The field is not provided; or the expressions "1D" or "2D" are not found in the field, and also the method mentioned is not available in the mapping between the method and dimensionality made with hard-coding; or the value is provided as N/A or other similar expressions; or the study "assays" value is "null"
+
Due to providing methods names in free text, much hard coding was needed
+
+
+
MW
+
semi-dedicated
+
NMR Eexperiment Type
+
free text
+
none
+
The field is not provided; or the expressions "1D" and "2D" are not found in the field, and also the method mentioned is not available in the mapping between the method and dimensionality made with hard-coding; or the value is provided as N/A or other similar expressions; or decoding the JSON file that contains the study details has failed due to syntax error there
+
Due to providing methods names in free text, much hard coding was needed
+
+
+
CENAPT
+
semi-dedicated
+
Description
+
machine-readable
+
none
+
Description field is always available, so missing means only that the expressions "1D" and "2D" are not found there
+
It was machine-readable as looking for "1D" and "2D" expressions was enough in all the texts
+
+
+
NMRShiftDB
+
semi-dedicated
+
[nmr:assignmentMethod, nmr:OBSERVENUCLEUS]
+
free text
+
none
+
The field is not provided; or the expressions "1D" and "2D" are not found in the field, and also the method mentioned is not available in the mapping between the method and dimensionality made with hard-coding. The value can also be given as "Unreported" or other similar expressions.
+
Due to providing methods names in free text, much hard coding was needed
+
+
+
+
+
+
+
Input Examples
+
Output
+
+
+
MTBLS
+
["1D NOESY with presaturation (tnnoesy)", "2D JRES with homonuclear J-resolved 2D correlation, presaturation during relaxation delay with gradients (jresgpprqf)", "1H_PROTON"]
+
"1d", "2d", "missing"
+
+
+
MW
+
["2D 1H-13C HSQC-TOCSY", "NOESY", "NOESY PR1D"]
+
"1d", "2d", "missing"
+
+
+
CENAPT
+
["NMR data of gossypol in DMSOd6 and CDCl3. The dataset contains 1D 1H 13C as well as 2D COSY, HSQC, HMBC, all acquired at 600MHz (Bruker 600MHz spectrometer with CryoProbe (CP DCH 600S3 C/H-D-05 Z)"]
+
+## Results
+The Dimensionality was possible to obtain in most studies and repositories. It can be either mentioned explicitly as "1D" or "2D", or it can be implied by the technique name (e.g., HSQC). None of the repositories used ontologies to describe the value.
+
+Most of the studies were only one-dimensional. Here you can see the percentage of studies based on their dimensionalities. If a study has both 1D and 2D spectra, it will appear twice.
+
+
+
+The percentages of all studies in the four repositories based on the Dimensionality
+
+
+[CENAPT](https://dataverse.harvard.edu/dataverse/cenapt) was the only exception to provide 2D NMR for almost all the studies as one can see below (NMRShiftDB data were not added due to the huge number of studies there).
+
+
+
+The number of studies in three repositories based on NMR dimensionalities
+
+
+However, NMRShiftDB similarly has mostly 1D NMR data.
+
+
+The number of studies in NMRShiftDB based on NMR dimensionalities
+
+
+And here you can find the whole view of the four repositories with a logarithmic scale.
+
+
+
+The number of studies in the four repositories based on NMR dimensionalities (with a logarithmic scale)
+
\ No newline at end of file
diff --git a/docs/advanced-guides/nmr-repositories/frequency.md b/docs/advanced-guides/nmr-repositories/frequency.md
new file mode 100644
index 00000000..e22be4a4
--- /dev/null
+++ b/docs/advanced-guides/nmr-repositories/frequency.md
@@ -0,0 +1,119 @@
+# Spectrometer Frequency
+[Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/frequency.ipynb) where you can find all the graphs.
+
+Data created on 17.10.2022 at 19:32:45
+
+Data updated on 17.10.2022 at 19:32:45
+
+## Support by Ontologies
+
+Frequency-wise, the NMR field seems to be full of terms such as Larmor frequency, instrument frequency, offset frequency, and others. Still, there is rare, if any, mention of them in NMR and Chemistry related ontologies. Being said, repositories still have the option to define this field, where the value of it is simply a float. The main issue here was the absence of an ontology-driven unit of frequency. Although it is somehow safe to assume that the unit is [MHz](https://terminology.nfdi4chem.de/ts/ontologies/uo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000325), assumptions aren't ideal. More importantly, providing the unit was often the only possible way to deduct that a certain number corresponds to frequency.
+
+When talking about "Spectrometer Frequency" here, we mean during the NMR assay, not the instrument maximum frequency, except for Metabolights, as this is the value provided there.
+
+## Data Sanitisation and Missing Values
+
+
+
+
Field Type
+
Field Name
+
Values Readability
+
Unit
+
Missing
+
Comment
+
+
+
MTBLS
+
absent
+
none
+
none
+
none
+
Slugified MHz was not found in the instrument name
+
There is no field for the frequency. It can be available in the description, but still, it is difficult to extract due to possible confusion with the instrument's maximum frequency value. The pulse sequence name is provided, but it doesn't contain numerical values. Here, we only provide the instrument's maximum frequency value, not what was used in the study
+
+
+
MW
+
dedicated
+
Spectrometer Frequency
+
machine-readable
+
integrated
+
The field is not provided; or multiple values were provided; or the value is provided as N/A or other similar expressions.
+
+
+
+
CENAPT
+
semi-dedicated
+
Name
+
machine-readable
+
integrated
+
The name is always provided, so "missing" means that a number plus slugified "MHz" were not found there.
+
+
+
+
NMRShiftDB
+
dedicated
+
cml:field
+
float
+
separate field
+
The value is given as "Unreported" or other similar expressions
+
+## Results
+The four repositories provided frequency values in one way or another. However, Metabolights only provided the instrument's maximum frequency value. Only NMRShiftDB provided a field for the unit. Including the large number of studies in NMRShiftDB, the most used spectrometer frequency was 100-150MHz.
+
+
+
+The percentages of all studies in three repositories (without MTBLS) based on the Spectrometer frequency
+
+
+However, when NMRShiftDB is excluded, the most used spectrometer frequency is 600-650MHz.
+
+
+
+The number of studies in MW and CENAPT based on Spectrometer frequency
+
+
+Looking into the instruments in Metabolights, the most used maximum frequency was also 600-650MHz.
+
+
+
+The number of studies in MTBLS based on Maximum spectrometer frequency
+
+
+
+And here you can find the whole view of the three repositories with a logarithmic scale.
+
+
+
+The number of studies in the three repositories based on Spectrometer frequency (with a logarithmic scale)
+
\ No newline at end of file
diff --git a/docs/advanced-guides/nmr-repositories/instrument.md b/docs/advanced-guides/nmr-repositories/instrument.md
new file mode 100644
index 00000000..0e2145a9
--- /dev/null
+++ b/docs/advanced-guides/nmr-repositories/instrument.md
@@ -0,0 +1,75 @@
+# Instruments Names
+[Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/instruments-names.ipynb) where you can find all the graphs.
+
+Data created on 17.10.2022 at 19:32:45
+
+Data updated on 17.10.2022 at 19:32:45
+
+## Support by Ontologies
+
+[NMR instrument](https://terminology.nfdi4chem.de/ts/ontologies/nmrcv/terms?iri=http%3A%2F%2FnmrML.org%2FnmrCV%23NMR%3A1400059)s are already provided in [nmr CV](https://terminology.nfdi4chem.de/ts/ontologies/nmrcv), along with [instruments parts](https://terminology.nfdi4chem.de/ts/ontologies/nmrcv/terms?iri=http%3A%2F%2FnmrML.org%2FnmrCV%23NMR%3A1000463&viewMode=All&siblings=false).
+
+## Data Sanitisation and Missing Values
+Instrument names are found only in MTBLS and MW.
+
+
+
+
+
Field Type
+
Field Name
+
Values Readability
+
Unit
+
Missing
+
+
+
MTBLS
+
dedicated
+
Instrument
+
free text
+
none
+
The field is not provided; or the value is provided as N/A or other similar expressions; or the study "assays" value is "null".
+
+
+
MW
+
dedicated
+
Instrument
+
free text
+
none
+
The field is not provided; or the value is provided as N/A or other similar expressions; or decoding the JSON file containing the study details has failed due to syntax error there.
+
+
+
+
+
+
+
Input Examples
+
Output
+
+
+
MTBLS
+
["Bruker AVANCE 700 MHz spectrometer", "Bruker AVANCE II 700 MHz spectrometer", "Bruker AVANCE III 700 MHz spectrometer", "Bruker AVANCE III HD 700 MHz spectrometer"]
+
["600-mhz-varian-inova-spectrometer", etc.]
+
+
+
MW
+
["Bruker 18.8 Tesla (800 MHz) NMR spectrometer ascend", "Bruker 500MHz spectrometer", "Bruker 600 MHz", "Bruker 600 MHz Avance III HD spectrometer", "Bruker 600-MHz AVANCE III solution NMR spectrometer", "Bruker 600MHZ", "FT NMR", "INOVA"]
+
["600-mhz-varian-inova-spectrometer", etc.]
+
+
+
+## Results
+
+Both repositories have a dedicated field for the instrument name, making it easily obtainable. However, none used ontology terms. As a result, one can see in the graph of the percentages of studies using the same instruments how small and plenty the sections are due to variations in the names used to indicate the same instrument. One can easily tell that Bruker and Agilent are the most used instruments, but getting exact numbers on how much a specific instrument is used was quite difficult.
+
+
+
+A rough estimate of the percentages of all studies in the two repositories based on the NMR instrument
+
+
+
+Looking at the distribution of instrument names in the two repositories, one can see that the same value (except for once) was never used in both, although the same instrument actually was.
+
+
+
+The number of studies in MW and MTBLS based on the instrument name.
+
diff --git a/docs/advanced-guides/nmr-repositories/nuclei.md b/docs/advanced-guides/nmr-repositories/nuclei.md
new file mode 100644
index 00000000..61296a87
--- /dev/null
+++ b/docs/advanced-guides/nmr-repositories/nuclei.md
@@ -0,0 +1,110 @@
+# Atomic Nuclei
+[Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/nuclei.ipynb) where you can find all the graphs.
+
+Data created on 17.10.2022 at 19:32:45
+
+Data updated on 17.10.2022 at 19:32:45
+
+## Support by Ontologies
+The term [acquisition nucleus](https://terminology.nfdi4chem.de/ts/ontologies/nmrcv/terms?iri=http%3A%2F%2FnmrML.org%2FnmrCV%23NMR%3A1400083) is already provided in [nmr CV](https://terminology.nfdi4chem.de/ts/ontologies/nmrcv). However, 2D NMR isotope-related terms are largely missing. The possible values such as "1H" are very well annotated, either simply as atoms ([in CHEBI](https://terminology.nfdi4chem.de/ts/ontologies/chebi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHEBI_33250&viewMode=All&siblings=false)), or encoded in the name of the NMR method ([in CHMO](https://terminology.nfdi4chem.de/ts/ontologies/chmo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FCHMO_0000613&viewMode=All&siblings=false) despite the lack of consistency with dimensionality there). Currently, available ontologies are adequate to cover the atomic nuclei values in most cases.
+
+## Data Sanitisation and Missing Values
+
+
+
+
+
Field Type
+
Field Name
+
Values Readability
+
Unit
+
Missing
+
+
+
MTBLS
+
semi-dedicated
+
Pulse sequence name
+
free text
+
none
+
The field is not provided; or the regular expressions '\d+[A-CE-Z]\-\d+[A-CE-Z]' or '\d+[A-CE-Z]\-\d+[A-CE-Z]' are not found in the field; or the value is provided as N/A or other similar expressions; or the study "assays" value is "null".
+
+
+
MW
+
semi-dedicated
+
NMR Experiment Type
+
machine-readable
+
none
+
The field is not provided; or an expression of numbers followed directly with letters (but not 1D or 2D) is not found in the field; or the value is provided as N/A or other similar expressions; or decoding the JSON file that contains the study details has failed due to syntax error there.
+
+
+
CENAPT
+
semi-dedicated
+
Description
+
free text
+
none
+
"1h" and "13c" were not found in the description, and checking for the regular expressions '\d+[a-zA-Z]+' didn't match any isotope.
["NMR data of gossypol in DMSOd6 and CDCl3. The dataset contains 1D 1H 13C as well as 2D COSY, HSQC, HMBC, all acquired at 600MHz (Bruker 600MHz spectrometer with CryoProbe (CP DCH 600S3 C/H-D-05 Z)"]
+
"1h", "1h-13c", "h-h", "missing"
+
+
+
NMRShiftDB
+
["1H", "13C", "H,H-COSY"]
+
"1h", "1h-13c", "h-h", "missing"
+
+
+
+## Results
+Taking the large number of studies from NMRShiftDB into account or not, the most reported atomic nuclei are "1H" and "13C". But NMRSiftDB adds more 1D nuclei to the scene, such as "19F" and "11B".
+
+
+
+The percentages of all studies in the four repositories based on the acquisition nucleus (only nuclei appearing in more than 200 studies can be seen here.)
+
+
+Excluding NMRShiftDB, we see that the other repositories have only 1D and 2D NMR based on proton and carbon.
+
+
+
+The number of studies in three repositories based on the acquisition nucleus
+
+
+Here one can see the variation in nuclei reported in NMRShiftDB.
+
+
+The number of studies in NMRShiftDB based on the acquisition nucleus
+
+
+And here you can find the whole view of the four repositories with a logarithmic scale.
+
+
+
+The number of studies in the four repositories based on the acquisition nucleus (with a logarithmic scale)
+
\ No newline at end of file
diff --git a/docs/advanced-guides/nmr-repositories/organism.md b/docs/advanced-guides/nmr-repositories/organism.md
new file mode 100644
index 00000000..510f5c84
--- /dev/null
+++ b/docs/advanced-guides/nmr-repositories/organism.md
@@ -0,0 +1,74 @@
+# Organism
+[Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/organism.ipynb) where you can find all the graphs.
+
+Data created on 17.10.2022 at 19:32:45
+
+Data updated on 17.10.2022 at 19:32:45
+
+## Support by Ontologies
+[NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy) provides an excellent source for organisms.
+
+## Data Sanitisation and Missing Values
+Organisms are found only in metabolomics-related repositories, i.e., MTBLS and MW.
+
+
+
+
+
Field Type
+
Field Name
+
Values Readability
+
Unit
+
Missing
+
+
+
MTBLS
+
dedicated
+
Organism
+
ontology-driven
+
none
+
The field is not provided; or the value is provided as N/A or other similar expressions; or the study "assays" value is "null"; or the organism is not found in NCBI taxonomy.
+
+
+
MW
+
dedicated
+
Subject Species
+
free text
+
none
+
The field is not provided; or the value is provided as N/A or other similar expressions; or decoding the JSON file containing the study details has failed due to syntax error there; or the organism was not found in NCBI taxonomy.
