1
|
Kondinski A, Bai J, Mosbach S, Akroyd J, Kraft M. Knowledge Engineering in Chemistry: From Expert Systems to Agents of Creation. Acc Chem Res 2022; 56:128-139. [PMID: 36516456 PMCID: PMC9850921 DOI: 10.1021/acs.accounts.2c00617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Passing knowledge from human to human is a natural process that has continued since the beginning of humankind. Over the past few decades, we have witnessed that knowledge is no longer passed only between humans but also from humans to machines. The latter form of knowledge transfer represents a cornerstone in artificial intelligence (AI) and lays the foundation for knowledge engineering (KE). In order to pass knowledge to machines, humans need to structure, formalize, and make knowledge machine-readable. Subsequently, humans also need to develop software that emulates their decision-making process. In order to engineer chemical knowledge, chemists are often required to challenge their understanding of chemistry and thinking processes, which may help improve the structure of chemical knowledge.Knowledge engineering in chemistry dates from the development of expert systems that emulated the thinking process of analytical and organic chemists. Since then, many different expert systems employing rather limited knowledge bases have been developed, solving problems in retrosynthesis, analytical chemistry, chemical risk assessment, etc. However, toward the end of the 20th century, the AI winters slowed down the development of expert systems for chemistry. At the same time, the increasing complexity of chemical research, alongside the limitations of the available computing tools, made it difficult for many chemistry expert systems to keep pace.In the past two decades, the semantic web, the popularization of object-oriented programming, and the increase in computational power have revitalized knowledge engineering. Knowledge formalization through ontologies has become commonplace, triggering the subsequent development of knowledge graphs and cognitive software agents. These tools enable the possibility of interoperability, enabling the representation of more complex systems, inference capabilities, and the synthesis of new knowledge.This Account introduces the history, the core principles of KE, and its applications within the broad realm of chemical research and engineering. In this regard, we first discuss how chemical knowledge is formalized and how a chemist's cognition can be emulated with the help of reasoning algorithms. Following this, we discuss various applications of knowledge graph and agent technology used to solve problems in chemistry related to molecular engineering, chemical mechanisms, multiscale modeling, automation of calculations and experiments, and chemist-machine interactions. These developments are discussed in the context of a universal and dynamic knowledge ecosystem, referred to as The World Avatar (TWA).
Collapse
Affiliation(s)
- Aleksandar Kondinski
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Jiaru Bai
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.
| | - Sebastian Mosbach
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.,CARES,
Cambridge Centre for Advanced Research and Education in Singapore, 1 Create Way, CREATE Tower, #05-05, 138602 Singapore
| | - Jethro Akroyd
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.,CMCL
Innovations, Sheraton
House, Castle Park, Cambridge CB3 0AX, U.K.
| | - Markus Kraft
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K.,CARES,
Cambridge Centre for Advanced Research and Education in Singapore, 1 Create Way, CREATE Tower, #05-05, 138602 Singapore,School
of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459 Singapore,E-mail:
| |
Collapse
|
2
|
Mosbach S, Menon A, Farazi F, Krdzavac N, Zhou X, Akroyd J, Kraft M. Multiscale Cross-Domain Thermochemical Knowledge-Graph. J Chem Inf Model 2020; 60:6155-6166. [PMID: 33242243 DOI: 10.1021/acs.jcim.0c01145] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In this paper, we develop a set of software agents which improve a knowledge-graph containing thermodynamic data of chemical species by means of quantum chemical calculations and error-canceling balanced reactions. The knowledge-graph represents species-associated information by making use of the principles of linked data, as employed in the Semantic Web, where concepts correspond to vertices and relationships between the concepts correspond to edges of the graph. We implement this representation by means of ontologies, which formalize the definition of concepts and their relationships, as a critical step to achieve interoperability between heterogeneous data formats and software. The agents, which conduct quantum chemical calculations and derive the estimates of standard enthalpies of formation, update the knowledge-graph with newly obtained results, improving data values, and adding nodes and connections between them. A key distinguishing feature of our approach is that it extends an existing, general-purpose knowledge-graph, called J-Park Simulator (http://theworldavatar.com), and its ecosystem of autonomous agents, thus enabling seamless cross-domain applications in wider contexts. To this end, we demonstrate how quantum calculations can directly affect the atmospheric dispersion of pollutants in an industrial emission use-case.
