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There is a significant amount of data available about students and their learning activities in many educational systems today. However, these datasets are frequently spread across several different digital services, making it challenging to use them strategically. In addition, there are no established standards for collecting, processing, analyzing, and presenting such data. As a result, school leaders, teachers, and students do not capitalize on the possibility of making decisions based on data. This is a serious barrier to the improvement of work in schools, teacher and student progress, and the development of effective Educational Technology (EdTech) products and services. Data standards can be used as a protocol on how different IT systems communicate with each other. When working with data from different public and private institutions simultaneously (e.g., different municipalities and EdTech companies), having a trustworthy data pipeline for retrieving the data and storing it in a secure warehouse is critical. In this study, we propose a technical solution containing a data pipeline by employing a secure warehouse—the Swedish University Computer Network (SUNET), which is an interface for information exchange between operational processes in schools. We conducted a user study in collaboration with four municipalities and four EdTech companies based in Sweden. Our proposal involves introducing a data standard to facilitate the integration of educational data from diverse resources in our SUNET drive. To accomplish this, we created customized scripts for each stakeholder, tailored to their specific data formats, with the aim of merging the students’ data. The results of the first four steps show that our solution works. Once the results of the next three steps are in, we will contemplate scaling up our technical solution nationwide. With the implementation of the suggested data standard and the utilization of the proposed technical solution, diverse stakeholders, Bibliografiskt granskad

The Draco laboratory at HZDR is a versatile, multi-arm and multi-target-area facility, consisting of several, independent subsystems. The lack of an overarching DAQ is balanced by interfaces of the subsystems and custom inter-linking agents. We present recent progress of implementing such software agents, connecting to the center’s electronic lab documentation system. First, manual logging of shot parameters and observations is lifted from spreadsheet software to a flexible web-app, writing to a database (DB). The laser-internal logging is exported to a DB and internal software triggering is forwarded to experiments. That provides a connection between laser-internal indexing and experiment-based indexing (another DB) and enables near-online data processing. The latter comprises file path logging and validation according to the shot’s acquisition settings for further analysis as well as basic on-shot analysis scripts, both enabling near-online visualization to better guide the course of experiments. Likewise, parameters and results from simulations are logged to databases, enabling machine learning techniques and better computing resource management. For a long-term, FAIR storage, the HELPMI project starts exploring the possibilities of openPMD and NeXus to ingest experimental data. That project shall serve as initiative for the global LPA community to find a data and metadata standard.

HELPMI is a 2-year project, subsidized by the Helmholtz Metadata Collaboration, conducted by GSI, HI Jena and HZDR (lead). The aim is to start the development of a F.A.I.R. data standard for experimental data of the entire laser-plasma (LPA) community. Such standard does not yet exist. It will facilitate management and analysis of usually quite heterogeneous experimental data and logs by rich and machine-actionable metadata, allowing automated processing of broad and long data sets. To date, the LPA community is widely using openPMD, an open meta-standard, well-established for simulations. NeXus is a similarly hierarchical and extensible standard for various experimental methods of the Photon and Neutron science community. Within HELPMI, we plan to adopt NeXus for LPA experimental data and simultaneously to make openPMD and its API extensible for custom hierarchies like NeXus. Thereby we can achieve interoperability of the standards, circumventing the need for another standard. Alongside we will start developing a glossary of LPA experimental terms in order to achieve re-usability. The glossary shall be community-driven and technically open, extensible and implementation-independent.

HELPMI is a 2-year project, subsidized by the Helmholtz Metadata Collaboration, conducted by GSI, HI Jena and HZDR (lead). The aim is to start the development of a F.A.I.R. data standard for experimental data of the entire laser-plasma (LPA) community. Such standard does not yet exist. It will facilitate management and analysis of usually quite heterogeneous experimental data and logs by rich and machine-actionable metadata, allowing automated processing of broad and long data sets. To date, the LPA community is widely using openPMD, an open meta-standard, well-established for simulations. NeXus is a similarly hierarchical and extensible standard for various experimental methods of the Photon and Neutron science community. Within HELPMI, we plan to adopt NeXus for LPA experimental data and simultaneously to make openPMD and its API extensible for custom hierarchies like NeXus. Thereby we can achieve interoperability of the standards, circumventing the need for another standard. Alongside we will start developing a glossary of LPA experimental terms in order to achieve re-usability. The glossary shall be community-driven and technically open, extensible and implementation-independent.

The Internet of Things (IoT) notion is quickly influencing t he architectures of data-driven systems d ue to the ever-increasing rapid technological progress in all sectors. The IoT involves the collection and exchange of data from a large number of interconnected devices or sensors. The collected data is structured and transmitted in a variety of different data formats such as JSON, CBOR, BSON, or simply a binary format. The data format used by an IoT device can have a significant i mpact on t he efficiency of its data transmission. In general, using a more compact and efficient data format can help to reduce t he amount of data that needs to be transmitted, which can improve the overall speed and performance of the device. For example, using a binary data format rather than a text-based format can often result in smaller data sizes and faster transmission times. Similarly, using a binary format in a more compressed form can further help to reduce the size of the data being transmitted, which can further improve the efficiency of the transmission. In this paper, we propose Delta Binary (i.e., DeltaBin) to reduce the binary data format by transmitting only changed data. We assess DeltaBin using a real IoT deployment scenario.

ModelCIF (github.com/ihmwg/ModelCIF) is a data information framework developed for and by computational structural biologists to enable delivery of Findable, Accessible, Interoperable, and Reusable (FAIR) data to users worldwide. ModelCIF describes the specific set of attributes and metadata associated with macromolecular structures modeled by solely computational methods and provides an extensible data representation for deposition, archiving, and public dissemination of predicted three-dimensional (3D) models of macromolecules. It is an extension of the Protein Data Bank Exchange / macromolecular Crystallographic Information Framework (PDBx/mmCIF), which is the global data standard for representing experimentally-determined 3D structures of macromolecules and associated metadata. The PDBx/mmCIF framework and its extensions (e.g., ModelCIF) are managed by the Worldwide Protein Data Bank partnership (wwPDB, wwpdb.org) in collaboration with relevant community stakeholders such as the wwPDB ModelCIF Working Group (wwpdb.org/task/modelcif). This semantically rich and extensible data framework for representing computed structure models (CSMs) accelerates the pace of scientific discovery. Herein, we describe the architecture, contents, and governance of ModelCIF, and tools and processes for maintaining and extending the data standard. Community tools and software libraries that support ModelCIF are also described.

