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We aim to make it suitable for NMR repositories and the supplementary materials of publications, not for the metadata in the experiment section. Therefore, we want to emphasize that the chemist doesn't need to enter their data in the recommended format as long as the repository is capable of converting it. For instance, the user might only upload NMR datasets, then NMRium extracts the solvent, and the repository does the mapping to the CHEBI instance."),(0,o.kt)("p",null,"While forging this standard, we have considered two aspects: How to make sense of the data on the first hand, where we need the minimum mentioned here in the first level, and data traceability and reproducibility, where details like the number of scans and the instrument become very useful, so we asked for them in the second level."),(0,o.kt)("p",null,"The recommendations started with metadata for reporting NMR analyses of synthetic compounds only, covering the reaction leading to the analyzed product. Then the decision was taken to split the recommendations and remove the synthetic compounds section to make them more modular and broader to cover all small molecules, including natural products, synthetic compounds, and mixtures where we have known molecules. They also started by making crucial and automatically extractable metadata (",(0,o.kt)("a",{parentName:"p",href:"https://www.nmrium.org/"},"by NMRium"),") mandatory, which can encourage chemists to use automatic workflows, and we made metadata relevant to impurities recommended. 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We aim to make it suitable for NMR repositories and the supplementary materials of publications, not for the metadata in the experiment section. Therefore, we want to emphasize that the chemist doesn't need to enter their data in the recommended format as long as the repository is capable of converting it. For instance, the user might only upload NMR datasets, then NMRium extracts the solvent, and the repository does the mapping to the CHEBI instance."),(0,n.kt)("p",null,"While forging this standard, we have considered two aspects: How to make sense of the data on the first hand, where we need the minimum mentioned here in the first level, and data traceability and reproducibility, where details like the number of scans and the instrument become very useful, so we asked for them in the second level."),(0,n.kt)("p",null,"The recommendations started with metadata for reporting NMR analyses of synthetic compounds only, covering the reaction leading to the analyzed product. Then the decision was taken to split the recommendations and remove the synthetic compounds section to make them more modular and broader to cover all small molecules, including natural products, synthetic compounds, and mixtures where we have known molecules. They also started by making crucial and automatically extractable metadata (",(0,n.kt)("a",{parentName:"p",href:"https://www.nmrium.org/"},"by NMRium"),") mandatory, which can encourage chemists to use automatic workflows, and we made metadata relevant to impurities recommended. However, for historical data, authors might fail to submit with restricted minimum information (MI), which led to the decision to keep automatically extractable metadata recommended if it wasn't crucial."),(0,n.kt)("p",null,(0,n.kt)("a",{parentName:"p",href:"https://docs.google.com/document/d/1fPltMeYXRmpCnzSOznekDpavrbIqzrpMyd8plNnrYcU/edit"},"Here is the link to the recommendations draft"),", which will be open for editing until publication."),(0,n.kt)("h2",{id:"scientific-applications-development---nmrium"},"Scientific Applications Development - NMRium"),(0,n.kt)("p",null,'Here we show Zakodium approach for the development of NMRium and how to make programming fair. Central to their methodology is the creation of highly sought-after libraries, such as React components including parsers, jcamp or Bruker converters, and tools for generating jcamp from other data.Zakodium adopts the practice of conventional committing to facilitate the automated generation of the change log based on bug fixes and new features, seamlessly closing associated issues. They harness continuous integration and leverage automatic GitHub testing. "Coverage" tells how much of the code was tested and which lines weren\'t, usually over 80% of the code is tested. '),(0,n.kt)("p",null,'To ensure the visibility and accessibility of their projects, Zakodium utilizes the Zenodo platform for publication, thereby obtaining Digital Object Identifiers (DOIs). Furthermore, they incorporate a "CITATION.cff" file, streamlining the generation of project citations in various formats, such as plain text or BibTeX. '),(0,n.kt)("h3",{id:"building-react-application"},"Building React Application:"),(0,n.kt)("p",null,"In the construction of React Applicationa, Zakodium employs a modular approach, relying on a multitude of specialized libraries for the graphical user interface (GUI), React components, and other functionalities. Impressively, over 60 libraries managed by Zakodium are integrated into NMRium, each serving specific purposes such as converters, structure viewing, and data loading and saving. A notable example is the 'nmr-load-save' library, capable of extracting comprehensive metadata from raw files within NMRium. Another case in point is 'Pixelium,' a library primarily focused on image processing. While not directly related to NMR, Pixelium extensively utilizes libraries originally created for NMRium, showcasing the versatility and cross-applicability of their development efforts. The team employs GitHub projects feature, providing a comprehensive overview of ongoing work and enabling the archiving of completed tasks. Automation is key in their workflow, with automatic bug reporting integrated into NMRium to promptly flag and address issues as they arise."),(0,n.kt)("h3",{id:"new-nmrium-features"},"New NMRium Features"),(0,n.kt)("p",null,"NMRium introduces a range of new features that enhance its capabilities:"),(0,n.kt)("ul",null,(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Multiplet analysis"),": Conduct multiplet analysis directly within the browser without the need for downloads, where you can display multiplicity trees, show the structure and do the assignment.The relation between the tables, molecule and spectra is interactive."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Databases"),": NMRium incorporates a versatile database featur to have databases for solvent or references for instance. Users can perform searches based on structure, substructure, or shifts. Additionally, there is advanced search to look for specific atoms.\nSimulation:"),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Prediction"),": Offering both 1D and 2D prediction capabilities, NMRium predicts spectra based on user-provided structures. It is also interactive. "),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Simulation"),": A novel addition, the simulation feature enables spectrum generation by entering values directly into the table, which is particularly beneficial for educational purposes"),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Metabolomics"),": NMRium excels in handling substantial gigabyte-sized files even within the browser. Filtering options enable users to navigate and extract relevant information from large amount of files based on specific criteria such as the type."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"e-learning"),": You process the spectrum and and propose a structure and you find if correct or not.")),(0,n.kt)("h3",{id:"formats-discussion"},"Formats Discussion"),(0,n.kt)("p",null,"In our considerations of data formats, it's crucial to draw a distinction between archival formats and those tailored for processing. A case in point is mzML, which, despite its stability over time, has faced reservations among users for certain applications. In Massbank, there exists a diversity of formats, including the less-documented Bruker MS, in contrast to the well-documented Bruker NMR.\nIn the context of NMRium, an approach encapsulating both original and processed data within a single JSON file is adopted. Notably, the utilization of JSON holds the promise of longevity, as its readability is anticipated to endure over the next 30 years. Audit trails are needed and we need to be able to read the data in 30 years from now."),(0,n.kt)("h2",{id:"towards-open-nmr-data-formats---what-we-want-and-what-we-can-have"},"Towards Open NMR Data Formats - What We Want and What We Can Have"),(0,n.kt)("p",null,(0,n.kt)("a",{parentName:"p",href:"https://docs.google.com/presentation/d/1QFzXAtckjrZBRC-RhCfl1dPXBVNx7wFiLdT-7kz_cGc/edit#slide=id.g255fdc7fa39_0_0"},"Dr. Johannes Liermann Presentation")),(0,n.kt)("p",null,"We prepare a sample with a molecule and in the spectrometer we get information that we want to assign to the molecule, which results in several layers of NMR data: raw data, processed data, assignment data and another layer that is the metadata. In higher levels in NMR it is difficult to tell what is data and what is metadata."),(0,n.kt)("p",null,"There are several NMR formats available:"),(0,n.kt)("ul",null,(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"JCAMP"),": Text-based format with tags defining both metadata and actual data along with the binary data, making it lengthy if uncompressed."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Bruker"),": Utilizes a folder structure with various files. 'fid' file holds binary data from acquisition. 'acqu' file relates to JCAMP and provides metadata. Bruker dataset is comprehensive, containing all necessary elements to reproduce an NMR experiment."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"nmrML"),": Employs an embedded ontology, distinguishing itself as probably the only one of the NMR formats utilizing ontology. Predominantly recognized in the metabolomics and biology domains but can be adapted for broader use."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"NMReData"),": Focuses beyond spectral data, extending into sdf structure and enriching it with 1D, 2D, assignments, coupling constants, and correlations.")),(0,n.kt)("p",null,"The landscape: JCAMP and Bruker cover raw and processed data and if at all assignment data.\nnmrML covers a little assignment but not designed for that. NMReDara is covers only assignment data."),(0,n.kt)("h3",{id:"challenges-examples"},"Challenges Examples:"),(0,n.kt)("pre",null,(0,n.kt)("code",{parentName:"pre"},"Challenge: \nSolution: Establishing a machine-readable syntax for pulse sequences can aid in identifying experiments and their parameters within the repository.\n")),(0,n.kt)("ul",null,(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Flip angle in Bruker"),": Obtaining the flip angle information requires reference to the pulse sequence, which may be clear for chemists but poses difficulty for developers. Recognizing the specific NMR experiment, such as HMBC, within a repository can indeed be challenging due to the diverse pulse sequence names. However, they all follow a machine readable syntax that can identify the experiment."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"TOCSY Experiment Naming Complexity"),': TOCSY experiment names can be intricate, especially when the term "TOCSY" is not explicitly mentioned.'),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Deciphering Pulse Program Information"),": In cases like d8 representing the mixing time, finding the relevant information in the dataset file (D field) may be challenging as you have to find the 8th one."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Locating Coupling Constants"),": Coupling constants may be embedded in the pulse sequence, requiring additional steps for retrieval."