Collapse
Affiliation(s)
- Sebastian Mosbach
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom.,Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower #05-05, 1 Create Way, Singapore, 138602
| | - Angiras Menon
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Feroz Farazi
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Nenad Krdzavac
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower #05-05, 1 Create Way, Singapore, 138602
| | - Xiaochi Zhou
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Jethro Akroyd
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom.,Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower #05-05, 1 Create Way, Singapore, 138602
| | - Markus Kraft
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom.,Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower #05-05, 1 Create Way, Singapore, 138602.,School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore, 637459
| |
Collapse
|
3
|
Farazi F, Salamanca M, Mosbach S, Akroyd J, Eibeck A, Aditya LK, Chadzynski A, Pan K, Zhou X, Zhang S, Lim MQ, Kraft M. Knowledge Graph Approach to Combustion Chemistry and Interoperability. ACS OMEGA 2020; 5:18342-18348. [PMID: 32743209 PMCID: PMC7391961 DOI: 10.1021/acsomega.0c02055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
In this paper, we demonstrate through examples how the concept of a Semantic Web based knowledge graph can be used to integrate combustion modeling into cross-disciplinary applications and in particular how inconsistency issues in chemical mechanisms can be addressed. We discuss the advantages of linked data that form the essence of a knowledge graph and how we implement this in a number of interconnected ontologies, specifically in the context of combustion chemistry. Central to this is OntoKin, an ontology we have developed for capturing both the content and the semantics of chemical kinetic reaction mechanisms. OntoKin is used to represent the example mechanisms from the literature in a knowledge graph, which itself is part of the existing, more general knowledge graph and ecosystem of autonomous software agents that are acting on it. We describe a web interface, which allows users to interact with the system, upload and compare the existing mechanisms, and query species and reactions across the knowledge graph. The utility of the knowledge-graph approach is demonstrated for two use-cases: querying across multiple mechanisms from the literature and modeling the atmospheric dispersion of pollutants emitted by ships. As part of the query use-case, our ontological tools are applied to identify variations in the rate of a hydrogen abstraction reaction from methane as represented by 10 different mechanisms.
Collapse
Affiliation(s)
- Feroz Farazi
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Maurin Salamanca
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Cambridge
Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
| | - Sebastian Mosbach
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Cambridge
Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
| | - Jethro Akroyd
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Cambridge
Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
| | - Andreas Eibeck
- Cambridge
Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
| | - Leonardus Kevin Aditya
- School
of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459
| | - Arkadiusz Chadzynski
- Cambridge
Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
| | - Kang Pan
- Cambridge
Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
| | - Xiaochi Zhou
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - Shaocong Zhang
- Cambridge
Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
| | - Mei Qi Lim
- Cambridge
Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
| | - Markus Kraft
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
- Cambridge
Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, Singapore 138602
- School
of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, Singapore 637459
| |
Collapse
|
4
|
Farazi F, Akroyd J, Mosbach S, Buerger P, Nurkowski D, Salamanca M, Kraft M. OntoKin: An Ontology for Chemical Kinetic Reaction Mechanisms. J Chem Inf Model 2019; 60:108-120. [DOI: 10.1021/acs.jcim.9b00960] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Feroz Farazi
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Jethro Akroyd
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, 138602, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore
| | - Sebastian Mosbach
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, 138602, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore
| | - Philipp Buerger
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
| | - Daniel Nurkowski
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore
| | - Maurin Salamanca
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, 138602, Singapore
| | - Markus Kraft
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcett Drive, Cambridge CB3 0AS, U.K
- Cambridge Centre for Advanced Research and Education in Singapore (CARES), CREATE Tower, 1 Create Way, 138602, Singapore
- CMCL Innovations, Sheraton House, Castle Park, Castle Street, Cambridge CB3 0AX, U.K
- School of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore
| |
Collapse
|
5
|
|
6
|
Krallinger M, Rabal O, Lourenço A, Oyarzabal J, Valencia A. Information Retrieval and Text Mining Technologies for Chemistry. Chem Rev 2017; 117:7673-7761. [PMID: 28475312 DOI: 10.1021/acs.chemrev.6b00851] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Efficient access to chemical information contained in scientific literature, patents, technical reports, or the web is a pressing need shared by researchers and patent attorneys from different chemical disciplines. Retrieval of important chemical information in most cases starts with finding relevant documents for a particular chemical compound or family. Targeted retrieval of chemical documents is closely connected to the automatic recognition of chemical entities in the text, which commonly involves the extraction of the entire list of chemicals mentioned in a document, including any associated information. In this Review, we provide a comprehensive and in-depth description of fundamental concepts, technical implementations, and current technologies for meeting these information demands. A strong focus is placed on community challenges addressing systems performance, more particularly CHEMDNER and CHEMDNER patents tasks of BioCreative IV and V, respectively. Considering the growing interest in the construction of automatically annotated chemical knowledge bases that integrate chemical information and biological data, cheminformatics approaches for mapping the extracted chemical names into chemical structures and their subsequent annotation together with text mining applications for linking chemistry with biological information are also presented. Finally, future trends and current challenges are highlighted as a roadmap proposal for research in this emerging field.