+
+## Results
+Organism details are available in metabolomics repositories. The users usually use the scientific name that can be obtained from [NCBI Taxonomy](https://www.ncbi.nlm.nih.gov/taxonomy). However, some inconsistencies were encountered such as with writing the scientific name (e.g., Mus Musculus instead of Mus musculus), providing a common name (Goat instead of Capra hircus), or providing the source along with the value (e.g., NCBITAXON:Homo sapiens), or even typos.
+
+Some values were ambiguous such as "Various", "Extract", "Multi-species non-defined biofilm consortium" or not even species, such as NMR buffer. Additionally, sometimes, more than one species was mentioned. The combination of species is usually standardized by putting ";" or "/" between the names, but still, the relation between the species is not clear (samples from multiple species vs one sample from a species tissue infected by another species). Lastly, the organism provided varys in rank. Mostly the species is provided, but sometimes it is the genus or strain.
+
+However, even after taking all that was mentioned above, it is still clear that the most studied species are humans (Homo sapiens) and mice (Mus musculus)
+
+
+A rough estimate of the percentages of all studies in MTBLS and MW repositories based on the organism
+
+
+Here one can see the number of studies providing the organism and its value.
+
+
+The number of studies in MTBLS and MW based on the organism
+
\ No newline at end of file
diff --git a/docs/advanced-guides/nmr-repositories/part.md b/docs/advanced-guides/nmr-repositories/part.md
new file mode 100644
index 00000000..e5d3431b
--- /dev/null
+++ b/docs/advanced-guides/nmr-repositories/part.md
@@ -0,0 +1,74 @@
+# Organism Part
+[Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/organism-part.ipynb) where you can find all the graphs.
+
+Data created on 17.10.2022 at 19:32:45
+
+Data updated on 17.10.2022 at 19:32:45
+
+## Support by Ontologies
+[The BRENDA Tissue Ontology - BTO](https://www.ebi.ac.uk/ols/ontologies/bto) and [Experimental Factor Ontology - EFO](https://www.ebi.ac.uk/ols/ontologies/efo) are excellent sources for organisms parts.
+
+## Data Sanitisation and Missing Values
+Organisms parts are found only in metabolomics-related repositories, i.e., MTBLS and MW.
+
+
+
+
+
+
Field Type
+
Field Name
+
Values Readability
+
Unit
+
Missing
+
+
+
MTBLS
+
dedicated
+
Organism part
+
ontology-driven
+
none
+
The field is not provided; or the value is provided as N/A or other similar expressions; or the study "assays" value is "null"; or the organism is not found in NCBI taxonomy.
+
+
+
MW
+
dedicated
+
SAMPLE_TYPE
+
free text
+
none
+
The field is not provided; or the value is provided as N/A or other similar expressions; or decoding the JSON file containing the study details has failed due to syntax error there; or the organism was not found in NCBI taxonomy.
+
+## Results
+Organism parts details are available in metabolomics repositories. The use of different sources of ontologies was easy to see when using terms such as "Blood" vs "blood". Additionally, values other than organism parts were sometimes provided, such as "Acetonitrile:H2O (1:3)".
+
+The most used part was the blood serum, then come the urine, blood plasma, liver, and others.
+
+
+
+A rough estimate of the percentages of all studies in MTBLS and MW repositories based on the organism part
+
+
+Here one can see the number of studies providing the organism part and its value.
+
+
+The number of studies in MTBLS and MW based on the organism part
+
\ No newline at end of file
diff --git a/docs/advanced-guides/nmr-repositories/ph.md b/docs/advanced-guides/nmr-repositories/ph.md
new file mode 100644
index 00000000..1e309850
--- /dev/null
+++ b/docs/advanced-guides/nmr-repositories/ph.md
@@ -0,0 +1,46 @@
+# Sample pH
+[Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/ph.ipynb) where you can find all the graphs.
+
+Data created on 17.10.2022 at 19:32:45
+
+Data updated on 17.10.2022 at 19:32:45
+
+## Support by Ontologies
+The [definition of the pH](https://terminology.nfdi4chem.de/ts/search?q=ph) is easily [found in ontologies](https://terminology.nfdi4chem.de/ts/search?q=ph), the definition of [Sample pH](https://terminology.nfdi4chem.de/ts/ontologies/nmrcv/terms?iri=http%3A%2F%2FnmrML.org%2FnmrCV%23NMR%3A1000019) too. However, when users provide this value, it is not clear whether it really means the pH of the sample, the solvent, the solvent with the buffer, or another value. Due to the possible confusion, users tend to provide a detailed explanation within the solvent field as a free text, which unfortunately affects the machine-readability of both the solvent and the pH. You can find examples in the [solvent](/advanced-guides/nmr-repositories/solvent.md) page.
+
+## Data Sanitisation and Missing Values
+It was possible to get the pH details only from [MetaboLights](https://www.ebi.ac.uk/metabolights/).
+
+
+
+
+
Field Type
+
Field Name
+
Values Readability
+
Unit
+
Missing
+
+
+
MTBLS
+
dedicated
+
Sample pH
+
free text
+
none
+
The field is not provided; or the value is provided as N/A or other similar expressions; or the study "assays" value is "null"; or the value cannot be converted into a float.
+
+
+
+## Results
+
+It was possible to obtain the pH only from MTBLS, even though most of the studies didn't provide this metadata. Most samples' pHs were leaning towards the neutral 7, while a small percentage was around 4.
+
+
+
+A rough estimate of the percentages of all studies in MTBLS repository based on the sample pH
+
+
+Here one can see the number of studies providing the pH of the sample and its value.
+
+
+The number of studies in MTBLS based on the sample pH
+
\ No newline at end of file
diff --git a/docs/advanced-guides/nmr-repositories/sanitisation.md b/docs/advanced-guides/nmr-repositories/sanitisation.md
new file mode 100644
index 00000000..a5436614
--- /dev/null
+++ b/docs/advanced-guides/nmr-repositories/sanitisation.md
@@ -0,0 +1,19 @@
+# Data Sanitisation and Missing Values
+
+Due to the data being reported, in most cases, as free text; in addition to the databases having their own schemas for data modeling (with few exceptions, as [MetaboLights](https://www.ebi.ac.uk/metabolights/) complies to [ISA Model](https://isa-specs.readthedocs.io/en/latest/isamodel.html)), we had to generate “personalized” scripts for each database to handle its specific way of data reporting; with data being exposed via standard API or not; within a dedicated field or not; as an ontology term or a free text; with a unit in the same field, or in another one, or completely absent. That also led to a lot of cleaning through hard coding, and also to considering some data as missing as the unit is not provided, making the data vague even for human reading, while sometimes cleaning even with hard coding wasn’t possible as each value will need its own cleaning (e.g., with the solvents, unless mapped to an ontology which is out of the scope of this analysis).
+
+We provide a detailed description of the data sanitization we performed based on the repository and the parameter in the dedicated pages of the parameters.
+- We describe the **Field Type** from which the parameter can be extracted as either:
+ - **dedicated** when the field purpose is to provide this parameter.
+ - **semi-dedicated** when it is not mainly concerned with providing the desired parameter, but still, it can be found there in most cases.
+ - **absent** means that no such field was found in the database.
+- Then, the field name is mentioned.
+- Afterwards, given that there is a dedicated or semi-dedicated field, we describe the **Values Readability** whether they are:
+ - **ontology-driven**.
+ - **machine-readable** when they are free text, but reasonable cleaning makes them machine-readable in most cases.
+ - **free text**
+- We describe whether the **Unit** was provided as a
+ - **separate field**
+ - **integrated** with the values (as this option usually results from free text input, it leads to the possibility of not providing the unit in some cases).
+ - If no unit is needed, we write it in the table as **none**.
+- We also provide examples of the **Input** (the values the parameter got in the repository) with the **Output** we generated from them, with clarification of the meaning of the value **missing** as an output.
diff --git a/docs/advanced-guides/nmr-repositories/solvent.md b/docs/advanced-guides/nmr-repositories/solvent.md
new file mode 100644
index 00000000..d1e90064
--- /dev/null
+++ b/docs/advanced-guides/nmr-repositories/solvent.md
@@ -0,0 +1,98 @@
+# Solvent
+[Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/solvent.ipynb) where you can find all the graphs.
+
+Data created on 17.10.2022 at 19:32:45
+
+Data updated on 17.10.2022 at 19:32:45
+
+## Support by Ontologies
+The concept of [NMR solvent](https://terminology.nfdi4chem.de/ts/ontologies/nmrcv/terms?iri=http%3A%2F%2FnmrML.org%2FnmrCV%23NMR%3A1000330) already exists in [nmr CV](https://terminology.nfdi4chem.de/ts/ontologies/nmrcv), unfortunately, without a definition. The same happens with [NMR buffer](https://terminology.nfdi4chem.de/ts/ontologies/nmrcv/terms?iri=http%3A%2F%2FnmrML.org%2FnmrCV%23NMR%3A1000331). Despite that, the values for [solvents, buffers,](https://terminology.nfdi4chem.de/ts/ontologies/chebi) and their [concentrations units](https://terminology.nfdi4chem.de/ts/ontologies/uo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000051&viewMode=All&siblings=false) can be ideally provided with ontology terms.
+
+## Data Sanitisation and Missing Values
+
+
+
+
+
Field Type
+
Field Name
+
Values Readability
+
Unit
+
Missing
+
+
+
MTBLS
+
dedicated
+
Solvent
+
free text
+
none
+
The field is not provided; or the value is provided as N/A or other similar expressions; or the study "assays" value is "null".
+
+
+
MW
+
dedicated
+
NMR Solvent
+
free text
+
none
+
The field is not provided; or the value is provided as N/A or other similar expressions; or decoding the JSON file containing the study details has failed due to syntax error there.
+
+
+
CENAPT
+
semi-dedicated
+
Description
+
free text
+
none
+
'in ' was not found in the description, or it was not relevant to the solvent (hard-coding).
+
+
+
NMDShiftDB
+
dedicated
+
cml:solvent
+
free text
+
none
+
The value is 'unreported' or 'unknown'
+
+
+
+
+
+
+
+
Input Examples
+
Output
+
+
+
MTBLS
+
["0.01 M phosphate buffered D2O", "0.154 M saline D20", "0.6 ml of 0.1M phosphate buffered D2O (pH=7.0) solution containing 0.5 mM 3-trimethylsilyl-propionate-2, 2, 3, 3, -d4 (TMSP, δ =0.0 ppm) ", "CD3OD", "H20 + D20", "water"]
+
["0-01-m-phosphate-buffered-d2o", etc.]
+
+
+
MW
+
["10%D20", "100 mM phosphate buffer at pH 7.4 (prepared in D2O) containing 0.1 mM 3-(trimethylsilyl)-propionic-2,2,3,3-d4 acid", "90:10 H2O/D2O (99.96% atom D2O; Cambridge Isotope Labs) with 0.2 mM phosphate buffer (pH 7.4) and 0.25 mM 3-(trimethylsilyl)propionic-2,2,3,3d4-acid", "CDCl3", "D2O and MeOD"]
+
["0-01-m-phosphate-buffered-d2o", etc.]
+
+
+
CENAPT
+
["NMR data of gossypol in DMSOd6 and CDCl3. The dataset contains 1D 1H 13C as well as 2D COSY, HSQC, HMBC, all acquired at 600MHz (Bruker 600MHz spectrometer with CryoProbe (CP DCH 600S3 C/H-D-05 Z)"]
+
+## Results
+The solvent was possible to obtain in most studies and repositories, but it was rarely machine-readable, with a high level of inconsistencies. The following graph can give a rough estimate of popular solvents. However, it is far from accurate when it comes to exact numbers, as one solvent can be mentioned tens of times with different expressions.
+
+
+
+A rough estimate of the percentages of all studies in the four repositories based on the NMR solvent (only solvent used in more than 50 studies are shown)
+
+
+Here you can find the whole view of the four repositories with a logarithmic scale where you can easily notice how some solvents get repeated with different expressions.
+
+
+
+The number of studies in the four repositories based on NMR solvent (with a logarithmic scale)
+
\ No newline at end of file
diff --git a/docs/advanced-guides/nmr-repositories/temperature.md b/docs/advanced-guides/nmr-repositories/temperature.md
new file mode 100644
index 00000000..20047a0d
--- /dev/null
+++ b/docs/advanced-guides/nmr-repositories/temperature.md
@@ -0,0 +1,97 @@
+# Temperature
+[Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/temperature.ipynb) where you can find all the graphs.
+
+Data created on 17.10.2022 at 19:32:45
+
+Data updated on 17.10.2022 at 19:32:45
+
+## Support by Ontologies
+While searching in NMR-related ontologies, finding terms about the temperature through an NMR assay wasn't possible. When saying "Temperature" here, we mean the temperature at which the NMR spectroscopy was conducted. Unit-wise, one can easily use [ontology-driven units](https://terminology.nfdi4chem.de/ts/ontologies/uo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUO_0000005&viewMode=All&siblings=false).
+
+## Data Sanitisation and Missing Values
+
+
+
+
+
Field Type
+
Field Name
+
Values Readability
+
Unit
+
Missing
+
Comment
+
+
+
MTBLS
+
dedicated
+
Temperature
+
float
+
separate field
+
The field is not provided; or the unit was not found in the list of units we provided; or the value is provided as N/A or other similar expressions; or the study "assays" value is "null".
+
The provided list of units is ['UO:kelvin', 'UO:kelvin:K','Kelvin','kelvin', 'degree Celsius','celsius', 'degree celsius']
+
+
+
MW
+
dedicated
+
Temperature
+
machine-readable
+
integrated
+
The field is not provided; or an expression of numbers was not found in the field; or the value is provided as N/A or other similar expressions; or the unit (words with c or d for Celsius and k for Kelvin) was not found; or decoding the JSON file that contains the study details has failed due to syntax error there.
+
+
+
+
CENAPT
+
none
+
none
+
none
+
none
+
+
+
+
+
NMRShiftDB
+
dedicated
+
cml:temp
+
float
+
separate field
+
none
+
The unit is ontology-driven as it is always Kelvin
+
+## Results
+The temperature was easy to obtain in all the three repositories that provide it. However, the inconsistency encountered in the values and units made it time-consuming to harmonize the data. In the end, having units coming (or possibly to be mapped) from ontologies made most of the data clear and machine-readable. The temperature provided in Celsius was converted to Kelvin, and with visualization, one can see that most of the assays were held around room temperature.
+
+
+
+The percentages of all studies in the three repositories based on the Temperature
+
+
+Still, some of the values were reported wrongly in Kelvin, as values like 0 and 37 can be seen in the graph showing the number of studies for each temperature (with a logarithmic scale).
+
+
+
+The number of studies in the three repositories based on the Temperature (with a logarithmic scale)
+
diff --git a/docs/advanced-guides/nmr-repositories/variant.md b/docs/advanced-guides/nmr-repositories/variant.md
new file mode 100644
index 00000000..6f74e3d3
--- /dev/null
+++ b/docs/advanced-guides/nmr-repositories/variant.md
@@ -0,0 +1,70 @@
+# Variant
+[Notebook link](https://github.com/NFDI4Chem/repo-scripts/blob/main/notebooks/variant.ipynb) where you can find all the graphs.
