Challenges of Connecting Chemistry to Pharmacology: Perspectives from Curating the IUPHAR/BPS Guide to PHARMACOLOGY

Connecting chemistry to pharmacology (c2p) has been an objective of GtoPdb and its precursor IUPHAR-DB since 2003. This has been achieved by populating our database with expert-curated relationships between documents, assays, quantitative results, chemical structures, their locations within the documents and the protein targets in the assays (D-A-R-C-P). A wide range of challenges associated with this are described in this perspective, using illustrative examples from GtoPdb entries. Our selection process begins with judgements of pharmacological relevance and scientific quality. Even though we have a stringent focus for our small-data extraction we note that assessing the quality of papers has become more difficult over the last 15 years. We discuss ambiguity issues with the resolution of authors’ descriptions of A-R-C-P entities to standardised identifiers. We also describe developments that have made this somewhat easier over the same period both in the publication ecosystem as well as enhancements of our internal processes over recent years. This perspective concludes with a look at challenges for the future including the wider capture of mechanistic nuances and possible impacts of text mining on automated entity extraction

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Challenges of Connecting Chemistry to Pharmacology: Perspectives from Curating the IUPHAR/BPS Guide to PHARMACOLOGY

10.26434/chemrxiv.6211115 ◽

2018 ◽

Author(s):

Christopher Southan ◽

Joanna L Sharman ◽

Elena Faccenda ◽

Adam J Pawson ◽

Simon D Harding ◽

...

Keyword(s):

Selection Process ◽

Data Extraction ◽

Scientific Quality ◽

Small Data ◽

Entity Extraction ◽

Protein Targets ◽

Chemical Structures ◽

Wide Range ◽

Quantitative Results

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Quality of Systematic Reviews of the Foods with Function Claims in Japan: Comparative Before- and After-Evaluation of Verification Reports by the Consumer Affairs Agency

Nutrients ◽

10.3390/nu11071583 ◽

2019 ◽

Vol 11 (7) ◽

pp. 1583 ◽

Cited By ~ 1

Author(s):

Kamioka ◽

Tsutani ◽

Origasa ◽

Yoshizaki ◽

Kitayuguchi ◽

...

Keyword(s):

Systematic Reviews ◽

Data Extraction ◽

Meta Analysis ◽

Scientific Evidence ◽

Reporting Quality ◽

Health Claims ◽

Scientific Quality ◽

Before And After ◽

Product Effectiveness

Background: In Japan, a new type of foods with health claims, called Foods with Function Claims (FFC), was introduced in April 2015 in order to make more products available that are clearly labeled with certain health functions. Regarding substantiating product effectiveness, scientific evidence for the proposed function claims must be explained by systematic reviews (SRs), but the quality of SRs was not clear. The objectives of this review were to assess the quality of SRs based on the FFC registered on the Consumer Affairs Agency (CAA) website in Japan, and to determine whether the CAA’s verification report in 2016 was associated with improvement in the quality of SRs. Methods: We evaluated the reporting quality of each SR by the AMSTAR checklist on methodological quality. We searched the database from 1 April to 31 October 2015 as the before-SR and from 1 July 2017 to 31 January 2018 as the after-SR. Results: Among the 104 SRs reviewed, 96 final products were included: 51 (53.1%) were supplements, 42 (43.8%) were processed foods without supplements, and 3 (3.1%) were fresh foods. Of the 104 SRs, 92 (88.5%) were qualitative reviews (i.e., without meta-analysis) and 12 (11.5%) performed a meta-analysis. The average quality score of before-SRs and after-SRs was 6.2 ± 1.8 and 5.0 ± 1.9, respectively, a statistically significant decrease (p < 0.001). Conclusion: Overall, the methodology and reporting quality of after-SRs based on the FFC were poorer than those of before-SRs. In particular, there were very poor descriptions and/or implementations of study selection and data extraction, search strategy, evaluation methods for risk of bias, assessment of publication bias, and formulating conclusions based on methodological rigor and scientific quality of the included studies.

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CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding

10.33774/chemrxiv-2021-rzq4n ◽

2021 ◽

Author(s):

Suzanne Ackloo ◽

Rima Al-awar ◽

Rommie E. Amaro ◽

Cheryl H. Arrowsmith ◽

Hatylas Azevedo ◽

...