Collapse
Affiliation(s)
- Martin Krallinger
- Structural Computational Biology Group, Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre , C/Melchor Fernández Almagro 3, Madrid E-28029, Spain
| | - Obdulia Rabal
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra , Avenida Pio XII 55, Pamplona E-31008, Spain
| | - Anália Lourenço
- ESEI - Department of Computer Science, University of Vigo , Edificio Politécnico, Campus Universitario As Lagoas s/n, Ourense E-32004, Spain.,Centro de Investigaciones Biomédicas (Centro Singular de Investigación de Galicia) , Campus Universitario Lagoas-Marcosende, Vigo E-36310, Spain.,CEB-Centre of Biological Engineering, University of Minho , Campus de Gualtar, Braga 4710-057, Portugal
| | - Julen Oyarzabal
- Small Molecule Discovery Platform, Molecular Therapeutics Program, Center for Applied Medical Research (CIMA), University of Navarra , Avenida Pio XII 55, Pamplona E-31008, Spain
| | - Alfonso Valencia
- Life Science Department, Barcelona Supercomputing Centre (BSC-CNS) , C/Jordi Girona, 29-31, Barcelona E-08034, Spain.,Joint BSC-IRB-CRG Program in Computational Biology, Parc Científic de Barcelona , C/ Baldiri Reixac 10, Barcelona E-08028, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig de Lluís Companys 23, Barcelona E-08010, Spain
| |
Collapse
|
7
|
Bird C, Coles SJ, Frey JG. The Evolution of Digital Chemistry at Southampton. Mol Inform 2016; 34:585-97. [PMID: 27490710 DOI: 10.1002/minf.201500008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/16/2015] [Indexed: 11/06/2022]
Abstract
In this paper we take a historical view of e-Science and e-Research developments within the Chemical Sciences at the University of Southampton, showing the development of several stages of the evolving data ecosystem as Chemistry moves into the digital age of the 21(st) Century. We cover our research on aspects of the representation of chemical information in the context of the world wide web (WWW) and its semantic enhancement (the Semantic Web) and illustrate this with the example of the representation of quantities and units within the Semantic Web. We explore the changing nature of laboratories as computing power becomes increasing powerful and pervasive and specifically look at the function and role of electronic or digital notebooks. Having focussed on the creation of chemical data and information in context, we finish the paper by following the use and reuse of this data as facilitated by the features provided by digital repositories and their importance in facilitating the exchange of chemical information touching on the issues of open and or intelligent access to the data.
Collapse
Affiliation(s)
- Colin Bird
- Chemistry, University of Southampton, University of Southampton, Highfield, Southampton, SO17 1BJ, UK phone: +44 (0)2380593209
| | - Simon J Coles
- Chemistry, University of Southampton, University of Southampton, Highfield, Southampton, SO17 1BJ, UK phone: +44 (0)2380593209
| | - Jeremy G Frey
- Chemistry, University of Southampton, University of Southampton, Highfield, Southampton, SO17 1BJ, UK phone: +44 (0)2380593209.
| |
Collapse
|
8
|
Warr WA. Many InChIs and quite some feat. J Comput Aided Mol Des 2015; 29:681-94. [PMID: 26081259 DOI: 10.1007/s10822-015-9854-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 06/10/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Wendy A Warr
- Wendy Warr & Associates, Holmes Chapel, Crewe, Cheshire, CW4 7HZ, UK,
| |
Collapse
|
9
|
Bird CL, Frey JG. Chemical information matters: an e-Research perspective on information and data sharing in the chemical sciences. Chem Soc Rev 2014; 42:6754-76. [PMID: 23686012 DOI: 10.1039/c3cs60050e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Recently, a number of organisations have called for open access to scientific information and especially to the data obtained from publicly funded research, among which the Royal Society report and the European Commission press release are particularly notable. It has long been accepted that building research on the foundations laid by other scientists is both effective and efficient. Regrettably, some disciplines, chemistry being one, have been slow to recognise the value of sharing and have thus been reluctant to curate their data and information in preparation for exchanging it. The very significant increases in both the volume and the complexity of the datasets produced has encouraged the expansion of e-Research, and stimulated the development of methodologies for managing, organising, and analysing "big data". We review the evolution of cheminformatics, the amalgam of chemistry, computer science, and information technology, and assess the wider e-Science and e-Research perspective. Chemical information does matter, as do matters of communicating data and collaborating with data. For chemistry, unique identifiers, structure representations, and property descriptors are essential to the activities of sharing and exchange. Open science entails the sharing of more than mere facts: for example, the publication of negative outcomes can facilitate better understanding of which synthetic routes to choose, an aspiration of the Dial-a-Molecule Grand Challenge. The protagonists of open notebook science go even further and exchange their thoughts and plans. We consider the concepts of preservation, curation, provenance, discovery, and access in the context of the research lifecycle, and then focus on the role of metadata, particularly the ontologies on which the emerging chemical Semantic Web will depend. Among our conclusions, we present our choice of the "grand challenges" for the preservation and sharing of chemical information.
