Merge pull request #417 from jliermann/main

Broken links

Author: jliermann

docs/10_domains/20_physical_chemistry.mdx

@@ -9,11 +9,6 @@ import ElnFinder from "@site/src/components/eln/ElnFinder.js";
 <LbeChip title="physical chemistry" />
 <LbeChip title="cheminformatics" />
 
-{/* prettier-ignore */}
-{/* :::info Summary:
-Physical chemistry is an interdisciplinary science at the frontier between chemistry and physics, whose topics go beyond the classical areas of the respective individual sciences. While preparative chemistry focuses on questions of the methodology of chemical synthesis of known and new substances, physical chemistry attempts to describe the properties of substances and their transformation by applying concepts of physics to objects of chemistry by means of theoretical and experimental methods. Along with organic and inorganic chemistry, physical chemistry therefore represents one of the three key disciplines of "classical" chemistry, since it provides the theoretical basis for technical chemistry and process engineering. Its knowledge is also an integral part of many other disciplines and is used, for example, for description and understanding in biology and medicine, meteorology as well as the earth sciences. Due to this great interdisciplinarity and the use of numerous physicochemical methods in almost all areas of chemistry, a complete description of physical chemistry as profile is hardly possible, which is why this article explicitly makes no claim to do so.
-::: \*/}
-
 ## Introduction
 
 Physical Chemistry encompasses a variety of sub-disciplines, covering vast methodology, which, in turn, produce heterogenous data.
@@ -25,9 +20,9 @@ As mentioned, the data produced in physical chemistry and its diverse sub-discip
 
 ## ELNs and Other Tools
 
-For effective data management, software tools should be selected in a uniform manner within a project or research group with the aim to [organize](docs/data_organisation) and streamline workflows. This involves establishing clear usage guidelines, including metadata templates drawn from minimum information standards for a given method, where available. These should be outlined in a [data management plan (DMP)](docs/dmp) for each project. Many universities supply tools and templates for DMPs (see the [respective article](doc/dmp) for more information).
+For effective data management, software tools should be selected in a uniform manner within a project or research group with the aim to [organize](/docs/data_organisation) and streamline workflows. This involves establishing clear usage guidelines, including metadata templates drawn from minimum information standards for a given method, where available. These should be outlined in a [data management plan (DMP)](/docs/dmp) for each project. Many universities supply tools and templates for DMPs (see the [respective article](/docs/dmp) for more information).
 
-An [electronic lab notebooks (ELNs)](docs/eln) helps in the day-to-day planning and structured documentation of experiments, while some also assist in data workflow management. For disciplines with diverse research, ELNs must be flexible and customizable. Certain universities may have a central option, while each research group may chose what best fits their needs and resources if they are able to host or procure their own solution. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) lists many options and the article on [choosing an ELN](docs/chose_eln) provides further assistance:
+An [electronic lab notebooks (ELNs)](/docs/eln) helps in the day-to-day planning and structured documentation of experiments, while some also assist in data workflow management. For disciplines with diverse research, ELNs must be flexible and customizable. Certain universities may have a central option, while each research group may chose what best fits their needs and resources if they are able to host or procure their own solution. The [ELN-Finder](https://eln-finder.ulb.tu-darmstadt.de/search?f.K03=Pharmacy,equals&spc.page=1) lists many options and the article on [choosing an ELN](/docs/chose_eln) provides further assistance:
 
 <ElnFinder subDisc="Physical chemistry" />
 
@@ -41,12 +36,12 @@ As many physical chemists may establish their own workflows or develop their own
 
 ## Publishing Data
 
-[Publishing research data](docs/data_publication), especially that underlying a published article, is an important aspect that allows others in the research community to replicate and build upon a researchers work. [Research data repositories](docs/repositories) serve as platforms for data publication and can greatly assist in [FAIR](docs/fair) data publication. Such repositories range from subject-specific to general and institutional. For many in physical chemistry and its varied data, general repositories such as [RADAR4Chem](https://radar.products.fiz-karlsruhe.de/de/radarabout/radar4chem) presents an option for publishing data for which now (sub-)discipline-specific repository has been established. [ioChem-BD](https://www.iochem-bd.org/) serves as a computational chemistry repository and includes a conversion service for many common data types to ensure interoperability. The [Image Data Resource (IDR)](https://idr.openmicroscopy.org/) makes biological imaging data available to the community, while self-hosted Omero repositoy can assist those working with other types of imaging data. {/* <!--Nikki: as far as I know--> */} For more information on choices, head [here](docs/choose_repository).
+[Publishing research data](/docs/data_publication), especially that underlying a published article, is an important aspect that allows others in the research community to replicate and build upon a researchers work. [Research data repositories](/docs/repositories) serve as platforms for data publication and can greatly assist in [FAIR](/docs/fair) data publication. Such repositories range from subject-specific to general and institutional. For many in physical chemistry and its varied data, general repositories such as [RADAR4Chem](https://radar.products.fiz-karlsruhe.de/de/radarabout/radar4chem) presents an option for publishing data for which now (sub-)discipline-specific repository has been established. [ioChem-BD](https://www.iochem-bd.org/) serves as a computational chemistry repository and includes a conversion service for many common data types to ensure interoperability. The [Image Data Resource (IDR)](https://idr.openmicroscopy.org/) makes biological imaging data available to the community, while self-hosted Omero repositoy can assist those working with other types of imaging data. For more information on choices, head [here](/docs/choose_repository).
 
