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DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

The standardization of data, encompassing both primary and contextual information (metadata), plays a pivotal role in facilitating data (re-)use, integration, and knowledge generation. However, the biodiversity and omics communities, converging on omics biodiversity data, have historically developed and adopted their own distinct standards, hindering effective (meta)data integration and collaboration. In response to this challenge, the Task Group (TG) for Sustainable DwC-MIxS Interoperability was established. Convening experts from the Biodiversity Information Standards (TDWG) and the Genomic Standards Consortium (GSC) alongside external stakeholders, the TG aimed to promote sustainable interoperability between the Minimum Information about any (x) Sequence (MIxS) and Darwin Core (DwC) specifications. To achieve this goal, the TG utilized the Simple Standard for Sharing Ontology Mappings (SSSOM) to create a comprehensive mapping of DwC keys to MIxS keys. This mapping, combined with the development of the MIxS-DwC extension, enables the incorporation of MIxS core terms into DwC-compliant metadata records, facilitating seamless data exchange between MIxS and DwC user communities. Through the implementation of this translation layer, data produced in either MIxS- or DwC-compliant formats can now be efficiently brokered, breaking down silos and fostering closer collaboration between the biodiversity and omics communities. To ensure its sustainability and lasting impact, TDWG and GSC have both signed a Memorandum of Understanding (MoU) on creating a continuous model to synchronize their standards. These achievements mark a significant step forward in enhancing data sharing and utilization across domains, thereby unlocking new opportunities for scientific discovery and advancement. [ABSTRACT FROM AUTHOR]

A catalog of mercurian craters that retain their central peak or peak‐ring structure was created to aid target prioritization for the Mercury Imaging X‐ray Spectrometer (MIXS), now on its way to Mercury aboard BepiColombo. Preliminary analysis of the MIXS crater catalog suggested a potential spatial correlation between an abnormally high spatial density of peak‐ring basins and a region of Mercury with elevated Mg/Si values (High‐Magnesium Terrane [HMT]). Robust statistical analysis of previously published crater catalogs confirmed that the spatial correlation exists, with an overall confidence level of 97.7%, specifically between peak‐ring basins and the HMT, delineated by a contour of Mg/Si = mean + 2σ = 0.648. Applying empirical impact cratering scaling laws to the 15 basins intersecting the HMT suggested that all have excavated material from ~13 to 20 km depth. None of the basins excavated mantle material, predicting instead that deep crustal material contains elevated Mg/Si material. However, five of the basins are predicted to have melted underlying mantle material, which might be a contributing factor in the elevated Mg/Si signature. In the absence of resolvable volcanic features associated with the rise of basaltic melts from the mantle, we favor excavation of deep crustal, high Mg/Si material. MIXS‐T is capable of spatially resolving individual features associated with peak‐ring basins and it is proposed that the 15 basins within the HMT are prioritized targets for MIXS, to test the hypothesis of exposed deep‐crustal material. Plain Language Summary: A catalog of craters that retain a central peak, or peak‐ring structure, was created in order to prioritize targets for the Mercury Imaging X‐ray Spectrometer on the BepiColombo mission. Preliminary analysis of this catalog revealed a potential spatial correlation between a region with an abnormally high spatial density of peak‐ring basins and a region with high Magnesium‐to‐Silicon ratios. Robust statistical analysis of previously published crater catalogs was used to confirm that the spatial correlation exists. Investigation of the depth of excavation for material ejected during impact indicates that the impacts within the main high Mg/Si terrane excavated deep crustal, rather than mantle, material of high Mg/Si ratio. Current X‐ray data do not spatially resolve the basin features to confirm these hypotheses but future observations by the Mercury Imaging X‐ray Spectrometer are capable of doing so. Key Points: There is a statistically strong spatial correlation between a group of 15 peak‐ring basins on Mercury and the high Mg/Si regionCrater uplift modeling and an absence of associated volcanic landforms, suggest excavation of deep crustal material with high Mg/SiThe High Mg/Si region will be a key target for Mercury Imaging X‐ray Spectrometer‐T on BepiColombo to test the model of deep crustal excavation [ABSTRACT FROM AUTHOR]

