Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

Three steps towards comparability and standardization among molecular methods for characterizing insect communities

Molecular methods are currently some of the best-suited technologies for implementation in insect monitoring. However, the field is developing rapidly and lacks agreement on methodology or community standards. To apply DNA-based methods in large-scale monitoring, and to gain insight across commensurate data, we need easy-to-implement standards that improve data comparability. Here, we provide three recommendations for how to improve and harmonize efforts in biodiversity assessment and monitoring via metabarcoding: (i) we should adopt the use of synthetic spike-ins, which will act as positive controls and internal standards; (ii) we should consider using several markers through a multiplex polymerase chain reaction (PCR) approach; and (iii) we should commit to the publication and transparency of all protocol-associated metadata in a standardized fashion. For (i), we provide a ready-to-use recipe for synthetic cytochrome c oxidase spike-ins, which enable between-sample comparisons. For (ii), we propose two gene regions for the implementation of multiplex PCR approaches, thereby achieving a more comprehensive community description. For (iii), we offer guidelines for transparent and unified reporting of field, wet-laboratory and dry-laboratory procedures, as a key to making comparisons between studies. Together, we feel that these three advances will result in joint quality and calibration standards rather than the current laboratory-specific proof of concepts. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

A template wizard for the cocreation of machine-readable data-reporting to harmonize the evaluation of (nano)materials

Making research data findable, accessible, interoperable and reusable (FAIR) is typically hampered by a lack of skills in technical aspects of data management by data generators and a lack of resources. We developed a Template Wizard for researchers to easily create templates suitable for consistently capturing data and metadata from their experiments. The templates are easy to use and enable the compilation of machine-readable metadata to accompany data generation and align them to existing community standards and databases, such as eNanoMapper, streamlining the adoption of the FAIR principles. These templates are citable objects and are available as online tools. The Template Wizard is designed to be user friendly and facilitates using and reusing existing templates for new projects or project extensions. The wizard is accompanied by an online template validator, which allows self-evaluation of the template (to ensure mapping to the data schema and machine readability of the captured data) and transformation by an open-source parser into machine-readable formats, compliant with the FAIR principles. The templates are based on extensive collective experience in nanosafety data collection and include over 60 harmonized data entry templates for physicochemical characterization and hazard assessment (cell viability, genotoxicity, environmental organism dose-response tests, omics), as well as exposure and release studies. The templates are generalizable across fields and have already been extended and adapted for microplastics and advanced materials research. The harmonized templates improve the reliability of interlaboratory comparisons, data reuse and meta-analyses and can facilitate the safety evaluation and regulation process for (nano) materials.

Minimum Information for Conducting and Reporting In Vitro Intracellular Infection Assays

Bacterial pathogens are constantly evolving to outsmart the host immune system and antibiotics developed to eradicate them. One key strategy involves the ability of bacteria to survive and replicate within host cells, thereby causing intracellular infections. To address this unmet clinical need, researchers are adopting new approaches, such as the development of novel molecules that can penetrate host cells, thus exerting their antimicrobial activity intracellularly, or repurposing existing antibiotics using nanocarriers (i.e., nanoantibiotics) for site-specific delivery. However, inconsistency in information reported across published studies makes it challenging for scientific comparison and judgment of experiments for future direction by researchers. Together with the lack of reproducibility of experiments, these inconsistencies limit the translation of experimental results beyond pre-clinical evaluation. Minimum information guidelines have been instrumental in addressing such challenges in other fields of biomedical research. Guidelines and recommendations provided herein have been designed for researchers as essential parameters to be disclosed when publishing their methodology and results, divided into four main categories: (i) experimental design, (ii) establishing an in vitro model, (iii) assessment of efficacy of novel therapeutics, and (iv) statistical assessment. These guidelines have been designed with the intention to improve the reproducibility and rigor of future studies while enabling quantitative comparisons of published studies, ultimately facilitating translation of emerging antimicrobial technologies into clinically viable therapies that safely and effectively treat intracellular infections.

Coordinating virus research: The Virus Infectious Disease Ontology

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies-structured, controlled, vocabularies-are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects.

ISCEV standard pattern reversal VEP development: paediatric reference limits from 649 healthy subjects

PURPOSE

To establish the extent of agreement for ISCEV standard reference pattern reversal VEPs (prVEPs) acquired at three European centres, to determine any effect of sex, and to establish reference intervals from birth to adolescence.

METHODS

PrVEPs were recorded from healthy reference infants and children, aged 2 weeks to 16 years, from three centres using closely matched but non-identical protocols. Amplitudes and peak times were modelled with orthogonal quadratic and sigmoidal curves, respectively, and two-sided limits, 2.5th and 97.5th centiles, estimated using nonlinear quantile Bayesian regression. Data were compared by centre and by sex using median quantile confidence intervals. The 'critical age', i.e. age at which P100 peak time ceased to shorten, was calculated.

RESULTS

Data from the three centres were adequately comparable. Sex differences were not clinically meaningful. The pooled data showed rapid drops in P100 peak time which stabilised by 27 and by 34 weeks for large and small check widths, respectively. Post-critical-age reference limits were 87-115 ms and 96-131 ms for large and small check widths, respectively. Amplitudes varied markedly and reference limits for all ages were 5-57 μV and 3.5-56 μV for large and small check widths, respectively.

CONCLUSIONS

PrVEP reference data could be combined despite some methodology differences within the tolerances of the ISCEV VEP Standard, supporting the clinical benefit of ISCEV Standards. Comparison with historical data is hampered by lack of minimum reporting guidelines. The reference data presented here could be validated or transformed for use elsewhere.

No assembly required: Time for stronger, simpler publishing standards for DNA sequences

Uniformly accessible DNA sequences are needed to improve experimental reproducibility and automation. Rather than descriptions of how engineered DNA is assembled, publishers should require complete and empirically validated sequences.