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Ontologies"),": Maintaining consistency in units, solvent values, and experiment types can be challenging without standardized ontologies. We need to actively contribute to and utilize available NMR ontologies")),(0,n.kt)("h3",{id:"discussion"},"Discussion:"),(0,n.kt)("p",null,"Establishing a mapping between ontology descriptions and vendors' datasets emerges as a crucial step. Later on, software can take an ontology and select a relevant branch of it for example to ask the user to pick a solvent. To initiate the effective integration of ontologies into a format, the we need following considerations: The primary requirement is to incorporate unique identifiers for ontology terms, as the software doesn\u2019t need to understand the semantic of the term at this level. Integration of a unit ontology can enhance the consistency and accuracy of data representation. "),(0,n.kt)("p",null,"What do we want from an open NMR format? Do we need one to start with?"),(0,n.kt)("ul",null,(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("p",{parentName:"li"},"Bruker's documentation being open is a positive step. If it becomes even more widely adopted, it could potentially fulfill the needs of the NMR community, and it might reduce the immediate need for a separate open format. Developing and maintaining an open format requires considerable resources and collaboration. Modernizing Bruker formats might be a pragmatic approach, given their widespread usage.")),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("p",{parentName:"li"},"JCAMP's popularity for Electronic Lab Notebooks (ELNs) makes it challenging to replace with Bruker formats,. Overlapping documentation for various analytical techniques using JCAMP can lead to confusion and hinder effective utilization. Despite JCAMP's capacity for metadata, there are limitations in including crucial information, emphasizing the need for enhancements. JCAMP's textual nature poses challenges for modern parsers, discouraging efforts to update and modernize it. The lack of a standardized way to validate JCAMP, requiring parsers writing for all \"standard\" versions, adds complexity to the format. Introducing ontologies into JCAMP may face resistance due to concerns that such modifications might not align with the preferences or understanding of chemists."))),(0,n.kt)("p",null,"Collaborating with IUPAC by incorporating elements from Bruker and seeking IUPAC recommendations could be a strategic approach to improving and modernizing JCAMP. We can enhance JCAMP by identifying and determining the minimum information missing there and incorporating them. Utilizing the dot in JCAMP for optional fields could offer a structured way to add relevant information specific to NMR."),(0,n.kt)("h3",{id:"we-are-still-stuck-with-the-question-of-what-format-to-go-with"},"We Are Still Stuck With The Question of What Format to Go With"),(0,n.kt)("ul",null,(0,n.kt)("li",{parentName:"ul"},"The consensus is to focus on enhancing existing formats rather than developing entirely new ones. The applied modifications should remain minimal. "),(0,n.kt)("li",{parentName:"ul"},"Acknowledgment that JCAMP, while popular, has limitations and misses important elements. This serves as a motivation to enhance and improve the format to capture more comprehensive data. A suggestion to take the JCAMP model and provide an additional serialization in JSON format, while emphasizing the importance of validation and testing, particularly for industry use.")),(0,n.kt)("p",null,"Conclusion:"),(0,n.kt)("ul",null,(0,n.kt)("li",{parentName:"ul"},'Considering the option of having the existing files with an additional JSON file for metadata. We need use cases where available formats fall short is highlighted. Existing NMR formats are not perceived as "bad enough" to warrant the development of entirely new formats. This reflects a pragmatic approach to evolving the current standards.')),(0,n.kt)("h2",{id:"nmrxiv--nmrium-as-the-open-source-choice-for-nmr-platforms"},"nmrXiv + NMRium as The Open Source Choice for NMR Platforms"),(0,n.kt)("p",null,(0,n.kt)("a",{parentName:"p",href:"https://drive.google.com/file/d/1xXmRkBTjp-Q3IbBDZZMkUgKN3SKHevFE/view?usp=sharing"},"Dr. Nils Schl\xf6rer Presentation")),(0,n.kt)("p",null,"The focus is on academia, not the industry. What tasks in the lab and the ideal workflow and what bottlenecks we have. What features we could have by merging nmrium with nmrXiv in such environment.\nLaboratories lack standardization, with variations in tools, systems, and practices, including the use of various systems such as LIMS (Laboratory Information Management Systems) and servers. Exploring the potential benefits of open access and automation in academic labs, with a particular emphasis on facilitating data submission without the need for a formal paper submission process, and providing the data to the user with accounts."),(0,n.kt)("p",null,"The repository, especially when integrated with applications like NMRium, becomes a valuable resource not only for visualization but also for data processing and assignment. Repositories have\ntwo aspects:"),(0,n.kt)("ul",null,(0,n.kt)("li",{parentName:"ul"},"Administrator's Role: Involves quality checks, ranking, and overall management of the repository."),(0,n.kt)("li",{parentName:"ul"},"User Expectations: Consideration of user expectations and the importance of user-friendly interfaces. Understanding user needs is crucial, and overly complex or needy submission processes may deter users.")),(0,n.kt)("p",null,"Highlighting the importance of providing added value to users. For example, NMRium suggesting assignments for 2D spectra, which is a common need in routine analyses. "),(0,n.kt)("h3",{id:"ideal-laboratory-nmr-workflow"},"Ideal Laboratory NMR Workflow"),(0,n.kt)("p",null,"The ideal laboratory NMR workflow for generating data ready for submission involves several key considerations to streamline the process and enhance user experience:"),(0,n.kt)("ul",null,(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Hosted Data Storage"),": Encourage the hosting of data in repositories rather than relying on local storage. Overcoming the preference for local storage by chemists can enhance data accessibility and sharing."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Structure Linkage"),": Ensure that each spectrum is linked to at least one corresponding chemical structure. Despite being common, the practice of not submitting structures should be hindered"),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Consistent Local and Public Format"),": Promote the use of a consistent format for both local and public data storage. This minimizes the need for users to switch between different systems, ensuring a seamless workflow."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Integrated Visualization and Processing"),": Provide tools for direct visualization and processing of data on the same platform after data is created. Integrated capabilities eliminate the need for users to rely on external software, enhancing efficiency."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Living Data with NMRium"),': Implement the concept of "living data" with tools like NMRium in platforms such as nmrXiv. This approach ensures that data remains dynamic and interactive, allowing users to explore and analyze it comprehensively.'),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Digital Availability of 2D Information"),": Shift from the current practice where people distribute some digital data and do paper assignment and the 2D information is usually mainly ignored."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Unified Interface for All Tasks"),": Provide a unified interface that caters to all tasks, from data submission to visualization and processing."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Suggested Assignment Feature"),": Incorporate a feature that suggests assignments to users. This not only adds value, but also makes the platform more attractive and user-friendly."),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("strong",{parentName:"li"},"Assignment Control"),": There should be some assignment control to check the plausibility by chemical shift comparisons but also can be used with case environment including logic, and if people do some assignment the system should be capable of continuing the job.")),(0,n.kt)("h3",{id:"success-factors"},"Success Factors:"),(0,n.kt)("p",null,"The success factors for an ideal NMR repository revolve around simplifying the user experience. Here's a breakdown of the key success factors:"),(0,n.kt)("ul",null,(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("p",{parentName:"li"},(0,n.kt)("strong",{parentName:"p"},"Minimizing Interfaces"),": Chemists are averse to handling multiple interfaces, potentially leading them to revert to traditional paper methods. The repository should provide a unified interface, streamlining all steps of the NMR workflow featured below:\n",(0,n.kt)("img",{alt:"Ideal NMR Workflow",src:a(170).Z,width:"1574",height:"1174"}))),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("p",{parentName:"li"},(0,n.kt)("strong",{parentName:"p"},"Consistent Structure Provision"),": Ensuring that structures are consistently provided with every NMR dataset submission.")),(0,n.kt)("li",{parentName:"ul"},(0,n.kt)("p",{parentName:"li"},(0,n.kt)("strong",{parentName:"p"},"Privacy and Data Sharing Options"),": Privacy concerns users and we need flexible data sharing options, offering robust privacy features, including the ability to publish data with restricted access to specific groups. Providing users with options for controlling data visibility fosters trust and compliance instead of just missing the data."))),(0,n.kt)("p",null,(0,n.kt)("img",{alt:"Ideal NMR Compilation",src:a(6495).Z,width:"1538",height:"902"})),(0,n.kt)("h3",{id:"discussion-1"},"Discussion:"),(0,n.kt)("p",null,"The discussion underscores the importance of including Electronic Lab Notebooks (ELNs) in the vision for NMR data management. Core facilities should play the role of raising the bar for data digitization. However, not all facilities may currently have the autonomy to enforce these practices, but they still should try for the better. Funders, such as DFG, can influence data quality by tying funding to specific standards. This creates a mechanism for control over data quality from the funder's perspective. The use of commercial management systems in the Jena platform lead to replacing traditional paper-based workflows. This shift underscores the practical adoption of digital tools. However, searching is based on people and groups rather than molecules. This limitation is attributed to the non-mandatory submission of structures."),(0,n.kt)("p",null,"nmrXiv repository layer is ready, with ongoing enhancements to the submission and molecule layers. Plans include building prediction and search layers separate from nmrXiv to facilitate broader usage. We already work with Chemotion, an open-source ELN that we found to be the best in the chemistry domain."),(0,n.kt)("h2",{id:"nmr-data-packaging-with-metadata-in-nfdi4chem"},"NMR Data Packaging with Metadata in NFDI4Chem"),(0,n.kt)("p",null,(0,n.kt)("a",{parentName:"p",href:"https://docs.google.com/presentation/d/1w72LL1qQl27pSHHPIV3uS79tTyZq5LD-c9Eu5cjgXFQ/edit#slide=id.g25304c5fa4f_0_0"},"Ms. Noura Rayya Presentation")),(0,n.kt)("p",null,"NMR Metadata Availability in NFDI4Chem: NFDI4Chem services, including nmrXiv (NMR data repository) and Chemotion (Repository for samples, reactions, and the accompanying analytical data), provide NMR metadata in a structured JSON format. This format adheres to schema.org and Bioschemas types, ensuring standardized representation. The use of NMRium in nmrXiv and Chemotion ensures a high extraction of metadata. This metadata can be translated into schema JSON and further optimized to include all the minimum information, while recommended and optional data can still partially depends on user's input. The platforms already provide the means for users to input some of this data."),(0,n.kt)("p",null,"Metadata Loss during Data Download: Currently, for both repositories, when users download data, no structured metadata files are automatically added within the folder. This lack of inclusion poses a risk of potential metadata loss during the download process. In Chemotion, even datasets belonging to the same reaction need to be downloaded individually. This can be cumbersome and may contribute to a fragmented dataset. Users need to go through a separate download/export process to obtain metadata. This involves using separate download buttons (Chemotion) or making API calls (nmrXiv), adding an extra step to access metadata."),(0,n.kt)("p",null,'In Chemotion, it is common to find additional chemical materials in the "description" field that may not be present in the reaction table. This adds complexity when deciding what metadata to export, as there may be supplementary information in unstructured fields.'),(0,n.kt)("p",null,"The need to package related data and metadata together in one folder is crucial for efficient data management. Data packaging involves using tools to containerize data along with its associated metadata in a format that is both human- and machine-readable. "),(0,n.kt)("p",null,"Data packaging tools request metadata to be structured, ensuring that it follows a standardized format that is both human- and machine-readable. Some tools incorporate data integrity checks to monitor the data and ensure its consistency throughout different processes, such as downloading, zipping/unzipping, and transferring. The tools also provide packaged data in formats that are convenient to transfer and download."))}m.isMDXComponent=!0},6495:(e,t,a)=>{a.d(t,{Z:()=>i});const i=a.p+"assets/images/compilation-9d5750aa9b4cea88ebc4a5ce71b341e7.png"},170:(e,t,a)=>{a.d(t,{Z:()=>i});const i=a.p+"assets/images/nils-cdda2cef52f81ea7ae7a20b2594ce949.png"}}]); \ No newline at end of file diff --git a/assets/js/runtime~main.d7a44e63.js b/assets/js/runtime~main.726c7d1b.js similarity index 98% rename from assets/js/runtime~main.d7a44e63.js rename to assets/js/runtime~main.726c7d1b.js index 4097b0e..a940717 100644 --- a/assets/js/runtime~main.d7a44e63.js +++ b/assets/js/runtime~main.726c7d1b.js @@ -1 +1 @@ -(()=>{"use strict";var e,a,f,r,t,d={},c={};function b(e){var a=c[e];if(void 0!==a)return a.exports;var f=c[e]={id:e,loaded:!1,exports:{}};return d[e].call(f.exports,f,f.exports,b),f.loaded=!0,f.exports}b.m=d,b.c=c,e=[],b.O=(a,f,r,t)=>{if(!f){var 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e={1303:0,532:0};b.f.j=(a,f)=>{var r=b.o(e,a)?e[a]:void 0;if(0!==r)if(r)f.push(r[2]);else if(/^(1303|532)$/.test(a))e[a]=0;else{var t=new Promise(((f,t)=>r=e[a]=[f,t]));f.push(r[2]=t);var d=b.p+b.u(a),c=new Error;b.l(d,(f=>{if(b.o(e,a)&&(0!==(r=e[a])&&(e[a]=void 0),r)){var t=f&&("load"===f.type?"missing":f.type),d=f&&f.target&&f.target.src;c.message="Loading chunk "+a+" failed.\n("+t+": "+d+")",c.name="ChunkLoadError",c.type=t,c.request=d,r[1](c)}}),"chunk-"+a,a)}},b.O.j=a=>0===e[a];var a=(a,f)=>{var r,t,d=f[0],c=f[1],o=f[2],n=0;if(d.some((a=>0!==e[a]))){for(r in c)b.o(c,r)&&(b.m[r]=c[r]);if(o)var i=o(b)}for(a&&a(f);n Archive | Minimum Information Requirements - +