Keyword(s):

Drug Discovery ◽

Computational Methods ◽

Open Science ◽

Critical Assessment ◽

Great Promise ◽

Crowd Sourcing ◽

Protein Targets ◽

Computational Approaches ◽

Chemical Structures ◽

Wide Range

Computational approaches in drug discovery and development hold great promise, with artificial intelligence methods undergoing widespread contemporary use, but the experimental validation of these new approaches is frequently inadequate. We are initiating Critical Assessment of Computational Hit-finding Experiments (CACHE) as a public benchmarking project that aims to accelerate the development of small molecule hit-finding algorithms by competitive assessment. Compounds will be identified by participants using a wide range of computational methods for dozens of protein targets selected for different types of prediction scenarios, as well as for their potential biological or pharmaceutical relevance. Community-generated predictions will be tested centrally and rigorously in an experimental hub(s), and all data, including the chemical structures of experimentally tested compounds, will be made publicly available without restrictions. The ability of a range of computational approaches to find novel compounds will be evaluated, compared, and published. The overarching goal of CACHE is to accelerate the development of computational chemistry methods by providing rapid and unbiased feedback to those developing methods, with an ancillary and valuable benefit of identifying new compound-protein binding pairs for biologically interesting targets. The initiative builds on the power of crowd sourcing and expands the open science paradigm for drug discovery.

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A systematic review of persistent symptoms and residual abnormal functioning following acute COVID-19: Ongoing symptomatic phase vs. post-COVID-19 syndrome

10.1101/2021.06.25.21259372 ◽

2021 ◽

Author(s):

Glenn Jennings ◽

Ann Monaghan ◽

Feng Xue ◽

David Mockler ◽

Román Romero-Ortuño

Keyword(s):

Quality Of Life ◽

Systematic Review ◽

Data Extraction ◽

Signs And Symptoms ◽

Psychological Disorder ◽

Research Database ◽

Chest Imaging ◽

Wide Range ◽

Two Phases

Objective | To compare the two phases of long COVID, namely ongoing symptomatic COVID-19 (OSC; signs and symptoms from 4 to 12 weeks from initial infection) and post-COVID-19 syndrome (PCS; signs and symptoms beyond 12 weeks) with respect to symptomatology, abnormal functioning, psychological burden, and quality of life. Design | Systematic review. Data Sources | Electronic search of EMBASE, MEDLINE, ProQuest Coronavirus Research Database, LitCOVID, and Google Scholar between January and April 2021, and manual search for relevant citations from review articles. Eligibility Criteria | Cross-sectional studies, cohort studies, randomised control trials, and case-control studies with participant data concerning long COVID symptomatology or abnormal functioning. Data Extraction | Studies were screened and assessed for risk of bias by two independent reviewers, with conflicts resolved with a third reviewer. The AXIS tool was utilised to appraise the quality of the evidence. Data were extracted and collated using a data extraction tool in Microsoft Excel. Results | Of the 1,145 studies screened, 39 were included, all describing adult cohorts with long COVID and sample sizes ranging from 32 to 1,733. Studies included data pertaining to symptomatology, pulmonary functioning, chest imaging, cognitive functioning, psychological disorder, and/or quality of life. Fatigue presented as the most prevalent symptom during both OSC and PCS at 43% and 44%, respectively. Sleep disorder (36%; 33%), dyspnoea (31%; 40%), and cough (26%; 22%) followed in prevalence. Abnormal spirometry (FEV1 <80% predicted) was observed in 15% and 11%, and abnormal chest imaging observed in 34% and 28%, respectively. Cognitive impairments were also evident (20%; 15%), as well as anxiety (28%; 34%) and depression (25%; 32%). Decreased quality of life was reported by 40% of patients with OSC and 57% by those with PCS. Conclusions | The prevalences of OSC and PCS were highly variable. Reported symptoms covered a wide range of body systems, with general overlap in frequencies between the two phases. However, abnormalities in lung function and imaging seemed to be more common in OSC, whilst anxiety, depression, and poor quality of life seemed more frequent in PCS. In general, the quality of the evidence was moderate and further research is needed to better understand the complex interplay of somatic versus psychosocial drivers in long COVID. Systematic Review Registration | Registered with PROSPERO with ID #CRD42021247846.