+
+Data created on 17.10.2022 at 19:32:45
+
+Data updated on 17.10.2022 at 19:32:45
+
+## Support by Ontologies
+[The BRENDA Tissue Ontology - BTO](https://www.ebi.ac.uk/ols/ontologies/bto) and [Experimental Factor Ontology - EFO](https://www.ebi.ac.uk/ols/ontologies/efo) are good sources for variants.
+
+Variants are found only in metabolomics-related repositories, i.e., MTBLS and MW.
+
+
+
+
+
Field Type
+
Field Name
+
Values Readability
+
Unit
+
Missing
+
+
+
MTBLS
+
dedicated
+
Variant
+
free text
+
none
+
The field is not provided; or the value is provided as N/A or other similar expressions; or the study "assays" value is "null"; or the organism is not found in NCBI taxonomy.
+
+
+
MW
+
dedicated
+
GENOTYPE_STRAIN
+
free text
+
none
+
The field is not provided; or the value is provided as N/A or other similar expressions; or decoding the JSON file containing the study details has failed due to syntax error there; or the organism was not found in NCBI taxonomy.
+
+
+
+
+
+
+
Input Examples
+
Output
+
+
+
MTBLS
+
["Mus musculus str. SAMP1/YitFc", "BY4741", "Thoroughbred", "EFO:Thalassiosira pseudonana CCMP1335"]
+
["c57Bl-6", "c3h-hen", etc.]
+
+
+
MW
+
["C57BL/6", "Swiss Webster Mice", "C3H/HeN"]
+
["c57Bl-6", "c3h-hen", etc.]
+
+
+
+## Results
+Variants details are available in metabolomics repositories. The most used variant was "C57BL/6J".
+
+
+
+A rough estimate of the percentages of all studies in MTBLS and MW repositories based on the variant
+
+
+Here one can see the number of studies providing the variant and its value.
+
+
+The number of studies in MTBLS and MW based on the variant
+
\ No newline at end of file
diff --git a/docs/advanced-guides/nmrium/nmrium.md b/docs/advanced-guides/nmrium/nmrium.md
new file mode 100644
index 00000000..c7fd79c1
--- /dev/null
+++ b/docs/advanced-guides/nmrium/nmrium.md
@@ -0,0 +1,35 @@
+# NMRium
+
+[NMRium](https://www.nmrium.org/) is an open-source NMR spectra processing tool.
+
+
+
+
+It provides a bundle of handy features, such as:
+* Open various vendors and open file formats (JCAMP-DX file, a zipped Bruker folder, or a JEOL file).
+* It accepts 1D (FID and FT) and 2D spectra (FT only).
+* Advanced peak picking detection for 1D and 2D NMR spectra. Also, it can generate the NMR string required for publication or patent.
+* All the processing and assignment can be stored as a “.nmrium” file. This file contains the original data as well as all the processing that was applied on the spectrum. Assignments of the molecule are also saved in the file. Additionally, export in NMReData is possible as well.
+
+## Demo
+
+
+
+
+
+## Integrating NMRium in nmrXiv
+
+Development: https://nmriumdev.nmrxiv.org
+Production: https://nmrium.nmrxiv.org
+
+Since **[nmrXiv](https://nmrxiv.org/)** supports open-source initiatives natively, NMRium is our preferred NMR spectra processing and analysis tool. NMRium is available as a standalone, React component that can be integrated into other applications.
+
+To enable and ensure that the integration is framework independent, we wrapped NMRium in a React App and can now be integrated into any third-party application via an iframe, irrespective of the underlying javascript framework. This layer one solution (nmrium-react-wrapper) enables us to extend and expose the NMRium APIs and integrate other NMR tools seamlessly.
+
+This nmrium-react-wrapper is released under MIT opensource license - [GitHub](https://github.com/NFDI4Chem/nmrium-react-wrapper)
+
+Please find the installation instructions and other documentation on the github readme page.
+
+## Documentation
+NMRium provides rich documentation on their webiste. [Here is the link for more details](https://docs.nmrium.org/).
+
diff --git a/docs/community/media-kit.md b/docs/community/media-kit.md
new file mode 100644
index 00000000..3e904f03
--- /dev/null
+++ b/docs/community/media-kit.md
@@ -0,0 +1,21 @@
+# Media Kit
+
+## Publications
+
+### 2020
+
+- Research Data in Chemistry ‐ Results of the first NFDI4Chem Community Survey
+
+- NFDI4Chem - Towards a National Research Data Infrastructure for Chemistry in Germany
+
+## Presentations
+### 2021
+- nmrXiv Specs (Functional and Technical details) Internal presentation WIP
+### 2022
+- Schema (Sample, Assay, Spectra) and Ontologies - Internal presentation WIP
+- Metadata in the wild (Analysis of meta-data from public NMR data sets) - Internal presentation WIP
+
+## Logos
+- Figma project - here
+
+
diff --git a/docs/community/training.md b/docs/community/training.md
new file mode 100644
index 00000000..05e4a94e
--- /dev/null
+++ b/docs/community/training.md
@@ -0,0 +1,3 @@
+# Training
+
+[NFDI4Chem](https://www.nfdi4chem.de/) provides training to the community in the shape of workshops and webinars. Additionally, any aspect that remains unclear can be further discussed through the [helpdesk](mailto:helpdesk@nfdi4chem.de).
\ No newline at end of file
diff --git a/docs/community/workshops.md b/docs/community/workshops.md
new file mode 100644
index 00000000..ceb5c477
--- /dev/null
+++ b/docs/community/workshops.md
@@ -0,0 +1,23 @@
+# NMR MIChI Workshops in NFDI4Chem
+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. Here you can find all the workshops related to NMR and analytical chemistry. For a full-list of the workshops, please visit [this link](https://nfdi4chem.github.io/workshops/).
+
+## FAIR NMR Research Data Management
+NFDI4Chem, in collaboration with IUPAC, has organized a workshop about FAIR NMR Research Data Management where experts contributing to the FAIRness and standardization of NMR data have participated 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. For more details, please visit [this link](https://nfdi4chem.github.io/workshops/category/fair-nmr-research-data-management)
+
+- Date and Location: Karlsruhe: 07.06.2022 - 08.06.2022
+
+- Participants (Alphabetically): [Dr. Damien Jeannerat](https://orcid.org/0000-0001-7018-4288), Dr. Gerhard Fink, Prof. Henry Rzepa](https://orcid.org/0000-0002-8635-8390), [Dr. Ian Bruno](https://orcid.org/0000-0003-4901-9936), [Dr. Johannes Liermann](https://orcid.org/0000-0003-2060-842X), [Mr. Mark Archibald](https://orcid.org/0000-0001-8687-7134), [Dr. Nicole Jung](https://orcid.org/0000-0001-9513-2468), Ms. Nisha Sharma, Ms. Noura Rayya, [Prof. Robert Hanson](https://orcid.org/0000-0001-5411-2356), Dr. Stefan Kuhn, [Prof. Steffen Neumann](https://orcid.org/0000-0002-7899-7192), [Mr. Venkata Chandra Sekhar Nainala](https://orcid.org/0000-0002-2564-3243)
+
+## NFDI4Chem Workshop Data Formats
+Discussion on available data formats in analytical chemistry, can we make any available open formats a standard? And how can they evolve to be so? For more details, please visit [this link](https://nfdi4chem.github.io/workshops/standard-formats/overview)
+
+- Date and Location: Hannover: 11.10.2022
+
+- Participants (Alphabetically): Mr. Adam Basha, Mr. Bhavin Katabathuni, [Prof. Christoph Steinbeck](https://orcid.org/0000-0001-6966-0814), Ms. Claire Lin, [Dr. David Rauh](https://orcid.org/0000-0001-7499-1693), [Dr.-Ing Felix Bach](https://orcid.org/0000-0002-5035-7978), [Dr. Giacomo Lanza](https://orcid.org/0000-0002-2239-3955), Dr. Holger Israel, Dr. Joachim Richert, [Dr. Johannes Liermann](https://orcid.org/0000-0003-2060-842X), [Ms. Leah McEwen](https://orcid.org/0000-0003-2968-1674), [Michael Klix](https://orcid.org/0000-0002-0591-6582), Ms. Nikki Parks, Ms. Nisha Sharma, Ms. Noura Rayya, Ms. Pei-Chi Huang, [Philip Strömert](https://orcid.org/0000-0002-1595-3213), [Dr. René Meier](https://orcid.org/0000-0002-1501-1349), [Dr. Rukeia El-Athman](https://orcid.org/0000-0003-0749-160X), [Dr. Steffen Neumann](https://orcid.org/0000-0002-7899-7192), Dr. Timothy holbrook, [Dr. Tobias Schulze](https://orcid.org/0000-0002-9744-8914)
+
+
+## Coming Soon
+### Minimum Information Standards in Analytical Chemistry
+Work in Progress.
+
+
diff --git a/docs/contribution/contributors.md b/docs/contribution/contributors.md
new file mode 100644
index 00000000..68e10672
--- /dev/null
+++ b/docs/contribution/contributors.md
@@ -0,0 +1,28 @@
+# Contributors and Steering Committee
+
+## Contributors
+- Annett Schröter
+- Christian Popp
+- Christoph Steinbeck
+- Darina Storozhuk
+- David Rauh
+- Hamed Musallam
+- Johannes Liermann
+- Kohulan Rajan
+- Markus Lange
+- Nazar Stefaniuk
+- Nisha Sharma
+- Noura Rayya
+- Pascal Scherreiks
+- Steffen Neumann
+- Tillmann Fischer
+- Timothy Holbrook
+- Venkata chandrasekhar Nainala (Chandu)
+
+## Steering committee
+- Guido Pauli
+- Julien Wist
+- Luc Patiny
+- Nils Schlörer
+- Stephan Kuhn
+
diff --git a/docs/contribution/nmrxiv-docs.md b/docs/contribution/nmrxiv-docs.md
new file mode 100644
index 00000000..3e9317bc
--- /dev/null
+++ b/docs/contribution/nmrxiv-docs.md
@@ -0,0 +1,285 @@
+This website is based on the [Docusaurus framework](https://docusaurus.io) that uses [Markdown](https://www.markdownguide.org/) with [JavaScript](https://www.javascript.com/) [(MDX)](https://mdxjs.com/). Therefore, the content is stored as a mixture mainly containing [Markdown](https://www.markdownguide.org/) with elements from [HTML](https://html.com/) and from the [JavaScript](https://www.javascript.com/) framework [React](https://reactjs.org/). The most important and used components are explained below. More information about [Markdown](https://www.markdownguide.org/) in Docusaurus can be found in the [official Docusaurus documentation](https://docusaurus.io/markdown-features).
+
+# Contributing to nmrXiv Documentation
+
+## Forking
+First, you need to fork the [documentation repository on GitHub](https://github.com/NFDI4Chem/nmrxiv-docs.git)
+
+## Installation
+Although one can edit the page directly on GitHub by clicking on **Edit this page** at the bottom of each page, please avoid it as this option doesn't enable you to see the changes applied before pushing them to GitHub. Also because you need to make the changes on your fork first. Therefore, a local installation is needed first.
+### Dependencies
+* [git](https://git-scm.com/).
+* [Docker Desktop](https://www.docker.com/products/docker-desktop).
+
+### Setup:
+* Start Docker.
+* Open your chosen directory in the terminal.
+* Clone your fork.
+* Go to the project directory:
+```bash
+cd nmrxiv-docs
+```
+* Install the project dependencies by running:
+```bash
+yarn install
+```
+* Start the local development server and open up the browser window by running:
+```bash
+yarn start
+```
+Most changes are reflected live without having to restart the server as soon as you save them.
+
+## Branching
+Whenever you want to edit a page, please do the following:
+* Create a new branch for that page from the "development" branch.
+* Make your modifications on that branch.
+* Create a pull request on GitHub for your fork to "development".
+
+Afterwards, the maintainers will review your changes and merge them.
+
+## How to
+
+### Adding a New Page
+* Go to the chosen directory.
+* Add a new file there.
+* Name your file complying with our conventions (kebab-case-of-small-letters).
+* Give it the extension ".mdx".
+* Insert at the top of the file, e.g.:
+
+```bash
+---
+sidebar_position: 2
+id: contributing-to-nmrxiv-docs.mdx
+title: Contributing to nmrxiv Docs.mdx
+---
+```
+| Name | Type | Default | Description |
+|---|---|
+| sidebar_position | Number | Default ordering | Controls the position of a doc inside the generated sidebar slice when using autogenerated sidebar items. See also [Autogenerated sidebar metadatas](https://docusaurus.io/sidebar#autogenerated-sidebar-metadatas).|
+| id | String | File path (including folders, without the extension) | A unique document id.|
+| title | String | Markdown title or id | The text title of your document. Used for the page metadata and as a fallback value in multiple places (sidebar, next/previous buttons...). Automatically added at the top of your doc if it does not contain any Markdown title. |
+
+More fields, and the Description of each field, can be found in [docusaurus documentation](https://docusaurus.io/api/plugins/@docusaurus/plugin-content-docs).
+
+### Headings
+To create a heading, add one or more # signs in front of the word or phrase. The number of # you use should correspond to the heading level. Many # indicates a low level.
+
+### Escaping Signs
+To show signs specified in the Markdown syntax, escape them with "\".
+
+### Links
+Links can be added via [Markdown](https://www.markdownguide.org/) or [React](https://reactjs.org/):
+
+In Markdown:
+```md
+[Text to be shown on the page](actual link)
+```
+In React:
+```js
+import Link from '@docusaurus/Link';
+
+Title
+```
+### Lists
+#### Ordered List
+Enter the number you want your list to start with, enter a dot and a space, then enter your text. When you hit enter, the next number will be generated automatically.
+```
+2. First line.
+3. Second line.
+4. Third line.
+```
+Output:
+
+2. First line.
+3. Second line.
+4. Third line.
+
+Please note, if you enter random numbers with dots, the generated list will still be ordered based on the first number!
+```
+2. First line.
+5. Second line.
+2. Third line.
+```
+
+Output:
+
+2. First line.
+5. Second line.
+2. Third line.
+
+
+#### Unordered Lists:
+Use either * or - at the beginning of the line, then enter a space and then your text.
+```
+* First line.
+- Second line.
+```
+
+Output:
+* First line.
+- Second line.
+
+### Code Blocks
+Code blocks enable highlighting your code and its syntax based on the language. To use code blocks:
+1. Wrap your code with three backticks.
+2. Add the right language.
+3. Insert your code.
+4. Optionally, you can add a title or highlight certain lines in the code. For more details, please refer to [Docusaurus Code blocks](https://docusaurus.io/markdown-features/code-blocks).