* NeXus provides a plethora of data structures that can be immediately used. * openPMD provides scalability to bigdata workflows and flexibility with respect to data format used. * Vocabulary extensions for describing meta-data for laser-plasma experiments mainly require Lasers, Targetry and Timing. * Candidate NeXus/H5 software packages for early openPMD migration: ** NeXus-API: NeXpy ** NeXus-Validator: punx ** NeXus-data source for browsing: h5wasm * To achieve critical mass: Provide value for Laser-Plasma experiments, stay pragmatic with design discussions, do small steps, but with an idea where to go.

PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular Crystallographic Information Framework (mmCIF), has become the data standard for structural biology. With its early roots in the domain of small-molecule crystallography, PDBx/mmCIF provides an extensible data representation that is used for deposition, archiving, remediation, and public dissemination of experimentally determined three-dimensional (3D) structures of biological macromolecules by the Worldwide Protein Data Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for computed structure models by ModelArchive (modelarchive.org), integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small angle scattering data by Small Angle Scattering Biological Data Bank SASBDB (sasbdb.org), and for models computed generated with the AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk). Community-driven development of PDBx/mmCIF spans three decades, involving contributions from researchers, software and methods developers in structural sciences, data repository providers, scientific publishers, and professional societies. Having a semantically rich and extensible data framework for representing a wide range of structural biology experimental and computational results, combined with expertly curated 3D biostructure data sets in public repositories, accelerates the pace of scientific discovery. Herein, we describe the architecture of the PDBx/mmCIF data standard, tools used to maintain representations of the data standard, governance, and processes by which data content standards are extended, plus community tools/software libraries available for processing and checking the integrity of PDBx/mmCIF data. Use cases exemplify how the members of the Worldwide Protein Data Bank have used PDBx/mmCIF as the foundation for its pipeline for delivering Findable, Accessible, Interoperable, and Reusable (FAIR) data to many millions of users worldwide.

The neurophysiology of cells and tissues are monitored electrophysiologically and optically in diverse experiments and species, ranging from flies to humans. Understanding the brain requires integration of data across this diversity, and thus these data must be findable, accessible, interoperable, and reusable (FAIR). This requires a standard language for data and metadata that can coevolve with neuroscience. We describe design and implementation principles for a language for neurophysiology data. Our open-source software (Neurodata Without Borders, NWB) defines and modularizes the interdependent, yet separable, components of a data language. We demonstrate NWB's impact through unified description of neurophysiology data across diverse modalities and species. NWB exists in an ecosystem, which includes data management, analysis, visualization, and archive tools. Thus, the NWB data language enables reproduction, interchange, and reuse of diverse neurophysiology data. More broadly, the design principles of NWB are generally applicable to enhance discovery across biology through data FAIRness.

Research data is an essential part of research and almost every publication in chemistry. The data itself can be valuable for reuse if sustainably deposited, annotated and archived. Thus, it is important to publish data following the FAIR principles, to make it findable, accessible, interoperable and reusable not only for humans but also in machine-readable form. This also improves transparency and reproducibility of research findings and fosters analytical work with scientific data to generate new insights, being only accessible with manifold and diverse datasets. Research data requires complete and informative metadata and use of open data formats to obtain interoperable data. Generic data formats like AnIML and JCAMP-DX have been used for many applications. Special formats for some analytical methods are already accepted, like mzML for mass spectrometry or nmrML and NMReDATA for NMR spectroscopy data. Other methods still lack common standards for data. Only a joint effort of chemists, instrument and software vendors, publishers and infrastructure maintainers can make sure that the analytical data will be of value in the future. In this review, we describe existing data formats in analytical chemistry and introduce guidelines for the development and use of standardized and open data formats.

Food microbiology researchers, risk assessment agencies and food business operators rely heavily on the reuse of knowledge that is available as data, models and tools. Unfortunately, such knowledge reuse remains challenging, as food safety data sets, models and tools are usually only available in platform-dependent or software-dependent formats that rarely comply to the Findability, Accessibility, Interoperability, and Reusability data principles. In recent years, the Risk Assessment Modelling and Knowledge Integration Platform (RAKIP) Initiative developed the so-called Food Safety Knowledge Exchange (FSKX) format. This development was accompanied by the creation of open-source software that facilitates the adoption of FSKX. Future work within RAKIP will focus on creating semantic interoperability in FSKX-related solutions and on the extension of the FSKX format towards other food microbiology knowledge.

Field observations of the soil-to-atmosphere CO2 flux—soil respiration, RS—are a prime example of ‘long tail’ data that historically have had neither centralized databases nor an agreed-upon reporting format. This has hindered scientific transparency, analytical reproducibility, and syntheses with respect to this globally-important component of the carbon cycle. Here we propose a new data and metadata reporting format for RS data, based on engagement with a wide range of researchers in the earth and ecological sciences as well as expert advisory panels. Our goal was a reporting format that would be relevant and useful for synthesis activities, optimizing data discoverability and usability while not placing an undue burden on data contributors. We describe previous RS data collection efforts, lessons learned from related databases and data-oriented networks (e.g., FLUXNET) in earth and ecological sciences, and the process of community consultation. The proposed reporting format focuses on chamber-level data and metadata, specifying measurement conditions and, for a given measurement period defined by beginning and ending timestamps, a mean RS flux (or CO2 concentration) and associated ancillary measurements. With input from the research community, we have also developed research data and metadata templates to support data collection adhering to the reporting format. Fundamentally, this format aims to enable findable, accessible, interoperable, and reusable data, while providing ‘future-proofing’ capabilities to support reanalyses using as yet unknown algorithms or approaches. This proposed RS reporting format is openly available online and is intended to be a dynamic document, subject to further community feedback and/or change.