Archive

Archive

2019

2021

- + \ No newline at end of file diff --git a/blog/first-blog-post/index.html b/blog/first-blog-post/index.html index ab7138b..2d9e2e2 100644 --- a/blog/first-blog-post/index.html +++ b/blog/first-blog-post/index.html @@ -6,13 +6,13 @@ First Blog Post | Minimum Information Requirements - +

First Blog Post

· One min read
Gao Wei

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

- + \ No newline at end of file diff --git a/blog/index.html b/blog/index.html index f4c45b1..99e7575 100644 --- a/blog/index.html +++ b/blog/index.html @@ -6,13 +6,13 @@ Blog | Minimum Information Requirements - +

· One min read
Sébastien Lorber
Yangshun Tay

Docusaurus blogging features are powered by the blog plugin.

Simply add Markdown files (or folders) to the blog directory.

Regular blog authors can be added to authors.yml.

The blog post date can be extracted from filenames, such as:

  • 2019-05-30-welcome.md
  • 2019-05-30-welcome/index.md

A blog post folder can be convenient to co-locate blog post images:

Docusaurus Plushie

The blog supports tags as well!

And if you don't want a blog: just delete this directory, and use blog: false in your Docusaurus config.

· One min read
Gao Wei

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

- + \ No newline at end of file diff --git a/blog/long-blog-post/index.html b/blog/long-blog-post/index.html index 3af0bc2..de5ad41 100644 --- a/blog/long-blog-post/index.html +++ b/blog/long-blog-post/index.html @@ -6,13 +6,13 @@ Long Blog Post | Minimum Information Requirements - +

Long Blog Post

· 3 min read
Endilie Yacop Sucipto

This is the summary of a very long blog post,

Use a <!-- truncate --> comment to limit blog post size in the list view.

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

- + \ No newline at end of file diff --git a/blog/mdx-blog-post/index.html b/blog/mdx-blog-post/index.html index de1d778..4e5ba29 100644 --- a/blog/mdx-blog-post/index.html +++ b/blog/mdx-blog-post/index.html @@ -6,13 +6,13 @@ MDX Blog Post | Minimum Information Requirements - +
- + \ No newline at end of file diff --git a/blog/tags/docusaurus/index.html b/blog/tags/docusaurus/index.html index e7cfcf9..fa7b379 100644 --- a/blog/tags/docusaurus/index.html +++ b/blog/tags/docusaurus/index.html @@ -6,13 +6,13 @@ 4 posts tagged with "docusaurus" | Minimum Information Requirements - +

4 posts tagged with "docusaurus"

View All Tags

· One min read
Sébastien Lorber
Yangshun Tay

Docusaurus blogging features are powered by the blog plugin.

Simply add Markdown files (or folders) to the blog directory.

Regular blog authors can be added to authors.yml.

The blog post date can be extracted from filenames, such as:

  • 2019-05-30-welcome.md
  • 2019-05-30-welcome/index.md

A blog post folder can be convenient to co-locate blog post images:

Docusaurus Plushie

The blog supports tags as well!

And if you don't want a blog: just delete this directory, and use blog: false in your Docusaurus config.

· One min read
Gao Wei

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

- + \ No newline at end of file diff --git a/blog/tags/facebook/index.html b/blog/tags/facebook/index.html index 18dfe59..dea7aef 100644 --- a/blog/tags/facebook/index.html +++ b/blog/tags/facebook/index.html @@ -6,13 +6,13 @@ One post tagged with "facebook" | Minimum Information Requirements - +

One post tagged with "facebook"

View All Tags

· One min read
Sébastien Lorber
Yangshun Tay

Docusaurus blogging features are powered by the blog plugin.

Simply add Markdown files (or folders) to the blog directory.

Regular blog authors can be added to authors.yml.

The blog post date can be extracted from filenames, such as:

  • 2019-05-30-welcome.md
  • 2019-05-30-welcome/index.md

A blog post folder can be convenient to co-locate blog post images:

Docusaurus Plushie

The blog supports tags as well!

And if you don't want a blog: just delete this directory, and use blog: false in your Docusaurus config.

- + \ No newline at end of file diff --git a/blog/tags/hello/index.html b/blog/tags/hello/index.html index 2744475..f3f8936 100644 --- a/blog/tags/hello/index.html +++ b/blog/tags/hello/index.html @@ -6,13 +6,13 @@ 2 posts tagged with "hello" | Minimum Information Requirements - +

2 posts tagged with "hello"

View All Tags

· One min read
Sébastien Lorber
Yangshun Tay

Docusaurus blogging features are powered by the blog plugin.

Simply add Markdown files (or folders) to the blog directory.

Regular blog authors can be added to authors.yml.

The blog post date can be extracted from filenames, such as:

  • 2019-05-30-welcome.md
  • 2019-05-30-welcome/index.md

A blog post folder can be convenient to co-locate blog post images:

Docusaurus Plushie

The blog supports tags as well!

And if you don't want a blog: just delete this directory, and use blog: false in your Docusaurus config.

- + \ No newline at end of file diff --git a/blog/tags/hola/index.html b/blog/tags/hola/index.html index 557d075..584c21f 100644 --- a/blog/tags/hola/index.html +++ b/blog/tags/hola/index.html @@ -6,13 +6,13 @@ One post tagged with "hola" | Minimum Information Requirements - +

One post tagged with "hola"

View All Tags

· One min read
Gao Wei

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Pellentesque elementum dignissim ultricies. Fusce rhoncus ipsum tempor eros aliquam consequat. Lorem ipsum dolor sit amet

- + \ No newline at end of file diff --git a/blog/tags/index.html b/blog/tags/index.html index 683d31e..ca52003 100644 --- a/blog/tags/index.html +++ b/blog/tags/index.html @@ -6,13 +6,13 @@ Tags | Minimum Information Requirements - +

Tags

- + \ No newline at end of file diff --git a/blog/welcome/index.html b/blog/welcome/index.html index 4439f4e..eeeeef0 100644 --- a/blog/welcome/index.html +++ b/blog/welcome/index.html @@ -6,13 +6,13 @@ Welcome | Minimum Information Requirements - +

Welcome

· One min read
Sébastien Lorber
Yangshun Tay

Docusaurus blogging features are powered by the blog plugin.