Collapse
Affiliation(s)
- Colin L Bird
- Chemistry, Faculty of Natural and Environmental Sciences, University of Southampton, University Road, Highfield, Southampton SO17 1BJ, UK
| | | |
Collapse
|
10
|
Milsted AJ, Hale JR, Frey JG, Neylon C. LabTrove: a lightweight, web based, laboratory "blog" as a route towards a marked up record of work in a bioscience research laboratory. PLoS One 2013; 8:e67460. [PMID: 23935832 PMCID: PMC3720848 DOI: 10.1371/journal.pone.0067460] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 05/17/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The electronic laboratory notebook (ELN) has the potential to replace the paper notebook with a marked-up digital record that can be searched and shared. However, it is a challenge to achieve these benefits without losing the usability and flexibility of traditional paper notebooks. We investigate a blog-based platform that addresses the issues associated with the development of a flexible system for recording scientific research. METHODOLOGY/PRINCIPAL FINDINGS We chose a blog-based approach with the journal characteristics of traditional notebooks in mind, recognizing the potential for linking together procedures, materials, samples, observations, data, and analysis reports. We implemented the LabTrove blog system as a server process written in PHP, using a MySQL database to persist posts and other research objects. We incorporated a metadata framework that is both extensible and flexible while promoting consistency and structure where appropriate. Our experience thus far is that LabTrove is capable of providing a successful electronic laboratory recording system. CONCLUSIONS/SIGNIFICANCE LabTrove implements a one-item one-post system, which enables us to uniquely identify each element of the research record, such as data, samples, and protocols. This unique association between a post and a research element affords advantages for monitoring the use of materials and samples and for inspecting research processes. The combination of the one-item one-post system, consistent metadata, and full-text search provides us with a much more effective record than a paper notebook. The LabTrove approach provides a route towards reconciling the tensions and challenges that lie ahead in working towards the long-term goals for ELNs. LabTrove, an electronic laboratory notebook (ELN) system from the Smart Research Framework, based on a blog-type framework with full access control, facilitates the scientific experimental recording requirements for reproducibility, reuse, repurposing, and redeployment.
Collapse
Affiliation(s)
- Andrew J. Milsted
- Department of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Jennifer R. Hale
- Department of Chemistry, University of Southampton, Southampton, United Kingdom
| | - Jeremy G. Frey
- Department of Chemistry, University of Southampton, Southampton, United Kingdom
- * E-mail:
| | - Cameron Neylon
- ISIS Neutron Facility, Science and Technology Facilities Council Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot, United Kingdom
| |
Collapse
|
11
|
Frey JG, Bird CL. Cheminformatics and the Semantic Web: adding value with linked data and enhanced provenance. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013; 3:465-481. [PMID: 24432050 PMCID: PMC3884755 DOI: 10.1002/wcms.1127] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 01/08/2013] [Indexed: 12/16/2022]
Abstract
Cheminformatics is evolving from being a field of study associated primarily with drug discovery into a discipline that embraces the distribution, management, access, and sharing of chemical data. The relationship with the related subject of bioinformatics is becoming stronger and better defined, owing to the influence of Semantic Web technologies, which enable researchers to integrate heterogeneous sources of chemical, biochemical, biological, and medical information. These developments depend on a range of factors: the principles of chemical identifiers and their role in relationships between chemical and biological entities; the importance of preserving provenance and properly curated metadata; and an understanding of the contribution that the Semantic Web can make at all stages of the research lifecycle. The movements toward open access, open source, and open collaboration all contribute to progress toward the goals of integration.