Leaf-level gas exchange data support the mechanistic understanding of plant fluxes of carbon and water. These fluxes inform our understanding of ecosystem function, are an important constraint on parameterization of terrestrial biosphere models, are necessary to understand the response of plants to global environmental change, and are integral to efforts to improve crop production. Collection of these data using gas analyzers can be both technically challenging and time consuming, and individual studies generally focus on a small range of species, restricted time periods, or limited geographic regions. The high value of these data is exemplified by the many publications that reuse and synthesize gas exchange data, however the lack of metadata and data reporting conventions make full and efficient use of these data difficult. Here we propose a reporting format for leaf-level gas exchange data and metadata to provide guidance to data contributors on how to store data in repositories to maximize their discoverability, facilitate their efficient reuse, and add value to individual datasets. For data users, the reporting format will better allow data repositories to optimize data search and extraction, and more readily integrate similar data into harmonized synthesis products. The reporting format specifies data table variable naming and unit conventions, as well as metadata characterizing experimental conditions and protocols. For common data types that were the focus of this initial version of the reporting format, i.e., survey measurements, dark respiration, carbon dioxide and light response curves, and parameters derived from those measurements, we took a further step of defining required additional data and metadata that would maximize the potential reuse of those data types. To aid data contributors and the development of data ingest tools by data repositories we provided a translation table comparing the outputs of common gas exchange instruments. Extensive consult

Field observations of the soil-to-atmosphere CO2 flux—soil respiration, RS—are a prime example of ‘long tail’ data that historically have had neither centralized databases nor an agreed-upon reporting format. This has hindered scientific transparency, analytical reproducibility, and syntheses with respect to this globally-important component of the carbon cycle. Here we propose a new data and metadata reporting format for RS data, based on engagement with a wide range of researchers in the earth and ecological sciences as well as expert advisory panels. Our goal was a reporting format that would be relevant and useful for synthesis activities, optimizing data discoverability and usability while not placing an undue burden on data contributors. We describe previous RS data collection efforts, lessons learned from related databases and data-oriented networks (e.g., FLUXNET) in earth and ecological sciences, and the process of community consultation. The proposed reporting format focuses on chamber-level data and metadata, specifying measurement conditions and, for a given measurement period defined by beginning and ending timestamps, a mean RS flux (or CO2 concentration) and associated ancillary measurements. With input from the research community, we have also developed research data and metadata templates to support data collection adhering to the reporting format. Fundamentally, this format aims to enable findable, accessible, interoperable, and reusable data, while providing ‘future-proofing’ capabilities to support reanalyses using as yet unknown algorithms or approaches. This proposed RS reporting format is openly available online and is intended to be a dynamic document, subject to further community feedback and/or change.

Leaf-level gas exchange data support the mechanistic understanding of plant fluxes of carbon and water. These fluxes inform our understanding of ecosystem function, are an important constraint on parameterization of terrestrial biosphere models, are necessary to understand the response of plants to global environmental change, and are integral to efforts to improve crop production. Collection of these data using gas analyzers can be both technically challenging and time consuming, and individual studies generally focus on a small range of species, restricted time periods, or limited geographic regions. The high value of these data is exemplified by the many publications that reuse and synthesize gas exchange data, however the lack of metadata and data reporting conventions make full and efficient use of these data difficult. Here we propose a reporting format for leaf-level gas exchange data and metadata to provide guidance to data contributors on how to store data in repositories to maximize their discoverability, facilitate their efficient reuse, and add value to individual datasets. For data users, the reporting format will better allow data repositories to optimize data search and extraction, and more readily integrate similar data into harmonized synthesis products. The reporting format specifies data table variable naming and unit conventions, as well as metadata characterizing experimental conditions and protocols. For common data types that were the focus of this initial version of the reporting format, i.e., survey measurements, dark respiration, carbon dioxide and light response curves, and parameters derived from those measurements, we took a further step of defining required additional data and metadata that would maximize the potential reuse of those data types. To aid data contributors and the development of data ingest tools by data repositories we provided a translation table comparing the outputs of common gas exchange instruments. Extensive consult

The nuclear magn etic resonance extracted data (NMReDATA) format has beenproposed as a way to store, exchange, and disseminate nuclear magneticresonance (NMR) data and physical and chemical metadata of chemical com-pounds. In this paper, we report on analytical workflows that take advantageof the uniform and standardized NMReDATA format. We also give access to arepository of sample data, which can serve for validating software packagesthat encode or decode files in NMReDATA format.

The nuclear magn etic resonance extracted data (NMReDATA) format has beenproposed as a way to store, exchange, and disseminate nuclear magneticresonance (NMR) data and physical and chemical metadata of chemical com-pounds. In this paper, we report on analytical workflows that take advantageof the uniform and standardized NMReDATA format. We also give access to arepository of sample data, which can serve for validating software packagesthat encode or decode files in NMReDATA format.

The nuclear magn etic resonance extracted data (NMReDATA) format has beenproposed as a way to store, exchange, and disseminate nuclear magneticresonance (NMR) data and physical and chemical metadata of chemical com-pounds. In this paper, we report on analytical workflows that take advantageof the uniform and standardized NMReDATA format. We also give access to arepository of sample data, which can serve for validating software packagesthat encode or decode files in NMReDATA format.

The nuclear magn etic resonance extracted data (NMReDATA) format has beenproposed as a way to store, exchange, and disseminate nuclear magneticresonance (NMR) data and physical and chemical metadata of chemical com-pounds. In this paper, we report on analytical workflows that take advantageof the uniform and standardized NMReDATA format. We also give access to arepository of sample data, which can serve for validating software packagesthat encode or decode files in NMReDATA format.