Keep It Simple: Using README Files to Advance Standardization in Chronobiology

Standardization plays a crucial role in ensuring the reliability, reproducibility, and interoperability of research data in the biomedical sciences. Metadata standards are one foundation for the FAIR (Findable, Accessible, Interoperable, and Reusable) principles of data management. They facilitate data discovery, understanding, and reuse. However, the adoption of metadata standards in biological research lags in practice. Barriers such as complexity, lack of incentives, technical challenges, resource constraints, and resistance to change hinder widespread adoption. In the field of chronobiology, standardization is essential but faces particular challenges due to the longitudinal nature of experimental data, diverse model organisms, and varied measurement techniques. To address these challenges, we propose an approach that emphasizes simplicity and practicality: the development of README templates tailored for particular data types and species. Through this opinion article, our intention is to initiate a dialogue and commence a community-driven standardization process by engaging potential contributors and collaborators.

The NanoFlow Repository

MOTIVATION

Extracellular particles (EPs) are the focus of a rapidly growing area of exploration due to the widespread interest in understanding their roles in health and disease. However, despite the general need for EP data sharing and established community standards for data reporting, no standard repository for EP flow cytometry data captures rigor and minimum reporting standards such as those defined by MIFlowCyt-EV (https://doi.org/10.1080/20013078.2020.1713526). We sought to address this unmet need by developing the NanoFlow Repository.

RESULTS

We have developed The NanoFlow Repository to provide the first implementation of the MIFlowCyt-EV framework.

AVAILABILITY AND IMPLEMENTATION

The NanoFlow Repository is freely available and accessible online at https://genboree.org/nano-ui/. Public datasets can be explored and downloaded at https://genboree.org/nano-ui/ld/datasets. The NanoFlow Repository's backend is built using the Genboree software stack that powers the ClinGen Resource, specifically the Linked Data Hub (LDH), a REST API framework written in Node.js, developed initially to aggregate data within ClinGen (https://ldh.clinicalgenome.org/ldh/ui/about). NanoFlow's LDH (NanoAPI) is available at https://genboree.org/nano-api/srvc. NanoAPI is supported by a Node.js Genboree authentication and authorization service (GbAuth), a graph database called ArangoDB, and an Apache Pulsar message queue (NanoMQ) to manage data inflows into NanoAPI. The website for NanoFlow Repository is built with Vue.js and Node.js (NanoUI) and supports all major browsers.

A Case for Accelerating Standards to Achieve the FAIR Principles of Environmental Health Research Experimental Data

BACKGROUND

Funding agencies, publishers, and other stakeholders are pushing environmental health science investigators to improve data sharing; to promote the findable, accessible, interoperable, and reusable (FAIR) principles; and to increase the rigor and reproducibility of the data collected. Accomplishing these goals will require significant cultural shifts surrounding data management and strategies to develop robust and reliable resources that bridge the technical challenges and gaps in expertise.

OBJECTIVE

In this commentary, we examine the current state of managing data and metadata-referred to collectively as (meta)data-in the experimental environmental health sciences. We introduce new tools and resources based on in vivo experiments to serve as examples for the broader field.

METHODS

We discuss previous and ongoing efforts to improve (meta)data collection and curation. These include global efforts by the Functional Genomics Data Society to develop metadata collection tools such as the Investigation, Study, Assay (ISA) framework, and the Center for Expanded Data Annotation and Retrieval. We also conduct a case study of in vivo data deposited in the Gene Expression Omnibus that demonstrates the current state of in vivo environmental health data and highlights the value of using the tools we propose to support data deposition.

DISCUSSION

The environmental health science community has played a key role in efforts to achieve the goals of the FAIR guiding principles and is well positioned to advance them further. We present a proposed framework to further promote these objectives and minimize the obstacles between data producers and data scientists to maximize the return on research investments. https://doi.org/10.1289/EHP11484.

Features of a FAIR vocabulary

BACKGROUND

The Findable, Accessible, Interoperable and Reusable(FAIR) Principles explicitly require the use of FAIR vocabularies, but what precisely constitutes a FAIR vocabulary remains unclear. Being able to define FAIR vocabularies, identify features of FAIR vocabularies, and provide assessment approaches against the features can guide the development of vocabularies.

RESULTS

We differentiate data, data resources and vocabularies used for FAIR, examine the application of the FAIR Principles to vocabularies, align their requirements with the Open Biomedical Ontologies principles, and propose FAIR Vocabulary Features. We also design assessment approaches for FAIR vocabularies by mapping the FVFs with existing FAIR assessment indicators. Finally, we demonstrate how they can be used for evaluating and improving vocabularies using exemplary biomedical vocabularies.

CONCLUSIONS

Our work proposes features of FAIR vocabularies and corresponding indicators for assessing the FAIR levels of different types of vocabularies, identifies use cases for vocabulary engineers, and guides the evolution of vocabularies.

Measurement of Prosocial Tendencies: Meta-Analysis of the Generalization of the Reliability of the Instrument

The Prosocial Tendencies Measure (PTM) and its revised version (PTM-R) are used internationally to measure prosocial behaviors in different life situations. To obtain accumulated evidence of the report and the reliability of its scores, a meta-analysis of the reliability of internal consistency was performed. The databases of Web of Science (WoS) and Scopus were reviewed and all the studies that applied it from 2002 to 2021 were selected. Results: Only 47.9% of the studies presented the index of reliability of PTM and PTM-R. The meta-analytic results of the reliability report of the subscales that the PTM and the PTM-R have in common were: Public 0.78 (95% CI: 0.76-0.80), Anonymous 0.80 (95% CI: 0.79-0.82), Dire 0.74 (95% CI: 0.71-0.76), and Compliant 0.71 (95% CI: 0.72-0.78). Each one of them presents high levels of heterogeneity derived from the gender of the participants (percentage of women), the continent of the population, the validation design, the incentive to participate, and the form of application. It is concluded that both versions present acceptable reliabilities to measure prosocial behavior in different groups and situations, as adolescents and young people, but their clinical use is discouraged.

Minimum Information Standards in Chemistry: A Call for Better Research Data Management Practices

Research data management (RDM) is needed to assist experimental advances and data collection in the chemical sciences. Many funders require RDM because experiments are often paid for by taxpayers and the resulting data should be deposited sustainably for posterity. However, paper notebooks are still common in laboratories and research data is often stored in proprietary and/or dead-end file formats without experimental context. Data must mature beyond a mere supplement to a research paper. Electronic lab notebooks (ELN) and laboratory information management systems (LIMS) allow researchers to manage data better and they simplify research and publication. Thus, an agreement is needed on minimum information standards for data handling to support structured approaches to data reporting. As digitalization becomes part of curricular teaching, future generations of digital native chemists will embrace RDM and ELN as an organic part of their research.