Simply add Markdown files (or folders) to the blog directory.

Regular blog authors can be added to authors.yml.

The blog post date can be extracted from filenames, such as:

  • 2019-05-30-welcome.md
  • 2019-05-30-welcome/index.md

A blog post folder can be convenient to co-locate blog post images:

Docusaurus Plushie

The blog supports tags as well!

And if you don't want a blog: just delete this directory, and use blog: false in your Docusaurus config.

- + \ No newline at end of file diff --git a/docs/category/data-formats/index.html b/docs/category/data-formats/index.html index 3a18c2b..a2f43c0 100644 --- a/docs/category/data-formats/index.html +++ b/docs/category/data-formats/index.html @@ -6,13 +6,13 @@ Data Formats | Minimum Information Requirements - +

Data Formats

Attached to its third consortium meeting, NFDI4Chem has organised a workshop on data formats to discuss the current status and the future steps.

- + \ No newline at end of file diff --git a/docs/category/fair-nmr-research-data-management/index.html b/docs/category/fair-nmr-research-data-management/index.html index b32698a..5c47910 100644 --- a/docs/category/fair-nmr-research-data-management/index.html +++ b/docs/category/fair-nmr-research-data-management/index.html @@ -6,13 +6,13 @@ FAIR NMR Research Data Management | Minimum Information Requirements - +

FAIR NMR Research Data Management

NFDI4Chem in collaboration with IUPAC have organised a workshop on FAIR NMR Research Data Management where we had experts who have been contributing to the FAIRness and standardisation of NMR data to participate in identifying challenges and finding solutions in this area. The discussions covered NMR repositories in NFDI4Chem and how to make their data more findable and interoperable, along with terminology, file formats, implementations and validations. We aimed at establishing a solid ground for a broader discussion that will follow in the next analytical chemistry MIChI workshops.

- + \ No newline at end of file diff --git a/docs/category/michi/index.html b/docs/category/michi/index.html index 4ab48db..fc7e0f5 100644 --- a/docs/category/michi/index.html +++ b/docs/category/michi/index.html @@ -6,13 +6,13 @@ MIChI | Minimum Information Requirements - +

MIChI

Here you can find all the MIChI that are still in the draft phase along with published ones.

- + \ No newline at end of file diff --git a/docs/category/minimum-information-standards-in-polymer-chemistry/index.html b/docs/category/minimum-information-standards-in-polymer-chemistry/index.html index 5c3ed0a..96ce571 100644 --- a/docs/category/minimum-information-standards-in-polymer-chemistry/index.html +++ b/docs/category/minimum-information-standards-in-polymer-chemistry/index.html @@ -6,13 +6,13 @@ Minimum Information Standards in Polymer Chemistry | Minimum Information Requirements - +

Minimum Information Standards in Polymer Chemistry

NFDI4Chem is organizing a workshop on minimum information standards in polymer chemistry. We would like to have experts for polymer chemistry to participate in the development and definition of these standards – aiming for a recommendation of the results as a general practice for scientists.

- + \ No newline at end of file diff --git a/docs/category/nmr-task-force-meeting/index.html b/docs/category/nmr-task-force-meeting/index.html index 1bf9993..4ec3389 100644 --- a/docs/category/nmr-task-force-meeting/index.html +++ b/docs/category/nmr-task-force-meeting/index.html @@ -6,13 +6,13 @@ NMR Task Force Meeting | Minimum Information Requirements - +

NMR Task Force Meeting

NMR Task Force Meeting was held for more detailed discussions on NMR across the several task areas within NFDI4Chem taking place in Jena.

- + \ No newline at end of file diff --git a/docs/category/recommendation-standard-for-reporting-liquid-state-nmr-experiments-of-small-molecules/index.html b/docs/category/recommendation-standard-for-reporting-liquid-state-nmr-experiments-of-small-molecules/index.html index 3100cec..760073a 100644 --- a/docs/category/recommendation-standard-for-reporting-liquid-state-nmr-experiments-of-small-molecules/index.html +++ b/docs/category/recommendation-standard-for-reporting-liquid-state-nmr-experiments-of-small-molecules/index.html @@ -6,13 +6,13 @@ Recommendation Standard for Reporting Liquid-State NMR Experiments of Small Molecules | Minimum Information Requirements - +

Recommendation Standard for Reporting Liquid-State NMR Experiments of Small Molecules

This recommendation standard is a proposal from NFDI4Chem to outline essential metadata required for documenting liquid-state NMR experiments of small molecules. We aim to make it suitable for NMR repositories and the supplementary materials of publications.The standard consists of textual guidelines explaining the meaning and purpose of the more concise tabular recommendations. Both can be found below.

- + \ No newline at end of file diff --git a/docs/category/surveysrequests-for-comments/index.html b/docs/category/surveysrequests-for-comments/index.html index f8a3281..65faef9 100644 --- a/docs/category/surveysrequests-for-comments/index.html +++ b/docs/category/surveysrequests-for-comments/index.html @@ -6,13 +6,13 @@ Surveys/Requests for comments | Minimum Information Requirements - +

Surveys/Requests for comments

Here we provide the forms to collect community feedback on our recommendations

- + \ No newline at end of file diff --git a/docs/category/workshops/index.html b/docs/category/workshops/index.html index 30e5e0d..76e977f 100644 --- a/docs/category/workshops/index.html +++ b/docs/category/workshops/index.html @@ -6,13 +6,13 @@ Workshops | Minimum Information Requirements - +

Workshops

Here you can find all the MIChI workshops held by NFDI4Chem

📄️ Introduction

NFDI4Chem is facilitating and organising a series of international workshops in different subdisciplines of chemistry to develop domain-specific MI standards. Each of the developed standards will be a modular recommendation for Minimum Information on Chemical Investigations due to the sheer size and variability of the field. Prior to the publication of the standards, there will be a Request for Comments (RFC) as part of a public review of the standards. We are providing this platform to receive the comments from the broadest possible community.

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Introduction

Here you can find all the MIChI that are still in the draft phase along with published ones.

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Tabular Guidelines

No.

Metadata

NFDI4Chem ID

Definition

Export Format

C

FAIRspec Property

Human-Readable Example

Machine-Readable Example

Comments

1

NMR Sample

NFDI.nmr.sample

NMR:1400128

1

1.1

Analyzed Compound

NFDI.nmr.sample.compound

All the compounds found in the NMR sample after running the NMR investigation

  • ChEBI ID or IRI that is a leaf of the ontology term molecular entity (CHEBI:23367) or

  • Pubchem ID or

  • Standard InChI or

  • SMILES

1-n

caffeine

CHEBI:27732

This value is to be filled after the assignment.

1.2

NMR Solvent

NFDI.nmr.sample.solvent

NMR:1000330

ChEBI ID which belongs to this extendible list

1-n

IFD.property.dataobject.fairspec.nmr.expt_solvent

D₂O

CHEBI:41981

1.2.1

NMR Solvent Volume/Volume Ratio

NFDI.nmr.sample.solvent.ratio

SNOMED:282380000 of NMR:1000330

ChEBI ID: ratio; ChEBI ID: ratio

0-n

D₂O: 90; CH₃OD: 10

CHEBI:41981: 90; CHEBI:193133: 10

1.3

Chemical Shift Reference

NFDI.nmr.sample.chemical_shift_reference

NMR:1400033

An nmrCV ID for a leaf from NMR:1400033

1

TMS

NMR:1000029

The term NMR:1400033 used in the defintion means chemical shift reference as it appears in the synonyms and considering its children

1.4.1

NMR Sample Tube Diameter

NFDI.nmr.sample.tube.diameter

The outer diameter of NMR:1400132

A number with unit: millimeter (UO:0000016)

0-1

5 mm

5 UO:0000016

1.4.2

NMR Sample Tube Type

NFDI.nmr.sample.tube.type

The type of NMR:1400132

A leaf of NMR:1400132

0-1

Young, coaxial, Shigemi...

NMR:1000269

2

NMR Acquisition Parameter

NFDI.nmr.acquisition

NMR:1001954

1-n

2.1

Acquisition Nucleus

NFDI.nmr.acquisition.nucleus

NMR:1400083

The nuclei of atoms identified by ChEBI IDs that are leaves of the ontology term atom (CHEBI:33250)

1-n

IFD.property.dataobject.fairspec.nmr.expt_nucl<n>

13C

The nucleus of CHEBI:36928

2.2

Irradiation Frequency

NFDI.nmr.acquisition.frequency

NMR:1400026

A number with unit:megaHertz (UO:0000325)

1

IFD.property.dataobject.fairspec.nmr.expt_freq<n>

400.02313552 MHz

400.02313552 UO:0000325

Users must provide precision of 8 decimal digits

2.3

NMR Method

NFDI.nmr.acquisition.method

Defines class of pulse sequence, for example 1D, 1D with decoupling, HSQC etc.

Values from nmrCV when available. In the meantime, free text as clarified in the definition (1D, 1D with decoupling, HSQC, etc.)

1

IFD.property.dataobject.fairspec.nmr.expt_title

HSQC

HSQC

2.4

Flip Angle

NFDI.nmr.acquisition.flip_angle

Rotation that the net magnetization experiences during the application of a radiofrequency pulse in nuclear magnetic resonance spectroscopy.