Leaf-level gas exchange data support the mechanistic understanding of plant fluxes of carbon and water. These fluxes inform our understanding of ecosystem function, are an important constraint on parameterization of terrestrial biosphere models, are necessary to understand the response of plants to global environmental change, and are integral to efforts to improve crop production. Collection of these data using gas analyzers can be both technically challenging and time consuming, and individual studies generally focus on a small range of species, restricted time periods, or limited geographic regions. The high value of these data is exemplified by the many publications that reuse and synthesize gas exchange data, however the lack of metadata and data reporting conventions make full and efficient use of these data difficult. Here we propose a reporting format for leaf-level gas exchange data and metadata to provide guidance to data contributors on how to store data in repositories to maximize their discoverability, facilitate their efficient reuse, and add value to individual datasets. For data users, the reporting format will better allow data repositories to optimize data search and extraction, and more readily integrate similar data into harmonized synthesis products. The reporting format specifies data table variable naming and unit conventions, as well as metadata characterizing experimental conditions and protocols. For common data types that were the focus of this initial version of the reporting format, i.e., survey measurements, dark respiration, carbon dioxide and light response curves, and parameters derived from those measurements, we took a further step of defining required additional data and metadata that would maximize the potential reuse of those data types. To aid data contributors and the development of data ingest tools by data repositories we provided a translation table comparing the outputs of common gas exchange instruments. Extensive consult

The nuclear magn etic resonance extracted data (NMReDATA) format has beenproposed as a way to store, exchange, and disseminate nuclear magneticresonance (NMR) data and physical and chemical metadata of chemical com-pounds. In this paper, we report on analytical workflows that take advantageof the uniform and standardized NMReDATA format. We also give access to arepository of sample data, which can serve for validating software packagesthat encode or decode files in NMReDATA format.

In 2010, the Conference of the Parties of the Convention on Biological Diversity agreed on the Strategic Plan for Biodiversity 2011-2020 in Aichi Prefecture, Japan. As this plan approaches its end, we discussed whether marine biodiversity and prediction studies were nearing the Aichi Targets during the 4th World Conference on Marine Biodiversity held in Montreal, Canada in June 2018. This article summarises the outcome of a five-day group discussion on how global marine biodiversity studies should be focused further to better understand the patterns of biodiversity. We discussed and reviewed seven fundamental biodiversity priorities related to nine Aichi Targets focusing on global biodiversity discovery and predictions to improve and enhance biodiversity data standards (quantity and quality), tools and techniques, spatial and temporal scale framing, and stewardship and dissemination. We discuss how identifying biodiversity knowledge gaps and promoting efforts have and will reduce such gaps, including via the use of new databases, tools and technology, and how these resources could be improved in the future. The group recognised significant progress toward Target 19 in relation to scientific knowledge, but negligible progress with regard to Targets 6 to 13 which aimed to safeguard and reduce human impacts on biodiversity.

In 2010, the Conference of the Parties of the Convention on Biological Diversity agreed on the Strategic Plan for Biodiversity 2011-2020 in Aichi Prefecture, Japan. As this plan approaches its end, we discussed whether marine biodiversity and prediction studies were nearing the Aichi Targets during the 4th World Conference on Marine Biodiversity held in Montreal, Canada in June 2018. This article summarises the outcome of a five-day group discussion on how global marine biodiversity studies should be focused further to better understand the patterns of biodiversity. We discussed and reviewed seven fundamental biodiversity priorities related to nine Aichi Targets focusing on global biodiversity discovery and predictions to improve and enhance biodiversity data standards (quantity and quality), tools and techniques, spatial and temporal scale framing, and stewardship and dissemination. We discuss how identifying biodiversity knowledge gaps and promoting efforts have and will reduce such gaps, including via the use of new databases, tools and technology, and how these resources could be improved in the future. The group recognised significant progress toward Target 19 in relation to scientific knowledge, but negligible progress with regard to Targets 6 to 13 which aimed to safeguard and reduce human impacts on biodiversity.

Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for "Reporting" and "Serving" data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7th Framework Programme "Ocean of Tomorrow", and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science.

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML-based format, capable of representing data about two-dimensional features from LC-MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java-based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)-level quantification values from peptide-level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC-MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in-built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq-lib/.

Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for "Reporting" and "Serving" data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7th Framework Programme "Ocean of Tomorrow", and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science.

Contextual data collected concurrently with molecular samples are critical to the use of metagenomics in the fields of marine biodiversity, bioinformatics and biotechnology. We present here Marine Microbial Biodiversity, Bioinformatics and Biotechnology (M2B3) standards for "Reporting" and "Serving" data. The M2B3 Reporting Standard (1) describes minimal mandatory and recommended contextual information for a marine microbial sample obtained in the epipelagic zone, (2) includes meaningful information for researchers in the oceanographic, biodiversity and molecular disciplines, and (3) can easily be adopted by any marine laboratory with minimum sampling resources. The M2B3 Service Standard defines a software interface through which these data can be discovered and explored in data repositories. The M2B3 Standards were developed by the European project Micro B3, funded under 7th Framework Programme "Ocean of Tomorrow", and were first used with the Ocean Sampling Day initiative. We believe that these standards have value in broader marine science.

The mzQuantML standard has been developed by the Proteomics Standards Initiative for capturing, archiving and exchanging quantitative proteomic data, derived from mass spectrometry. It is a rich XML-based format, capable of representing data about two-dimensional features from LC-MS data, and peptides, proteins or groups of proteins that have been quantified from multiple samples. In this article we report the development of an open source Java-based library of routines for mzQuantML, called the mzqLibrary, and associated software for visualising data called the mzqViewer. The mzqLibrary contains routines for mapping (peptide) identifications on quantified features, inference of protein (group)-level quantification values from peptide-level values, normalisation and basic statistics for differential expression. These routines can be accessed via the command line, via a Java programming interface access or a basic graphical user interface. The mzqLibrary also contains several file format converters, including import converters (to mzQuantML) from OpenMS, Progenesis LC-MS and MaxQuant, and exporters (from mzQuantML) to other standards or useful formats (mzTab, HTML, csv). The mzqViewer contains in-built routines for viewing the tables of data (about features, peptides or proteins), and connects to the R statistical library for more advanced plotting options. The mzqLibrary and mzqViewer packages are available from https://code.google.com/p/mzq-lib/.

