Sysrev: A FAIR Platform for Data Curation and Systematic Evidence Review

Bozada, Thomas; Borden, James; Workman, Jeffrey; Cid, Mardo Del; Malinowski, Jennifer; Luechtefeld, Thomas

doi:10.3389/frai.2021.685298

Cited by 59 publications

(40 citation statements)

References 30 publications

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“…For this paper, we use the online platform sysrev (Bozada et al, 2021) to screen the GAMI database for island case studies. For the initial screening, we include any papers dealing with an inhabited island case study.…”

Section: Methodsmentioning

confidence: 99%

Between tinkering and transformation: A contemporary appraisal of climate change adaptation research on the world's islands

Petzold

Joe²,

Kelman³

et al. 2023

Front. Clim.

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Islands are at the center of discourses on climate change. Yet despite extensive work on diverse island systems in a changing climate, we still lack an understanding of climate change-related responses amongst islands and what shifting from what might be called “tinkering” (perhaps heat warnings) to “transformational” adaptation (perhaps relocation) means for these vastly different landmasses which are often grouped together by default. Through a systematic review of the climate change adaptation scientific literature, this paper critically reflects on how considering islands as a homogenous ensemble and the use of buzzwords such as “transformational adaptation” may be problematic for diverse island realities under climate change. Our findings show that the adaptation evidence base actually provides literature on contrasting island types and cultural and political contexts, including Small Island Developing States as well as other island territories. This study finds research gaps with respect to regions (e.g., South America, Africa, and Mediterranean) and that there is overall both little evidence of and a lack of context-specific definitions of transformational adaptation in island contexts. The adaptation literature does not yet fully reflect the experiences or needs of islands regarding transitions and transformations throughout history.

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Section: Methodsmentioning

confidence: 99%

Between tinkering and transformation: A contemporary appraisal of climate change adaptation research on the world's islands

Petzold

Joe²,

Kelman³

et al. 2023

Front. Clim.

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“…Labels are boolean, string, categorical, or tabular forms that constrain user input in order to build consistent, structured data. Data were accessed and analyzed in R using the rsr package (Bozada et al, 2021 ).…”

Section: Methodsmentioning

confidence: 99%

“…The reviewer(s), time of review, and extracted data for each document can be looked up by readers and updated easily. We used Sysrev (Bozada et al, 2021 ), a web application designed to facilitate data curation and systematic evidence reviews (SER). It has an integrated machine learning (ML) platform with natural language processing (NLP) tools for searching, tagging, and extracting data from database sources.…”

Section: Introductionmentioning

confidence: 99%

Applications for open access normalized synthesis in metastatic prostate cancer trials

Luechtefeld¹,

Bozada²,

Goel

et al. 2022

Front. Artif. Intell.

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Recent metastatic castration-resistant prostate cancer (mCRPC) clinical trials have integrated homologous recombination and DNA repair deficiency (HRD/DRD) biomarkers into eligibility criteria and secondary objectives. These trials led to the approval of some PARP inhibitors for mCRPC with HRD/DRD indications. Unfortunately, biomarker-trial outcome data is only discovered by reviewing publications, a process that is error-prone, time-consuming, and laborious. While prostate cancer researchers have written systematic evidence reviews (SERs) on this topic, given the time involved from the last search to publication, an SER is often outdated even before publication. The difficulty in reusing previous review data has resulted in multiple reviews of the same trials. Thus, it will be useful to create a normalized evidence base from recently published/presented biomarker-trial outcome data that one can quickly update. We present a new approach to semi-automating normalized, open-access data tables from published clinical trials of metastatic prostate cancer using a data curation and SER platform. Clinicaltrials.gov and Pubmed.gov were used to collect mCRPC clinical trial publications with HRD/DRD biomarkers. We extracted data from 13 publications covering ten trials that started before 22nd Apr 2021. We extracted 585 hazard ratios, response rates, duration metrics, and 543 adverse events. Across 334 patients, we also extracted 8,180 patient-level survival and biomarker values. Data tables were populated with survival metrics, raw patient data, eligibility criteria, adverse events, and timelines. A repeated strong association between HRD and improved PARP inhibitor response was observed. Several use cases for the extracted data are demonstrated via analyses of trial methods, comparison of treatment hazard ratios, and association of treatments with adverse events. Machine learning models are also built on combined and normalized patient data to demonstrate automated discovery of therapy/biomarker relationships. Overall, we demonstrate the value of systematically extracted and normalized data. We have also made our code open-source with simple instructions on updating the analyses as new data becomes available, which anyone can use even with limited programming knowledge. Finally, while we present a novel method of SER for mCRPC trials, one can also implement such semi-automated methods in other clinical trial domains to advance precision medicine.