+
+For instance:
+
+\```js
+
+Example
+
+\```
+
+Which will look like this:
+
+```js
+Example
+```
+
+For a list of the supported languages, please visit the [link](https://github.com/FormidableLabs/prism-react-renderer/blob/master/src/vendor/prism/includeLangs.js). It is common to use "bash", "html", "js", and "md" in this documentation. Please use "Bash" code blocks for errors too.
+
+### Images/gifs
+
+Images/gifs can be inserted in a centered mode with a specified width using HTML. Please use the following block and change the path to your image, along with the width and caption. If you have many images related to one topic, please group them in one folder. All images are to be added to `/static/img` folder.
+
+```html
+
+
+Private project view
+
+```
+
+#### SVG
+SVGs need special treatment. First import them as [React component](https://reactjs.org/react-component.html), and then insert them in your text with `className="logo"`:
+
+``` js
+import Sun from '@site/static/img/sun.svg'
+
+```
+### Tables
+```
+| Header 1 | Header 2 |
+|---|---|
+| Field 1 | Field 2 |
+```
+Output:
+
+| Header 1 | Header 2 |
+|---|---|
+| Field 1 | Field 2 |
+
+### Info Boxes
+Highlighted info boxes with further information are called "Admonitions" in [Docusaurus](https://docusaurus.io/markdown-features/admonitions). There are three possible admonitions in nmrXiv Docs:
+
+:::danger Caution
+Caution: When there is a risk of losing data, breaking things down, and so on.
+:::
+
+:::caution Recommendation
+Recommendation: When a certain behavior is recommended, but not necessary.
+:::
+
+:::info Info
+Info: Any important piece of information to be highlighted.
+:::
+
+### Inserting Downloadable Files
+If you want to provide one or multiple file(s) to be downloaded directly from the documentation, upload them to the [files folder in GitHub](https://github.com/NFDI4Chem/nmrxiv-docs/tree/development/static/files), and insert a Download Button with the file path(s), separated by a comma, in `files` and the text to be shown on the button in `text`:
+
+```
+import { DownloadBtn } from '@site/download-files.js'
+
+
+```
+
+### Formatting
+
+#### Bold
+
+```
+Example
+```
+Output:
+Example
+
+#### Italics
+```
+Example
+```
+Output:
+Example
+
+#### Highlighted Elements
+
+```
+`Example`
+```
+Output:
+`Example`
+
+#### Line Breaks
+Add two blank lines (two "enter"s) where the line break is needed to be.
+
+#### Color
+* Colored letters:
+```js
+Example
+```
+Output:
+Example
+
+* Colored background:
+```js
+Example
+```
+
+Output:
+Example
+
+#### Strikethrough
+```html
+Example
+```
+Output:
+Example
+
+
+## Conventions
+
+### Hyperlinks
+We would recommend the intensive use of hyperlinks instead of plain text whenever possible. The intro of this page is a good example of that.
+
+### Bold Text
+All bolded terms in this documentation can also be found within the user/developer interface.
+
+### Tables
+To maintain a consistent view throughout the table, the first letter from the first word will always be capitalized (unless it is a unit). Full stops will be used when the correct language requires them. The following table provides more details and examples.
+
+| Case | Capitalization | Full stop | Example |
+|---|---|---|---|
+| Unit | to be written as provided by [The International System of Units (SI)](https://www.bipm.org/en/measurement-units) | No | "Hz", "°C", "cm" |
+| Single word| Only first letter, unless the word is usually written differently| No | "No", "True", "NMR" |
+| Phrase | Only first letter from the first word, unless other words require so | No | "NMR technique", "Chemical formula" |
+| Sentence | To be written according to the correct use of language | Yes | "Fields with description are usually provided as sentences which requires adding a full stop at the end of the sentence." |
+
+### Capitalization
+Please always capitalize:
+* The first letter of the first word, unless it is officially written with small letters, e.g., "nmrXiv".
+* Headings: The first letter of each word except articles, conjunctions, and prepositions with less than four letters. e.g., "Contributing to nmrXiv Docs".
+
+Please note: Prepositions are dealt with as normal words and are capitalized when applicable in the following cases:
+* If they are part of the verb: "Starting Up the Application".
+* If they have more than four letters: "Further Steps After Installation".
+
+### Highlighting Elements
+[Highlighted Elements](https://docs.nmrxiv.org/contributing/contributing-to-nmrxiv-docs/#highlighted-elements) should be used with files and folders names, and to highlight words where bolding is not applicable.
+
+### Images
+Images are to be added directly after the corresponding paragraph.
+
+### Citations
+When citing nother resource, please add a number at the end of the cited section within brackets. For instance: "This is a cited line.[1]". At the bottom of the page, pleas add a new paragraph highlighted with one "\#" and name it as "References". Then provide the numbered list of references as persistent links.
diff --git a/docs/contribution/nmrxiv.md b/docs/contribution/nmrxiv.md
new file mode 100644
index 00000000..f4817832
--- /dev/null
+++ b/docs/contribution/nmrxiv.md
@@ -0,0 +1,34 @@
+### Did you find a bug?
+
+* **Do not open up a GitHub discussion issue if the bug is a security vulnerability in nmrXiv**, and instead contact us here: info.nmrxiv@uni-jena.de (This email is not ready yet).
+
+* **Ensure the bug was not already reported** by searching on GitHub under [nmrXiv issues](https://github.com/NFDI4Chem/nmrxiv/issues).
+ When searching change the filter box to both open and closed issues like this:
+ ```bash
+ is:issue is open
+ ```
+ to
+ ```bash
+ is:issue
+ ```
+ e.g.
+ ```bash
+ is: issue theme
+ ```
+
+* If you're unable to find an open issue addressing the problem, [open a new issue](https://github.com/NFDI4Chem/nmrxiv/issues/new/choose) under the approriate category. Be sure to include a Title and clear Description, with as much relevant information as possible, and a **code sample** or an **executable test case** demonstrating the expected behavior that is not occurring.
+
+### **Did you write a patch that fixes a bug?**
+Please read the [Development workflow](https://docs.nmrxiv.org/developer-guides/development-workflow) guide to learn more about coding conventions, opening an issue, creating a PR, reviewing, and merging the PR.
+
+### **Do you intend to add a new feature or change an existing one?**
+
+* Do not open an issue on GitHub or suggest your change in the nmrXiv mailing list before you start coding.
+
+### **Do you have questions about the source code?**
+
+* Ask any question about how to use nmrXiv in the nmrXiv mailing list.
+
+Thanks!
+
+nmrXiv Team
diff --git a/docs/developer-guides/api.md b/docs/developer-guides/api.md
new file mode 100644
index 00000000..6e61748b
--- /dev/null
+++ b/docs/developer-guides/api.md
@@ -0,0 +1,16 @@
+# API
+
+nmrXiv infrastructure supports API through which software developers can interact with the data programmatically. Postman tool is used to document how nmrXiv API should be used, methods, status, and error codes supported.
+
+Postman allows you to publish documentation quickly and easily. Postman automatically pulls your sample requests, headers, code snippets, etc., to populate your documentation page with dynamic examples and machine-readable instructions so you can easily share your API with the rest of the world.
+
+## [nmrXiv APIs](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17173369-2ef7d5a8-0121-418b-8762-cc47d7a5b7cd)
+
+
+
+
+If you are interested in specific endpoints, check out the following quick links:
+
+- [Authentication and Authorisation](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/collection/17173369-f372ec15-9b92-4902-8844-b129ab0c17d1?ctx=documentation)
+- [Projects/Studies/Dataset](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/collection/17173369-b00475c3-6171-4e58-97ab-cb88b3ac4c59?ctx=documentation)
+- [Bioschemas](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/folder/17195598-561a4bcc-7c84-4669-b245-c8416dfc8e90?ctx=documentation)
diff --git a/docs/developer-guides/architecture.md b/docs/developer-guides/architecture.md
new file mode 100644
index 00000000..9e3f6376
--- /dev/null
+++ b/docs/developer-guides/architecture.md
@@ -0,0 +1,5 @@
+# Architecture
+
+
+
+
diff --git a/docs/developer-guides/code-contribution-guidelines.md b/docs/developer-guides/code-contribution-guidelines.md
new file mode 100644
index 00000000..a813f64c
--- /dev/null
+++ b/docs/developer-guides/code-contribution-guidelines.md
@@ -0,0 +1,104 @@
+# Code Contribution Guidelines
+
+Thank you for investing your time in contributing to our project! Any contribution you make will be reflected on [nmrxiv.org](https://nmrxiv.org) after it has passed all the test cases on [dev.nmrxiv.org](https://dev.nmrxiv.org).
+In this guide you will get an overview of the contribution workflow from opening an issue, creating a PR, reviewing, and merging the PR.
+
+### Getting started
+
+Before you start contributing, make sure:
+
+- You have a GitHub account, for information on how to create an account, see [Signing up for GitHub.](https://docs.github.com/en/get-started/signing-up-for-github).
+- You have proper access to the [repo](https://github.com/NFDI4Chem/nmrxiv) for your GitHub account, for which you can contact repository owners.
+- You have a code editor installed in your local system, we recommend using [Visual Studio Code](https://code.visualstudio.com/).
+- You have cloned the code and have nmrXiv running locally, for which you can follow the steps provided [here](https://docs.nmrxiv.org/developer-guides/installation/development).
+
+#### Create a new issue
+
+If you spot a problem with the application, [search if an issue already exists](https://github.com/NFDI4Chem/nmrxiv/issues). If a related issue doesn't exist, you can open a [new issue](https://github.com/NFDI4Chem/nmrxiv/issues/new/choose) with the appropriate form.
+[Click here](/FAQs#how-to-report-a-bug) to learn more about how to create an issue or report a bug.
+
+#### Solve an issue
+
+Scan through our [existing issues](https://github.com/NFDI4Chem/nmrxiv/issues) to find one that interests you. You can narrow down the search using `labels` as filters.
+
+### Workflow
+
+#### Create a branch
+
+Never push your code directly to the `development` or `main` branch. Switch to the `development` branch and create a new branch in your repository. A short, descriptive branch name enables your collaborators to see ongoing work at a glance. The branch name should be all small with words separated by a hyphen, [click here](https://github.com/NFDI4Chem/nmrxiv/branches) to follow some examples.
+
+#### Make Changes
+
+On your branch, make the desired changes to the repository. Your branch is a safe place to make changes. If you make a mistake, you can revert your changes or push additional changes to fix the mistake. Your changes will not end up on the default branch until you merge your branch. Commit and push your changes to your branch. Once your changes are ready, don't forget to self-review to speed up the review process. Also, you have proper comments all over your code so that it's easy and clean to understand.
+
+#### Format
+
+For formatting, you can simply run below command which will help saving your time in code formatting and makes it simple to ensure that your code style stays clean, consistent and properly indented.
+
+```bash
+npm run format
+./vendor/bin/sail pint
+```
+
+#### Commit
+
+To facilitate auto CHANGELOG generation, creation of GitHub releases, and version bumps(as per [Semantic Versioning](https://semver.org/)), please follow the structure of [Conventional Commit](https://www.conventionalcommits.org/en/v1.0.0/) for your commit messages.
+Each commit should also be descriptive enough to help you and future contributors to understand what changes the commit contains.
+
+```bash
+[optional scope]:
+
+[optional body]
+
+[optional footer(s)]
+```
+
+choose your `` from below:
+
+1. `fix` : a commit of the type fix patches a bug in your codebase (this correlates with PATCH in Semantic Versioning).
+1. `feat` : a commit of the type feat introduces a new feature to the codebase (this correlates with MINOR in Semantic Versioning).
+1. `BREAKING CHANGE` : a commit that has a footer BREAKING CHANGE:, or appends a ! after the type/scope, introduces a breaking API change (correlating with MAJOR in Semantic Versioning). A BREAKING CHANGE can be part of commits of any type.
+
+An example would look like this:
+
+```bash
+fix: update iframe reference point
+
+Resolves the connection issue for the upload view.
+
+Reviewed-by: XYZ
+Fixes: #123
+```
+
+Click here to learn more about [Conventional Commit](https://www.conventionalcommits.org/en/v1.0.0/).
+
+#### Create a pull request
+
+When you're finished with the changes, create a pull request(also known as a PR) to the `development` branch.
+When you create a pull request, make sure
+
+- You include a summary of the changes and what problem they solve.
+- Your branch has no conflicts with the base branch.
+- You have [linked the issue](https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue), if your pull request addresses an issue. If you link with a keyword, the issue will close automatically when the pull request merges.
+- You have assigned a reviewer for faster code review.
+
+
+#### Address review comments
+
+Reviewers can leave questions, comments, and suggestions. Reviewers can comment on the whole pull request or add comments to specific lines. You and reviewers can insert images or code suggestions to clarify comments.
+You can continue to commit and push changes in response to the reviews. Your pull request will update automatically.
+
+#### Merge your pull request
+
+Your pull request can be merged once it is approved by the reviewer. The primary merge should always be made to the `development` branch, from where your code will be deployed to the [dev environment](https://dev.nmrxiv.org) via our [CI/CD pipeline](https://docs.nmrxiv.org/developer-guides/ci-cd). The [dev environment](https://dev.nmrxiv.org) provides the room to test your feature or code changes. Once it has passed all the test cases, your code changes will now be included as part of a release and be deployed finally to the [production environment](https://nmrxiv.org). These actions are restrictive and should only be performed by our repo admins and owners.
+
+#### Delete your branch
+
+After your branch is merged and the pull request is closed please don't forget to delete your stale branch. This indicates that the work on the branch is complete and prevents you or others from accidentally using old branches. For more information, see [Deleting and restoring branches in a pull request](https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/managing-branches-in-your-repository/deleting-and-restoring-branches-in-a-pull-request).
+
+
+:::info Info
+
+- Never leak your secrets or commit local config files(.env) into source control.
+- Follow the link to learn more about [Laravel](https://laravel.com/9.x/readme) and [Inertia.js](https://inertiajs.com/) best practices.
+ :::
diff --git a/docs/developer-guides/configurations/_category_.json b/docs/developer-guides/configurations/_category_.json
new file mode 100644
index 00000000..64ff4fc7
--- /dev/null
+++ b/docs/developer-guides/configurations/_category_.json
@@ -0,0 +1,7 @@
+{
+ "label": "Configurations",
+ "position": 2,
+ "link": {
+ "type": "generated-index"
+ }
+}
\ No newline at end of file
diff --git a/docs/developer-guides/configurations/oauth.md b/docs/developer-guides/configurations/oauth.md
new file mode 100644
index 00000000..01bcbc47
--- /dev/null
+++ b/docs/developer-guides/configurations/oauth.md
@@ -0,0 +1,36 @@
+______________________________________________________________________
+
+## sidebar_position: 2 id: oauth title: OAuth
+
+In addition to basic username/password authentication, nmrXiv also supports authentication via [OAuth 2.0](https://www.digitalocean.com/community/tutorials/an-introduction-to-oauth-2), which is an authorization framework that enables third party clients to obtain limited access to user accounts on an HTTP service.