A number with unit: degree (UO:0000185)

1

90°

90 UO:0000185

2.5

Relaxation Delay

NFDI.nmr.acquisition.relaxation_delay

NMR:1400090

A number with unit: second based unit (UO:1000010)

0-1

2 sec

2 UO:0000010

2.6

Number of Acquisition Data Points

NFDI.nmr.acquisition.number_of_acquisition_data_points

NMR:1400017

A number with unit: data point (AFR:0000186)

0-1

32768 data points

32768 AFR:0000186

2.7

Sample Temperature Information

NFDI.nmr.acquisition.temperature

NMR:1400262

A number with unit: kelvin (UO:0000012)

0-1

IFD.property.dataobject.fairspec.nmr.expt_absolute_temperature

298.15 Kelvin

298.15 UO:0000012

2.8

Number of Scans

NFDI.nmr.acquisition.number_of_scans

NMR:1400087

A number

0-1

8

8

2.9

  • Pulse Power or
  • Pulse Power Gradient

NFDI.nmr.acquisition.pulse_power

  • The power of the applied RF pulse. or
  • The power gradient of the applied RF pulse.

numbers with unit: watt based uni (UO:1000114)

0-n

10 Watt

10 UO:0000114

2.10

Acquisition Time

NFDI.nmr.acquisition.acquisition_time

AFR:0001158

A number with unit:second based unit (UO:1000010)

0-1

20 sec

20 UO:0000010

2.11

Usage of Shaped Radio Frequency Pulse

NFDI.nmr.acquisition.shaped_pulse

Whether a shaped radio frequency pulse was used

A truth value: True or False

0-1

TRUE

SIO:000269

2.A

2D NMR

NFDI.nmr.acquisition.2d

CHMO:0000598

0-n

2.A.1

Mixing Time

NFDI.nmr.acquisition.2d.mixing_time

Delay for dipolar cross-relaxation in NOE, TOCSY, exchange spectroscopy

A number with unit:second based unit (UO:1000010)

0-1

0.5 sec

0.5 UO:0000010

Mandatory for NOE, TOCSY

2.A.2

Constant Time

NFDI.nmr.acquisition.2d.constant _time

The fixed time period in a constant time method

A number with unit:second based unit (UO:1000010)

0-1

0.5 sec

0.5 UO:0000010

3

NMR Instrument

NFDI.nmr.instrument

NMR:1400059

0-n

3.1

NMR Instrument Manufacturer

NFDI.nmr.instrument.manufacturer

NMR:1400255

An nmrCV ID which is a leaf from NMR:1400255

0-1

IFD.property.dataobject.fairspec.nmr.instr_manufacturer_name

Bruker

NMR:1400256

3.2

NMR Instrument Model

NFDI.nmr.instrument.model

NMR:1000031

An nmrCV ID for a leaf from NMR:1400059

0-1

AVANCE III HD

NMR:1000371

3.3

NMR Probe

NFDI.nmr.instrument.probe

NMR:1400014

An nmrCV ID which is a leaf from NMR:1400014

0-1

IFD.property.dataobject.fairspec.nmr.instr_probe_type

5mm inverse detection cryoprobe

NMR:1000326

4

NMR Data Processing

NFDI.nmr.processing

NMR:1400042

0-n

4.1

Number of Zero Filling Points

NFDI.nmr.processing.zero_filling

Number of data points of the FID after zero filling

A number with unit: data point (AFR:0000186)

0-1

256000 data points

256000 AFR:0000186

4.2

Window Function for Apodization

NFDI.nmr.processing.apodization_function

NMR:1400068

An nmrCV ID for a leaf from NMR:1400068

0-1

gaussian broadening

NMR:1400070

4.2.1

Window Function Parameters

NFDI.nmr.processing.apodization_function.parameters

NMR:1400096

Depends on the function

0-n

4.3

Baseline Correction

NFDI.nmr.processing.baseline_correction

NMR:1400074

An nmrCV ID for a leaf from NMR:1400074

0-1

polynomial

NMR:1000225

4.3.1

Baseline Correction Parameters

NFDI.nmr.processing.baseline_correction.parameters

A parameter to a baseline correction function

Depends on the function

0-n

4.4

Phase Correction

NFDI.nmr.processing.phase_correction

NMR:1000071

An nmrCV ID for a leaf from NMR:1000071

0-1

manual

NMR:1000096

4.4.1

Zero Order Phase Correction (ph0)

NFDI.nmr.processing.phase_correction.ph0

NMR:1400079

A number with unit: degree (UO:0000185)

0-1

-3.45684728°

-3.45684728 UO:0000185

4.4.2

First Order Phase Correction (ph1)

NFDI.nmr.processing.phase_correction.ph1

NMR:1400080

A number with unit: degree (UO:0000185)

0-1

4.457289234°

4.457289234 UO:0000185

4.5

Usage of Absolute Correction

NFDI.nmr.processing.absolute_correction

Whether a method was used that removes phase information like power or magnitude mode.

A truth value: True or False

0-1

TRUE

SIO:000269

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Textual Guidelines

These textual guidelines explaining the meaning and purpose of the more concise tabular standard, which enumerates the requested metadata, each item assigned a number in the "No." column, indicating the hierarchical relationship between rows. For example, "NMR sample" is assigned the number "1," the “solvent” included in the sample is prefixed with "1" and has its own number "2" (1.2), and then the “ratio of solvents” is labeled as "1.2.1."

No Column

We assign a unique NFDI4Chem identifier to each requested metadata point. All identifiers start with "NFDI.nmr." and further extend in a structured manner, reflecting the hierarchical relationship between the respective elements:

  • NFDI.nmr.sample
  • NFDI.nmr.sample.solvent
  • NFDI.nmr.sample.solvent.ratio

ID Column

Whenever possible, we provide a definition for each element using a controlled vocabulary term within the "Definition" column.

cv Column

The “Export Format” clarifies the expected format of the metadata when exported by the digital platforms, i.e. if the user submits a raw data file from which metadata can be extracted, the platform is not required to request the same metadata anew. Instead, it should be capable of mapping it to the mentioned format.

For instance, the Jeol format incorporates temperature values in Celsius, here the user doesn’t need to enter that value. Nevertheless, when the platform provides an export/download of the metadata, the system should map this temperature value to Kelvin, which comes from the UO ontology.

Format Column

The cardinality column (C) indicates how often to report the metadata point. It splits the recommendations into two levels:

  • Level 1 (required): This level encompasses the absolute minimum information (MI) that must be reported for NMR experiments. Infrastructure implementing this standard must not accept data missing this metadata. It can be identified in the table by a cardinality of no less than 1. The second sheet in the file summaries again all the MI in one table. For enhanced visibility, these entries are highlighted in red.
  • Level 2 (recommended): This level comprises metadata that is advisable to accompany the data whenever possible. However, in cases where this metadata is absent, the primary data can still be interpreted meaningfully. Infrastructure adhering to this standard must raise a warning when such metadata is missing. Level 2 entries can be identified in the table by cardinality starting from 0. For enhanced visibility, these entries are highlighted in green.

Cardinality Column

The cardinality of the four groups of requested metadata (highlighted in gray) is outlined as follows:

  1. NMR Sample: Cardinality = 1, as this recommendation considers NMR experiments conducted on 1 sample.
  2. NMR Acquisition Parameter: Cardinality = 1 - n, indicating that each sample must possess at least one NMR assay with reported acquisition parameters. Moreover, it can have more than one assay.
    • 2D NMR: Cardinality = 0 - n, as one sample may not have any 2D assays, or it might have several (Recommended to have).
  3. NMR Instrument: Cardinality = 0 - n, as reporting instrument metadata is not mandatory (0), and a single sample can be studied in more than one instrument (n).
  4. NMR Data Processing: Cardinality = 0 - n, as it is not mandatory to report processing metadata, but if the sample has n assays, then there will be n times of NMR Data Processing reports.

Furthermore, we offer mapping to FAIRspec properties whenever feasible. Finally, both human-readable and machine-readable examples are provided for enhanced clarity and utility.

FAIRspec Column

Next version: In the upcoming version, in addition to incorporating expected edits from the community, our aim is to actively contribute to NMR controlled vocabularies, and to expand the integration of these vocabularies into our recommendations.

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Related Links

nmrXiv​

Chemotion​

NMRShiftDB​

Terminology​

Schema​

IUPAC FAIRData Metadata Object Model​

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  • Anyone can add any new parameter, while properties are controlled and more agreed on.
  • Parameters are not ontology driven.
  • Parameters are not mandatory, It is the choice of ,e.g., the repository owner, but if they want to include them, then they should comply with FAIRspec specifications.
  • Parameters depend on the pulse sequence.
  • We will focus on finding the properties easily with the finding aid without much digging into the data. The photo shows some possible spectrum properties annd parameters. fid.json content
    • - + \ No newline at end of file diff --git a/docs/workshops/intro/index.html b/docs/workshops/intro/index.html index 75133e8..55d9645 100644 --- a/docs/workshops/intro/index.html +++ b/docs/workshops/intro/index.html @@ -6,13 +6,13 @@ Introduction | Minimum Information Requirements - +

    Introduction

    NFDI4Chem is facilitating and organising a series of international workshops in different subdisciplines of chemistry to develop domain-specific MI standards. Each of the developed standards will be a modular recommendation for Minimum Information on Chemical Investigations due to the sheer size and variability of the field. Prior to the publication of the standards, there will be a Request for Comments (RFC) as part of a public review of the standards. We are providing this platform to receive the comments from the broadest possible community.

    Content​

    For each workshop, we provide an overview about the topics discussed with a link to the full workshop record, along with forms to hear from you about your comments and thoughts, and other related links.