Understanding the importance of quality control and quality assurance in preclinical PET/CT imaging

The fundamental principle of experimental design is to ensure efficiency and efficacy of the performed experiments. Therefore, it behoves the researcher to gain knowledge of the technological equipment to be used. This should include an understanding of the instrument quality control and assurance requirements to avoid inadequate or spurious results due to instrumentation bias whilst improving reproducibility. Here, the important role of preclinical positron emission tomography/computed tomography and the scanner's required quality control and assurance is presented along with the suggested guidelines for quality control and assurance. There are a multitude of factors impeding the continuity and reproducibility of preclinical research data within a single laboratory as well as across laboratories. A more robust experimental design incorporating validation or accreditation of the scanner performance can reduce inconsistencies. Moreover, the well-being and welfare of the laboratory animals being imaged is prime justification for refining experimental designs to include verification of instrumentation quality control and assurance. Suboptimal scanner performance is not consistent with the 3R principle (Replacement, Reduction, and Refinement) and potentially subjects animals to unnecessary harm. Thus, quality assurance and control should be of paramount interest to any scientist conducting animal studies. For this reason, through this work, we intend to raise the awareness of researchers using PET/CT regarding quality control/quality assurance (QC/QA) guidelines and instil the importance of confirming that these are routinely followed. We introduce a basic understanding of the PET/CT scanner, present the purpose of QC/QA as well as provide evidence of imaging data biases caused by lack of QC/QA. This is shown through a review of the literature, QC/QA accepted standard protocols and our research. We also want to encourage researchers to have discussions with the PET/CT facilities manager and/or technicians to develop the optimal designed PET/CT experiment for obtaining their scientific objective. Additionally, this work provides an easy gateway to multiple resources not only for PET/CT knowledge but for guidelines and assistance in preclinical experimental design to enhance scientific integrity of the data and ensure animal welfare.

Machine actionable metadata models

Community-developed minimum information checklists are designed to drive the rich and consistent reporting of metadata, underpinning the reproducibility and reuse of the data. These reporting guidelines, however, are usually in the form of narratives intended for human consumption. Modular and reusable machine-readable versions are also needed. Firstly, to provide the necessary quantitative and verifiable measures of the degree to which the metadata descriptors meet these community requirements, a requirement of the FAIR Principles. Secondly, to encourage the creation of standards-driven templates for metadata authoring, especially when describing complex experiments that require multiple reporting guidelines to be used in combination or extended. We present new functionalities to support the creation and improvements of machine-readable models. We apply the approach to an exemplar set of reporting guidelines in Life Science and discuss the challenges. Our work, targeted to developers of standards and those familiar with standards, promotes the concept of compositional metadata elements and encourages the creation of community-standards which are modular and interoperable from the onset.

Pericyte derived chemokines amplify neutrophil recruitment across the cerebrovascular endothelial barrier

Excessive neutrophil extravasation can drive immunopathology, exemplified in pyogenic meningitis caused by Streptococcus pneumoniae infection. Insufficient knowledge of the mechanisms that amplify neutrophil extravasation has limited innovation in therapeutic targeting of neutrophil mediated pathology. Attention has focussed on neutrophil interactions with endothelia, but data from mouse models also point to a role for the underlying pericyte layer, as well as perivascular macrophages, the only other cell type found within the perivascular space in the cerebral microvasculature. We tested the hypothesis that human brain vascular pericytes (HBVP) contribute to neutrophil extravasation in a transwell model of the cerebral post-capillary venule. We show that pericytes augment endothelial barrier formation. In response to inflammatory cues, they significantly enhance neutrophil transmigration across the endothelial barrier, without increasing the permeability to small molecules. In our model, neither pericytes nor endothelia responded directly to bacterial stimulation. Instead, we show that paracrine signalling by multiple cytokines from monocyte derived macrophages drives transcriptional upregulation of multiple neutrophil chemokines by pericytes. Pericyte mediated amplification of neutrophil transmigration was independent of transcriptional responses by endothelia, but could be mediated by direct chemokine translocation across the endothelial barrier. Our data support a model in which microbial sensing by perivascular macrophages generates an inflammatory cascade where pericytes serve to amplify production of neutrophil chemokines that are translocated across the endothelial barrier to act directly on circulating neutrophils. In view of the striking redundancy in inflammatory cytokines that stimulate pericytes and in the neutrophil chemokines they produce, we propose that the mechanism of chemokine translocation may offer the most effective therapeutic target to reduce neutrophil mediated pathology in pyogenic meningitis.

ENDOCELL-Seud: a Delphi protocol to harmonise methods in endometrial cell culturing

In vitro

culturing of endometrial cells obtained from the uterine mucosa or ectopic sites is used to study molecular and cellular signalling relevant to physiologic and pathologic reproductive conditions. However, the lack of consensus on standard operating procedures for deriving, characterising and maintaining primary cells in two- or three-dimensional cultures from eutopic or ectopic endometrium may be hindering progress in this area of research. Guidance for unbiased in vitro research methodologies in the field of reproductive science remains essential to increase confidence in the reliability of in vitro models. We present herein the protocol for a Delphi process to develop a consensus on in vitro methodologies using endometrial cells (ENDOCELL-Seud Project). A steering committee composed of leading scientists will select critical methodologies, topics and items that need to be harmonised and that will be included in a survey. An enlarged panel of experts (ENDOCELL-Seud Working Group) will be invited to participate in the survey and provide their ratings to the items to be harmonised. According to Delphi, an iterative investigation method will be adopted. Recommended measures will be finalised by the steering committee. The study received full ethical approval from the Ethical Committee of the Maastricht University (ref. FHML-REC/2021/103). The study findings will be available in both peer-reviewed articles and will also be disseminated to appropriate audiences at relevant conferences.

Lay summary

Patient-derived cells cultured in the lab are simple and cost-effective methods used to study biological and dysfunctional or disease processes. These tools are frequently used in the field of reproductive medicine. However, the lack of clear recommendations and standardised methodology to guide the laboratory work of researchers can produce results that are not always reproducible and sometimes are incorrect. To remedy this situation, we define here a method to ascertain if researchers who routinely culture cells in the lab agree or disagree on the optimal laboratory techniques. This method will be used to make recommendations for future researchers working in the field of reproductive biology to reproducibly culture endometrial cells in the laboratory.