+Currently nmrXiv supports login via below three clients:
+
+- [Twitter](https://twitter.com/)
+- [GitHub](https://github.com/)
+- [ORCID](https://orcid.org/)
+
+In order to get this feature available in your application, you need to register your application with the service. This is done through a registration form in the **developer** or **API** portion of the service's website, where you will provide following information (and probably details about your application):
+
+- Application Name
+- Application Website
+- Redirect URI or Callback URL
+
+Once your application is registered, the service will issue client credentials in the form of a *Client Id* and *Client Secret*. These details should be added to the .env file against the below values.
+
+```
+GITHUB_CLIENT_ID=
+GITHUB_CLIENT_SECRET=
+GITHUB_REDIRECT_URL=
+
+ORCID_CLIENT_ID=
+ORCID_CLIENT_SECRET=
+ORCID_REDIRECT_URL=
+
+TWITTER_CLIENT_ID=
+TWITTER_CLIENT_SECRET=
+TWITTER_REDIRECT_URL=
+```
+
+Once done restart or refresh your application and you would be able to find the single sign-on section added in the Login page.
+
+To know more about how nmrXiv works with OAuth visit the official site of [Laravel](https://laravel.com/8.x/socialite) for more details.
diff --git a/docs/developer-guides/configurations/storage.md b/docs/developer-guides/configurations/storage.md
new file mode 100644
index 00000000..17f1756b
--- /dev/null
+++ b/docs/developer-guides/configurations/storage.md
@@ -0,0 +1,34 @@
+______________________________________________________________________
+
+## sidebar_position: 3 id: storage title: Storage
+
+Files in [nmrxiv](https://nmrxiv.org) are stored as [objects](https://en.wikipedia.org/wiki/Object_storage) and are [S3](https://en.wikipedia.org/wiki/Amazon_S3) compatible which provides below three big benefits.
+
+- **Backup/redundancy** - S3 and similar have built-in backups and redundancy
+- **Scaling** - Savings files off-server becomes necessary in modern hosting, such as serverless or containerized environments, as well as in traditional load-balanced environments
+- **Disk usage** - You won't need as much disk space when storing files in the cloud
+- **Features** - S3 (and other clouds) have some great features, such as versioning support for files, lifecycle rules for deleting old files (or storing them in a cheaper way), deletion protection, and more
+
+#### Configuration
+
+There are just two place where the configuration needs to be done.
+
+- Within your Object Storage or Amazon S3 you need to.
+
+ - Create the bucket.
+ - Create a service account to get Key/Secret Key.
+
+- Within the [nmrxiv](https://nmrxiv.org) you just need to configure below values in the `.env` file.
+
+```
+FILESYSTEM_DRIVER=
+
+AWS_ACCESS_KEY_ID=xxxxxx
+AWS_SECRET_ACCESS_KEY=xxxxxxs
+AWS_DEFAULT_REGION=us-east-1
+AWS_BUCKET=nmrxiv
+AWS_BUCKET_PUBLIC=nmrxiv-public
+AWS_ENDPOINT=
+AWS_URL=
+
+```
diff --git a/docs/developer-guides/deployment/ci-cd.md b/docs/developer-guides/deployment/ci-cd.md
new file mode 100644
index 00000000..98318f20
--- /dev/null
+++ b/docs/developer-guides/deployment/ci-cd.md
@@ -0,0 +1,16 @@
+# Continous Integration and Continous Deployment
+
+To simplify the process of development, releasing of software, and also keeping the [agile](https://en.wikipedia.org/wiki/Agile_software_development) development practices in mind, we have a [CI/CD](https://en.wikipedia.org/wiki/CI/CD) workflow intact with our repository which will enforce the automation of the whole deployment process.
+The workflow focuses on automating the software delivery process so that the team can easily deploy their code to [production](https://www.nmrxiv.org/) at any time without compromising on quality.
+
+We have used [Github Actions](https://docs.github.com/en/actions) for building the [CI/CD](https://en.wikipedia.org/wiki/CI/CD) pipeline and below is the diagram to briefly describe how the current setup works. The workflow gets triggered the moment the code is pushed to the respective branches ([dev-helm-deploy](https://github.com/NFDI4Chem/nmrxiv/tree/dev-helm-deploy) to deploy code to [development](https://dev.nmrxiv.org) and [prod-helm-deploy](https://github.com/NFDI4Chem/nmrxiv/tree/prod-helm-deploy) to deploy code to [production](https://www.nmrxiv.org/)). Once the workflow is triggered (which you can find in the Actions tab) it will perform the below actions.
+
+- **Test** - Execute automated tests(WIP).
+- **Build and Push** - Build the Docker images and push to [Google Artifact Registry](https://cloud.google.com/artifact-registry/docs).
+- **Deploy** - Pull the latest image, deploy and restart the deployment in the [Google Kubernetes Engine](https://cloud.google.com/kubernetes-engine/docs) cluster.
+
+All the jobs defined above are synchronous and failure at any step will abort the consecutive jobs. After the successful completion of the workflow, the code changes will be reflected on the server with minimum or zero downtime.
+
+Click [here](/developer-guides/deployment/environment) to learn more about our current infrastructure environment.
+
+
diff --git a/docs/developer-guides/deployment/environment.md b/docs/developer-guides/deployment/environment.md
new file mode 100644
index 00000000..27a03470
--- /dev/null
+++ b/docs/developer-guides/deployment/environment.md
@@ -0,0 +1,19 @@
+# Environment
+
+### [Development](https://dev.nmrxiv.org)
+
+The [Development](https://dev.nmrxiv.org)(pre-production) environment is the replica of [production](https://www.nmrxiv.org/) one (except for its content), and it provides a space to test all the installation/configuration/migration scripts and procedures before they get applied to the [production](https://www.nmrxiv.org/) environment. Stake Holders and Reviewers have access to [development site](https://dev.nmrxiv.org), where they can test/preview new or existing features and use them for demo purposes.
+All the code changes, features, or any bug fixes have to pass through [development](https://dev.nmrxiv.org) before getting released to [production](https://www.nmrxiv.org/).
+Another important use of [development](https://dev.nmrxiv.org) is performance or stress testing.
+
+:::danger Caution
+Caution: The [development](https://dev.nmrxiv.org) environment is for demonstration purpose only. You can test most of the nmrXiv features but DO NOT use the dev site for your work. All the data stored here can be reset anytime.
+:::
+
+### [Production](https://www.nmrxiv.org/)
+
+The [Production](https://www.nmrxiv.org/) environment is also known as live, particularly for servers, as it is the environment with which users directly interact. It is where the software or products are made live for the intended users to use. Code should go in the [production](https://www.nmrxiv.org/) after all known bugs have already been fixed, and the product or update must work perfectly.
+
+**References**
+
+1. [Deployment environment](https://en.wikipedia.org/wiki/Deployment_environment)
diff --git a/docs/developer-guides/deployment/gke.md b/docs/developer-guides/deployment/gke.md
new file mode 100644
index 00000000..8420ffdd
--- /dev/null
+++ b/docs/developer-guides/deployment/gke.md
@@ -0,0 +1,107 @@
+# Google Kubernetes Engine (GKE)
+
+nmrXiv application is deployed and setup in Google Kubernetes Engine. This page provides the complete guide on how the current deployment is setup in Google Cloud Platform.
+
+### Google Artifact Registry:
+
+nmrXiv docker container images are public and is stored in Google Artifact.
+To pull the latest image for application and Nginx use the below command:
+
+Application
+
+```bash
+docker pull \
+ europe-west3-docker.pkg.dev/nmrxiv/nmrxiv-prod/nmrxiv-app:latest
+```
+
+Nginx
+
+```bash
+docker pull \
+ europe-west3-docker.pkg.dev/nmrxiv/nmrxiv-prod/nmrxiv-nginx:latest
+```
+
+Steps to configure the Artifact Registry:
+
+1. Enable the Artifact Registry API
+1. [Setup](https://cloud.google.com/sdk/install) gcloud CLI in your local system.
+1. [Authenticate](https://cloud.google.com/artifact-registry/docker/pushing-and-pulling#auth) your repository to allow Docker to have access.
+
+```bash
+ gcloud auth configure-docker europe-west3-docker.pkg.dev
+```
+
+4. Push the image:
+
+ - Build the docker image locally:
+ ```bash
+ docker build -f ./resources/ops/docker/app/app.dockerfile .
+ ```
+ - Tag the image with repository name:
+ ```bash
+ docker tag europe-west3-docker.pkg.dev/nmrxiv/nmrxiv-prod/nmrxiv-app
+ ```
+ - Push the image:
+ ```bash
+ docker push europe-west3-docker.pkg.dev/nmrxiv/nmrxiv-prod/nmrxiv-app
+ ```
+
+### Cluster Configuration:
+
+To start with, create a GKE-Standard Cluster with e2-standard-2(dual core, 8GB memory) machine type (or higher) with single or multiple Node Pool. Choose the other basic options as relevant such as Location and zone of your resources, Boot Disk size and type, Maximum Nodes per node etc.
+Once your cluster is ready open the cloud shell and configure the kubectl command line access to your cluster.
+Helm is already installed in Google Cloud Shell to check the version type
+
+```bash
+ helm version
+```
+
+### Deploy with Helm:
+
+Next step is to just add the repo as follows and install the chart.
+Follow the steps provided [here](https://docs.nmrxiv.org/developer-guides/deployment/helm) to install the chart using helm.
+You might need to have your own values.yml file instead of using the default one.
+Once the helm deployment is successfully completed you can check the status of your resources in the workloads and services tab.
+
+### Ingress Setup:
+
+Your services are deployed but not exposed to the internet yet. Kubernetes allows administrators to bring their own Ingress Controllers instead of using the cloud provider's built-in offering. So to do so we can use Nginx or any other server of your choice. But here we are using Nginx(deployed via helm). Deploy and configure Nginx by following the steps provided in the [link](https://cloud.google.com/community/tutorials/nginx-ingress-gke). We have already done a few steps so you can directly jump to the Deploy ingress controller section.
+You might have to create your own ingress-resource file by taking the reference from below.
+
+```bash
+ apiVersion: networking.k8s.io/v1
+ kind: Ingress
+ metadata:
+ name: ingress-resource-dev
+ annotations:
+ kubernetes.io/ingress.class: "nginx"
+ nginx.ingress.kubernetes.io/ssl-redirect: "true"
+ cert-manager.io/issuer: "letsencrypt-dev"
+
+ spec:
+ tls:
+ - hosts:
+ - dev.nmrxiv.org
+ secretName: nmrxiv-app-dev-tls
+
+ rules:
+ - host: dev.nmrxiv.org
+ http:
+ paths:
+ - pathType: Prefix
+ path: "/"
+ backend:
+ service:
+ name: nmrxiv-nmrxiv-app
+ port:
+ number: 80
+
+```
+
+### Certificate Installation:
+
+Now that the ingress is established and we can access the application via the domain name in the browser, next step would be to install the TLS or certificate for your domain name. To do so we have various [option](https://kubernetes.github.io/ingress-nginx/user-guide/tls/) but here we have used [cert-manager](https://cert-manager.io/) which will automatically request missing or expired certificates from a range of supported issuer(Let's Encrypt) by monitoring ingress-resource.
+
+1. Install cert-manager using [helm](https://cert-manager.io/installation/helm/).
+1. Configure [Let's Encrypt Issuer](https://cert-manager.io/tutorials/acme/nginx-ingress/#step-6---configure-a-lets-encrypt-issuer).
+1. Deploy a [TLS Ingress Resource](https://cert-manager.io/tutorials/acme/nginx-ingress/#step-7---deploy-a-tls-ingress-resource).
diff --git a/docs/developer-guides/deployment/helm.md b/docs/developer-guides/deployment/helm.md
new file mode 100644
index 00000000..8a67049f
--- /dev/null
+++ b/docs/developer-guides/deployment/helm.md
@@ -0,0 +1,35 @@
+# Helm Chart
+
+nmrXiv is packaged and published as [Helm](https://helm.sh/) for Kubernetes deployment, which makes the installation easy to define, install, and upgrade.
+You need to install Helm first to use the charts. Please refer to the Helm's [documentation](https://helm.sh/docs) to get started.
+
+The chart comes with following optional dependencies which you can opt to have in your deployment if you wish to:
+
+- [Meilisearch](https://docs.meilisearch.com/) (Search Engine)
+- [RabbitMQ](https://www.rabbitmq.com/documentation.html) (Message Broker)
+- [Redis](https://redis.io/documentation) (Cache)
+
+Once Helm has been set up correctly, add the repo as follows:
+
+```bash
+helm repo add repo-helm-charts https://nfdi4chem.github.io/repo-helm-charts/
+```
+
+If you had already added this repo earlier, run `helm repo update` to retrieve
+the latest versions of the packages. You can then run `helm search repo repo-helm-charts` to see the charts.
+
+Before you install [generate your own application key](https://stackoverflow.com/questions/33370134/when-to-generate-a-new-application-key-in-laravel) and provide that value in the .Values.appProperties.key property.
+
+To install the nmrxiv-app chart:
+
+```
+helm install my-nmrxiv-app repo-helm-charts/nmrxiv-app
+```
+
+To uninstall the chart:
+
+```
+helm delete my-nmrxiv-app
+```
+
+To learn more about the structure of the chart, visit our [Github repo](https://github.com/NFDI4Chem/repo-helm-charts).
diff --git a/docs/developer-guides/deployment/production.md b/docs/developer-guides/deployment/production.md
new file mode 100644
index 00000000..c84f108e
--- /dev/null
+++ b/docs/developer-guides/deployment/production.md
@@ -0,0 +1,116 @@
+# Production
+
+### Introduction
+
+When deploying the nmrXiv application to production, there are some needed steps to make sure our application is running as efficiently as possible. In this document, we will cover some basic configuration required for the same in production environment.
+
+### Server Configuration
+
+#### Nginx
+
+If deploying the application in `nginx` the following configuration file can be referred as a starting point for configuring the web server.
+It should be ensured, like the configuration below, that the web server directs all requests to the application's public/index.php file. The index.php file should not be moved to the project's root, as serving the application from the project root will expose many sensitive configuration files to the public Internet.
+
+```bash
+server {
+ listen 80 default_server;
+ listen [::]:80 default_server;
+ server_name ;
+ server_tokens off;
+
+ root /var/www/html;
+
+ add_header X-Frame-Options "SAMEORIGIN";
+ add_header X-XSS-Protection "1; mode=block";
+ add_header X-Content-Type-Options "nosniff";
+
+ charset utf-8;
+ location / {
+ try_files $uri $uri/ /public/index.php?$query_string;
+ }
+
+ index /public/index.html /public/index.htm /public/index.php;
+ error_page 404 /public/index.php;
+
+ location ~ \.php$ {
+ fastcgi_pass localhost:9000;
+ fastcgi_param SCRIPT_FILENAME $document_root$fastcgi_script_name;
+ fastcgi_param SCRIPT_NAME $fastcgi_script_name;
+ fastcgi_split_path_info ^(.+\.php)(/.+)$;
+ fastcgi_index index.php;
+ include fastcgi_params;
+ fastcgi_read_timeout 300;
+ }
+
+ location ~* \.(png|jpg|jpeg|gif|svg|ico|woff2|woff)$ {
+ expires 7d;
+ }
+
+ location ~ /\.(?!well-known).* {
+ deny all;
+ }
+}
+```
+
+### Optimization
+
+When deploying the application to production, the below command should be considered and run during your deployment process for better optimization and performance.