 For work that includes developing in-house research software solutions: **software is data and an integral part of research and should be published as such**. While only GitHub currently offers an automatic workflow for publishing software releases to [zenodo](https://zenodo.org/), there are methods to assign the [software a DOI, therefore making it citable](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/gitlab/repo-doi/).
 
 ## Challenges
 
 Common challenges in physical chemistry and FAIR data often go hand-in-hand with the large variety of sub-disciplines, methodology, and thus diverse data types. Many working in physical chemistry labs may have established their own personal workflows. Working within a group streamline and unify common steps and to establish reusable templates for metadata, be it in ELNs or in the local file system, can provide structured information not just for fellow researchers, but also for those working on FAIR data infrastructure, such as ELNs and research data repositories.
 
-Especially in imaging, large data volume can strain the local [storage](docs/data_storage) resources. Central storage solution can provide assistance and should be used in combination with best research data management practices to ensure the data's re-usability and avoid unorganized and inefficient use of large storage systems.
+Especially in imaging, large data volume can strain the local [storage](/docs/data_storage) resources. Central storage solution can provide assistance and should be used in combination with best research data management practices to ensure the data's re-usability and avoid unorganized and inefficient use of large storage systems.

docs/10_domains/40_synthetic_chemistry.mdx

@@ -36,7 +36,7 @@ Chemotion is especially suitable for synthetic chemistry as it originally starte
 
 ## Publishing Data
 
-[Publishing research data](/docs/data_publication/) is important in order to allow for the reuse of data by other researchers or for machine learning. Especially for machine learning, it is crucial that the data is published in a structured and standardised way. Where can you publish your data? Open access [data repositories](/docs/repositories/) are a good solution to provide your data for reuse by others. Choosing the right repository is crucial and as a general rule of thumb it is better to deposit your data in data-specific or discipline-specific repositories as these enforce more standardisation in how the data are published thus allowing for better machine-readability.
+[Publishing research data](/docs/data_publishing/) is important in order to allow for the reuse of data by other researchers or for machine learning. Especially for machine learning, it is crucial that the data is published in a structured and standardised way. Where can you publish your data? Open access [data repositories](/docs/repositories/) are a good solution to provide your data for reuse by others. Choosing the right repository is crucial and as a general rule of thumb it is better to deposit your data in data-specific or discipline-specific repositories as these enforce more standardisation in how the data are published thus allowing for better machine-readability.
 
 In order to reach as many researchers as possible, choosing the right repository can be crucial (more on this in the [article on choosing the right repository](/docs/choose_repository/)).
 

docusaurus.config.js

@@ -11,14 +11,14 @@ const title = "NFDI4Chem Knowledge Base";
 const description =
     "Supporting scientists to digitalise all steps of chemical research: to collect, store, process, analyse, publish, and reuse research data";
 const url = "https://knowledgebase.nfdi4chem.de/";
-// const baseUrl = "/knowledge_base/";
+const baseUrl = "/knowledge_base/";
 
 const navbar = require("./navbar.json");
 const footerLinks = require("./footer.json");
 
 // Use for stagging:
 // const baseUrl = '/staging/knowledge_base_matomo/';
-const baseUrl = "/staging_eln/knowledge_base/";
+// const baseUrl = "/staging_eln/knowledge_base/";
 
 const config = {
     title: title,

scripts/getElns.sh

@@ -1,8 +1,7 @@
 #!/bin/bash
 
-targetDir="/var/www/html/staging_eln/knowledge_base/assets"
-# targetDir="/var/www/html/knowledge_base/assets"
-# targetDir="/git/n4c-kb_jl/static/assets"
+# targetDir="/var/www/html/staging_eln/knowledge_base/assets"
+targetDir="/var/www/html/knowledge_base/assets"
 
 # get the data from the eln-finder