The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file containing the experimental data. In 1984, the first Flow Cytometry Standard format for data files was adopted as FCS 1.0. This standard was modified in 1990 as FCS 2.0 and again in 1997 as FCS 3.0. We report here on the next generation flow cytometry standard data file format. FCS 3.1 is a minor revision based on suggested improvements from the community. The unchanged goal of the standard is to provide a uniform file format that allows files created by one type of acquisition hardware and software to be analyzed by any other type. The FCS 3.1 standard retains the basic FCS file structure and most features of previous versions of the standard. Changes included in FCS 3.1 address potential ambiguities in the previous versions and provide a more robust standard. The major changes include simplified support for international characters and improved support for storing compensation. The major additions are support for preferred display scale, a standardized way of capturing the sample volume, information about originality of the data file, and support for plate and well identification in high throughput, plate based experiments. Please see the normative version of the FCS 3.1 specification in Supporting Information for this manuscript (or at http://www.isac-net.org/ in the Current standards section) for a complete list of changes.

The flow cytometry data file standard provides the specifications needed to completely describe flow cytometry data sets within the confines of the file containing the experimental data. In 1984, the first Flow Cytometry Standard format for data files was adopted as FCS 1.0. This standard was modified in 1990 as FCS 2.0 and again in 1997 as FCS 3.0. We report here on the next generation flow cytometry standard data file format. FCS 3.1 is a minor revision based on suggested improvements from the community. The unchanged goal of the standard is to provide a uniform file format that allows files created by one type of acquisition hardware and software to be analyzed by any other type. The FCS 3.1 standard retains the basic FCS file structure and most features of previous versions of the standard. Changes included in FCS 3.1 address potential ambiguities in the previous versions and provide a more robust standard. The major changes include simplified support for international characters and improved support for storing compensation. The major additions are support for preferred display scale, a standardized way of capturing the sample volume, information about originality of the data file, and support for plate and well identification in high throughput, plate based experiments. Please see the normative version of the FCS 3.1 specification in Supporting Information for this manuscript (or at http://www.isac-net.org/ in the Current standards section) for a complete list of changes.

Úkolem bakalářské práce bylo prostudovat datový standard Ministerstva zdravotnictví České republiky a možnosti přístupu do NIS Clinicom. Je zde popsána chronologie změn v blokové struktuře a popisu dat. Byl navržen a realizován webový přístup do NIS Clinicomu pomocí CSP, ve kterém lze generovat datové zprávy o pacientech se zvolenou infekční diagnózou odpovídající povinnému hlášení do Národního zdravotnického informačního systému., This work attempts at exploring the data standard of the Ministry of Health of the Czech Republic and the possibility of access to NIS Clinicom. The chronology of changes in the block structure and data description has been described. The web acces to NIS Clinicom has been designed and put into effect by means of CSP which can be used to generate data messages concerning patients with a selected infectious diagnosis corresponding with the compulsory report to the National Medical Information System.

Práce „Datový standard zdravotnických informačních systémů“ se zabývá strukturou datového standardu Ministerstva zdravotnictví České republiky, včetně jazyka XML. Dále se práce zaměřuje na nemocniční informační systém CLINICOM včetně přístupu k záznamům databáze Caché firmy InterSystems. Součástí práce je rovněž popis Národních zdravotních registrů. Hlavní cíl této práce je návrh webové aplikace, která umožňuje generovat zprávy v DS MZ k povinnému hlášení do registrů NZIS v zadaném časovém intervalu z databáze Caché. Nalezené záznamy z databáze lze vytisknout k archivaci. Práce se také zabývá zabezpečením přístupu k serveru NIS a datové komunikaci mezi zdravotnickými organizacemi., The diploma thesis "Data Standard of the Health Information Systems" deals with the structure of data standard including XML language. Further the thesis is focusing on hospital information system CLINICOM with the inclusion of the access to data records from its database Caché company InterSystems. Description of the National registers of health is also included.The concept of web application is also one part of the thesis which enables to generate reports in the data standard of the Ministry of Healt of the Czech Republic for mandatory reporting by NHIS registers in the time interval from the Caché database. Found records from the database can be printed for archiving. The work also deals with security access to the HIS server and data communication between health organizations.

Nemocniční informační systémy slouží k ukládání pacientských dat a k jejich sdílení. Mají několik výhod. Lékaři mají okamžitě přístupnou anamnézu, která pomáhá k rychlejší diagnostice, zabraňuje nadbytečnému plýtvání léky a duplicitním vyšetřením. Cílem mé bakalářské práce bylo vytvoření dálkového přístupu k nemocničnímu informačnímu systému Clinicom prostřednictvím internetu. Data jsou v informačním systému spravována databázovým systémem Caché. Z této databáze byly informace získávány pomocí SQL dotazů. Pro prezentaci dat na internetu bylo navrženo a realizováno uživatelské rozhraní v programovacím jazyce PHP, které umožňuje vzdálenou správu databáze systému Clinicom., Hospital information systems to store patient data and to share them. Have several advantages. Doctors are immediately accessible to history, which helps to quickly diagnose, prevent unnecessary wastage of drugs and duplicate tests. The goal of this work was to develop remote access to hospital information system CLINICOM via the Internet. The data in the information system managed by the database system Caché. From this database information was obtained using SQL queries. For the presentation of data on the Internet was designed and implemented user interface in the PHP programming language, which enables remote database management system CLINICOM.