+
+- Autoloader Optimization -
+
+Below command will optimize Composer's class autoloader map.
+
+```bash
+composer install --optimize-autoloader --no-dev
+```
+
+:::info Info
+Info: In addition to above, the composer.lock file should be present in the project's source control repository, which will make the project's dependencies installation much faster.
+:::
+
+- Optimizing Configuration Loading -
+
+To greatly reduce the number of trips the framework would make to filesystem when loading the configuration files, below command should be executed to combine all the configuration files into a single, cached file.
+
+```bash
+php artisan config:cache
+```
+
+- Optimizing Route Loading -
+
+This command reduces all of the route registration into a single method call within a cached file, improving the performance of route registration when registering hundreds of routes.
+
+```bash
+php artisan route:cache
+```
+
+- Optimizing View Loading -
+
+To precompile all the Blade views and improve the performance of each request that returns a view.
+
+```bash
+php artisan view:cache
+```
+
+### Debug Mode
+
+The `APP_DEBUG` value which is stored in .env file should always be set to `false` and `APP_ENV` value to `production` in production environment. Setting the debug value as true may expose some sensitive configuration values to your application end users.
+
+### Environment File Security
+
+The .env file should not be committed to application's source control, as this could be security risk in the event and any sensitive information would be exposed.
+
+### Database and Backup
+
+nmrXiv uses `PostgreSQL` database and details regarding the connection could be established against below values in the .env file.
+
+```bash
+DB_CONNECTION=pgsql
+DB_HOST=pgsql
+DB_PORT=5432
+DB_DATABASE=nmrxiv
+DB_USERNAME=****
+DB_PASSWORD=****
+```
+
+A comprehensive data backup plan should be implemented so that data can be restored and recovered effectively at the time of disaster.
diff --git a/docs/developer-guides/installation/centos.md b/docs/developer-guides/installation/centos.md
new file mode 100644
index 00000000..92fa06fe
--- /dev/null
+++ b/docs/developer-guides/installation/centos.md
@@ -0,0 +1,194 @@
+# Centos
+
+nmrXiv project is built with [Laravel](https://laravel.com/8.x) web application framework which comes with [Sail](https://laravel.com/8.x/sail), a built-in solution for running your Laravel project using Docker.
+The whole project is a package of below services and features.
+
+- [PostgreSQL](https://www.postgresql.org/)
+- [Redis](https://redis.io/)
+- [Selenium](https://www.selenium.dev/documentation/)
+- [Meilisearch](https://docs.meilisearch.com/)
+- [MailHog](https://mailtrap.io/blog/mailhog-explained/)
+
+### Dependencies
+
+- \[git\]
+- \[PHP 8.0 or more\]
+- \[Composer\]
+- \[Docker Engine\]
+- \[Docker Compose\]
+
+### Setup:
+
+Install GIT
+
+```
+$ sudo dnf update -y
+$ sudo dnf install git -y
+$ git --version
+```
+
+Install docker
+
+```
+$ sudo yum remove docker \
+ docker-client \
+ docker-client-latest \
+ docker-common \
+ docker-latest \
+ docker-latest-logrotate \
+ docker-logrotate \
+ docker-engine
+
+# Install using the repository
+$ sudo yum install -y yum-utils
+$ sudo yum-config-manager \
+ --add-repo \
+ https://download.docker.com/linux/centos/docker-ce.repo
+
+$ sudo yum install docker-ce docker-ce-cli containerd.io
+
+# If podman / buildah packages conflict with the docker installation. You need to remove those packages using the following command and reinstall docker again
+
+$ sudo yum erase podman buildah
+$ sudo systemctl start docker
+$ sudo docker run hello-world
+```
+
+Install docker compose
+
+```
+$ curl -L "https://github.com/docker/compose/releases/download/1.27.4/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
+$ chmod +x /usr/local/bin/docker-compose
+```
+
+Now that we have installed docker and docker-compose. Let's install PHP >8.0 and composer to get started with Laravel sail
+
+Install PHP 8.0
+
+```
+$ sudo dnf -y install https://dl.fedoraproject.org/pub/epel/epel-release-latest-8.noarch.rpm
+$ sudo dnf -y install https://rpms.remirepo.net/enterprise/remi-release-8.rpm
+$ sudo dnf -y install yum-utils
+$ sudo dnf module reset php
+$ sudo dnf module install php:remi-8.0 -y
+$ sudo dnf install php -y
+$ sudo dnf -y install php-{cli,fpm,mysqlnd,zip,devel,gd,mbstring,curl,xml,pear,bcmath,json}
+```
+
+Install composer
+
+Please replace the 'hash' in the command below from the composer site [here](https://getcomposer.org/download/)
+
+```
+$ php -r "copy('https://getcomposer.org/installer', 'composer-setup.php');"
+$ php -r "if (hash_file('sha384', 'composer-setup.php') === '') { echo 'Installer verified'; } else { echo 'Installer corrupt'; unlink('composer-setup.php'); } echo PHP_EOL;"
+$ php composer-setup.php
+$ php -r "unlink('composer-setup.php');"
+```
+
+Now with composer installed lets go ahead and install all the php dependencies. But before we can do that we need to clone the project locally.
+
+```bash
+git clone https://github.com/NFDI4Chem/nmrxiv.git
+```
+
+- Go to the project directory:
+
+```bash
+cd nmrxiv
+```
+
+- Navigate to the development branch:
+
+```bash
+git checkout development
+```
+
+- Create an `.env` file, and copy the existing `.env.example` into it:
+
+```bash
+cp .env.example .env
+```
+
+- Install the dependencies from the `composer.lock` file:
+
+```bash
+composer install
+```
+
+- Start [Sail](https://laravel.com/8.x/sail#starting-and-stopping-sail) to build application containers on your machine:
+
+```bash
+./vendor/bin/sail up
+```
+
+If your sail could not find the docker you need to open up the docker binary permissions using the following command
+
+```
+$ sudo chmod 666 /var/run/docker.sock
+```
+
+If your docker is failing to download os packages you need to update your firewall settings
+
+In your config file
+
+```
+$ sudo nano /etc/firewalld/firewalld.conf
+```
+
+please change
+
+```
+FirewallBackend=nftables
+```
+
+to
+
+```
+FirewallBackend=iptables
+```
+
+Save this change and reload firewall
+
+```
+$ sudo systemctl restart firewalld.service
+```
+
+Once the application's Docker containers have been started, you can access the application in your web browser at [http://localhost](http://localhost).
+
+If you find the error message indicating the app key doesn't exist. You will be prompted to Generate app key (you will find the button on the error page below the error message). After pressing the generation button, the following message is shown on the screen: "The solution was executed successfully. Refresh now." After refreshing, you access the application.
+
+At this stage, you haven't run the application migrations (no database tables for the application to connect to). Again you will be prompted with an error message. You will also find a button just below the message to run migrations. Please click it and you are good to go.
+
+For local development, you will need nodejs and npm to install and compile node packages
+
+```
+$ sudo dnf install -y gcc-c++ make
+$ curl -sL https://rpm.nodesource.com/setup_16.x | sudo -E bash -
+```
+
+Install all the npm packages
+
+```
+$ npm install
+```
+
+Compile Javascript code
+
+```
+$ npm run build
+```
+
+In order to actively watch and compile changes
+
+```
+$ npm run watch
+```
+
+:::caution Recommendation
+Follow our [code contribution guidelines](/developer-guides/code-contribution-guidelines) to make a pull request.
+:::
+
+:::info Info
+Click to learn more about [Laravel](https://laravel.com/9.x) and [installation guides](https://laravel.com/9.x/installation).
+:::
diff --git a/docs/developer-guides/installation/development-workflow.md b/docs/developer-guides/installation/development-workflow.md
new file mode 100644
index 00000000..18b4ffcc
--- /dev/null
+++ b/docs/developer-guides/installation/development-workflow.md
@@ -0,0 +1,5 @@
+### Email Registration
+
+To be able to develop locally, you have to install [Node.js](https://nodejs.org/en/download/) to compile [JavaScript](https://developer.mozilla.org/en-US/Web/JavaScript).
+
+After having nmrXiv successfully installed and accessing the application in the web browser at http://localhost:8025 , you need to create a new account. Press Register button. You will be prompted to enter registration details (Name, Email, Password). Agreeing to the Terms of Service and Privacy Policy by checking the corresponding box is required for the registration. After clicking Register, you will receive an email to confirm your email address, you can access it through [MailHog](https://github.com/mailhog/MailHog). Open a new window in your browser, and go to http://localhost:8025 . Open the received email and click Verify Email Address. You will be forwarded to the Dashboard.
diff --git a/docs/developer-guides/installation/mac.md b/docs/developer-guides/installation/mac.md
new file mode 100644
index 00000000..0d79cc3e
--- /dev/null
+++ b/docs/developer-guides/installation/mac.md
@@ -0,0 +1,113 @@
+# MacOS
+
+nmrXiv project is built with [Laravel](https://laravel.com/8.x) web application framework which comes with [Sail](https://laravel.com/8.x/sail), a built-in solution for running your Laravel project using Docker.
+The whole project is a package of below services and features.
+
+- [PostgreSQL](https://www.postgresql.org/)
+- [Redis](https://redis.io/)
+- [Selenium](https://www.selenium.dev/documentation/)
+- [Meilisearch](https://docs.meilisearch.com/)
+- [MailHog](https://mailtrap.io/blog/mailhog-explained/)
+
+### Dependencies
+
+- [git](https://git-scm.com/).
+- [Docker Desktop](https://www.docker.com/products/docker-desktop).
+- [Composer](https://getcomposer.org/)
+
+### Setup:
+
+- Start Docker.
+- Open your chosen directory in the terminal.
+- Clone the [project from Github](https://github.com/NFDI4Chem/nmrxiv) by running:
+
+```bash
+git clone https://github.com/NFDI4Chem/nmrxiv.git
+```
+
+- Go to the project directory:
+
+```bash
+cd nmrxiv
+```
+
+- Navigate to the development branch:
+
+```bash
+git checkout development
+```
+
+- Create an `.env` file, and copy the existing `.env.example` into it:
+
+```bash
+cp .env.example .env
+```
+
+- Update the dependencies from the `composer.json` file:
+
+```bash
+composer update
+```
+
+- Install the dependencies from the `composer.lock` file:
+
+```bash
+composer install
+```
+
+- Start [Sail](https://laravel.com/8.x/sail#starting-and-stopping-sail) to build application containers on your machine:
+
+```bash
+./vendor/bin/sail up
+```
+
+- Run the below command to migrate the database with some dummy values. Don't forget to note down the admin's user id and password provided at the end of migration output.
+
+```bash
+./vendor/bin/sail artisan migrate:refresh --seed
+```
+
+- Open another terminal and run the below command to boot up your local static web server.
+
+```bash
+npm install && npm run dev
+```
+
+- For all background jobs to run, nmrXiv is powered with [Redis](https://redis.com/) and packaged with [Horizon](https://github.com/laravel/horizon).
+ Run the below command to publish all the jobs and start the worker for the background jobs to execute.
+
+```bash
+./vendor/bin/sail artisan horizon:publish
+./vendor/bin/sail artisan horizon
+```
+
+- To configure file object storage, you should have [Minio](https://min.io/) instance already running in your local(for more details check your docker-compose file). For the first time you have to generate the Access Keys, create the buckets and configure that in your `.env` file.
+ - Open the Minio instance running in your [http://localhost:8900](http://localhost:8900/)
+ - Login with user - `sail` and password - `password`
+ - Go to Access Keys and create a new access key.
+ - Create the two buckets with Read Write Access as `nmrxiv` and `nmrxiv-public`
+ - Update the Filesystem driver and the AWS Keys as below in the `.env` file. Make sure you point your `AWS_URL` to Minio API endpoint which is running in port 9000. Please define both the public and private driver. The public bucket is used to store all the files which can be publicly accessible through out the application, such as profile & project images. All the private files uploaded by the user will end up in the private bucket.
+
+```bash
+FILESYSTEM_DRIVER=minio
+FILESYSTEM_DRIVER_PUBLIC=minio_public
+
+AWS_ACCESS_KEY_ID=**********
+AWS_SECRET_ACCESS_KEY=************
+AWS_DEFAULT_REGION=us-east-1
+AWS_BUCKET=nmrxiv
+AWS_ENDPOINT=http://localhost:9000/
+AWS_URL=http://localhost:9000/
+AWS_USE_PATH_STYLE_ENDPOINT=false
+AWS_BUCKET_PUBLIC=nmrxiv-public
+```
+
+Once the application's Docker containers have been started, you can access the application in your web browser at [http://localhost](http://localhost). But first, you will be prompted to Generate app key. After pressing the generation button, the following message is shown on the screen: "The solution was executed successfully. Refresh now." After refreshing, you access the application.
+
+:::caution Recommendation
+Follow our [code contribution guidelines](/developer-guides/code-contribution-guidelines) to make a pull request.
+:::
+
+:::info Info
+Click to learn more about [Laravel](https://laravel.com/9.x) and [installation guides](https://laravel.com/9.x/installation).
+:::
diff --git a/docs/developer-guides/installation/ubuntu.md b/docs/developer-guides/installation/ubuntu.md
new file mode 100644
index 00000000..d1a4d061
--- /dev/null
+++ b/docs/developer-guides/installation/ubuntu.md
@@ -0,0 +1,119 @@
+# Ubuntu
+
+nmrXiv project is built with [Laravel](https://laravel.com/8.x) web application framework which comes with [Sail](https://laravel.com/8.x/sail), a built-in solution for running your Laravel project using Docker.
+The whole project is a package of below services and features.
+
+- [PostgreSQL](https://www.postgresql.org/)
+- [Redis](https://redis.io/)
+- [Selenium](https://www.selenium.dev/documentation/)
+- [Meilisearch](https://docs.meilisearch.com/)
+- [MailHog](https://mailtrap.io/blog/mailhog-explained/)
+- [Minio](https://min.io/)
+
+#### Ubuntu 20.04
+
+### Dependencies
+
+- [git](https://git-scm.com/).
+- [PHP](https://www.php.net/manual/en/install.php).
+- [Composer](https://getcomposer.org/download/).
+- [Docker Engine](https://docs.docker.com/engine/install/ubuntu/).
+- [Docker Compose](https://docs.docker.com/compose/install/) for Linux.
+
+### Setup:
+
+- Start Docker.
+- Open your chosen directory in the terminal.