Collapse
Affiliation(s)
- Jeremy G Frey
- Chemistry, Faculty of Natural Environmental Science, University of Southampton Highfield, Southampton, SO17 1BJ, UK
| | - Colin L Bird
- Chemistry, Faculty of Natural Environmental Science, University of Southampton Highfield, Southampton, SO17 1BJ, UK
| |
Collapse
|
12
|
Kruger FA, Overington JP. Global analysis of small molecule binding to related protein targets. PLoS Comput Biol 2012; 8:e1002333. [PMID: 22253582 PMCID: PMC3257267 DOI: 10.1371/journal.pcbi.1002333] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 11/16/2011] [Indexed: 11/29/2022] Open
Abstract
We report on the integration of pharmacological data and homology information for a large scale analysis of small molecule binding to related targets. Differences in small molecule binding have been assessed for curated pairs of human to rat orthologs and also for recently diverged human paralogs. Our analysis shows that in general, small molecule binding is conserved for pairs of human to rat orthologs. Using statistical tests, we identified a small number of cases where small molecule binding is different between human and rat, some of which had previously been reported in the literature. Knowledge of species specific pharmacology can be advantageous for drug discovery, where rats are frequently used as a model system. For human paralogs, we demonstrate a global correlation between sequence identity and the binding of small molecules with equivalent affinity. Our findings provide an initial general model relating small molecule binding and sequence divergence, containing the foundations for a general model to anticipate and predict within-target-family selectivity. Many drugs are small molecules that specifically bind to proteins involved in disease related processes. In this way, drugs modulate the function of a targeted protein and ultimately the process causing the disease. The development of drugs crucially relies on assays that measure the potency of the effect a small molecule exerts on its protein target. We compared the potencies of small molecules measured for human proteins and the corresponding (orthologous) protein in rat. Our results suggest that, after subtraction of statistical noise, most human proteins are equally susceptible to small molecule binding as their orthologs in rats. However, we identified a small number of exceptions to this rule, for example the histamine H3 receptor, a protein of the central nervous system. We also compared the potency of small molecules measured against a human protein and another member of the same protein family. In drug development it is often desired to target a protein selectively over other related proteins. The observed differences were generally greater than the statistical noise, indicating that most of the small molecules in our study have some degree of selectivity within protein families.
Collapse
|
13
|
Hastings J, Chepelev L, Willighagen E, Adams N, Steinbeck C, Dumontier M. The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web. PLoS One 2011; 6:e25513. [PMID: 21991315 PMCID: PMC3184996 DOI: 10.1371/journal.pone.0025513] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 09/07/2011] [Indexed: 11/19/2022] Open
Abstract
Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA).
Collapse
Affiliation(s)
- Janna Hastings
- Chemoinformatics and Metabolism, European Bioinformatics Institute, Hinxton, United Kingdom.
| | | | | | | | | | | |
Collapse
|
14
|
De Roure D, Page KR, Fields B, Crawford T, Downie JS, Fujinaga I. An e-Research approach to Web-scale music analysis. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2011; 369:3300-3317. [PMID: 21768141 DOI: 10.1098/rsta.2011.0171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The growing quantity of digital recorded music available in large-scale resources such as the Internet archive provides an important new resource for musical analysis. An e-Research approach has been adopted in order to create a very substantive web-accessible corpus of musical analyses in a common framework for use by music scholars, students and beyond, and to establish a methodology and tooling that will enable others to add to the resource in the future. The enabling infrastructure brings together scientific workflow and Semantic Web technologies with a set of algorithms and tools for extracting features from recorded music. It has been used to deliver a prototype system, described here, that demonstrates the utility of LINKED DATA for enhancing the curation of collections of music signal data for analysis and publishing results that can be simply and readily correlated to these and other sources. This paper describes the motivation, infrastructure design and the proof-of-concept case study and reflects on emerging e-Research practice as researchers embrace the scale of the Web.
Collapse
Affiliation(s)
- David De Roure
- Oxford e-Research Centre, University of Oxford, Oxford, UK.
| | | | | | | | | | | |
Collapse
|
15
|
Schuffenhauer A, Varin T. Rule-Based Classification of Chemical Structures by Scaffold. Mol Inform 2011; 30:646-64. [PMID: 27467257 DOI: 10.1002/minf.201100078] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2011] [Accepted: 07/14/2011] [Indexed: 01/25/2023]
Abstract
Databases for small organic chemical molecules usually contain millions of structures. The screening decks of pharmaceutical companies contain more than a million of structures. Nevertheless chemical substructure searching in these databases can be performed interactively in seconds. Because of this nobody has really missed structural classification of these databases for the purpose of finding data for individual chemical substructures. However, a full deck high-throughput screen produces also activity data for more than a million of substances. How can this amount of data be analyzed? Which are the active scaffolds identified by an assays? To answer such questions systematic classifications of molecules by scaffolds are needed. In this review it is described how molecules can be hierarchically classified by their scaffolds. It is explained how such classifications can be used to identify active scaffolds in an HTS data set. Once active classes are identified, they need to be visualized in the context of related scaffolds in order to understand SAR. Consequently such visualizations are another topic of this review. In addition scaffold based diversity measures are discussed and an outlook is given about the potential impact of structural classifications on a chemically aware semantic web.