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Predictors and triggers of incivility within healthcare teams: a systematic review of the literature

BMJ Open ◽

10.1136/bmjopen-2019-035471 ◽

2020 ◽

Vol 10 (6) ◽

pp. e035471

Author(s):

Sandra Keller ◽

Steven Yule ◽

Vivian Zagarese ◽

Sarah Henrickson Parker

Keyword(s):

Data Extraction ◽

Empirical Studies ◽

Individual Characteristics ◽

Qualitative Studies ◽

Publication Date ◽

Eligibility Criteria ◽

Medical Specialties ◽

Healthcare Teams ◽

Wide Range

ObjectivesTo explore predictors and triggers of incivility in medical teams, defined as behaviours that violate norms of respect but whose intent to harm is ambiguous.DesignSystematic literature review of quantitative and qualitative empirical studies.Data sourcesDatabase searches according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guideline in Medline, CINHAL, PsychInfo, Web of Science and Embase up to January 2020.Eligibility criteriaOriginal empirical quantitative and qualitative studies focusing on predictors and triggers of incivilities in hospital healthcare teams, excluding psychiatric care.Data extraction and synthesisOf the 1397 publications screened, 53 were included (44 quantitative and 9 qualitative studies); publication date ranged from 2002 to January 2020.ResultsBased on the Medical Education Research Study Quality Instrument (MERSQI) scores, the quality of the quantitative studies were relatively low overall (mean MERSQI score of 9.93), but quality of studies increased with publication year (r=0.52; p<0.001). Initiators of incivility were consistently described as having a difficult personality, yet few studies investigated their other characteristics and motivations. Results were mostly inconsistent regarding individual characteristics of targets of incivilities (eg, age, gender, ethnicity), but less experienced healthcare professionals were more exposed to incivility. In most studies, participants reported experiencing incivilities mainly within their own professional discipline (eg, nurse to nurse) rather than across disciplines (eg, physician to nurse). Evidence of specific medical specialties particularly affected by incivility was poor, with surgery as one of the most cited uncivil specialties. Finally, situational and cultural predictors of higher incivility levels included high workload, communication or coordination issues, patient safety concerns, lack of support and poor leadership.ConclusionsAlthough a wide range of predictors and triggers of incivilities are reported in the literature, identifying characteristics of initiators and the targets of incivilities yielded inconsistent results. The use of diverse and high-quality methods is needed to explore the dynamic nature of situational and cultural triggers of incivility.

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Health-related quality of life issues, including symptoms, in patients with active COVID-19 or post COVID-19; a systematic literature review

Quality of Life Research ◽

10.1007/s11136-021-02908-z ◽

2021 ◽

Author(s):

Cecilie Delphin Amdal ◽

Madeline Pe ◽

Ragnhild Sørum Falk ◽

Claire Piccinin ◽

Andrew Bottomley ◽

...

Keyword(s):

Quality Of Life ◽

Systematic Review ◽

Data Extraction ◽

Health Related Quality ◽

Psychological Issues ◽

Wide Range ◽

Related Quality ◽

Health Related

Abstract Purpose This systematic review was performed to identify all relevant health-related quality of life (HRQoL) issues associated with COVID-19. Methods A systematic literature search was undertaken in April 2020. In four teams of three reviewers each, all abstracts were independently reviewed for inclusion by two reviewers. Using a pre-defined checklist of 93 criteria for each publication, data extraction was performed independently by two reviewers and subsequently compared and discussed. If necessary, a third reviewer resolved any discrepancies. The search was updated in February 2021 to retrieve new publications on HRQoL issues including issues related to the long-term consequences of COVID-19. Results The search in April 2020 identified 3342 potentially relevant publications, and 339 publications were selected for full-text review and data extraction. We identified 75 distinct symptoms and other HRQoL issues categorized into 12 thematic areas; from general symptoms such as fever, myalgia, and fatigue, to neurological and psychological issues. The updated search revealed three extra issues experienced during active disease and long-term problems with fatigue, psychological issues and impaired cognitive function. Conclusion This first comprehensive systematic review provides a detailed overview of the wide range of HRQoL issues experienced by patients with COVID-19 throughout the course of the disease. It demonstrates the devastating impact of the disease and provides critically important information for clinicians, to enable them to better recognize the disease and to provide knowledge important for treatment and follow-up. The results provided the foundation for the international development of a COVID-19 specific patient-reported HRQoL questionnaire.