Abstract Background The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association studies which identify genetic determinants of pathogen virulence and drug resistance, as well as phylogenetic studies designed to track the origin and spread of disease outbreaks. These omics studies are complex and often employ multiple assay technologies including genomics, metagenomics, transcriptomics, proteomics, and metabolomics. To maximize the impact of omics studies, it is essential that data be accompanied by detailed contextual metadata (e.g., specimen, spatial-temporal, phenotypic characteristics) in clear, organized, and consistent formats. Over the years, many metadata standards developed by various metadata standards initiatives have arisen; the Genomic Standards Consortium’s minimal information standards (MIxS), the GSCID/BRC Project and Sample Application Standard. Some tools exist for tracking metadata, but they do not provide event based capabilities to configure, collect, validate, and distribute metadata. To address this gap in the scientific community, an event based data-driven application, OMeta, was created that allows users to quickly configure, collect, validate, distribute, and integrate metadata. Results A data-driven web application, OMeta, has been developed for use by researchers consisting of a browser-based interface, a command-line interface (CLI), and server-side components that provide an intuitive platform for configuring, capturing, viewing, and sharing metadata. Project and sample metadata can be set based on existing standards or based on projects goals. Recorded information includes details on the biological samples, procedures, protocols, and experimental technologies, etc. This information can be organized based on events, including sample collection, sample quantification, sequencing assay, and analysis results. OMeta enables configuration in various presentation types: checkbox, file, drop-box, ontology, and fields can be configured to use the National Center for Biomedical Ontology (NCBO), a biomedical ontology server. Furthermore, OMeta maintains a complete audit trail of all changes made by users and allows metadata export in comma separated value (CSV) format for convenient deposition of data into public databases. Conclusions We present, OMeta, a web-based software application that is built on data-driven principles for configuring and customizing data standards, capturing, curating, and sharing metadata.

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields-isotope, isotopolog, isotopolog label, labeling approach, and gradient position-and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology., (© Published by Oxford University Press on behalf of GigaScience 2024.)

Background: The development of high-throughput sequencing and analysis has accelerated multi-omics studies of thousands of microbial species, metagenomes, and infectious disease pathogens. Omics studies are enabling genotype-phenotype association studies which identify genetic determinants of pathogen virulence and drug resistance, as well as phylogenetic studies designed to track the origin and spread of disease outbreaks. These omics studies are complex and often employ multiple assay technologies including genomics, metagenomics, transcriptomics, proteomics, and metabolomics. To maximize the impact of omics studies, it is essential that data be accompanied by detailed contextual metadata (e.g., specimen, spatial-temporal, phenotypic characteristics) in clear, organized, and consistent formats. Over the years, many metadata standards developed by various metadata standards initiatives have arisen; the Genomic Standards Consortium's minimal information standards (MIxS), the GSCID/BRC Project and Sample Application Standard. Some tools exist for tracking metadata, but they do not provide event based capabilities to configure, collect, validate, and distribute metadata. To address this gap in the scientific community, an event based data-driven application, OMeta, was created that allows users to quickly configure, collect, validate, distribute, and integrate metadata. Results: A data-driven web application, OMeta, has been developed for use by researchers consisting of a browser-based interface, a command-line interface (CLI), and server-side components that provide an intuitive platform for configuring, capturing, viewing, and sharing metadata. Project and sample metadata can be set based on existing standards or based on projects goals. Recorded information includes details on the biological samples, procedures, protocols, and experimental technologies, etc. This information can be organized based on events, including sample collection, sample quantification, sequencing assay, and analysis results. OMeta enables configuration in various presentation types: checkbox, file, drop-box, ontology, and fields can be configured to use the National Center for Biomedical Ontology (NCBO), a biomedical ontology server. Furthermore, OMeta maintains a complete audit trail of all changes made by users and allows metadata export in comma separated value (CSV) format for convenient deposition of data into public databases. Conclusions: We present, OMeta, a web-based software application that is built on data-driven principles for configuring and customizing data standards, capturing, curating, and sharing metadata. [ABSTRACT FROM AUTHOR]

