1
|
Kanza S, Willoughby C, Bird CL, Frey JG. eScience Infrastructures in Physical Chemistry. Annu Rev Phys Chem 2021; 73:97-116. [PMID: 34882434 DOI: 10.1146/annurev-physchem-082120-041521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
As the volume of data associated with scientific research has exploded over recent years, the use of digital infrastructures to support this research and the data underpinning it has increased significantly. Physical chemists have been making use of eScience infrastructures since their conception, but in the last five years their usage has increased even more. While these infrastructures have not greatly affected the chemistry itself, they have in some cases had a significant impact on how the research is undertaken. The combination of the human effort of collaboration to create open source software tools and semantic resources, the increased availability of hardware for the laboratories, and the range of data management tools available has made the life of a physical chemist significantly easier. This review considers the different aspects of eScience infrastructures and explores how they have improved the way in which we can conduct physical chemistry research. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 73 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Samantha Kanza
- School of Chemistry, University of Southampton, Southampton, United Kingdom; , , ,
| | - Cerys Willoughby
- School of Chemistry, University of Southampton, Southampton, United Kingdom; , , ,
| | - Colin Leonard Bird
- School of Chemistry, University of Southampton, Southampton, United Kingdom; , , ,
| | - Jeremy Graham Frey
- School of Chemistry, University of Southampton, Southampton, United Kingdom; , , ,
| |
Collapse
|
2
|
Shah SG, Mandloi T, Kunte P, Natu A, Rashid M, Reddy D, Gadewal N, Gupta S. HISTome2: a database of histone proteins, modifiers for multiple organisms and epidrugs. Epigenetics Chromatin 2020; 13:31. [PMID: 32746900 PMCID: PMC7398201 DOI: 10.1186/s13072-020-00354-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/28/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Epigenetics research is progressing in basic, pre-clinical and clinical studies using various model systems. Hence, updating the knowledge and integration of biological data emerging from in silico, in vitro and in vivo studies for different epigenetic factors is essential. Moreover, new drugs are being discovered which target various epigenetic proteins, tested in pre-clinical studies, clinical trials and approved by the FDA. It brings distinct challenges as well as opportunities to update the existing HIstome database for implementing and applying enormous data for biomedical research. RESULTS HISTome2 focuses on the sub-classification of histone proteins as variants and isoforms, post-translational modifications (PTMs) and modifying enzymes for humans (Homo sapiens), rat (Rattus norvegicus) and mouse (Mus musculus) on one interface for integrative analysis. It contains 232, 267 and 350 entries for histone proteins (non-canonical/variants and canonical/isoforms), PTMs and modifying enzymes respectively for human, rat, and mouse. Around 200 EpiDrugs for various classes of epigenetic modifiers, their clinical trial status, and pharmacological relevance have been provided in HISTome2. The additional features like 'Clustal omega' for multiple sequence alignment, link to 'FireBrowse' to visualize TCGA expression data and 'TargetScanHuman' for miRNA targets have been included in the database. CONCLUSION The information for multiple organisms and EpiDrugs on a common platform will accelerate the understanding and future development of drugs. Overall, HISTome2 has significantly increased the extent and diversity of its content which will serve as a 'knowledge Infobase' for biologists, pharmacologists, and clinicians. HISTome2: The HISTone Infobase is freely available on http://www.actrec.gov.in/histome2/ .
Collapse
Affiliation(s)
- Sanket G. Shah
- Epigenetics and Chromatin Biology Group, Gupta Laboratory, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210 India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH 400085 India
| | - Tushar Mandloi
- Bioinformatics Centre, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210 India
| | - Pooja Kunte
- Epigenetics and Chromatin Biology Group, Gupta Laboratory, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210 India
- Present Address: Diabetes Unit, King Edward Memorial Hospital Research Centre, Rasta Peth, Pune, Maharashtra 411 011 India
| | - Abhiram Natu
- Epigenetics and Chromatin Biology Group, Gupta Laboratory, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210 India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH 400085 India
| | - Mudasir Rashid
- Epigenetics and Chromatin Biology Group, Gupta Laboratory, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210 India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH 400085 India
| | - Divya Reddy
- Epigenetics and Chromatin Biology Group, Gupta Laboratory, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210 India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH 400085 India
- Present Address: Stowers Institute for Medical Research, Kansas City, MO 64110 USA
| | - Nikhil Gadewal
- Bioinformatics Centre, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210 India
| | - Sanjay Gupta
- Epigenetics and Chromatin Biology Group, Gupta Laboratory, Cancer Research Institute, Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, MH 410210 India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, MH 400085 India
| |
Collapse
|
4
|
Frey JG, Bird CL. Scientific and technical data sharing: a trading perspective. J Comput Aided Mol Des 2014; 28:989-96. [PMID: 25113779 PMCID: PMC4196031 DOI: 10.1007/s10822-014-9785-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 07/31/2014] [Indexed: 11/29/2022]
Abstract
It is arguably a precept that the open sharing of data maximises the scientific utility of the research that generated that data. Indeed, progress depends on individual scientists being able to build on the results produced by others. The means to facilitate sharing undoubtedly exist, but various studies have identified reluctance among researchers to share information with their peers, at least until the professional priorities of the original researchers have been accommodated. With a view to encouraging less inhibited collaboration, we appraise the processes of data exchange from the perspective of a trading environment and consider how data exchanges might promote (or perhaps hinder) collaboration in data-rich scientific research disciplines and how such an exchange might be set up. We suggest an exchange with trusted brokers (akin to the commodity markets) as a way to overcome the challenges of the current environment. We conclude by encouraging the scientific and technical community to debate the merits of a trading perspective on data sharing and exchange.
Collapse
Affiliation(s)
- Jeremy G Frey
- Chemistry, University of Southampton, Southampton, SO17 1BJ, UK,
| | | |
Collapse
|
5
|
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
|
6
|
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
|