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Abstract P158: Lower Extremity Peripheral Artery Disease and Quality of Life among Older Individuals in the Community: The Atherosclerosis Risk in Communities (ARIC) Study

Circulation ◽

10.1161/circ.131.suppl_1.p158 ◽

2015 ◽

Vol 131 (suppl_1) ◽

Author(s):

Aozhou Wu ◽

Josef Coresh ◽

Elizabeth Selvin ◽

Hirofumi Tanaka ◽

Gerardo Heiss ◽

...

Keyword(s):

Quality Of Life ◽

Health Status ◽

Lower Extremity ◽

Ankle Brachial Index ◽

Small Data ◽

Older Individuals ◽

Limited Ability ◽

Wide Range ◽

The Impact

Background: Lower extremity peripheral arterial disease (PAD), commonly identified by an ankle-brachial Index (ABI) <0.9, increases mortality risk and may impair mobility as well as quality of life (QOL). However, most studies assessing reduced QOL in the relation to PAD rely on small data from vascular clinics, leaving uncertainty about the impact of PAD on QOL in the community. Method: Using 5,610 ARIC visit 5 (2011-2013) participants aged 66-90 years, we assessed the associations of ABI with several QOL parameters, including self-evaluated general health status, mental status (the Center for Epidemiologic Studies Depression [CES-D] score and hopeless feeling), social aspect (work interfered by pain and social activity interfered by health status), and physical ability (limited ability to climb stairs and need of walking assistance). Logistic regression models were applied to assess the association of ABI with each QOL parameter, adjusting for potential confounders including comorbidities such as history of heart failure, coronary heart disease, and stroke. Result: With ABI 1.1-1.2 as a reference, lower ABI was consistently associated with poor status of all QOL parameters tested (Table), with overall evident dose-response relationship. Interestingly, a poor status of various QOL parameters was observed even in borderline low ABI (0.9-1.0) and low normal (1.0-1.1). High ABI (>1.3), indicative of arterial stiffness, was only significantly associated with limited ability to climb stairs. Similar results for low ABI and QOL were observed in both genders and white and black participants. Conclusion: Low ABI was independently and consistently associated with poor status of wide range of QOL domains, with potential important implications on quality-maintained life in older individuals. Further studies are warranted to assess whether the association is due to PAD-related leg symptoms or weakness and/or reflects the impact of systemic atherosclerosis on QOL.

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Academy Journal No.7(19), 2020/ Chief Editors Susan Belih /OEAPS Inc.(Open European Academy of Public Sciences) & Estonian Academy of Sciences. Tallinn, Estonia. 31.10.2020: OEAPS Inc., 2020. - 128 P. ISSN : 2733-0923

10.31219/osf.io/mxzyu ◽

2020 ◽

Author(s):

OEAPS ◽

Saparbaev Bunyodbek

Keyword(s):

Scientific Quality ◽

Final Decision ◽

European Academy ◽

Wide Range ◽

Verification Process ◽

Academy Of Sciences

journal. It is devoted to the publication of original scientificresearch articles dealing with various academic disciplines.Articles that may be of interest to a wide range of researchersare welcome, and not limited to those who work on specificresearch subjects."Academy Journal" has an open archive, according to whichpublished articles are available immediately after publication,excluding embargoes.Expert reviewThere is one blind verification process in the journal. Allarticles will be initially evaluated by the editor for compliancewith the journal. Manuscripts that are considered appropriateare then usually sent to at least two independent peer reviewersto assess the scientific quality of the article. The editor isresponsible for the final decision on whether to accept or rejectthe article. The editor's decision is final.