The Mercury Imaging X-ray Spectrometer (MIXS) will be launched on board of the 5th ESA cornerstone mission BepiColombo. The two channel instrument MIXS is dedicated to the exploration of the elemental composition of the mercurian surface by imaging x-ray spectroscopy of the elemental fluorescence lines. One of the main scientific goals of MIXS is to provide spatially resolved elemental abundance maps of key rock-forming elements. MIXS will be the successor of the XRS instrument, which is currently orbiting Mercury on board of NASAs satellite MESSENGER. MIXS will provide unprecedented spectral and spatial resolution due to its innovative detector and optics concepts. The MIXS target energy band ranges from 0.5 to 7 keV and allows to directly access the Fe-L line at 0.7 keV, which was not accessible to previous missions. In addition, the high spectroscopic resolution of FWHM ≤ 200 eV at the reference energy of 1 keV after one year in Mercury orbit, allows to separate the x-ray fluorescence emission lines of important elements like Mg (1.25 keV) and Al (1.49 keV) without the need for any filter. The detectors for the energy and spatially resolved detection of x-rays for both channels are identical DEPFET (DEpleted P-channel FET) active pixel detectors. We report on the calibration of the MIXS flight and flight spare detector modules at the PTB (Physikalisch-Technische Bundesanstalt) beamlines at the BESSY II synchrotron radiation facility. Each detector was calibrated at least at 10 discrete energies in the energy range from 0.5 to 10 keV. The excellent spectroscopic performance of all three detector modules was verified. [ABSTRACT FROM AUTHOR]

The Mercury imaging X-ray spectrometer (MIXS) on board of ESA's fifth cornerstone mission BepiColombo will be the first space instrument using DEpleted P-channel FET (DEPFET) based detectors. The MIXS spectrometer comprises two channels with identical focal plane detectors and is dedicated to energy resolved imaging of X-ray fluorescence from the mercurial surface. [ABSTRACT FROM PUBLISHER]

MIxS (Minimum Information about any Sequence) (Yilmaz et al. 2011) is a metadata standard of the Genomics Standards Consortium (GSC), designed to make sequence data findable, accessible, and interoperable. It contains fields for recording physical and chemical characteristics of the sampling environment, geographical and habitat information, and other metadata about the sample and its provenance, which are critical for downstream intepretation of data derived from the sample. We will present our experience implementing MIxS in two metagenomic information systems -- the Earth Microbiome Project (EMP) and the Government of Canada (GoC) Ecobiomics project. The EMP (Gilbert et al. 2014) is an ongoing effort to crowdsource environmental microbiome samples from around Earth, then sequence and analyze them using a standardized workflow. The EMP has aggregated and sequenced over 50,000 samples, which are queryable using a publicly available catalogue. A meta-analysis of the first 25,000 samples is currently in review. MIxS and the Environment Ontology (ENVO) (Buttigieg et al. 2016) have been useful in structuring environmental metadata from EMP studies. For the particular application of the EMP meta-analysis, however, several issues were encountered: often there are multiple possible 'correct' assignments to the biome, feature, and material fields; the fields are not hierarchical, limiting logical organization; and the primary ecological factors differentiating microbial communites are not captured. In response to these challenges, the EMP team worked with the ENVO team to devise a new hierarchical structure, the EMP ontology (EMPO), that captures the primary axes along which microbial communities tend to be structured (host-associated or not, saline or not). EMPO is an application ontology, with a formally defined W3C Web Ontology Language (OWL) document mapping to existing ontologies, enabling reuse by the microbial ecology community. Ecobiomics is a joint project of multiple GoC departments and involves the complete workflow, from sampling in a variety of aquatic, soil, and benthic environments, through sample prep, DNA extraction, library prep, sequencing, and analysis. In contrast to the EMP--where some of the samples and metadata had been collected before the establishment of the MIxS standards--the Ecobiomics project has been able to create metadata profiles for each sub-project to conform to, extend, and build, upon the existing MIxS standards. Despite these two different contexts, EMP and Ecobiomics encountered a number of common issues that prevented a complete implementation of MIxS. These issues include ambiguous term names and definitions; inconsistencies amongst the environmental packages; non-standard ways of dealing with units; and a number of issues surrounding ENVO (the Environment Ontology), which is required for filling out the mandatory MIxS fields "Environmental material", "Biome", and "Environmental feature". We will describe these issues, and, more generally, the successes and challenges of our implementations. [ABSTRACT FROM AUTHOR]