NExtSEEK: Extending SEEK for Active Management of Interoperable Metadata

Data management is a critical challenge required to improve the rigor and reproducibility of large projects. Adhering to Findable, Accessible, Interoperable, and Reusable (FAIR) standards provides a baseline for meeting these requirements. Although many existing repositories handle data in a FAIR-compliant manner, there are limited tools in the public domain to handle the metadata burden required to connect data from multi-omic projects that span multiple institutions and are deposited in diverse repositories. One promising approach is the SEEK platform, which allows for diverse metadata and provides an established repository. SEEK is challenged by the assumption of single deposition events where a sample is immutable once entered in the database. This is structured for published data but presents a limitation for ongoing studies where multiple sequential events may occur in a single sample at different sites. To address this issue, we have created a modified wrapper around the SEEK platform that allows for active data management by establishing more discrete sample types that are mutable to permit the expansion of the types of metadata, allowing researchers to track additional information. The use of discrete nodes also converts assays from nodes to edges, creating a network model of the study and more accurately representing the experimental process. With these changes to SEEK, users are able to collect and organize the information that researchers need to improve reusability and reproducibility as well as make data and metadata available to the scientific community through public repositories.

MITI minimum information guidelines for highly multiplexed tissue images

The imminent release of tissue atlases combining multi-channel microscopy with single cell sequencing and other omics data from normal and diseased specimens creates an urgent need for data and metadata standards that guide data deposition, curation and release. We describe a Minimum Information about highly multiplexed Tissue Imaging (MITI) standard that applies best practices developed for genomics and other microscopy data to highly multiplexed tissue images and traditional histology.

Intent Parser: A Tool for Codification and Sharing of Experimental Design

Communicating information about experimental design among a team of collaborators is challenging because different people tend to describe experiments in different ways and with different levels of detail. Sometimes, humans can interpret missing information by making assumptions and drawing inferences from information already provided. Doing so, however, is error-prone and typically requires a high level of interpersonal communication. In this paper, we present a tool that addresses this challenge by providing a simple interface for incremental formal codification of experiment designs. Users interact with a Google Docs word-processing interface with structured tables, backed by assisted linking to machine-readable definitions in a data repository (SynBioHub) and specification of available protocols and requests for execution in the Open Protocol Interface Language (OPIL). The result is an easy-to-use tool for generating machine-readable descriptions of experiment designs with which users in the DARPA SD2 program have collected data from 80 208 samples using a variety of protocols and instruments over the course of 181 experiment runs.

End-to-End provenance representation for the understandability and reproducibility of scientific experiments using a semantic approach

BACKGROUND

The advancement of science and technologies play an immense role in the way scientific experiments are being conducted. Understanding how experiments are performed and how results are derived has become significantly more complex with the recent explosive growth of heterogeneous research data and methods. Therefore, it is important that the provenance of results is tracked, described, and managed throughout the research lifecycle starting from the beginning of an experiment to its end to ensure reproducibility of results described in publications. However, there is a lack of interoperable representation of end-to-end provenance of scientific experiments that interlinks data, processing steps, and results from an experiment's computational and non-computational processes.

RESULTS

We present the "REPRODUCE-ME" data model and ontology to describe the end-to-end provenance of scientific experiments by extending existing standards in the semantic web. The ontology brings together different aspects of the provenance of scientific studies by interlinking non-computational data and steps with computational data and steps to achieve understandability and reproducibility. We explain the important classes and properties of the ontology and how they are mapped to existing ontologies like PROV-O and P-Plan. The ontology is evaluated by answering competency questions over the knowledge base of scientific experiments consisting of computational and non-computational data and steps.

CONCLUSION

We have designed and developed an interoperable way to represent the complete path of a scientific experiment consisting of computational and non-computational steps. We have applied and evaluated our approach to a set of scientific experiments in different subject domains like computational science, biological imaging, and microscopy.

Basic Empathy Scale: A Systematic Review and Reliability Generalization Meta-Analysis

The Basic Empathy Scale (BES) has been internationally used to measure empathy. A systematic review including 74 articles that implement the instrument since its development in 2006 was carried out. Moreover, an evidence validity analysis and a reliability generalization meta-analysis were performed to examine if the scale presented the appropriate values to justify its application. Results from the systematic review showed that the use of the BES is increasing, although the research areas in which it is being implemented are currently being broadened. The validity analyses indicated that both the type of factor analysis and reliability are reported in validation studies much more than the consequences of testing are. Regarding the meta-analysis results, the mean of Cronbach's α for cognitive empathy was 0.81 (95% CI: 0.77-0.85), with high levels of heterogeneity (I2 = 98.81%). Regarding affective empathy, the mean of Cronbach's α was 0.81 (95% CI: 0.76-0.84), with high levels of heterogeneity. It was concluded that BES is appropriate to be used in general population groups, although not recommended for clinical diagnosis; and there is a moderate to high heterogeneity in the mean of Cronbach's α. The practical implications of the results in mean estimation and heterogeneity are discussed.

Guidelines for the use of flow cytometry and cell sorting in immunological studies (third edition)

The third edition of Flow Cytometry Guidelines provides the key aspects to consider when performing flow cytometry experiments and includes comprehensive sections describing phenotypes and functional assays of all major human and murine immune cell subsets. Notably, the Guidelines contain helpful tables highlighting phenotypes and key differences between human and murine cells. Another useful feature of this edition is the flow cytometry analysis of clinical samples with examples of flow cytometry applications in the context of autoimmune diseases, cancers as well as acute and chronic infectious diseases. Furthermore, there are sections detailing tips, tricks and pitfalls to avoid. All sections are written and peer-reviewed by leading flow cytometry experts and immunologists, making this edition an essential and state-of-the-art handbook for basic and clinical researchers.