Práce „Datový standard Ministerstva zdravotnictví České republiky“ se zabývá strukturou datového standardu včetně jazyka XML. Dále se práce zaměřuje na nemocniční informační systém CLINICOM včetně přístupu k záznamům z jeho databáze Caché firmy InterSystems. Součástí této práce je rovněž návrh webové aplikace, která umožňuje vyhledat záznamy se zvolenou diagnózou z databáze Caché a jejich zobrazení v datovém standardu Ministerstva zdravotnictví České republiky., Diploma thesis "Data standard of the Ministry of Health" deals with the structure of data standard including XML language. Further the thesis is focusing on hospital information system CLINICOM with the inclusion of the access to data records from its database Caché company InterSystems. The concept of web application is also one part of the thesis which enables to find out records with selective diagnosis from Caché database and their depictions in data standard of the Ministry of Health of the Czech Republic.

Úkolem bakalářské práce bylo prostudovat datový standard Ministerstva zdravotnictví České republiky a možnosti přístupu do NIS Clinicom. Je zde popsána chronologie změn v blokové struktuře a popisu dat. Byl navržen a realizován webový přístup do NIS Clinicomu pomocí CSP, ve kterém lze generovat datové zprávy o pacientech se zvolenou infekční diagnózou odpovídající povinnému hlášení do Národního zdravotnického informačního systému., This work attempts at exploring the data standard of the Ministry of Health of the Czech Republic and the possibility of access to NIS Clinicom. The chronology of changes in the block structure and data description has been described. The web acces to NIS Clinicom has been designed and put into effect by means of CSP which can be used to generate data messages concerning patients with a selected infectious diagnosis corresponding with the compulsory report to the National Medical Information System.

Úkolem bakalářské práce je prostudovat datový standard Ministerstva zdravotnictví České republiky a moţnosti přístupu do nemocničního informačního systému CLINICOM. Jsou zde popsány základní informace o datovém standardu, mezinárodní klasifikaci nemocí a skupinách vztaţených k diagnóze. Je zde popsána databázová platforma Caché a základy práce s ní. Dále je zde popsána platná legislativa pro národní zdravotní registry a pro povinné hlášení do Národního registru hospitalizovaných. Nakonec jezde popsána realizace programu pro přípravu datových zpráv o pacientech k povinnému hlášení do Národního registru hospitalizovaných, kde jsou pacienti filtrováni podle časového období a skupiny diagnóz. Je zde diskutována funkčnost programu a bezpečnost přenosu dat po veřejné internetové síti., This work attempts at exploring the data standard of the Ministry of Health of the Czech Republic and the possibilities of access to the hospital information system CLINICOM. At the beginning basic information about data standards in the health care, international classification of diseases and diagnosis related groups are described. The next part is focused at the database platform Caché and possibilities of word wide web access into the system via Caché server pages. Then it describes valid legislature for nation medicine registries and for mandatory reports to the Nation Medicine Registry of Inpatients. In the end of work it describes the realized program in Cache server pages for on-line data message reports about anonym patients into the National Registry of Inpatients. Patients are sort in agreement with time period and diagnosis related groups. Program utility and Internet data transfer security are discussed.

Tato diplomová práce popisuje nemocniční informační systém (NIS) CLINICOM se zaměřením na oddělení radiologie. Rozebírá problematiku přenosu obrazové dokumentace pacientů prostřednictvím sítě Internet a poskytuje návod pro realizaci rozhraní dálkového přístupu na oddělení radiologie. Kromě toho slouží jako podrobný průvodce instalací a konfigurací programových komponent NIS CLINICOM., This thesis describes the hospital information system (HIS) CLINICOM, focusing on the department of radiology. It analyses the problems linked with Internet transport of patient image documentation and it provides instructions how to create remote access interface on the department of radiology. It gives also a detailed guide describing installation and components configuration of HIS CLINICOM.

Práce „Datový standard zdravotnických informačních systémů“ se zabývá strukturou datového standardu Ministerstva zdravotnictví České republiky, včetně jazyka XML. Dále se práce zaměřuje na nemocniční informační systém CLINICOM včetně přístupu k záznamům databáze Caché firmy InterSystems. Součástí práce je rovněž popis Národních zdravotních registrů. Hlavní cíl této práce je návrh webové aplikace, která umožňuje generovat zprávy v DS MZ k povinnému hlášení do registrů NZIS v zadaném časovém intervalu z databáze Caché. Nalezené záznamy z databáze lze vytisknout k archivaci. Práce se také zabývá zabezpečením přístupu k serveru NIS a datové komunikaci mezi zdravotnickými organizacemi., The diploma thesis "Data Standard of the Health Information Systems" deals with the structure of data standard including XML language. Further the thesis is focusing on hospital information system CLINICOM with the inclusion of the access to data records from its database Caché company InterSystems. Description of the National registers of health is also included.The concept of web application is also one part of the thesis which enables to generate reports in the data standard of the Ministry of Healt of the Czech Republic for mandatory reporting by NHIS registers in the time interval from the Caché database. Found records from the database can be printed for archiving. The work also deals with security access to the HIS server and data communication between health organizations.

Úkolem bakalářské práce je prostudovat datový standard Ministerstva zdravotnictví České republiky a moţnosti přístupu do nemocničního informačního systému CLINICOM. Jsou zde popsány základní informace o datovém standardu, mezinárodní klasifikaci nemocí a skupinách vztaţených k diagnóze. Je zde popsána databázová platforma Caché a základy práce s ní. Dále je zde popsána platná legislativa pro národní zdravotní registry a pro povinné hlášení do Národního registru hospitalizovaných. Nakonec jezde popsána realizace programu pro přípravu datových zpráv o pacientech k povinnému hlášení do Národního registru hospitalizovaných, kde jsou pacienti filtrováni podle časového období a skupiny diagnóz. Je zde diskutována funkčnost programu a bezpečnost přenosu dat po veřejné internetové síti., This work attempts at exploring the data standard of the Ministry of Health of the Czech Republic and the possibilities of access to the hospital information system CLINICOM. At the beginning basic information about data standards in the health care, international classification of diseases and diagnosis related groups are described. The next part is focused at the database platform Caché and possibilities of word wide web access into the system via Caché server pages. Then it describes valid legislature for nation medicine registries and for mandatory reports to the Nation Medicine Registry of Inpatients. In the end of work it describes the realized program in Cache server pages for on-line data message reports about anonym patients into the National Registry of Inpatients. Patients are sort in agreement with time period and diagnosis related groups. Program utility and Internet data transfer security are discussed.