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    - + \ No newline at end of file diff --git a/docs/workshops/nmr-michi/overview/index.html b/docs/workshops/nmr-michi/overview/index.html index ec9b2f9..909f9d5 100644 --- a/docs/workshops/nmr-michi/overview/index.html +++ b/docs/workshops/nmr-michi/overview/index.html @@ -6,13 +6,19 @@ Workshop Overview | Minimum Information Requirements - +
    -

    Workshop Overview

    Date and Location​

    Jena: 19.07.2023

    Participants (Alphabetically)​

    Prof. Christoph Steinbeck, Dr. Eva Ziegler, Dr. Johannes Liermann, prof Luc Patiny, Dr. Nils Schlörer , Ms. Nisha Sharma, Ms. Noura Rayya, Dr. Pavel Kessler, Dr. Stefan Kuhn, Dr. Steffen Neumann, Dr. Tillmann Fischer, Mr. Venkata Chandra Sekhar Nainala

    Recommendations Standard for Reporting Liquid-State NMR Experiments of Small Molecules​

    This recommendations standard is a proposal from NFDI4Chem of what metadata to report for liquid-state NMR experiments of small molecules. We aim to make it suitable for NMR repositories and the supplementary materials of publications, not for the metadata in the experiment section. Therefore, we want to emphasize that the chemist doesn't need to enter their data in the recommended format as long as the repository is capable of converting it. For instance, the user might only upload NMR datasets, then NMRium extracts the solvent, and the repository does the mapping to the CHEBI instance.

    While forging this standard, we have considered two aspects: How to make sense of the data on the first hand, where we need the minimum mentioned here in the first level, and data traceability and reproducibility, where details like the number of scans and the instrument become very useful, so we asked for them in the second level.

    The recommendations started with metadata for reporting NMR analyses of synthetic compounds only, covering the reaction leading to the analyzed product. Then the decision was taken to split the recommendations and remove the synthetic compounds section to make them more modular and broader to cover all small molecules, including natural products, synthetic compounds, and mixtures where we have known molecules. They also started by making crucial and automatically extractable metadata (by NMRium) mandatory, which can encourage chemists to use automatic workflows, and we made metadata relevant to impurities recommended. However, for historical data, authors might fail to submit with restricted minimum information (MI), which led to the decision to keep automatically extractable metadata recommended if it wasn't crucial.

    Here is the link to the recommendations draft, which will be open for editing until publication.

    - +

    Workshop Overview

    Date and Location​

    Jena: 19.07.2023

    Participants (Alphabetically)​

    Prof. Christoph Steinbeck, Dr. Eva Ziegler, Dr. Johannes Liermann, prof Luc Patiny, Dr. Nils Schlörer , Ms. Nisha Sharma, Ms. Noura Rayya, Dr. Pavel Kessler, Dr. Stefan Kuhn, Dr. Steffen Neumann, Dr. Tillmann Fischer, Mr. Venkata Chandra Sekhar Nainala

    Recommendations Standard for Reporting Liquid-State NMR Experiments of Small Molecules​

    This recommendations standard is a proposal from NFDI4Chem of what metadata to report for liquid-state NMR experiments of small molecules. We aim to make it suitable for NMR repositories and the supplementary materials of publications, not for the metadata in the experiment section. Therefore, we want to emphasize that the chemist doesn't need to enter their data in the recommended format as long as the repository is capable of converting it. For instance, the user might only upload NMR datasets, then NMRium extracts the solvent, and the repository does the mapping to the CHEBI instance.

    While forging this standard, we have considered two aspects: How to make sense of the data on the first hand, where we need the minimum mentioned here in the first level, and data traceability and reproducibility, where details like the number of scans and the instrument become very useful, so we asked for them in the second level.

    The recommendations started with metadata for reporting NMR analyses of synthetic compounds only, covering the reaction leading to the analyzed product. Then the decision was taken to split the recommendations and remove the synthetic compounds section to make them more modular and broader to cover all small molecules, including natural products, synthetic compounds, and mixtures where we have known molecules. They also started by making crucial and automatically extractable metadata (by NMRium) mandatory, which can encourage chemists to use automatic workflows, and we made metadata relevant to impurities recommended. However, for historical data, authors might fail to submit with restricted minimum information (MI), which led to the decision to keep automatically extractable metadata recommended if it wasn't crucial.

    Here is the link to the recommendations draft, which will be open for editing until publication.

    Scientific Applications Development - NMRium​

    Here we show Zakodium approach for the development of NMRium and how to make programming fair. Central to their methodology is the creation of highly sought-after libraries, such as React components including parsers, jcamp or Bruker converters, and tools for generating jcamp from other data.Zakodium adopts the practice of conventional committing to facilitate the automated generation of the change log based on bug fixes and new features, seamlessly closing associated issues. They harness continuous integration and leverage automatic GitHub testing. "Coverage" tells how much of the code was tested and which lines weren't, usually over 80% of the code is tested.

    To ensure the visibility and accessibility of their projects, Zakodium utilizes the Zenodo platform for publication, thereby obtaining Digital Object Identifiers (DOIs). Furthermore, they incorporate a "CITATION.cff" file, streamlining the generation of project citations in various formats, such as plain text or BibTeX.

    Building React Application:​

    In the construction of React Applicationa, Zakodium employs a modular approach, relying on a multitude of specialized libraries for the graphical user interface (GUI), React components, and other functionalities. Impressively, over 60 libraries managed by Zakodium are integrated into NMRium, each serving specific purposes such as converters, structure viewing, and data loading and saving. A notable example is the 'nmr-load-save' library, capable of extracting comprehensive metadata from raw files within NMRium. Another case in point is 'Pixelium,' a library primarily focused on image processing. While not directly related to NMR, Pixelium extensively utilizes libraries originally created for NMRium, showcasing the versatility and cross-applicability of their development efforts. The team employs GitHub projects feature, providing a comprehensive overview of ongoing work and enabling the archiving of completed tasks. Automation is key in their workflow, with automatic bug reporting integrated into NMRium to promptly flag and address issues as they arise.

    New NMRium Features​

    NMRium introduces a range of new features that enhance its capabilities:

    • Multiplet analysis: Conduct multiplet analysis directly within the browser without the need for downloads, where you can display multiplicity trees, show the structure and do the assignment.The relation between the tables, molecule and spectra is interactive.
    • Databases: NMRium incorporates a versatile database featur to have databases for solvent or references for instance. Users can perform searches based on structure, substructure, or shifts. Additionally, there is advanced search to look for specific atoms. +Simulation:
    • Prediction: Offering both 1D and 2D prediction capabilities, NMRium predicts spectra based on user-provided structures. It is also interactive.
    • Simulation: A novel addition, the simulation feature enables spectrum generation by entering values directly into the table, which is particularly beneficial for educational purposes
    • Metabolomics: NMRium excels in handling substantial gigabyte-sized files even within the browser. Filtering options enable users to navigate and extract relevant information from large amount of files based on specific criteria such as the type.
    • e-learning: You process the spectrum and and propose a structure and you find if correct or not.

    Formats Discussion​

    In our considerations of data formats, it's crucial to draw a distinction between archival formats and those tailored for processing. A case in point is mzML, which, despite its stability over time, has faced reservations among users for certain applications. In Massbank, there exists a diversity of formats, including the less-documented Bruker MS, in contrast to the well-documented Bruker NMR. +In the context of NMRium, an approach encapsulating both original and processed data within a single JSON file is adopted. Notably, the utilization of JSON holds the promise of longevity, as its readability is anticipated to endure over the next 30 years. Audit trails are needed and we need to be able to read the data in 30 years from now.

    Towards Open NMR Data Formats - What We Want and What We Can Have​

    Dr. Johannes Liermann Presentation

    We prepare a sample with a molecule and in the spectrometer we get information that we want to assign to the molecule, which results in several layers of NMR data: raw data, processed data, assignment data and another layer that is the metadata. In higher levels in NMR it is difficult to tell what is data and what is metadata.

    There are several NMR formats available:

    • JCAMP: Text-based format with tags defining both metadata and actual data along with the binary data, making it lengthy if uncompressed.
    • Bruker: Utilizes a folder structure with various files. 'fid' file holds binary data from acquisition. 'acqu' file relates to JCAMP and provides metadata. Bruker dataset is comprehensive, containing all necessary elements to reproduce an NMR experiment.
    • nmrML: Employs an embedded ontology, distinguishing itself as probably the only one of the NMR formats utilizing ontology. Predominantly recognized in the metabolomics and biology domains but can be adapted for broader use.
    • NMReData: Focuses beyond spectral data, extending into sdf structure and enriching it with 1D, 2D, assignments, coupling constants, and correlations.

    The landscape: JCAMP and Bruker cover raw and processed data and if at all assignment data. +nmrML covers a little assignment but not designed for that. NMReDara is covers only assignment data.

    Challenges Examples:​

    Challenge: 
    Solution: Establishing a machine-readable syntax for pulse sequences can aid in identifying experiments and their parameters within the repository.
    • Flip angle in Bruker: Obtaining the flip angle information requires reference to the pulse sequence, which may be clear for chemists but poses difficulty for developers. Recognizing the specific NMR experiment, such as HMBC, within a repository can indeed be challenging due to the diverse pulse sequence names. However, they all follow a machine readable syntax that can identify the experiment.
    • TOCSY Experiment Naming Complexity: TOCSY experiment names can be intricate, especially when the term "TOCSY" is not explicitly mentioned.
    • Deciphering Pulse Program Information: In cases like d8 representing the mixing time, finding the relevant information in the dataset file (D field) may be challenging as you have to find the 8th one.
    • Locating Coupling Constants: Coupling constants may be embedded in the pulse sequence, requiring additional steps for retrieval.
    • Ontologies: Maintaining consistency in units, solvent values, and experiment types can be challenging without standardized ontologies. We need to actively contribute to and utilize available NMR ontologies

    Discussion:​

    Establishing a mapping between ontology descriptions and vendors' datasets emerges as a crucial step. Later on, software can take an ontology and select a relevant branch of it for example to ask the user to pick a solvent. To initiate the effective integration of ontologies into a format, the we need following considerations: The primary requirement is to incorporate unique identifiers for ontology terms, as the software doesn’t need to understand the semantic of the term at this level. Integration of a unit ontology can enhance the consistency and accuracy of data representation.