Collapse
Affiliation(s)
- Ansgar Schuffenhauer
- Novartis Institutes for BioMedical Research, CPC/LFP, WSJ-88.11.11, Postfach, Basel, Switzerland, CH-4002; phone:+41 61 32 45385.
| | - Thibault Varin
- Novartis Institutes for BioMedical Research, CPC/LFP, WSJ-88.11.11, Postfach, Basel, Switzerland, CH-4002; phone:+41 61 32 45385
| |
Collapse
|
16
|
Shirley R, Phadungsukanan W, Kraft M, Downing J, Day NE, Murray-Rust P. First-principles thermochemistry for gas phase species in an industrial rutile chlorinator. J Phys Chem A 2011; 114:11825-32. [PMID: 20923209 DOI: 10.1021/jp106795p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work presents thermochemical data for possible gas phase intermediate species in an industrial rutile chlorinator. An algorithm developed for previous work is employed to ensure that all possible species are considered, reducing the number of important species neglected. Thermochemical data and enthalpies of formation are calculated for 22 new species using density functional theory, post Hartree-Fock coupled cluster calculations, and statistical mechanics. Equilibrium calculations are performed to identify whether any Ti/C intermediates are likely to be important to the high temperature industrial process. These new species are not present at high concentration in the exit stream. It is therefore likely that the two chemical processes do not interact. Rather, the Cl₂ rapidly reacts with the solid TiO₂ to form TiCl₄ and O₂. The latter then reacts with the solid C to form CO and CO₂ and provide the heat. Data for all the new species is provided as Supporting Information. Finally, a new methodology for data collaboration is investigated in which the data is made openly accessible using the resource description framework. Example scripts are provided to demonstrate how to query and retrieve the data automatically.
Collapse
Affiliation(s)
- Raphael Shirley
- Department of Chemical Engineering and Biotechnology, University of Cambridge, New Museums Site, Cambridge, United Kingdom
| | | | | | | | | | | |
Collapse
|
17
|
|
18
|
Abstract
This introductory chapter gives a brief overview of the history of cheminformatics, and then summarizes some recent trends in computing, cultures, open systems, chemical structure representation, docking, de novo design, fragment-based drug design, molecular similarity, quantitative structure-activity relationships (QSAR), metabolite prediction, the use of phamacophores in drug discovery, data reduction and visualization, and text mining. The aim is to set the scene for the more detailed exposition of these topics in the later chapters.
Collapse
Affiliation(s)
- Wendy A Warr
- Wendy Warr & Associates, Holmes Chapel, Cheshire, UK
| |
Collapse
|
19
|
Chebotko A, Lu S, Fei X, Fotouhi F. RDFProv: A relational RDF store for querying and managing scientific workflow provenance. DATA KNOWL ENG 2010. [DOI: 10.1016/j.datak.2010.03.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
20
|
Choi J, Davis MJ, Newman AF, Ragan MA. A Semantic Web Ontology for Small Molecules and Their Biological Targets. J Chem Inf Model 2010; 50:732-41. [DOI: 10.1021/ci900461j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- JooYoung Choi
- Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia, and Queensland Facility for Advanced Bioinformatics, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia
| | - Melissa J. Davis
- Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia, and Queensland Facility for Advanced Bioinformatics, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia
| | - Andrew F. Newman
- Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia, and Queensland Facility for Advanced Bioinformatics, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia
| | - Mark A. Ragan
- Institute for Molecular Bioscience and ARC Centre of Excellence in Bioinformatics, The University of Queensland, Brisbane, QLD 4072, Australia, and Queensland Facility for Advanced Bioinformatics, Queensland Bioscience Precinct, Brisbane, QLD 4072, Australia
| |
Collapse
|
21
|
Downing J, Harvey MJ, Morgan PB, Murray-Rust P, Rzepa HS, Stewart DC, Tonge AP, Townsend JA. SPECTRa-T: Machine-Based Data Extraction and Semantic Searching of Chemistry e-Theses. J Chem Inf Model 2010; 50:251-61. [DOI: 10.1021/ci9003688] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jim Downing
- Unilever Centre for Molecular Informatics, Department of Chemistry, Lensfield Rd., Cambridge CB2 1EW, U.K., Cambridge University Library, West Rd., Cambridge CB3 9DR, U.K., and Department of Chemistry and High Performance Computing Unit, ICT, Imperial College London, Exhibition Rd., London SW7 2AZ, U.K
| | - Matt J. Harvey