MISpheroID: a knowledgebase and transparency tool for minimum information in spheroid identity

Spheroids are three-dimensional cellular models with widespread basic and translational application across academia and industry. However, methodological transparency and guidelines for spheroid research have not yet been established. The MISpheroID Consortium developed a crowdsourcing knowledgebase that assembles the experimental parameters of 3,058 published spheroid-related experiments. Interrogation of this knowledgebase identified heterogeneity in the methodological setup of spheroids. Empirical evaluation and interlaboratory validation of selected variations in spheroid methodology revealed diverse impacts on spheroid metrics. To facilitate interpretation, stimulate transparency and increase awareness, the Consortium defines the MISpheroID string, a minimum set of experimental parameters required to report spheroid research. Thus, MISpheroID combines a valuable resource and a tool for three-dimensional cellular models to mine experimental parameters and to improve reproducibility.

Data Management and Modeling in Plant Biology

The study of plant-environment interactions is a multidisciplinary research field. With the emergence of quantitative large-scale and high-throughput techniques, amount and dimensionality of experimental data have strongly increased. Appropriate strategies for data storage, management, and evaluation are needed to make efficient use of experimental findings. Computational approaches of data mining are essential for deriving statistical trends and signatures contained in data matrices. Although, current biology is challenged by high data dimensionality in general, this is particularly true for plant biology. Plants as sessile organisms have to cope with environmental fluctuations. This typically results in strong dynamics of metabolite and protein concentrations which are often challenging to quantify. Summarizing experimental output results in complex data arrays, which need computational statistics and numerical methods for building quantitative models. Experimental findings need to be combined by computational models to gain a mechanistic understanding of plant metabolism. For this, bioinformatics and mathematics need to be combined with experimental setups in physiology, biochemistry, and molecular biology. This review presents and discusses concepts at the interface of experiment and computation, which are likely to shape current and future plant biology. Finally, this interface is discussed with regard to its capabilities and limitations to develop a quantitative model of plant-environment interactions.

Minimal information for chemosensitivity assays (MICHA): a next-generation pipeline to enable the FAIRification of drug screening experiments

Chemosensitivity assays are commonly used for preclinical drug discovery and clinical trial optimization. However, data from independent assays are often discordant, largely attributed to uncharacterized variation in the experimental materials and protocols. We report here the launching of Minimal Information for Chemosensitivity Assays (MICHA), accessed via https://micha-protocol.org. Distinguished from existing efforts that are often lacking support from data integration tools, MICHA can automatically extract publicly available information to facilitate the assay annotation including: 1) compounds, 2) samples, 3) reagents and 4) data processing methods. For example, MICHA provides an integrative web server and database to obtain compound annotation including chemical structures, targets and disease indications. In addition, the annotation of cell line samples, assay protocols and literature references can be greatly eased by retrieving manually curated catalogues. Once the annotation is complete, MICHA can export a report that conforms to the FAIR principle (Findable, Accessible, Interoperable and Reusable) of drug screening studies. To consolidate the utility of MICHA, we provide FAIRified protocols from five major cancer drug screening studies as well as six recently conducted COVID-19 studies. With the MICHA web server and database, we envisage a wider adoption of a community-driven effort to improve the open access of drug sensitivity assays.

Preprocessing of Public RNA-Sequencing Datasets to Facilitate Downstream Analyses of Human Diseases

Publicly available RNA-sequencing (RNA-seq) data are a rich resource for elucidating the mechanisms of human disease; however, preprocessing these data requires considerable bioinformatic expertise and computational infrastructure. Analyzing multiple datasets with a consistent computational workflow increases the accuracy of downstream meta-analyses. This collection of datasets represents the human intracellular transcriptional response to disorders and diseases such as acute lymphoblastic leukemia (ALL), B-cell lymphomas, chronic obstructive pulmonary disease (COPD), colorectal cancer, lupus erythematosus; as well as infection with pathogens including Borrelia burgdorferi, hantavirus, influenza A virus, Middle East respiratory syndrome coronavirus (MERS-CoV), Streptococcus pneumoniae, respiratory syncytial virus (RSV), severe acute respiratory syndrome coronavirus (SARS-CoV), and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We calculated the statistically significant differentially expressed genes and Gene Ontology terms for all datasets. In addition, a subset of the datasets also includes results from splice variant analyses, intracellular signaling pathway enrichments as well as read mapping and quantification. All analyses were performed using well-established algorithms and are provided to facilitate future data mining activities, wet lab studies, and to accelerate collaboration and discovery.

Tissue Transglutaminase Impairs HTR-8/SVneo Trophoblast Cell Invasion via the PI3K/AKT Signaling Pathway

OBJECTIVES

The pathogenesis of preeclampsia (PE) is associated with impaired trophoblast invasion, which results in placental insufficiency. Our earlier studies demonstrated that tissue transglutaminase (tTG) is highly expressed in human PE serum. However, whether tTG participates in trophoblast invasion remains unclear. The aim of the present study was to determine the role and mechanism of tTG in regulating matrix metalloproteinase (MMP)-2/MMP-9 expression to reduce trophoblast invasiveness in PE.

METHODS

HTR-8/SVneo cells were transfected with a lentivirus vector and small interfering RNA targeting tTG. The protein level was detected by Western blotting. Cell proliferation and apoptosis were assessed by MTS and flow cytometry assays, respectively. Cell invasion was investigated by Transwell assay. In addition, the influence of tTG on PI3K and AKT mRNA levels in HTR-8/SVneo cells was evaluated using reverse transcription-quantitative PCR.

RESULTS

tTG-overexpression inhibited HTR-8/SVneo cell proliferation and invasion and promoted apoptosis. In addition, upregulation of tTG induced an increase of PI3K and phosphorylated AKT and a decrease of MMP-2 and MMP-9 expression. tTG-knockdown significantly promoted the proliferation and invasion of HTR-8/SVneo cells and inhibited the apoptosis. Furthermore, the PI3K expression level was reduced, and the MMP-2/MMP-9 protein levels were increased.

CONCLUSION

Taken together, the present study demonstrated that tTG-overexpression inhibited HTR-8/SVneo cell invasion via reducing the expression of MMP-2 and MMP-9 by activating PI3K/AKT signaling pathway, which may lead to the occurrence or development of PE. The present data provide new insights into modulation of tTG expression as a potential therapeutic target for PE.

Effects of Manual Therapy on the Diaphragm in the Musculoskeletal System: A Systematic Review

OBJECTIVES

To analyze the effects at the musculoskeletal level of manual treatment of the diaphragm muscle in adults.