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“…The use of systematic methods to populate this framework will result in accuracy, consistency, and transparency in the collection and interpretation of the data underlying each AOP. In addition, advances in artificial intelligence (AI) such as natural language processing and machine learning may add efficiency to the process ( Marshall and Wallace, 2019 ; O’Connor et al, 2020 ; Bozada et al, 2021 ). These AI tools are already integral to SR workflows and include machine assisted topic clustering and prioritization of search results, machine assistance for study screening, normalization of terminology using controlled vocabularies and ontologies, etc., with the advantage of a human-in-the-loop model.…”

Section: Literature-based Aop Development (Theme 2)mentioning

confidence: 99%

Application of evidence-based methods to construct mechanism-driven chemical assessment frameworks

Hoffmann

Aiassa

Angrish

et al. 2022

ALTEX

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Although emissions of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) have been dramatically reduced, the persistence and bioaccumulation of these chemicals result in detectable levels in the U.S. population. Despite declining emissions, there is continued widespread exposure to both chemicals and a number of studies have reported potential PFOA-and PFOS-associated immunotoxicity in both humans and non-human animals. The NTP conducted a systematic review to evaluate the evidence on exposure to PFOS or PFOA and immune-related health effects to determine whether exposure to either chemical is associated with immunotoxicity for humans. The literature search and screening process identified 33 human studies, 93 animal studies, and 27 in vitro/mechanistic studies relevant for addressing the objective. The health effects data for PFOA and PFOS were considered separately in developing hazard identification conclusions. Conclusions for each chemical were reached by integrating evidence from human and animal studies with consideration of any mechanistic data. PEER REVIEW OF THE DRAFT NTP MONOGRAPHPeer review of the draft NTP Monograph was conducted by an ad hoc expert panel in a public meeting held July 19, 2016, at the National Institute of Environmental Health Sciences, Research triangle park and via WebEx (see http://ntp.niehs.nih.gov/go/37090 for meeting materials and peer review report). The selection of panel members and conduct of the peer review were performed in accordance with the Federal Advisory Committee Act and Federal policies and regulations. The panel members served as independent scientists, not as representatives of any institution, company, or governmental agency. In this capacity, panel members had two major responsibilities in reviewing the draft NTP Monograph:(1) to determine whether the scientific information cited in the draft monograph was technically correct and clearly stated, and whether NTP has objectively presented and assessed the scientific evidence;(2) to determine whether the scientific evidence presented in the draft monograph supported the NTP's conclusions regarding whether immunotoxicity is associated with exposure to PFOA or PFOS.The panel agreed with the draft conclusions that PFOA and PFOS are both presumed to be immune hazards to humans; however, they recommended changing the level of evidence conclusion for hypersensitivity-related outcomes for the animal body of evidence from "high" to "moderate". NTP concurred with this recommendation. Comments from the peer reviewers and written public comments were considered during finalization of the document.

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Sysrev: A FAIR Platform for Data Curation and Systematic Evidence Review

Cited by 59 publications

References 30 publications

Between tinkering and transformation: A contemporary appraisal of climate change adaptation research on the world's islands

Between tinkering and transformation: A contemporary appraisal of climate change adaptation research on the world's islands

Applications for open access normalized synthesis in metastatic prostate cancer trials

Application of evidence-based methods to construct mechanism-driven chemical assessment frameworks

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