- Unilever Centre for Molecular Informatics, Department of Chemistry, Lensfield Rd., Cambridge CB2 1EW, U.K., Cambridge University Library, West Rd., Cambridge CB3 9DR, U.K., and Department of Chemistry and High Performance Computing Unit, ICT, Imperial College London, Exhibition Rd., London SW7 2AZ, U.K
| | - Peter B. Morgan
- Unilever Centre for Molecular Informatics, Department of Chemistry, Lensfield Rd., Cambridge CB2 1EW, U.K., Cambridge University Library, West Rd., Cambridge CB3 9DR, U.K., and Department of Chemistry and High Performance Computing Unit, ICT, Imperial College London, Exhibition Rd., London SW7 2AZ, U.K
| | - Peter Murray-Rust
- Unilever Centre for Molecular Informatics, Department of Chemistry, Lensfield Rd., Cambridge CB2 1EW, U.K., Cambridge University Library, West Rd., Cambridge CB3 9DR, U.K., and Department of Chemistry and High Performance Computing Unit, ICT, Imperial College London, Exhibition Rd., London SW7 2AZ, U.K
| | - Henry S. Rzepa
- Unilever Centre for Molecular Informatics, Department of Chemistry, Lensfield Rd., Cambridge CB2 1EW, U.K., Cambridge University Library, West Rd., Cambridge CB3 9DR, U.K., and Department of Chemistry and High Performance Computing Unit, ICT, Imperial College London, Exhibition Rd., London SW7 2AZ, U.K
| | - Diana C. Stewart
- Unilever Centre for Molecular Informatics, Department of Chemistry, Lensfield Rd., Cambridge CB2 1EW, U.K., Cambridge University Library, West Rd., Cambridge CB3 9DR, U.K., and Department of Chemistry and High Performance Computing Unit, ICT, Imperial College London, Exhibition Rd., London SW7 2AZ, U.K
| | - Alan P. Tonge
- Unilever Centre for Molecular Informatics, Department of Chemistry, Lensfield Rd., Cambridge CB2 1EW, U.K., Cambridge University Library, West Rd., Cambridge CB3 9DR, U.K., and Department of Chemistry and High Performance Computing Unit, ICT, Imperial College London, Exhibition Rd., London SW7 2AZ, U.K
| | - Joe A. Townsend
- Unilever Centre for Molecular Informatics, Department of Chemistry, Lensfield Rd., Cambridge CB2 1EW, U.K., Cambridge University Library, West Rd., Cambridge CB3 9DR, U.K., and Department of Chemistry and High Performance Computing Unit, ICT, Imperial College London, Exhibition Rd., London SW7 2AZ, U.K
| |
Collapse
|
22
|
Fey N. The contribution of computational studies to organometallic catalysis: descriptors, mechanisms and models. Dalton Trans 2010:296-310. [DOI: 10.1039/b913356a] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
23
|
Frey JG. The value of the Semantic Web in the laboratory. Drug Discov Today 2009; 14:552-61. [DOI: 10.1016/j.drudis.2009.03.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2008] [Revised: 02/01/2009] [Accepted: 03/03/2009] [Indexed: 11/28/2022]
|
24
|
Adams N, Winter J, Murray-Rust P, Rzepa HS. Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language. J Chem Inf Model 2008; 48:2118-28. [DOI: 10.1021/ci8002123] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nico Adams
- Unilever Centre for Molecular Science Informatics, University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, Unilever HPC R&D Port Sunlight, Physical and Chemical Insights Group, Quarry Road East, Bebington, Wirral, CH63 3 JW, United Kingdom, Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
| | - Jerry Winter
- Unilever Centre for Molecular Science Informatics, University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, Unilever HPC R&D Port Sunlight, Physical and Chemical Insights Group, Quarry Road East, Bebington, Wirral, CH63 3 JW, United Kingdom, Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
| | - Peter Murray-Rust
- Unilever Centre for Molecular Science Informatics, University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, Unilever HPC R&D Port Sunlight, Physical and Chemical Insights Group, Quarry Road East, Bebington, Wirral, CH63 3 JW, United Kingdom, Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
| | - Henry S. Rzepa
- Unilever Centre for Molecular Science Informatics, University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom, Unilever HPC R&D Port Sunlight, Physical and Chemical Insights Group, Quarry Road East, Bebington, Wirral, CH63 3 JW, United Kingdom, Department of Chemistry, Imperial College London, SW7 2AZ, United Kingdom
| |
Collapse
|
25
|
Kell DB, Mendes P. The markup is the model: Reasoning about systems biology models in the Semantic Web era. J Theor Biol 2008; 252:538-43. [DOI: 10.1016/j.jtbi.2007.10.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2007] [Revised: 10/19/2007] [Accepted: 10/22/2007] [Indexed: 01/09/2023]
|
26
|
