Broadening the capture of natural products mentioned in FAERS using fuzzy string-matching and a Siamese neural network.

Increased sales of natural products (NPs) in the US and growing safety concerns highlight the need for NP pharmacovigilance. A challenge for NP pharmacovigilance is ambiguity when referring to NPs in spontaneous reporting systems. We used a combination of fuzzy string-matching and a neural network to reduce this ambiguity. Our aim is to increase the capture of reports involving NPs in the US Food and Drug Administration Adverse Event Reporting System (FAERS). For this, we utilized Gestalt pattern-matching (GPM) and Siamese neural network (SM) to identify potential mentions of NPs of interest in 389,386 FAERS reports with unmapped drug names. A team of health professionals refined the candidates identified in the previous step through manual review and annotation. After candidate adjudication, GPM identified 595 unique NP names and SM 504. There was little overlap between candidates identified by each (Non-overlapping: GPM 347, SM 248). We identified a total of 686 novel NP names from FAERS reports. Including these names in the FAERS collection yielded 3,486 additional reports mentioning NPs.

Broadening the Capture of Natural Products Mentioned in FAERS Using Fuzzy String-Matching and a Siamese Neural Network.

Increased sales of natural products (NPs) in the US and growing safety concerns highlight the need for NP pharmacovigilance. A challenge for NP pharmacovigilance is ambiguity when referring to NPs in spontaneous reporting systems. We used a combination of fuzzy string-matching and a neural network to reduce this ambiguity. We aim to increase the capture of reports involving NPs in the US Food and Drug Administration Adverse Event Reporting System (FAERS). Gestalt pattern-matching (GPM) and Siamese neural network (SM) were used to identify potential mentions of NPs of interest in 389,386 FAERS reports with unmapped drug names. We refined the identified candidates through manual review and annotation by health professionals. After adjudication, GPM identified 595 unique NP names and SM 504. There was little overlap between candidates identified by the approaches (Non-overlapping: GPM 347, SM 248). In total, 686 novel NP names were identified in the unmapped FAERS reports. Including these names in the FAERS collection yielded 3,486 additional reports mentioning NPs.

Applications of the microphysiology systems database for experimental ADME-Tox and disease models.

To accelerate the development and application of Microphysiological Systems (MPS) in biomedical research and drug discovery/development, a centralized resource is required to provide the detailed design, application, and performance data that enables industry and research scientists to select, optimize, and/or develop new MPS solutions, as well as to harness data from MPS models. We have previously implemented an open source Microphysiology Systems Database (MPS-Db), with a simple icon driven interface, as a resource for MPS researchers and drug discovery/development scientists (https://mps.csb.pitt.edu). The MPS-Db captures and aggregates data from MPS, ranging from static microplate models to integrated, multi-organ microfluidic models, and associates those data with reference data from chemical, biochemical, pre-clinical, clinical and post-marketing sources to support the design, development, validation, application and interpretation of the models. The MPS-Db enables users to manage their multifactor, multichip studies, then upload, analyze, review, computationally model and share data. Here we discuss how the sharing of MPS study data in the MS-Db is under user control and can be kept private to the individual user, shared with a select group of collaborators, or be made accessible to the general scientific community. We also present a test case using our liver acinus MPS model (LAMPS) as an example and discuss the use of the MPS-Db in managing, designing, and analyzing MPS study data, assessing the reproducibility of MPS models, and evaluating the concordance of MPS model results with clinical findings. We introduce the Disease Portal module with links to resources for the design of MPS disease models and studies and discuss the integration of computational models for the prediction of PK/PD and disease pathways using data generated from MPS models.

Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations.

Many groups within the broad field of nanoinformatics are already developing data repositories and analytical tools driven by their individual organizational goals. Integrating these data resources across disciplines and with non-nanotechnology resources can support multiple objectives by enabling the reuse of the same information. Integration can also serve as the impetus for novel scientific discoveries by providing the framework to support deeper data analyses. This article discusses current data integration practices in nanoinformatics and in comparable mature fields, and nanotechnology-specific challenges impacting data integration. Based on results from a nanoinformatics-community-wide survey, recommendations for achieving integration of existing operational nanotechnology resources are presented. Nanotechnology-specific data integration challenges, if effectively resolved, can foster the application and validation of nanotechnology within and across disciplines. This paper is one of a series of articles by the Nanomaterial Data Curation Initiative that address data issues such as data curation workflows, data completeness and quality, curator responsibilities, and metadata.

How should the completeness and quality of curated nanomaterial data be evaluated?

Nanotechnology is of increasing significance. Curation of nanomaterial data into electronic databases offers opportunities to better understand and predict nanomaterials' behaviour. This supports innovation in, and regulation of, nanotechnology. It is commonly understood that curated data need to be sufficiently complete and of sufficient quality to serve their intended purpose. However, assessing data completeness and quality is non-trivial in general and is arguably especially difficult in the nanoscience area, given its highly multidisciplinary nature. The current article, part of the Nanomaterial Data Curation Initiative series, addresses how to assess the completeness and quality of (curated) nanomaterial data. In order to address this key challenge, a variety of related issues are discussed: the meaning and importance of data completeness and quality, existing approaches to their assessment and the key challenges associated with evaluating the completeness and quality of curated nanomaterial data. Considerations which are specific to the nanoscience area and lessons which can be learned from other relevant scientific disciplines are considered. Hence, the scope of this discussion ranges from physicochemical characterisation requirements for nanomaterials and interference of nanomaterials with nanotoxicology assays to broader issues such as minimum information checklists, toxicology data quality schemes and computational approaches that facilitate evaluation of the completeness and quality of (curated) data. This discussion is informed by a literature review and a survey of key nanomaterial data curation stakeholders. Finally, drawing upon this discussion, recommendations are presented concerning the central question: how should the completeness and quality of curated nanomaterial data be evaluated?

Statistical method to evaluate the occurrence of PCB transformations in river sediments with application to Hudson River data.

Polychlorinated biphenyls (PCBs) were produced in the mid 1900s for industrial use. The term PCBs refers to 209 theoretically possible chlorinated compounds of the biphenyl molecule (congeners). The number and location of the chlorines govern both the environmental fate and toxicity of each congener. Changes in the distribution of congeners in river sediments can result from congener transformation and/or preferential congener transport. This study exploits the distribution of PCB congeners, specifically congeners that maintain a constant ratio relationship in the commercially manufactured PCB mixtures (Aroclors), to quantify the likelihood of congener distribution shifts in river sediment. By using relative abundances, the influence of total PCB bias is eliminated. Correlated congeners (tracker pairs) maintain a constant relative proportion in sequentially more-highly chlorinated Aroclors, thus there is no need to know the source contaminating Aroclors a priori. Using the Frame et al. database of Aroclor congener distributions, 276 pairs of correlated congeners, constructed from 95 individual congeners, are identified. A comparison study of Aroclors and Hudson River sediments included 218 of the 276 tracker pairs. Conclusive evidence of a shift in the congener proportions is found in 120 of the 218 cases, a much greater number than expected if no change in congener distribution had occurred.