Nemocniční informační systémy slouží k ukládání pacientských dat a k jejich sdílení. Mají několik výhod. Lékaři mají okamžitě přístupnou anamnézu, která pomáhá k rychlejší diagnostice, zabraňuje nadbytečnému plýtvání léky a duplicitním vyšetřením. Cílem mé bakalářské práce bylo vytvoření dálkového přístupu k nemocničnímu informačnímu systému Clinicom prostřednictvím internetu. Data jsou v informačním systému spravována databázovým systémem Caché. Z této databáze byly informace získávány pomocí SQL dotazů. Pro prezentaci dat na internetu bylo navrženo a realizováno uživatelské rozhraní v programovacím jazyce PHP, které umožňuje vzdálenou správu databáze systému Clinicom., Hospital information systems to store patient data and to share them. Have several advantages. Doctors are immediately accessible to history, which helps to quickly diagnose, prevent unnecessary wastage of drugs and duplicate tests. The goal of this work was to develop remote access to hospital information system CLINICOM via the Internet. The data in the information system managed by the database system Caché. From this database information was obtained using SQL queries. For the presentation of data on the Internet was designed and implemented user interface in the PHP programming language, which enables remote database management system CLINICOM.

Úkolem bakalářské práce bylo prostudovat datový standard Ministerstva zdravotnictví České republiky a možnosti přístupu do NIS Clinicom. Je zde popsána chronologie změn v blokové struktuře a popisu dat. Byl navržen a realizován webový přístup do NIS Clinicomu pomocí CSP, ve kterém lze generovat datové zprávy o pacientech se zvolenou infekční diagnózou odpovídající povinnému hlášení do Národního zdravotnického informačního systému., This work attempts at exploring the data standard of the Ministry of Health of the Czech Republic and the possibility of access to NIS Clinicom. The chronology of changes in the block structure and data description has been described. The web acces to NIS Clinicom has been designed and put into effect by means of CSP which can be used to generate data messages concerning patients with a selected infectious diagnosis corresponding with the compulsory report to the National Medical Information System.

Úkolem bakalářské práce bylo prostudovat datový standard Ministerstva zdravotnictví České republiky a možnosti přístupu do NIS Clinicom. Je zde popsána chronologie změn v blokové struktuře a popisu dat. Byl navržen a realizován webový přístup do NIS Clinicomu pomocí CSP, ve kterém lze generovat datové zprávy o pacientech se zvolenou infekční diagnózou odpovídající povinnému hlášení do Národního zdravotnického informačního systému., This work attempts at exploring the data standard of the Ministry of Health of the Czech Republic and the possibility of access to NIS Clinicom. The chronology of changes in the block structure and data description has been described. The web acces to NIS Clinicom has been designed and put into effect by means of CSP which can be used to generate data messages concerning patients with a selected infectious diagnosis corresponding with the compulsory report to the National Medical Information System.

Práce „Datový standard Ministerstva zdravotnictví České republiky“ se zabývá strukturou datového standardu včetně jazyka XML. Dále se práce zaměřuje na nemocniční informační systém CLINICOM včetně přístupu k záznamům z jeho databáze Caché firmy InterSystems. Součástí této práce je rovněž návrh webové aplikace, která umožňuje vyhledat záznamy se zvolenou diagnózou z databáze Caché a jejich zobrazení v datovém standardu Ministerstva zdravotnictví České republiky., Diploma thesis "Data standard of the Ministry of Health" deals with the structure of data standard including XML language. Further the thesis is focusing on hospital information system CLINICOM with the inclusion of the access to data records from its database Caché company InterSystems. The concept of web application is also one part of the thesis which enables to find out records with selective diagnosis from Caché database and their depictions in data standard of the Ministry of Health of the Czech Republic.

Predmetom tejto diplomovej práce je ukázať aplikáciu BIM modelu v líniových stavbách. Ako podklad poslúžila klasická 2D dokumentácia, z ktorej som vytvoril 3D model s využitím programu Civil 3D. Pre negrafické informácie bol využitý štandard SFDI pre studeň dokumentácie PDPS, nakoľko to bol v daný moment najvyšší možný stupeň. Po skompletizovaní grafických a negrafických informácii bola časť modelu spracovaná do 5D modelu pridaním časového faktora a rozpoč-tu. Táto diplomová práca má ukázať aplikáciu BIM v líniových stavbách, ale aj po-ukázať na problémy a súčasne limity, či už z hľadiska softwaru alebo chýbajúcich noriem a metodík., The subject of this thesis is to show implementation of BIM in linear structures such as roads. In this case there was a normal 2D project, which I must convert to 3D model, using programme Civil 3D. For non-graphical information, standard from SFDI was used at its highest level of documentation that time (PDPS level). After finalizing all graphical and non-graphical information, part of the model was later converted in 5D model, adding cost and schedule. This thesis is supposed to show application of BIM in linear structures such as roads and point out problems from software side such as norms and methodology.

Predmetom tejto diplomovej práce je ukázať aplikáciu BIM modelu v líniových stavbách. Ako podklad poslúžila klasická 2D dokumentácia, z ktorej som vytvoril 3D model s využitím programu Civil 3D. Pre negrafické informácie bol využitý štandard SFDI pre studeň dokumentácie PDPS, nakoľko to bol v daný moment najvyšší možný stupeň. Po skompletizovaní grafických a negrafických informácii bola časť modelu spracovaná do 5D modelu pridaním časového faktora a rozpoč-tu. Táto diplomová práca má ukázať aplikáciu BIM v líniových stavbách, ale aj po-ukázať na problémy a súčasne limity, či už z hľadiska softwaru alebo chýbajúcich noriem a metodík., The subject of this thesis is to show implementation of BIM in linear structures such as roads. In this case there was a normal 2D project, which I must convert to 3D model, using programme Civil 3D. For non-graphical information, standard from SFDI was used at its highest level of documentation that time (PDPS level). After finalizing all graphical and non-graphical information, part of the model was later converted in 5D model, adding cost and schedule. This thesis is supposed to show application of BIM in linear structures such as roads and point out problems from software side such as norms and methodology.