    What do we want from an open NMR format? Do we need one to start with?

    • Bruker's documentation being open is a positive step. If it becomes even more widely adopted, it could potentially fulfill the needs of the NMR community, and it might reduce the immediate need for a separate open format. Developing and maintaining an open format requires considerable resources and collaboration. Modernizing Bruker formats might be a pragmatic approach, given their widespread usage.

    • JCAMP's popularity for Electronic Lab Notebooks (ELNs) makes it challenging to replace with Bruker formats,. Overlapping documentation for various analytical techniques using JCAMP can lead to confusion and hinder effective utilization. Despite JCAMP's capacity for metadata, there are limitations in including crucial information, emphasizing the need for enhancements. JCAMP's textual nature poses challenges for modern parsers, discouraging efforts to update and modernize it. The lack of a standardized way to validate JCAMP, requiring parsers writing for all "standard" versions, adds complexity to the format. Introducing ontologies into JCAMP may face resistance due to concerns that such modifications might not align with the preferences or understanding of chemists.

    Collaborating with IUPAC by incorporating elements from Bruker and seeking IUPAC recommendations could be a strategic approach to improving and modernizing JCAMP. We can enhance JCAMP by identifying and determining the minimum information missing there and incorporating them. Utilizing the dot in JCAMP for optional fields could offer a structured way to add relevant information specific to NMR.

    We Are Still Stuck With The Question of What Format to Go With​

    • The consensus is to focus on enhancing existing formats rather than developing entirely new ones. The applied modifications should remain minimal.
    • Acknowledgment that JCAMP, while popular, has limitations and misses important elements. This serves as a motivation to enhance and improve the format to capture more comprehensive data. A suggestion to take the JCAMP model and provide an additional serialization in JSON format, while emphasizing the importance of validation and testing, particularly for industry use.

    Conclusion:

    • Considering the option of having the existing files with an additional JSON file for metadata. We need use cases where available formats fall short is highlighted. Existing NMR formats are not perceived as "bad enough" to warrant the development of entirely new formats. This reflects a pragmatic approach to evolving the current standards.

    nmrXiv + NMRium as The Open Source Choice for NMR Platforms​

    Dr. Nils Schlörer Presentation

    The focus is on academia, not the industry. What tasks in the lab and the ideal workflow and what bottlenecks we have. What features we could have by merging nmrium with nmrXiv in such environment. +Laboratories lack standardization, with variations in tools, systems, and practices, including the use of various systems such as LIMS (Laboratory Information Management Systems) and servers. Exploring the potential benefits of open access and automation in academic labs, with a particular emphasis on facilitating data submission without the need for a formal paper submission process, and providing the data to the user with accounts.

    The repository, especially when integrated with applications like NMRium, becomes a valuable resource not only for visualization but also for data processing and assignment. Repositories have +two aspects:

    • Administrator's Role: Involves quality checks, ranking, and overall management of the repository.
    • User Expectations: Consideration of user expectations and the importance of user-friendly interfaces. Understanding user needs is crucial, and overly complex or needy submission processes may deter users.

    Highlighting the importance of providing added value to users. For example, NMRium suggesting assignments for 2D spectra, which is a common need in routine analyses.

    Ideal Laboratory NMR Workflow​

    The ideal laboratory NMR workflow for generating data ready for submission involves several key considerations to streamline the process and enhance user experience:

    • Hosted Data Storage: Encourage the hosting of data in repositories rather than relying on local storage. Overcoming the preference for local storage by chemists can enhance data accessibility and sharing.
    • Structure Linkage: Ensure that each spectrum is linked to at least one corresponding chemical structure. Despite being common, the practice of not submitting structures should be hindered
    • Consistent Local and Public Format: Promote the use of a consistent format for both local and public data storage. This minimizes the need for users to switch between different systems, ensuring a seamless workflow.
    • Integrated Visualization and Processing: Provide tools for direct visualization and processing of data on the same platform after data is created. Integrated capabilities eliminate the need for users to rely on external software, enhancing efficiency.
    • Living Data with NMRium: Implement the concept of "living data" with tools like NMRium in platforms such as nmrXiv. This approach ensures that data remains dynamic and interactive, allowing users to explore and analyze it comprehensively.
    • Digital Availability of 2D Information: Shift from the current practice where people distribute some digital data and do paper assignment and the 2D information is usually mainly ignored.
    • Unified Interface for All Tasks: Provide a unified interface that caters to all tasks, from data submission to visualization and processing.
    • Suggested Assignment Feature: Incorporate a feature that suggests assignments to users. This not only adds value, but also makes the platform more attractive and user-friendly.
    • Assignment Control: There should be some assignment control to check the plausibility by chemical shift comparisons but also can be used with case environment including logic, and if people do some assignment the system should be capable of continuing the job.

    Success Factors:​

    The success factors for an ideal NMR repository revolve around simplifying the user experience. Here's a breakdown of the key success factors:

    • Minimizing Interfaces: Chemists are averse to handling multiple interfaces, potentially leading them to revert to traditional paper methods. The repository should provide a unified interface, streamlining all steps of the NMR workflow featured below: +Ideal NMR Workflow

    • Consistent Structure Provision: Ensuring that structures are consistently provided with every NMR dataset submission.

    • Privacy and Data Sharing Options: Privacy concerns users and we need flexible data sharing options, offering robust privacy features, including the ability to publish data with restricted access to specific groups. Providing users with options for controlling data visibility fosters trust and compliance instead of just missing the data.

    Ideal NMR Compilation

    Discussion:​

    The discussion underscores the importance of including Electronic Lab Notebooks (ELNs) in the vision for NMR data management. Core facilities should play the role of raising the bar for data digitization. However, not all facilities may currently have the autonomy to enforce these practices, but they still should try for the better. Funders, such as DFG, can influence data quality by tying funding to specific standards. This creates a mechanism for control over data quality from the funder's perspective. The use of commercial management systems in the Jena platform lead to replacing traditional paper-based workflows. This shift underscores the practical adoption of digital tools. However, searching is based on people and groups rather than molecules. This limitation is attributed to the non-mandatory submission of structures.

    nmrXiv repository layer is ready, with ongoing enhancements to the submission and molecule layers. Plans include building prediction and search layers separate from nmrXiv to facilitate broader usage. We already work with Chemotion, an open-source ELN that we found to be the best in the chemistry domain.

    NMR Data Packaging with Metadata in NFDI4Chem​

    Ms. Noura Rayya Presentation

    NMR Metadata Availability in NFDI4Chem: NFDI4Chem services, including nmrXiv (NMR data repository) and Chemotion (Repository for samples, reactions, and the accompanying analytical data), provide NMR metadata in a structured JSON format. This format adheres to schema.org and Bioschemas types, ensuring standardized representation. The use of NMRium in nmrXiv and Chemotion ensures a high extraction of metadata. This metadata can be translated into schema JSON and further optimized to include all the minimum information, while recommended and optional data can still partially depends on user's input. The platforms already provide the means for users to input some of this data.

    Metadata Loss during Data Download: Currently, for both repositories, when users download data, no structured metadata files are automatically added within the folder. This lack of inclusion poses a risk of potential metadata loss during the download process. In Chemotion, even datasets belonging to the same reaction need to be downloaded individually. This can be cumbersome and may contribute to a fragmented dataset. Users need to go through a separate download/export process to obtain metadata. This involves using separate download buttons (Chemotion) or making API calls (nmrXiv), adding an extra step to access metadata.

    In Chemotion, it is common to find additional chemical materials in the "description" field that may not be present in the reaction table. This adds complexity when deciding what metadata to export, as there may be supplementary information in unstructured fields.

    The need to package related data and metadata together in one folder is crucial for efficient data management. Data packaging involves using tools to containerize data along with its associated metadata in a format that is both human- and machine-readable.

    Data packaging tools request metadata to be structured, ensuring that it follows a standardized format that is both human- and machine-readable. Some tools incorporate data integrity checks to monitor the data and ensure its consistency throughout different processes, such as downloading, zipping/unzipping, and transferring. The tools also provide packaged data in formats that are convenient to transfer and download.

    + \ No newline at end of file diff --git a/docs/workshops/polymer/links/index.html b/docs/workshops/polymer/links/index.html index 92bf7b5..941fd22 100644 --- a/docs/workshops/polymer/links/index.html +++ b/docs/workshops/polymer/links/index.html @@ -6,13 +6,13 @@ Related Links | Minimum Information Requirements - +
    - + \ No newline at end of file diff --git a/docs/workshops/polymer/overview/index.html b/docs/workshops/polymer/overview/index.html index 45c5769..b533bce 100644 --- a/docs/workshops/polymer/overview/index.html +++ b/docs/workshops/polymer/overview/index.html @@ -6,7 +6,7 @@ Workshop Overview | Minimum Information Requirements - + @@ -16,7 +16,7 @@ We provide talks and receive questions. Registration is open, and we have many events coming. The workshops (online) are open to all people, and internationalization is part of our mission.

    The Minimum Information on Chemistry Investigations (MIChI)​

    Data needs to be associated with metadata, otherwise, data loses context. Metadata can be domain independent (funder, publisher, author, dates..) or specific, as in the domain of chemistry. We are especially interested in the Minimum Information subset out of the metadata, which we call minimum information on Chemistry investigation (MIChI). We can store the MIChI standards on specific repositories like FAIRsharing.

    We would like to provide our MIChI as:

    • Guidelines article: Useful for students and researchers.
    • Checklist for authors
    • Data Model: A conceptual idea for the programmers.
    • Ontology terms: to support the MIChI.
    • Implementation can happen in ELNs and repositories, and behind the scene, you have the APIs, databases, and the file formats.