DATA SOURCES

Systematic review using 4 databases: PubMed, Science Direct, Web of Science, and Scopus.

STUDY SELECTION AND DATA EXTRACTION

Two independent reviewers applied the selection criteria and assessed the quality of the studies using the Physiotherapy Evidence Database scale for experimental studies. A third reviewer intervened in cases where a consensus had not been reached. A total of 9 studies were included in the review.

DATA SYNTHESIS

Manual therapy directed to the diaphragm has been shown to be effective in terms of the immediate increase in diaphragmatic mobility and thoracoabdominal expansion. The immediate improvement in the posterior muscle chain flexibility test is another of the most frequently found findings in the evaluated studies. Limited studies show improvements at the lumbar and cervical level in the range of motion and in pain.

CONCLUSION

Manual diaphragm therapy has shown an immediate significant effect on parameters related to costal, spinal, and posterior muscle chain mobility. Further studies are needed, not only to demonstrate the effectiveness of manual diaphragm therapy in the long-term and in symptomatic populations, but also to investigate the specific neurophysiological mechanisms involved in this type of therapy.

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)

Motivation

A large variety of molecular interactions occurs between biomolecular components in cells. When a molecular interaction results in a regulatory effect, exerted by one component onto a downstream component, a so-called ‘causal interaction’ takes place. Causal interactions constitute the building blocks in our understanding of larger regulatory networks in cells. These causal interactions and the biological processes they enable (e.g. gene regulation) need to be described with a careful appreciation of the underlying molecular reactions. A proper description of this information enables archiving, sharing and reuse by humans and for automated computational processing. Various representations of causal relationships between biological components are currently used in a variety of resources.

Results

Here, we propose a checklist that accommodates current representations, called the Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). This checklist defines both the required core information, as well as a comprehensive set of other contextual details valuable to the end user and relevant for reusing and reproducing causal molecular interaction information. The MI2CAST checklist can be used as reporting guidelines when annotating and curating causal statements, while fostering uniformity and interoperability of the data across resources.

Availability and implementation

The checklist together with examples is accessible at https://github.com/MI2CAST/MI2CAST

Supplementary information

Supplementary data are available at Bioinformatics online.

Dataset search in biodiversity research: Do metadata in data repositories reflect scholarly information needs?

The increasing amount of publicly available research data provides the opportunity to link and integrate data in order to create and prove novel hypotheses, to repeat experiments or to compare recent data to data collected at a different time or place. However, recent studies have shown that retrieving relevant data for data reuse is a time-consuming task in daily research practice. In this study, we explore what hampers dataset retrieval in biodiversity research, a field that produces a large amount of heterogeneous data. In particular, we focus on scholarly search interests and metadata, the primary source of data in a dataset retrieval system. We show that existing metadata currently poorly reflect information needs and therefore are the biggest obstacle in retrieving relevant data. Our findings indicate that for data seekers in the biodiversity domain environments, materials and chemicals, species, biological and chemical processes, locations, data parameters and data types are important information categories. These interests are well covered in metadata elements of domain-specific standards. However, instead of utilizing these standards, large data repositories tend to use metadata standards with domain-independent metadata fields that cover search interests only to some extent. A second problem are arbitrary keywords utilized in descriptive fields such as title, description or subject. Keywords support scholars in a full text search only if the provided terms syntactically match or their semantic relationship to terms used in a user query is known.

A Minimal Information Model for Potential Drug-Drug Interactions

Despite the significant health impacts of adverse events associated with drug-drug interactions, no standard models exist for managing and sharing evidence describing potential interactions between medications. Minimal information models have been used in other communities to establish community consensus around simple models capable of communicating useful information. This paper reports on a new minimal information model for describing potential drug-drug interactions. A task force of the Semantic Web in Health Care and Life Sciences Community Group of the World-Wide Web consortium engaged informaticians and drug-drug interaction experts in in-depth examination of recent literature and specific potential interactions. A consensus set of information items was identified, along with example descriptions of selected potential drug-drug interactions (PDDIs). User profiles and use cases were developed to demonstrate the applicability of the model. Ten core information items were identified: drugs involved, clinical consequences, seriousness, operational classification statement, recommended action, mechanism of interaction, contextual information/modifying factors, evidence about a suspected drug-drug interaction, frequency of exposure, and frequency of harm to exposed persons. Eight best practice recommendations suggest how PDDI knowledge artifact creators can best use the 10 information items when synthesizing drug interaction evidence into artifacts intended to aid clinicians. This model has been included in a proposed implementation guide developed by the HL7 Clinical Decision Support Workgroup and in PDDIs published in the CDS Connect repository. The complete description of the model can be found at https://w3id.org/hclscg/pddi.

Adding Toxicological Context to Nanotoxicity Study Reporting Using the NanoTox Metadata List

This paper proposes a list of specifications (NanoTox metadata list) to be reported about nanotoxicity experiments (metadata) together with resultant data to add toxicological context to reported studies. In areas involving nanomaterials (NMs), existing metadata reporting standards include the reporting of experimental conditions and protocols (MIRIBEL) and material characteristics (MINChar and MIAN), as well as reporting focused on specific experiments (MINBE). NanoCRED is a similarly transparent and structured framework, however, it is developed to guide risk assessors in evaluating the reliability and relevance of NM ecotoxicity studies. There is no reporting standard which would include interpretation of the aims and outcomes of nanotoxicity studies beyond regulatory purposes. The proposed NanoTox metadata reporting checklist is elaborated to extend reporting toward describing nanotoxicological context and thus is a logical complement to technology/material-assay focused reporting checklists. It is further designed to allow for NM toxicity data and knowledge integration, reuse, and communication. Its ultimate goal is to adhere to the basic rules of toxicology when taking a stand on the toxicity of NMs and to limit speculations on safety. As nanotoxicology becomes more interdisciplinary with the advent of new tools and new materials to be tested, reporting standards will contribute to cross-disciplinary communication.

