambiguously define chemical structures using the International Chemical Identifier (InChI), which resolves the question of whether two compounds represented in different resources are the same molecule. ‘By deriving the InChi, you can be confident that any compound with that InChI, wherever you find it, is the same. It’s a very simple idea but also really quite powerful, which UniChem uses to easily allow users to navigate to data from different resources on the same compound.’ Challenges do still exist with respect to
16 Scientific Computing World Autumn 2021
managing the diversity and volume of data that is being produced in the chemical space, Leach further pointed out. ‘There are new data types being produced using the latest experimental methods, so there is a continual challenge with respect to managing and integrating these different kinds of data.’ So there will always be a need for expert curation, ‘especially when it comes to interpreting information from multiple sources, which can be challenging to interpret or might be ambiguous.’ The small molecule sector can,
nevertheless, perhaps learn from other biological data resources, Leach suggested. ‘The biological community already deposits large volumes of data directly into the relevant databases. The type of data in ChEMBL is much more heterogeneous than (say) DNA sequence data; in addition, it is often generated in individual academic labs, which may not have the necessary informatics systems nor expertise to undertake the necessary processing and validating steps. Nevertheless, it is important for us to continually explore how we might address this challenge and indeed, we continue to work with a number of laboratories who directly deposit data into ChEMBL.’ EMBL-EBI is funded by its member state
governments and other external funders, which include UK Research and Innovation (UKRI) and the UK’s Research Councils, as well as the European Commission, the US National Institutes of Health and the Wellcome Trust. The Wellcome Trust has been the most significant funder of the ChEMBL family of databases, Leach noted. EMBL-EBI is also a key partner in large-
scale collaborative projects, he continued. ‘We are involved in a large public-private collaboration called EUbOPEN, which is funded by the Innovative Medicines Initiative (IMI). This project aims to create a publicly available chemogenomics dataset that will comprise a set of compounds representative of a wide diversity of bioactivities and also to deliver at least 100 open-access chemical probes. The ChEMBL team is also involved in a number of other IMI collaborations, the NIH-funded Illuminating the Druggable Genome project, Open Targets and BioChemGraph, which aims to integrate data from ChEMBL, the Protein Data Bank in Europe, and the Cambridge Structural Database (CSD).
Increasing model reliability Alvascience is a young cheminformatics software company, established three years ago, which offers a suite of desktop
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