    Structured data can be tedious work, but it saves a lot of time later when we need to publish, it is also essential for reusability

    Publication with Chemotion​

    Using Chemotion ELN or repository, one can generate reports that contain the description, the reaction scheme, identifiers and information coming from the identifiers (such as the molecular mass). If the data comes from the repository, the report contains its DOI. Supplemental information then can be submitted to the journals. If the data is already published in journals, corresponding links can be added to the “Reference” section.

    Supplemental information is already partially standardized for organic chemistry but not completely, as standardized elements such as the names and identifiers are being used in larger non-standardized sections, such as the description and results.

    Introduction in Polymer Chemistry​

    Polymer 101​

    A macromolecule is the single chain while the polymer is an ensemble of macromolecules (multiple macromolecular chains), this is challenging as we need to look into both the macromolecule and the polymer. Additionally, polymers have distributions in their chain length, the broadness of distribution depends on the synthetic way and we don’t have those issues in the macromolecule. However, the information on the macromolecule level and the polymer level go hand in hand.

    One can synthesize aspirin by many methods, paths, and people, and the same material will always be obtained. But in the case of polymers, one will get another polymer each time, as the resulting polymers might have similar properties, but they still differ on the molecular level. This is why we are always dealing with statistical distribution when dealing with polymers.

    Naming Polymers​

    It is challenging as different principles are followed.

    • Source based naming: Starting from the monomer and adding poly in front of it. It is an easy way, but it doesn’t always work and it is not always correct.
    • IUPAC, based on constitutional repeating units: IUPAC naming works only for simple polymers, but then it becomes very long.
    • Abbreviations and acronyms: They can be not clear for non polymer chemists.
    • Trade names are useful for narrow fields.
    • There are also rules for SMILES and big SMILES that are not much easy to use regularly.

    From Small Molecules to Polymers - Challenges with Digitalization​

    • Small molecules can be analyzed by relatively simple methods, such as NMR, IR, and MS, but when they form a polymer or an oligomer, they need more difficult and specialized methods, such as SEC, MALDI-ToF, SEC/ESI MS.
    • The repeating units in the product polymer can be controlled during the reaction, but such details are difficult to mirror in ELNs (such as Chemotion ELN). The same happens with nested polymers structures, which are very common.
    • The materials generated from polymers can undergo further procedures (post modifications) that are difficult to include in ELNs.
    • When it comes to polymers, we have neither standardized names, reaction information, sample structures, nor repositories entries with identifiers.

    Polymers Minimum Information​

    Many MI are actually expanding to become "Maximum" standards and they are really extensive. This problem can be tackled by having several levels of mandations, e.i., mandatory, recommened, and optional. The ELN might be a great first data-entry spot where these levels can be tranlsated into flags. ELNs can also serve by collecting statistics on how people report their data, where all input fields can start as optional, and based on a certain suggested percentage of users reporting this data, it can become recommended or later mandatory. There remains the risk of people report random data when Forced to fill in the mandatory fields which they don't have.

    One point to keep in mind about MI is its dependency on the field, e.g., for battery science you might only care about ion connectivity where molecular weight might not be of concern. This can easily be noticed in the different journals.

    Polymers Description - On The Way to MIChI​

    There is some basic information that can be used to describe polymers and the procedures carried out to generate them. In the following table you can find a basic description of a polymer.

    InformationDetails
    Synthesismethod, yield, degree of polymerization
    Chemical identityWhich polymer is this? What additives are present? Is there contamination?
    MorphologyAmount of crystallinity (tacticity?), optical properties
    Molecular weightMn, Mw, etc. : Molecular weight distribution Ð = Mw/Mn
    Solution behaviorViscosity, flow, gel
    Solution behaviorViscosity, flow, gel
    Thermal behaviorGlass transition, melt and decomposition temperature, melt viscosity
    Mechanical propertiesTensile strength, modulus, impact, creep, dimensional stability

    And next you can find a basic description of a polymer generation process with its expected metadata. Most important ones are highlighted.

    StepSub-steps
    Humans
    • Idea
    • Affiliation
    • Partners
    • Funding
    Planning
    • Hypothesis
    • Arrays
    • Structures
    Synthesis
    • Method
    • Conditions
    • Repetition?
    • Multiple steps?
    • Online analytics
    • Failure?
    • Contamination
    Analytics
    • Hypothesis
    • Instruments
    • Preparation
    • Mw
    • Solubility
    • Thermal
    • Mechanical
    Processing Application
    • Prparation
    • Additives
    • Casting
    • Extrusion
    • Post-modification
    • Lifecycle
    • Recycling?
    • Performance

    Polymers in Electronic Structure Editors​

    There are several available electronic structure editors that can handle polymers and, from which, Chemotion ELN users can pick, including:

    • Ketcher
    • Marvin
    • ChemDraw
    • HELM

    ChemDraw​

    • Most people in the workshop only use Chemdraw, but:
    • It provides a wide span of functions which polymer chemists don’t actually use.
    • It needs more documentation.
    • It is not possible to define []x-y.

    chemDraw1 chemDraw2

    Polymers in Electronic Lab Notebooks​

    On top of what the editors provide, ELNs can describe procceses as planned, ongoing, succeeded, failed. This becomes handy remembering the importance of maintaining failure results, which people might not be interested in publishing at the beginning, but these results are very important on their own to show others what actually works, and also for machine learning as better training comes with a mixed of good and bad data. This is still challenging when it comes to publications as reviewers might not be interested, and such results are usually not provided in the supporting material. We need to record what the polymer community finds useful and we can work on it day to day.

    Furthermore, ELNs help in keeping notes on why you picked a certain parameter, e.g. why an experiment is done at a certain temperature, along with the random variables not thought of by the researcher, which they might miss recording.

    When it comes to MI, ELNs can prevent the scenario of needing to report a certain mandatory parameter, but failing to do so as it wasn't recorded during the experiment. But more discussion is needed for MIs in ELNs, for instance, in addition to showing and describing the polymer, we still need to provide the dataset, the repeating units, and how they are linked because it is something you can’t show in chemdraw and you need to describe in words, along with the application in mind, on which the polymer charectrisitcs depend.

    Future Discussions​

    • What is the Minimum Information in polymer synthesis?

    • What is the Minimum Information in structural characterization?

    • What is the Minimum Information in property characterization?

    • What is the most suitable structure editor for polymerstool?

    • Can all editors mentioned in this overview be used adequately?

    • What definitions are necessary in ELN/for documentation?

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    Related Links

    nmrXiv​

    Chemotion​

    Ontologies​

    Articles​

    Presentations​

    - + \ No newline at end of file diff --git a/docs/workshops/standard-formats/overview/index.html b/docs/workshops/standard-formats/overview/index.html index 6968835..7ed9002 100644 --- a/docs/workshops/standard-formats/overview/index.html +++ b/docs/workshops/standard-formats/overview/index.html @@ -6,13 +6,13 @@ Workshop Overview | Minimum Information Requirements - +

    Workshop Overview

    Date and Location​

    Hannover: 11.10.2022

    Participants (Alphabetically)​

    Mr. Adam Basha, Mr. Bhavin Katabathuni, Prof. Christoph Steinbeck, Ms. Claire Lin, Dr. David Rauh, Dr.-Ing Felix Bach, Dr. Giacomo Lanza, Dr. Holger Israel, Dr. Joachim Richert, Dr. Johannes Liermann, Ms. Leah McEwen, Michael Klix, Ms. Nikki Parks, Ms. Nisha Sharma, Ms. Noura Rayya, Ms. Pei-Chi Huang, Philip Strömert, Dr. René Meier, Dr. Rukeia El-Athman, Dr. Steffen Neumann, Dr. Timothy holbrook, Dr. Tobias Schulze

    Data Formats in General​

    Dr. Steffen Neumann Presentation

    There are several standards to specify files' content. Ontologies are of the most important. Here we provide some branches that provide definitions of file formats:

    Vibrational Spectroscopy​

    Dr. Timothy Holbrook Presentatioin

    Vibrational Spec Files' metadata often lacks normalization and standardization as it comes from different manufacturers. When it comes to ontologies, NFDI4Chem is developing the Vibrational Spectroscopy Ontology to represent execution and analysis of vibrational spectroscopy assays metadata. Building this ontology still requires more domain experts' involvement to provide the needed terms, such as the devices with their parts and configuration parameters.

    Nuclear Magnetic Resonance Spectroscopy​

    Ms. Noura Rayya Presentation

    Several open formats exist for NMR, but are any ready to be recommended as a community standard? So far, inadequate conversion seems to be the most urging pitfall to be solved before making a recommendation, as different converters output different files. This issue is faced with both JCAMP-DX and NMReData. Provided that vendor and software formats are standardly converted to NMReData and nmrML, an approach mentioned in the article NMReDATA: Tools and applications recommends combining those two formats in a zipped NMR record, which may be promising. Some vendors, such as Bruker, already provide NMReData export by default in their software, while importing scripts might be required first to enable this export in other software.

    Further development of an NMR standard will need to answer the question of what metadata to include there. Instrument names might be a suggestion as they considerably vary and show a lack of standardization whenever reported. However, such metadata is not required to reproduce the experiment as long as the pulse sequence is provided. Further similar discussions will be needed to decide the purpose of metadata included in the format, and thus, the metadata itself.

    Continuous Testing Approach for Data Conversion as a Service​

    Michael Klix Presentatioin

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    Minimum Information Requirements

    NFDI4Chem Workshop Series

    To Chemistry Disciplines Workshops ⮕

    Minimum Information about a Chemical Investigation

    Guides to support researchers in reporting metadata in selected areas of chemistry.

    FAIRness

    Focus on making the (meta)data more Findable, Accessible, Interoperable, and Reusable.

    Internalization

    We collaborate with international organizations and we strive to reach an international consensus about our MIChI to be.

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    Markdown page example

    You don't need React to write simple standalone pages.

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