The Coming of Age for Big Data in Systems Radiobiology, an Engineering Perspective

As high-throughput approaches in biological and biomedical research are transforming the life sciences into information-driven disciplines, modern analytics platforms for big data have started to address the needs for efficient and systematic data analysis and interpretation. We observe that radiobiology is following this general trend, with -omics information providing unparalleled depth into the biomolecular mechanisms of radiation response-defined as systems radiobiology. We outline the design of computational frameworks and discuss the analysis of big data in low-dose ionizing radiation (LDIR) responses of the mammalian brain. Following successful examples and best practices of approaches for the analysis of big data in life sciences and health care, we present the needs and requirements for radiation research. Our goal is to raise awareness for the radiobiology community about the new technological possibilities that can capture complex information and execute data analytics on a large scale. The production of large data sets from genome-wide experiments (quantity) and the complexity of radiation research with multidimensional experimental designs (quality) will necessitate the adoption of latest information technologies. The main objective was to translate research results into applied clinical and epidemiological practice and understand the responses of biological tissues to LDIR to define new radiation protection policies. We envisage a future where multidisciplinary teams include data scientists, artificial intelligence experts, DevOps engineers, and of course radiation experts to fulfill the augmented needs of the radiobiology community, accelerate research, and devise new strategies.

Method comparison studies of telomere length measurement using qPCR approaches: A critical appraisal of the literature

Use of telomere length (TL) as a biomarker for various environmental exposures and diseases has increased in recent years. Various methods have been developed to measure telomere length. Polymerase chain reaction (PCR)-based methods remain wide-spread for population-based studies due to the high-throughput capability. While several studies have evaluated the repeatability and reproducibility of different TL measurement methods, the results have been variable. We conducted a literature review of TL measurement cross-method comparison studies that included a PCR-based method published between January 1, 2002 and May 25, 2020. A total of 25 articles were found that matched the inclusion criteria. Papers were reviewed for quality of methodologic reporting of sample and DNA quality, PCR assay characteristics, sample blinding, and analytic approaches to determine final TL. Overall, methodologic reporting was low as assessed by two different reporting guidelines for qPCR-based TL measurement. There was a wide range in the reported correlation between methods (as assessed by Pearson’s r) and few studies utilized the recommended intra-class correlation coefficient (ICC) for assessment of assay repeatability and methodologic comparisons. The sample size for nearly all studies was less than 100, raising concerns about statistical power. Overall, this review found that the current literature on the relation between TL measurement methods is lacking in validity and scientific rigor. In light of these findings, we present reporting guidelines for PCR-based TL measurement methods and results of analyses of the effect of assay repeatability (ICC) on statistical power of cross-sectional and longitudinal studies. Additional cross-laboratory studies with rigorous methodologic and statistical reporting, adequate sample size, and blinding are essential to accurately determine assay repeatability and replicability as well as the relation between TL measurement methods.

KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling

The KiMoSys (https://kimosys.org), launched in 2014, is a public repository of published experimental data, which contains concentration data of metabolites, protein abundances and flux data. It offers a web-based interface and upload facility to share data, making it accessible in structured formats, while also integrating associated kinetic models related to the data. In addition, it also supplies tools to simplify the construction process of ODE (Ordinary Differential Equations)-based models of metabolic networks. In this release, we present an update of KiMoSys with new data and several new features, including (i) an improved web interface, (ii) a new multi-filter mechanism, (iii) introduction of data visualization tools, (iv) the addition of downloadable data in machine-readable formats, (v) an improved data submission tool, (vi) the integration of a kinetic model simulation environment and (vii) the introduction of a unique persistent identifier system. We believe that this new version will improve its role as a valuable resource for the systems biology community. Database URL:  www.kimosys.org.

Reporting of Hybrid Data and the Difficulties with Cross-Discipline Research Techniques

Peer review is the way in which we, as scientists, criticise, check, and confirm the findings of our colleagues. The process of peer review relies on individuals in all fields applying their particular expertise and determining if they agree with the findings submitted for publication. In recent years, there has been a significant rise in the number of manuscripts submitted for publication that draw from a range of disparate and complementary fields. This has created the curious situation where an expert may be requested to review a manuscript that is only partially within their immediate field of expertise. The issue that arises is that, without full knowledge of the data, techniques, methodologies, and principles that are presented, it is difficult for reviewers to make properly informed decisions, especially when it can take an entire career to reach that specific level of expertise in a single field. From this perspective, we explore these issues and also provide a commentary on how peer review could evolve in the context of a changing cross-disciplinarily-focused scientific landscape.

Metadata Stewardship in Nanosafety Research: Community-Driven Organisation of Metadata Schemas to Support FAIR Nanoscience Data

The emergence of nanoinformatics as a key component of nanotechnology and nanosafety assessment for the prediction of engineered nanomaterials (NMs) properties, interactions, and hazards, and for grouping and read-across to reduce reliance on animal testing, has put the spotlight firmly on the need for access to high-quality, curated datasets. To date, the focus has been around what constitutes data quality and completeness, on the development of minimum reporting standards, and on the FAIR (findable, accessible, interoperable, and reusable) data principles. However, moving from the theoretical realm to practical implementation requires human intervention, which will be facilitated by the definition of clear roles and responsibilities across the complete data lifecycle and a deeper appreciation of what metadata is, and how to capture and index it. Here, we demonstrate, using specific worked case studies, how to organise the nano-community efforts to define metadata schemas, by organising the data management cycle as a joint effort of all players (data creators, analysts, curators, managers, and customers) supervised by the newly defined role of data shepherd. We propose that once researchers understand their tasks and responsibilities, they will naturally apply the available tools. Two case studies are presented (modelling of particle agglomeration for dose metrics, and consensus for NM dissolution), along with a survey of the currently implemented metadata schema in existing nanosafety databases. We conclude by offering recommendations on the steps forward and the needed workflows for metadata capture to ensure FAIR nanosafety data.

Food Phenotyping: Recording and Processing of Non-Targeted Liquid Chromatography Mass Spectrometry Data for Verifying Food Authenticity

Experiments based on metabolomics represent powerful approaches to the experimental verification of the integrity of food. In particular, high-resolution non-targeted analyses, which are carried out by means of liquid chromatography-mass spectrometry systems (LC-MS), offer a variety of options. However, an enormous amount of data is recorded, which must be processed in a correspondingly complex manner. The evaluation of LC-MS based non-targeted data is not entirely trivial and a wide variety of strategies have been developed that can be used in this regard. In this paper, an overview of the mandatory steps regarding data acquisition is given first, followed by a presentation of the required preprocessing steps for data evaluation. Then some multivariate analysis methods are discussed, which have proven to be particularly suitable in this context in recent years. The publication closes with information on the identification of marker compounds.