Abstract: Focal plane instrumentation based on DEPFET Macropixel devices, being a combination of the Detector–Amplifier structure DEPFET with a silicon drift chamber (SDD), has been proposed for the MIXS (Mercury Imaging X-ray Spectrometer) instrument on ESA''s Mercury exploration mission BepiColombo. MIXS images X-ray fluorescent radiation from the Mercury surface with a lightweight X-ray mirror system on the focal plane detector to measure the spatially resolved element abundance in Mercury''s crust. The sensor needs to have an energy resolution better than 200eV FWHM at 1keV and is required to cover an energy range from 0.5 to 10keV, for a pixel size of . Main challenges for the instrument are radiation damage and the difficult thermal environment in the mercury orbit. The production of the first batch of flight devices has been finished at the MPI semiconductor laboratory. Prototype modules have been assembled to verify the electrical properties of the devices; selected results are presented here. The prototype devices, Macropixel prototypes for the SIMBOL-X focal plane, are electrically fully compatible, but have a pixel size of 0.5×0.5mm2. Excellent homogeneity and near Fano-limited energy resolution at high readout speeds have been observed on these devices. [Copyright &y& Elsevier]

Background: Data papers have emerged as a powerful instrument for open data publishing, obtaining credit, and establishing priority for datasets generated in scientific experiments. Academic publishing improves data and metadata quality through peer review and increases the impact of datasets by enhancing their visibility, accessibility, and reusability., Objective: We aimed to establish a new type of article structure and template for omics studies: the omics data paper. To improve data interoperability and further incentivize researchers to publish well-described datasets, we created a prototype workflow for streamlined import of genomics metadata from the European Nucleotide Archive directly into a data paper manuscript., Methods: An omics data paper template was designed by defining key article sections that encourage the description of omics datasets and methodologies. A metadata import workflow, based on REpresentational State Transfer services and Xpath, was prototyped to extract information from the European Nucleotide Archive, ArrayExpress, and BioSamples databases., Findings: The template and workflow for automatic import of standard-compliant metadata into an omics data paper manuscript provide a mechanism for enhancing existing metadata through publishing., Conclusion: The omics data paper structure and workflow for import of genomics metadata will help to bring genomic and other omics datasets into the spotlight. Promoting enhanced metadata descriptions and enforcing manuscript peer review and data auditing of the underlying datasets brings additional quality to datasets. We hope that streamlined metadata reuse for scholarly publishing encourages authors to create enhanced metadata descriptions in the form of data papers to improve both the quality of their metadata and its findability and accessibility., (© The Author(s) 2021. Published by Oxford University Press on behalf of The Royal Astronomical Society.)

Microbial organisms - including Archaea, Bacteria and unicellular Eukaryota - collectively dominate the Earth in terms of bio- and functional diversity. Their study, often constrained by technology, has strongly benefited from the recent advancements in high-throughput DNA sequencing techniques. The vast amounts of microbial data generated in the wake of these developments, however, remains severely underrepresented on open access biodiversity data repositories (e.g. the Global Biodiversity Information Facility; GBIF). Moreover, when sequencing data has been made publicly available, is often poorly annotated with metadata and environmental variables, making it difficult to find or query. Therefore, the microbial Antarctic Resource System (mARS) aims to fill this lacuna by documenting and geo-referencing microbial datasets and linking the sequence data in the International Nucleotide Sequence Database Collaboration (INSDC) repositories with the associated environmental measurements on mARS, which is aimed to be interoperable with both INSDC and GBIF. This way, mARS helps to preserve environmental data and the metadata that is crucial for the correct processing and interpretation of sequence data, while it also connects researchers via its webportal to the existing wealth of molecular information, and allows these datasets to be more effectively accessed. Given the general complexity of microbial ecological datasets, mARS needs to operate between different data archiving standards, such as MIxS (see https://press3.mcs.anl.gov/gensc/mixs/), which is oriented towards DNA sequence data, and the biodiversity-based DarwinCore standard. Currently, mARS tries to address the challenges of integrating microbial data with these existing systems as well as connecting with the communities behind them, by documenting the datasets on GBIF's extensions or investigate the feasibility of routinely processing raw sequence data into occurrence datasets using the open computing facilities offered by the European Molecular Biology Laboratory's (EMBL) MGnify resource. [ABSTRACT FROM AUTHOR]