Sankar P, Aghila G. Ontology aided modeling of organic reaction mechanisms with flexible and fragment based XML markup procedures. J Chem Inf Model 2007; 47:1747-62. [PMID: 17705463 DOI: 10.1021/ci700043u] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism models for primary organic reactions encoding the structural fragments undergoing substitution, addition, elimination, and rearrangements are developed. In the proposed models, each and every structural component of mechanistic pathways is represented with flexible and fragment based markup technique in XML syntax. A significant feature of the system is the encoding of the electron movements along with the other components like charges, partial charges, half bonded species, lone pair electrons, free radicals, reaction arrows, etc. needed for a complete representation of reaction mechanism. The rendering of reaction schemes described with the proposed methodology is achieved with a concise XML extension language interoperating with the structure markup. The reaction scheme is visualized as 2D graphics in a browser by converting them into SVG documents enabling the desired layouts normally perceived by the chemists conventionally. An automatic representation of the complex patterns of the reaction mechanism is achieved by reusing the knowledge in chemical ontologies and developing artificial intelligence components in terms of axioms.
Collapse
Affiliation(s)
- Punnaivanam Sankar
- Department of Chemistry and Computer Science & Engineering and Information Technology, Pondicherry Engineering College, Puducherry - 605 014, India
| | | |
Collapse
|
27
|
Casher O, Rzepa HS. SemanticEye: A Semantic Web Application to Rationalize and Enhance Chemical Electronic Publishing. J Chem Inf Model 2006; 46:2396-411. [PMID: 17125182 DOI: 10.1021/ci060139e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
SemanticEye, an ontology with associated tools, improves the classification and open accessibility of chemical information in electronic publishing. In a manner analogous to digital music management, RDF metadata encoded as Adobe XMP can be extracted from a variety of document formats, such as PDF, and managed in an RDF repository called Sesame. Users upload electronic documents containing XMP to a central server by "dropping" them into WebDAV folders. The documents can then be navigated in a Web browser via their metadata, and multiple documents containing identical metadata can then be aggregated. SemanticEye does not actually store any documents. By including unique identifiers within the XMP, such as the DOI, associated documents can be retrieved from the Web with the help of resolving agents. The power of this metadata driven approach is illustrated by including, within the XMP, InChI identifiers for molecular structures and finding relationships between articles based on their InChIs. SemanticEye will become increasingly more comprehensive as usage becomes more widespread. Furthermore, following the Semantic Web architecture enables the reuse of open software tools, provides a "semantically intuitive" alternative to search engines, and fosters a greater sense of trust in Web-based scientific information.
Collapse
Affiliation(s)
- Omer Casher
- Clinical Imaging Centre, GlaxoSmithKline, Harlow CM19 5AW, UK
| | | |
Collapse
|
28
|
Kell DB. Systems biology, metabolic modelling and metabolomics in drug discovery and development. Drug Discov Today 2006; 11:1085-92. [PMID: 17129827 DOI: 10.1016/j.drudis.2006.10.004] [Citation(s) in RCA: 219] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2006] [Revised: 09/25/2006] [Accepted: 10/09/2006] [Indexed: 01/03/2023]
Abstract
Unlike signalling pathways, metabolic networks are subject to strict stoichiometric constraints. Metabolomics amplifies changes in the proteome, and represents more closely the phenotype of an organism. Recent advances enable the production (and computer-readable encoding as SBML) of metabolic network models reconstructed from genome sequences, as well as experimental measurements of much of the metabolome. There is increasing convergence between the number of human metabolites estimated via genomics ( approximately 3000) and the number measured experimentally. It is thus both timely, and now possible, to bring these two approaches together as an integrated (if distributed) whole to help understand the genesis of metabolic biomarkers, the progress of disease, and the modes of action, efficacy, off-target effects and toxicity of pharmaceutical drugs.
Collapse
Affiliation(s)
- Douglas B Kell
- School of Chemistry, Faraday Building, The University of Manchester. PO Box 88, Manchester, M60 1QD, UK.
| |
Collapse
|
29
|
CombeChem: A Case Study in Provenance and Annotation Using the Semantic Web. PROVENANCE AND ANNOTATION OF DATA 2006. [DOI: 10.1007/11890850_27] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|