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A Systematic Review of Persistent Symptoms and Residual Abnormal Functioning following Acute COVID-19: Ongoing Symptomatic Phase vs. Post-COVID-19 Syndrome

Journal of Clinical Medicine ◽

10.3390/jcm10245913 ◽

2021 ◽

Vol 10 (24) ◽

pp. 5913

Author(s):

Glenn Jennings ◽

Ann Monaghan ◽

Feng Xue ◽

David Mockler ◽

Román Romero-Ortuño

Keyword(s):

Quality Of Life ◽

Systematic Review ◽

Data Extraction ◽

Signs And Symptoms ◽

Psychological Disorder ◽

Research Database ◽

Chest Imaging ◽

Wide Range ◽

Two Phases

Objective: To compare the two phases of long COVID, namely ongoing symptomatic COVID-19 (OSC; signs and symptoms from 4 to 12 weeks from initial infection) and post-COVID-19 syndrome (PCS; signs and symptoms beyond 12 weeks) with respect to symptomatology, abnormal functioning, psychological burden, and quality of life. Design: Systematic review. Data Sources: Electronic search of EMBASE, MEDLINE, ProQuest Coronavirus Research Database, LitCOVID, and Google Scholar between January and April 2021, and manual search for relevant citations from review articles. Eligibility Criteria: Cross-sectional studies, cohort studies, randomised control trials, and case-control studies with participant data concerning long COVID symptomatology or abnormal functioning. Data Extraction: Studies were screened and assessed for risk of bias by two independent reviewers, with conflicts resolved with a third reviewer. The AXIS tool was utilised to appraise the quality of the evidence. Data were extracted and collated using a data extraction tool in Microsoft Excel. Results: Of the 1145 studies screened, 39 were included, all describing adult cohorts with long COVID and sample sizes ranging from 32 to 1733. Studies included data pertaining to symptomatology, pulmonary functioning, chest imaging, cognitive functioning, psychological disorder, and/or quality of life. Fatigue presented as the most prevalent symptom during both OSC and PCS at 43% and 44%, respectively. Sleep disorder (36%; 33%), dyspnoea (31%; 40%), and cough (26%; 22%) followed in prevalence. Abnormal spirometry (FEV1 < 80% predicted) was observed in 15% and 11%, and abnormal chest imaging was observed in 34% and 28%, respectively. Cognitive impairments were also evident (20%; 15%), as well as anxiety (28%; 34%) and depression (25%; 32%). Decreased quality of life was reported by 40% in those with OSC and 57% with PCS. Conclusions: The prevalence of OSC and PCS were highly variable. Reported symptoms covered a wide range of body systems, with a general overlap in frequencies between the two phases. However, abnormalities in lung function and imaging seemed to be more common in OSC, whilst anxiety, depression, and poor quality of life seemed more frequent in PCS. In general, the quality of the evidence was moderate and further research is needed to understand longitudinal symptomatology trajectories in long COVID. Systematic Review Registration: Registered with PROSPERO with ID #CRD42021247846.

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Base on the Public Scientific Quality Improvement Research on Risk Early Warning of Online Shopping

10.21203/rs.3.rs-493778/v1 ◽

2021 ◽

Author(s):

Xiaoyan Li ◽

Lixia Cao ◽

Tonghui Wang ◽

Xiangchu Feng

Keyword(s):

Early Warning ◽

Online Shopping ◽

Popular Science ◽

Scientific Quality ◽

Science Knowledge ◽

The Public ◽

Quality Improvement Research ◽

Risk Warning ◽

Wide Range

Abstract In order to improve the scientific quality of the public, the Chinese Association for Science and Technology has put forward a call to combine popular science education with leisure and entertainment. In view of the fact that online shopping involves a wide range of areas, and the people pay more attention to it, the paper completed the innovation of online shopping risk warning science knowledge, the design of popular science mechanism and the dissemination of popular science knowledge. The paper used complex network’s knowledge discovery methods and decision theory to design online shopping risk warning science knowledge; Using the complex network public opinion dissemination trust analysis realize the dissemination of popular science knowledge and promote the improvement of the public's quality of popular science. The spread of risk early warning science knowledge in the network shows that the risk early warning mechanism designed can achieve the purpose of improving public science knowledge when the reward and punishment measures are appropriate.

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