A Systematic Approach to Review of in vitro Methods in Brain Tumour Research (SAToRI-BTR): Development of a Preliminary Checklist for Evaluating Quality and Human Relevance

Background

A wide range of human in vitro methods have been developed and there is considerable interest in the potential of these studies to address questions related to clinical (human) use of drugs, and the pathobiology of tumours. This requires agreement on how to assess the strength of evidence available (i.e., quality and quantity) and the human-relevance of such studies. The SAToRI-BTR (Systematic Approach To Review of in vitro methods in Brain Tumour Research) project seeks to identify relevant appraisal criteria to aid planning and/or evaluation of brain tumour studies using in vitro methods.

Objectives

To identify criteria for evaluation of quality and human relevance of in vitro brain tumour studies; to assess the general acceptability of such criteria to senior scientists working within the field.

Methods

Stage one involved identification of potential criteria for evaluation of in vitro studies through: (1) an international survey of brain tumour researchers; (2) interviews with scientists, clinicians, regulators, and journal editors; (3) analysis of relevant reports, documents, and published studies. Through content analysis of findings, an initial list of criteria for quality appraisal of in vitro studies of brain tumours was developed. Stage two involved review of the criteria by an expert panel (Delphi process).

Results

Results of stage one indicated that methods for and quality of review of in vitro studies are highly variable, and that improved reporting standards are needed. 129 preliminary criteria were identified; duplicate and highly context-specific items were removed, resulting in 48 criteria for review by the expert (Delphi) panel. 37 criteria reached agreement, resulting in a provisional checklist for appraisal of in vitro studies in brain tumour research.

Conclusion

Through a systematic process of collating assessment criteria and subjecting these to expert review, SAToRI-BTR has resulted in preliminary guidance for appraisal of in vitro brain tumour studies. Further development of this guidance, including investigating strategies for adaptation and dissemination across different sub-fields of brain tumour research, as well as the wider in vitro field, is planned.

Interactions of Osteoprogenitor Cells with a Novel Zirconia Implant Surface

Background: This study compared the in vitro response of a mouse pre-osteoblast cell line on a novel sandblasted zirconia surface with that of titanium. Material and Methods: The MC3T3-E1 subclone 4 osteoblast precursor cell line was cultured on either sandblasted titanium (SBCpTi) or sandblasted zirconia (SBY-TZP). The surface topography was analysed by three-dimensional laser microscopy and scanning electron microscope. The wettability of the discs was also assessed. The cellular response was quantified by assessing the morphology (day 1), proliferation (day 1, 3, 5, 7, 9), viability (day 1, 9), and migration (0, 6, 24 h) assays. Results: The sandblasting surface treatment in both titanium and zirconia increased the surface roughness by rendering a defined surface topography with titanium showing more apparent nano-topography. The wettability of the two surfaces showed no significant difference. The zirconia surface resulted in improved cellular spreading and a significantly increased rate of migration compared to titanium. However, the cellular proliferation and viability noted in our experiments were not significantly different on the zirconia and titanium surfaces. Conclusions: The novel, roughened zirconia surface elicited cellular responses comparable to, or exceeding that, of titanium. Therefore, this novel zirconia surface may be an acceptable substitute for titanium as a dental implant material.

NFDI4Chem - Towards a National Research Data Infrastructure for Chemistry in Germany

The vision of NFDI4Chem is the digitalisation of all key steps in chemical research to support scientists in their efforts to collect, store, process, analyse, disclose and re-use research data. Measures to promote Open Science and Research Data Management (RDM) in agreement with the FAIR data principles are fundamental aims of NFDI4Chem to serve the chemistry community with a holistic concept for access to research data. To this end, the overarching objective is the development and maintenance of a national research data infrastructure for the research domain of chemistry in Germany, and to enable innovative and easy to use services and novel scientific approaches based on re-use of research data. NFDI4Chem intends to represent all disciplines of chemistry in academia. We aim to collaborate closely with thematically related consortia. In the initial phase, NFDI4Chem focuses on data related to molecules and reactions including data for their experimental and theoretical characterisation.

This overarching goal is achieved by working towards a number of key objectives:

Key Objective 1: Establish a virtual environment of federated repositories for storing, disclosing, searching and re-using research data across distributed data sources. Connect existing data repositories and, based on a requirements analysis, establish domain-specific research data repositories for the national research community, and link them to international repositories.

Key Objective 2: Initiate international community processes to establish minimum information (MI) standards for data and machine-readable metadata as well as open data standards in key areas of chemistry. Identify and recommend open data standards in key areas of chemistry, in order to support the FAIR principles for research data. Finally, develop standards, if there is a lack.

Key Objective 3: Foster cultural and digital change towards Smart Laboratory Environments by promoting the use of digital tools in all stages of research and promote subsequent Research Data Management (RDM) at all levels of academia, beginning in undergraduate studies curricula.

Key Objective 4: Engage with the chemistry community in Germany through a wide range of measures to create awareness for and foster the adoption of FAIR data management. Initiate processes to integrate RDM and data science into curricula. Offer a wide range of training opportunities for researchers.

Key Objective 5: Explore synergies with other consortia and promote cross-cutting development within the NFDI.

Key Objective 6: Provide a legally reliable framework of policies and guidelines for FAIR and open RDM.

Standardization of the minimum information for publication of infrared-related data when microplastics are characterized

Infrared spectrometry (IR) became a workhorse to characterize microplastics (MPs) worldwide. However, reports on the experimental conditions to measure them decreased alarmingly. As complete, relevant information on the instrumental setup determining IR spectra is crucial for scientific reproducibility, ca. 50% of the papers that reported FTIR to measure MPs were evaluated and it was found that most studies cannot be replicated due to missing experimental details. To ameliorate this, the most critical parameters influencing IR spectra are depicted, their impact when matching a spectrum against databases exemplified, and, following efforts from other scientific fields, a minimum information for publication of IR-related data on MPs characterization (MIPIR-MP) is proposed, along with a brief, simple paragraph to resume the most critical information to be reported. This can be used to improve the worrying figures that point out to a reproducibility crisis in the field, as disclosed by the survey.