Predmetom tejto diplomovej práce je ukázať aplikáciu BIM modelu v líniových stavbách. Ako podklad poslúžila klasická 2D dokumentácia, z ktorej som vytvoril 3D model s využitím programu Civil 3D. Pre negrafické informácie bol využitý štandard SFDI pre studeň dokumentácie PDPS, nakoľko to bol v daný moment najvyšší možný stupeň. Po skompletizovaní grafických a negrafických informácii bola časť modelu spracovaná do 5D modelu pridaním časového faktora a rozpoč-tu. Táto diplomová práca má ukázať aplikáciu BIM v líniových stavbách, ale aj po-ukázať na problémy a súčasne limity, či už z hľadiska softwaru alebo chýbajúcich noriem a metodík., The subject of this thesis is to show implementation of BIM in linear structures such as roads. In this case there was a normal 2D project, which I must convert to 3D model, using programme Civil 3D. For non-graphical information, standard from SFDI was used at its highest level of documentation that time (PDPS level). After finalizing all graphical and non-graphical information, part of the model was later converted in 5D model, adding cost and schedule. This thesis is supposed to show application of BIM in linear structures such as roads and point out problems from software side such as norms and methodology.

Úkolem bakalářské práce je prostudovat datový standard Ministerstva zdravotnictví České republiky a moţnosti přístupu do nemocničního informačního systému CLINICOM. Jsou zde popsány základní informace o datovém standardu, mezinárodní klasifikaci nemocí a skupinách vztaţených k diagnóze. Je zde popsána databázová platforma Caché a základy práce s ní. Dále je zde popsána platná legislativa pro národní zdravotní registry a pro povinné hlášení do Národního registru hospitalizovaných. Nakonec jezde popsána realizace programu pro přípravu datových zpráv o pacientech k povinnému hlášení do Národního registru hospitalizovaných, kde jsou pacienti filtrováni podle časového období a skupiny diagnóz. Je zde diskutována funkčnost programu a bezpečnost přenosu dat po veřejné internetové síti., This work attempts at exploring the data standard of the Ministry of Health of the Czech Republic and the possibilities of access to the hospital information system CLINICOM. At the beginning basic information about data standards in the health care, international classification of diseases and diagnosis related groups are described. The next part is focused at the database platform Caché and possibilities of word wide web access into the system via Caché server pages. Then it describes valid legislature for nation medicine registries and for mandatory reports to the Nation Medicine Registry of Inpatients. In the end of work it describes the realized program in Cache server pages for on-line data message reports about anonym patients into the National Registry of Inpatients. Patients are sort in agreement with time period and diagnosis related groups. Program utility and Internet data transfer security are discussed.

Práce „Datový standard Ministerstva zdravotnictví České republiky“ se zabývá strukturou datového standardu včetně jazyka XML. Dále se práce zaměřuje na nemocniční informační systém CLINICOM včetně přístupu k záznamům z jeho databáze Caché firmy InterSystems. Součástí této práce je rovněž návrh webové aplikace, která umožňuje vyhledat záznamy se zvolenou diagnózou z databáze Caché a jejich zobrazení v datovém standardu Ministerstva zdravotnictví České republiky., Diploma thesis "Data standard of the Ministry of Health" deals with the structure of data standard including XML language. Further the thesis is focusing on hospital information system CLINICOM with the inclusion of the access to data records from its database Caché company InterSystems. The concept of web application is also one part of the thesis which enables to find out records with selective diagnosis from Caché database and their depictions in data standard of the Ministry of Health of the Czech Republic.

Úkolem bakalářské práce bylo prostudovat datový standard Ministerstva zdravotnictví České republiky a možnosti přístupu do NIS Clinicom. Je zde popsána chronologie změn v blokové struktuře a popisu dat. Byl navržen a realizován webový přístup do NIS Clinicomu pomocí CSP, ve kterém lze generovat datové zprávy o pacientech se zvolenou infekční diagnózou odpovídající povinnému hlášení do Národního zdravotnického informačního systému., This work attempts at exploring the data standard of the Ministry of Health of the Czech Republic and the possibility of access to NIS Clinicom. The chronology of changes in the block structure and data description has been described. The web acces to NIS Clinicom has been designed and put into effect by means of CSP which can be used to generate data messages concerning patients with a selected infectious diagnosis corresponding with the compulsory report to the National Medical Information System.

Nemocniční informační systémy slouží k ukládání pacientských dat a k jejich sdílení. Mají několik výhod. Lékaři mají okamžitě přístupnou anamnézu, která pomáhá k rychlejší diagnostice, zabraňuje nadbytečnému plýtvání léky a duplicitním vyšetřením. Cílem mé bakalářské práce bylo vytvoření dálkového přístupu k nemocničnímu informačnímu systému Clinicom prostřednictvím internetu. Data jsou v informačním systému spravována databázovým systémem Caché. Z této databáze byly informace získávány pomocí SQL dotazů. Pro prezentaci dat na internetu bylo navrženo a realizováno uživatelské rozhraní v programovacím jazyce PHP, které umožňuje vzdálenou správu databáze systému Clinicom., Hospital information systems to store patient data and to share them. Have several advantages. Doctors are immediately accessible to history, which helps to quickly diagnose, prevent unnecessary wastage of drugs and duplicate tests. The goal of this work was to develop remote access to hospital information system CLINICOM via the Internet. The data in the information system managed by the database system Caché. From this database information was obtained using SQL queries. For the presentation of data on the Internet was designed and implemented user interface in the PHP programming language, which enables remote database management system CLINICOM.