+- Clone the [project from Github](https://github.com/NFDI4Chem/nmrxiv) by running:
+
+```bash
+git clone https://github.com/NFDI4Chem/nmrxiv.git
+```
+
+- Go to the project directory:
+
+```bash
+cd nmrxiv
+```
+
+- Navigate to the development branch:
+
+```bash
+git checkout development
+```
+
+- Create an `.env` file, and copy the existing `.env.example` into it:
+
+```bash
+cp .env.example .env
+```
+
+- Update the dependencies from the `composer.json` file:
+
+```bash
+composer update
+```
+
+- Install the dependencies from the `composer.lock` file:
+
+```bash
+composer install
+```
+
+- Start [Sail](https://laravel.com/8.x/sail#starting-and-stopping-sail) to build application containers on your machine:
+
+```bash
+./vendor/bin/sail up
+```
+
+- Run the below command to migrate the database with some dummy values.
+ Don't forget to note down the admin's user id and password provided at the end of migration output.
+
+```bash
+./vendor/bin/sail artisan migrate:refresh --seed
+```
+
+- Open another terminal and run the below command to boot up your local static web server.
+
+```bash
+npm install && npm run dev
+```
+
+- For all background jobs to run, nmrXiv is powered with [Redis](https://redis.com/) and packaged with [Horizon](https://github.com/laravel/horizon).
+ Run the below command to publish all the jobs and start the worker for the background jobs to execute.
+
+```bash
+./vendor/bin/sail artisan horizon:publish
+./vendor/bin/sail artisan horizon
+```
+
+- To configure file object storage, you should have [Minio](https://min.io/) instance already running in your local(for more details check your docker-compose file). For the first time you have to generate the Access Keys, create the buckets and configure that in your `.env` file.
+ - Open the Minio instance running in your [http://localhost:8900](http://localhost:8900/)
+ - Login with user - `sail` and password - `password`
+ - Go to Access Keys and create a new access key.
+ - Create the two buckets with Read Write Access as `nmrxiv` and `nmrxiv-public`
+ - Update Filesystem driver and the AWS Keys as below in the `.env` file. Make sure you point your `AWS_URL` to Minio API which is running in port 9000. Please define both the public and private driver. The public bucket is used to store all the files which can be publicly accessible through out the application, such as profile & project images. All the private files uploaded by the user will end up in the private bucket.
+
+```bash
+FILESYSTEM_DRIVER=minio
+FILESYSTEM_DRIVER_PUBLIC=minio_public
+
+AWS_ACCESS_KEY_ID==**********
+AWS_SECRET_ACCESS_KEY===**********
+AWS_DEFAULT_REGION=us-east-1
+AWS_BUCKET=nmrxiv
+AWS_ENDPOINT=http://localhost:9000/
+AWS_URL=http://localhost:9000/
+AWS_USE_PATH_STYLE_ENDPOINT=false
+AWS_BUCKET_PUBLIC=nmrxiv-public
+```
+
+Once the application's Docker containers have been started, you can access the application in your web browser at [http://localhost](http://localhost). But first, you will be prompted to Generate app key. After pressing the generation button, the following message is shown on the screen: "The solution was executed successfully. Refresh now." After refreshing, you access the application.
+
+:::caution Recommendation
+Follow our [code contribution guidelines](/developer-guides/code-contribution-guidelines) to make a pull request.
+:::
+
+:::info Info
+Click to learn more about [Laravel](https://laravel.com/9.x) and [installation guides](https://laravel.com/9.x/installation).
+:::
diff --git a/docs/developer-guides/installation/windows.md b/docs/developer-guides/installation/windows.md
new file mode 100644
index 00000000..4805a8bf
--- /dev/null
+++ b/docs/developer-guides/installation/windows.md
@@ -0,0 +1,140 @@
+# Windows
+
+nmrXiv project is built with [Laravel](https://laravel.com/8.x) web application framework which comes with [Sail](https://laravel.com/8.x/sail), a built-in solution for running your Laravel project using Docker.
+The whole project is a package of below services and features.
+
+- [PostgreSQL](https://www.postgresql.org/)
+- [Redis](https://redis.io/)
+- [Selenium](https://www.selenium.dev/documentation/)
+- [Meilisearch](https://docs.meilisearch.com/)
+- [MailHog](https://mailtrap.io/blog/mailhog-explained/)
+
+### Dependencies
+
+- [git](https://git-scm.com/).
+- [Docker Desktop](https://www.docker.com/products/docker-desktop).
+- [Ubuntu app](https://www.microsoft.com/store/productId/9NBLGGH4MSV6) (Recommended).
+- [Composer](https://getcomposer.org/), which can be installed following the [Windows installer guidelines](https://getcomposer.org/download/).
+- [Windows Subsystem for Linux 2 (WSL2)](https://docs.microsoft.com/en-us/windows/wsl/).
+
+Make sure to enable and install WSL, and to upgrade it to WSL2 as described in the [guidelines](https://docs.microsoft.com/en-us/windows/wsl/install-win10). WSL allows you to run Linux binary executables natively on Windows 10.
+
+To check the WSL mode, open **Windows Powershell** and run:
+
+```bash
+wsl.exe -l -v
+```
+
+To upgrade your existing Linux distro to v2, run:
+
+```bash
+wsl.exe --set-version (distro name) 2
+```
+
+:::important
+
+After installing and enabling WSL2, you should ensure that Docker Desktop is [configured to use the WSL2 backend.](https://docs.docker.com/desktop/windows/wsl/)
+
+:::
+
+### Setup:
+
+- Start Docker.
+- Open [Ubuntu](https://www.microsoft.com/store/productId/9NBLGGH4MSV6) shell and clone the repo using the below command to your home directory.
+ We recommend running the project from your Linux directory and not from your local windows file system, for faster compilation and execution.
+
+```bash
+cd /home/
+git clone https://github.com/NFDI4Chem/nmrxiv.git
+```
+
+- Go to the project directory:
+
+```bash
+cd nmrxiv
+```
+
+- Navigate to the development branch:
+
+```bash
+git checkout development
+```
+
+- Create an `.env` file, and copy the existing `.env.example` into it:
+
+```bash
+cp .env.example .env
+```
+
+- Update the dependencies from the `composer.json` file:
+
+```bash
+composer update
+```
+
+- Install the dependencies from the `composer.lock` file:
+
+```bash
+composer install
+```
+
+- Start [Sail](https://laravel.com/8.x/sail#starting-and-stopping-sail) to build application containers on your machine:
+
+```bash
+./vendor/bin/sail up
+```
+
+- Run the below command to migrate the database with some dummy values.
+ Don't forget to note down the admin's user id and password provided at the end of migration output.
+
+```bash
+./vendor/bin/sail artisan migrate:refresh --seed
+```
+
+- Make sure you have node version > 16 installed in your WSL. Open another terminal and run the below command to boot up your local static web server.
+
+```bash
+npm install
+npm run dev
+```
+
+- For all background jobs to run, nmrXiv is powered with [Redis](https://redis.com/) and packaged with [Horizon](https://github.com/laravel/horizon).
+ Run the below command to publish all the jobs and start the worker for the background jobs to execute.
+
+```bash
+./vendor/bin/sail artisan horizon:publish
+./vendor/bin/sail artisan horizon
+```
+
+- To configure file object storage, you should have [Minio](https://min.io/) instance already running in your local(for more details check your docker-compose file). For the first time you have to generate the Access Keys, create the buckets and configure that in your `.env` file.
+ - Open the Minio instance running in your [http://localhost:8900](http://localhost:8900/)
+ - Login with user - `sail` and password - `password`
+ - Go to Access Keys and create a new access key.
+ - Create the two buckets with Read Write Access as `nmrxiv` and `nmrxiv-public`
+ - Update Filesystem driver and the AWS Keys as below in the `.env` file. Make sure you point your `AWS_URL` to Minio API which is running in port 9000. Please define both the public and private driver. The public bucket is used to store all the files which can be publicly accessible through out the application, such as profile & project images. All the private files uploaded by the user will end up in the private bucket.
+
+```bash
+FILESYSTEM_DRIVER=minio
+FILESYSTEM_DRIVER_PUBLIC=minio_public
+
+AWS_ACCESS_KEY_ID=**********
+AWS_SECRET_ACCESS_KEY==**********
+AWS_DEFAULT_REGION=us-east-1
+AWS_BUCKET=nmrxiv
+AWS_ENDPOINT=http://localhost:9000/
+AWS_URL=http://localhost:9000/
+AWS_USE_PATH_STYLE_ENDPOINT=false
+AWS_BUCKET_PUBLIC=nmrxiv-public
+```
+
+Once the application's Docker containers have been started, you can access the application in your web browser at [http://localhost](http://localhost). But first, you will be prompted to Generate app key. After pressing the generation button, the following message is shown on the screen: "The solution was executed successfully. Refresh now." After refreshing, you can access the application.
+
+Run `code .` to open the code base to your VSCode editor.
+Thanks to [Vite](https://vitejs.dev/guide/) that any changes you make to the javascript file would be reflected in your browser immediately without requiring any refresh.
+
+:::caution Recommendation
+Follow our [code contribution guidelines](/developer-guides/code-contribution-guidelines) to make a pull request.
+:::
+:::info Info
+Click to learn more about [Laravel](https://laravel.com/9.x) and [installation guides](https://laravel.com/9.x/installation).
+:::
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
index 00000000..f9c97964
--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,31 @@
+______________________________________________________________________
+
+# https://vitepress.dev/reference/default-theme-home-page
+
+layout: home
+
+hero:
+name: "nmrXiv"
+text: "Open, FAIR and Consensus-Driven NMR spectroscopy data repository and analysis platform"
+tagline: ""
+actions:
+\- theme: brand
+text: Get started
+link: /introduction/intro.md
+\- theme: alt
+text: Submission Guides
+link: /submission-guides/data-lifecycle.md
+\- theme: alt
+text: Developer Guides
+link: /developer-guides/architecture.md
+
+features:
+
+- title: Demo Version
+ details: Try our demo version to test or preview the features.
+- title: Submission Guides
+ details: Want to submit data? Read the submission guide.
+- title: Contribution Guides
+ details: Want to contribute? Read the contribution guide.
+
+______________________________________________________________________
diff --git a/docs/introduction/data/exemplary-data.md b/docs/introduction/data/exemplary-data.md
new file mode 100644
index 00000000..4360de66
--- /dev/null
+++ b/docs/introduction/data/exemplary-data.md
@@ -0,0 +1,63 @@
+# Exemplary Data
+In this section, you can find links and explanations about exemplary data ready for submission to **[nmrXiv](https://nmrxiv.org)**.
+
+## Bruker Datasets
+[Following this link](https://cloud.uni-jena.de/s/W3JHNPDY5isXo5F), you can download a project with two samples analyzed with Bruker instrument. After unzipping, the project "Bruker Example" is ready for submission.
+You can find the needed hierarchy for submission there :
+- The main folder "Bruker Example" corresponds to the project. This is the folder that should be submitted (dragged and dropped) to nmrXiv.
+ - Within "Bruker Example" you find two folders, each corresponding to a sample (Eserine and Cucurbitacin E).
+ - Within each sample folder, you find separate **folders** each corresponding to the spectrum/dataset folder. at the same level (within the sample folder), you can find additional files representing the whole sample, such as mol files for the structure or NMReData files and such.
+
+
+
+The hierarchy needed for a Bruker samples project
+
+
+### Wrong Bruker Hierarchy
+
+::: danger Wrong Hierarchy
+It is common in Bruker datasets to find, for instance, the 2D datasets provided in a parent folder with the experiment name (e.g., HSQC), and within this folder you find the traditional Bruker named folders such as 1,2,3, etc. Such hierarchy will result in considering the HSQC dataset as a separate sample by nmrXiv, thus you need to be careful and avoid such inconveniences
+:::
+
+In the following photo, because there is an "HSQC" folder above the actual spectrum folder "58", nmrXiv recognizes 3 studies (Eserine, Cucurbitacin E, and HSQC)
+
+
+
+Adding a parent "HSQC folder to dataset 58 makes that folder a new sample to nmrXiv system."
+
+
+
+
+The studies in nmrXiv resulting from submitting the project in the above image.
+
+
+## JCAMP Datasets
+
+[Following this link](https://cloud.uni-jena.de/s/CrNXN46N9GBQ7cG), you can download a project with two analyzed samples. The analysis output is provided in JCAMP format. After unzipping, the project "JCAMP Example" is ready for submission.
+You can find the needed hierarchy for submission there :
+- The main folder "JCAMP Example" corresponds to the project. This is the folder that should be submitted (dragged and dropped) to nmrXiv.
+ - Within "JCAMP Example" you find two folders, each corresponding to a sample (196793-29-0 and 1155308-25-0).
+ - Within each sample folder, you find separate **JCAMP files** each corresponding to the spectrum/dataset file. At the same level (within the sample folder), you can find additional files corresponding to the whole sample, such as mol files for the structure or NMReData files and such.
+
+
+
+The hierarchy needed for a Bruker samples project
+
+
+### Wrong JCAMP Hierarchy
+
+:::danger Wrong Hierarchy
+It is common in JCAMP datasets to find, for instance, the 2D datasets provided in a parent folder with the experiment name (e.g., HSQC), and within this folder, you find the jcamp file such as hsqc.dx. Such hierarchy will result in considering the HSQC dataset as a separate sample by nmrXiv, thus you need to be careful and avoid such inconveniences
+:::
+
+In the following photo, because there is an "HSQC" folder above the actual spectrum file "hsqc.dx", nmrXiv recognizes 3 studies (196793-29-0, 1155308-25-0, and HSQC)
+
+
+
+Adding a parent "hsqc folder to dataset hsqc.dx makes that folder a new sample to nmrXiv system."
+
+
+
+
+The studies in nmrXiv resulting from submitting the project in the above image.
+
\ No newline at end of file
diff --git a/docs/introduction/data/formats.md b/docs/introduction/data/formats.md
new file mode 100644
index 00000000..ef0edae4
--- /dev/null
+++ b/docs/introduction/data/formats.md
@@ -0,0 +1,186 @@
+# NMR File Formats
+
+**[nmrXiv](https://nmrxiv.org)** is the first FAIR and Open archive to preserve NMR data in its original instrument format, and promote Open Data and Open Standards to maximize the long-term sustainability of the resource and FAIRness of the archived data.
+
+To reduce user burden and foster immediate utility, **[nmrXiv](https://nmrxiv.org)** accepts raw NMR data in all original instrument formats. Upon uploading files, the platform converts all those files to available **Open** data formats, such as [JCAMP-DX](https://opg.optica.org/as/abstract.cfm?uri=as-47-8-1093), [NMReData](https://doi.org/10.1002/mrc.4737), and [nmrML](https://doi.org/10.1021/acs.analchem.7b02795). The content stored in existing formats is heterogeneous, and no single format is currently capable of fully capturing all information from NMR experiments and data processing.
+
+As native instrument formats represent the most available data, they will be preserved and made available to users. This approach ensures traceability and secure long-term access to every detail of measured data as new formats appear or existing ones evolve. At the same time, the availability and interoperability of several formats will facilitate the re-use of data with external tools.
+
+### NMR Vendor Formats
+FAIR sharing raw NMR data enhances the quality of research and dissemination quality. Historically, the sharing of original spectroscopic data has been hampered by technological limitations such as data storage size and gaps between digital data and paper/printed publishing format. Therefore, researchers are accustomed to extracting the (perceived most) important information from NMR spectra and summarising them in a very compact text form, typically in tables or text compilations of chemical shifts and coupling constants (e.g., ACS-style listings). More recently, they became accompanied by spectra images as evidence of discovering a new molecule. However, this practice constitutes a drastic loss of information relative to the wealth
+of detail in the raw NMR data. This approach leads to incomplete information and curbs peer review and re-use processes. It can lead to wrong or misidentified structures, affecting ~15% of terpenoid NPs, as shown here [1,2,3].
+
+Moreover, peaks associated with impurities or byproducts are not reported and remain invisible to the reader or reviewer. The AnaPurNa [4,5] and UIC CENAPT Raw Data Initiative studies [6] provide evidence that purity information can be gleaned from raw NMR data. Until such data are shared broadly, it remains difficult or even impossible for subsequent studies to resolve discrepancies about the structure, activity, and purity of a given compound or sample(s). **[nmrXiv](https://nmrxiv.org)** will allow the community to leverage the vast informational power of raw NMR data to enhance the reproducibility of reported outcomes, enable innovative re-evaluation and advance the quality of NP research more broadly.
+
+#### Vendor format examples
+
+| Short Name | Maintainer | File Extension |
+|------------|------------|----------------|
+| Bruker | Bruker | Folder |
+| JEOL | JEOL | .jdf |
+| Agilent | Agilent | Folder |
+| Magritek | Magritek | .1d, .2d |
+
+### Software-Specific NMR Formats
+
+Tools such as [TopSpin](https://www.bruker.com/en/products-and-solutions/mr/nmr-software/topspin.html), [Mnova](https://mestrelab.com/software/mnova/nmr/), and [ACD/Labs](https://www.acdlabs.com/solutions/nmr-spectroscopy/) are widely used among the NMR research community to process and analyze NMR spectra.
+
+It is impossible and highly undesirable to reproduce everything these tools offer on **[nmrXiv](https://nmrxiv.org)**. At the same time, we cannot request the researcher to recreate the analysis using the tools we support in **[nmrXiv](https://nmrxiv.org)**.
+
+These tools' output usually gets stored in proprietary formats, such as .spectrus and .mnova. These formats are closed, and they are often updated with breaking changes.
+
+To avoid losing all the rich (meta-)data from these third-party tools, it is advantageous to export it into standard formats (nmreData, Jcamp, nmrML) rather than being able to parse their proprietary output formats.
+
+These tools already support export in some of the standard/widely known formats, such as [JCAMP-DX](https://opg.optica.org/as/abstract.cfm?uri=as-47-8-1093) ([Mnova](https://resources.mestrelab.com/top-highlights-in-mnova-14-3/), [ACD/Labs](https://www.acdlabs.com/technical-support/supported-data-formats/) (for 1D NMR only)), and [NMReData](https://doi.org/10.1002/mrc.4737) ([Mnova, ACD/Labs, TopSpin](https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mrc.5146)), which contain a subset (molecular structure, assignments, peaks, integrals etc.) of the complete data but are still valuable.
+
+**[nmrXiv](https://nmrxiv.org)** will drive the collective efforts to collaborate with [ACD/Labs](https://www.acdlabs.com) and [Mestrelab](https://mestrelab.com/) to enable better or up to date export functions, and also to improve the parsers to process the standard output file format with the rich metadata.
+
+For further details on loading a script in Mnova, please check this [link](https://resources.mestrelab.com/how-to-get-started-with-mnova-scripts/)
+
+Example output:
+- [Mnova - nmredata](https://drive.google.com/file/d/1a6na29Gc8FHDP38QC19BLsOzWtj5H2sp/view?usp=sharing)
+- [ACD/Labs - jdx](https://drive.google.com/drive/folders/1P5NAVrI0tiIShLkhnckr2vHHMxMKnrzt)
+
+#### Software format examples
+
+| Short Name | Maintainer | File Extension |
+|------------|------------|----------------|
+| ACD/Labs | ACD/Labs | .spectrus |
+| Mnova | Mestrelab | .mnova |
+
+### NMR Open Formats
+
+[JCAMP-DX](https://opg.optica.org/as/abstract.cfm?uri=as-47-8-1093) is a widely used **Open** NMR data exchange format. However, due to the broad scope and complexity of this format, along with maintenance issues, alternative approaches with peer-maintained ontologies would be beneficial. In **[nmrXiv](https://nmrxiv.org)**, within NFDI4Chem, we are working on extending the available **Open** NMR formats [NMReData](https://doi.org/10.1002/mrc.4737) and [nmrML](https://doi.org/10.1021/acs.analchem.7b02795) as candidate alternatives.
+
+| Short Name | Maintainer | File Extension | Parent Format | Specification |
+|------------|---------------------|-----------------|---------------|---------------|
+| nmrML | COSMOS | .nmrML | XML | Open |
+| NMReDATA | NMReDATA Initiative | .sdf | SDF | Open |
+| JCAMP-DX | IUPAC | .dx, .jdx, .jcm | ASCII, Text | Open |
+
+#### nmrML
+It is an open XML-based exchange and storage format for NMR spectral data. It can capture raw NMR data, spectral data acquisition parameters, and- where available- spectral metadata, such as chemical structures associated with spectral assignments. The nmrML format is compatible with pure-compound NMR data for reference spectral libraries and NMR data from complex bio-mixtures. There already exists nmrML converters for Bruker, JEOL, and Agilent/Varian vendor formats. In addition, easy-to-use Web-based spectral viewing, processing, and spectral assignment tools that read and write nmrML have been developed. Software libraries and Web services for data validation are available for tool developers and end-users. The nmrML format has already been adopted for capturing and disseminating NMR data for small molecules by several open-source data processing tools and metabolomics reference spectral libraries, e.g., serving as a storage format for the [MetaboLights](https://www.ebi.ac.uk/metabolights/) data repository. The nmrML open access data standard has been endorsed by the Metabolomics Standards Initiative (MSI).
+
+
+
+Non-exhaustive list of nmrML compatible open source software, clustered by tool category
+
+
+#### NMReDATA
+NMReData is the only standard file format available for the NMR data relevant to the structural characterization of small molecules as it associates the NMR parameters extracted from 1D and 2D spectra of organic compounds to the proposed chemical structure. These NMR parameters include chemical shift values, signal integrals, intensities, multiplicities, scalar coupling constants, lists of 2D correlations, relaxation times, and diffusion rates. The file format is an extension of the existing Structure Data Format .sdf, which is compatible with the commonly used MOL format. The association of an NMReDATA file with the raw and spectral data from which it originates constitutes an NMR record.
+
+
+
+NMReData working compatible software and tools
+
+
+
+NMReData announced compatible software and tools
+
+
+#### JCAMP-DX
+It is one of the most used open data exchange formats for NMR data, but due to its broad scope and complexity many different vendor-dependent variants exist. Coordinated updating for all variants to reflect the state-of-the-art in NMR methodology is rarely seen in this 30-year-old format. This variability can lead to incompatibilities between different software packages, and as a result, no content-based (semantic) validation of JCAMP-DX is available. However, JCAMP-DX is likely to remain in use for NMR data capture for many years, and therefore it will be supported in **[nmrXiv](https://nmrxiv.org)**.
+
+## NMR File Formats Converters
+
+### [NMRium](https://www.nmrium.org/)
+[NMRium](https://www.nmrium.org/) can convert open and vendor file formats to other formats. As an input, it can handle:
+- Jcamp DX (.dx, .jdx, .jcamp)
+- zipped folder in Bruker format (raw data or processed)
+- Jeol (.jdf)
+- NMRium file (.nmrium)
+- NMReData (.nmredata, coming soon)
+
+And as output, it gives back:
+- NMRium file (.nmrium)
+- NMReData (.nmredata, coming soon)
+- images
+
+### nmrML Converters
+There are converters from vendor formats (Bruker, JEOL, and Agilent/Varian) to nmrML along with other converters covered in the following table from [nmrML: A Community Supported Open Data Standard for the Description, Storage, and Exchange of NMR Data](https://pubs.acs.org/doi/10.1021/acs.analchem.7b02795).
+
+
+| Converter Name | Key Functions | Developer |
+|--------------------------|----------------------------------------------------|--------------------------------------------------------------|
+| nmrML converter (Java) | Converts vendor to nmrML format (recommended) | Institut National de la Recherche Agronomique (INRA), France |
+| nmrML converter (Python) | Converts vendor to nmrML format | The Metabolomics Innovation Center (TMIC), Canada |
+| nmrML to ISA converter | Generates prepopulated ISA files from nmrML files | EMBL-EBI, United Kingdom |
+| BMSxNmrML | Converts BMRB metabolomics entries to nmrML format | Institute for Protein Research (IPR), Japan |
+
+### NMReData Converters
+Conversion to NMReData is already being worked on by the NMRium team. Furthermore, non-open software such as [Mnova, ACD/Labs, and TopSpin](https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/mrc.5146) also provide the possibility to export their data as NMReData.
+
+## nmrXiv approach
+
+By now, it is evident that the type of information stored in existing formats is heterogeneous (see below), and no single format is currently capable of fully capturing all information from NMR experiments and data processing. Currently, NMReData (co-developed by nmrXiv team members) is the most promising Open format, as it supports all data types except for raw spectral data (see below). As native instrument formats represent the majority of available data, they will be preserved and made available to users. This approach ensures traceability and secure, long-term access to every detail of measured data as new formats appear or existing ones evolve. At the same time, the availability and interoperability of several formats will facilitate the re-use of data with external tools.
+
+| Data Format | RAW Spectra | Peaks | Annotation | Meta data | Acquisition parameters | Spin parameters | Structure |
+|----------------|-------------|-----------------|------------|-----------|------------------------|-----------------|-----------|
+| Bruker | I | I | | I | I | | I |
+| JEOL | I | I | | I | I | | I |
+| Varian/Agilent | I | I | | I | I | | I |
+| Mnova | I | I | | I | I | | I |
+| NMReData | | I/O | I/O | I/O | I/O | I/O (partially) | I/O |
+| CML Spect | I/O | I/O | I/O | I/O | I/O | | |
+| nmrML | I/O | I/O | I/O | | |
+| Allotrope ADF | I/O | I/O | I/O | | |
+| JCAMP-DX | I/O | I/O (sometimes) | |
+| NMR Star | I/O | I/O | I/O |
+
+I: input
+O: output
+
+#### Column definitions
+
+- **RAW Spectra**: The availability of the raw spectral data (the free induction decays (FIDs), which represent the actual (raw) spectroscopic data from the excited nuclear spins in the NMR experiment). Here is an example from an nmrML on how this data looks like:
+
+ ```eJwMl4dfzl8Ux7U3lYZKy0qiomQLPd9zHlmhslMJ2aIoGe29hyhKKURIaWhoPd9zn6zEz46skFKKZMXPX3DPva/PPZ/3u9xlqVhxpdX8Udd0Gp02JIodL2UIN34vE/sdO4la8ZHCQ7lCseEBM/E981xh2fNnbNDxOyCwLRF+XBYhvrlcna1elI65.../jyvhLLF5zln64UoklPU75xwQ3IPL4Dx/Nfkc91ZJlO3dz/ABn2jzA=```
+
+- **Peaks**: The list of the peaks (the list of the chemical shifts and other possible attributes such as the peak type, as in doublets or multiplet). Here is an example from an NMReData on how this data looks like (Find more about NMReData [here](https://nmredata.org/wiki/NMReDATA_tag_format#Agregated_data_tags)):
+ - A, 48.301, 1 ;A corresponds to the carbon of CH2\
+ - B, 20.322, 2 ;B corresponds to the carbon of CH3\
+
+- **Annotation**: The possibility to annotate the data with more details provided by the users, as one can see in the same example from the NMReData file here,:
+ - A, 48.301, 1 ;A corresponds to the carbon of CH2\
+ - B, 20.322, 2 ;B corresponds to the carbon of CH3\
+
+ Where, in addition to the peaks and the atoms labels, the user was able to further clarify the chemical groups.
+
+- **Metadata**: The availability of Metadata, e.g., locations of files. Another example from the NMReData file:
+
+ ```Spectrum_Location=file:./nmr/11/1/pdata/1\```
+
+ ```> 1.1\```
+
+ ```> 0\```
+
+- **Acquisition parameters**: The availability of acquisition parameters related to the NMR assay, which can be usually provided by the instrument:
+
+```bash
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ ....
+
+
+```
+- **Structure**: The availability of the structure, where in some files, the mol data can be integrated with the rest of the data, and in others, it can be provided as a separate mol file.
+
+- Additionally to what traditional formats usually provide, NMReData associates the NMR parameters extracted from 1D and 2D spectra of organic compounds to the proposed chemical structure.
+
+For further details, please check [NFDI4Chem Knowledgebase - Data format standard](https://knowledgebase.nfdi4che/knowledge_base/topics/format_standards/)
\ No newline at end of file
diff --git a/docs/introduction/data/ontologies.md b/docs/introduction/data/ontologies.md
new file mode 100644
index 00000000..d550c022
--- /dev/null
+++ b/docs/introduction/data/ontologies.md
@@ -0,0 +1,69 @@
+# Ontologies
+nmrXiv aims to provide the data, present it unambiguously, and make it [FAIRer](https://www.go-fair.org/fair-principles) (Findable, Accessible, Interoperable, Reusable). It focuses on making the data not only human-readable, but machine-readable as well, so that researchers can leverage advanced Machine Learning, Named Entity Recognition, and other language processing techniques to re-analyze the data. This can be facilitated by using ontologies.
+
+## Ontologies usage in nmrXiv
+nmrXiv will use ontologies to annotate as many fields as possible, along with requesting some fields' values to be ontology-driven, including all units. In addition to being ontologies-consumers, being an NMR data repository, nmrXiv is suited for gathering missing terms via user submission and contributing them to ontologies relevant to NMR data, or repositories data in general (in other words, to domain-specific and domain-independent ontologies). This will be achieved through collaboration with the [NFDI4Chem Terminology Service](https://terminology.nfdi4chem.de/ts/index) from **Task Area 6** in NFDI4Chem.
+
+### Ontology Component
+The ontology component will be provided as an open-source, platform-agnostic tool compatible with JavaScript interfaces. This component will ensure a user-friendly experience in finding ontology values from any terminology service supported by the platform using the component ([NFDI4Chem Terminology Service](https://terminology.nfdi4chem.de/ts/index) in the case of nmrXiv). It will simplifiy the search for terms by providing auto-complete functionality, while enabling the platform to restrict the suggested terms to selected ontologies that are relavent to the field in hand. The development of the component is currently going on [this branch of nmrXiv repository](https://github.com/NFDI4Chem/nmrxiv/tree/ontology-component).
+
+nmrXiv will make use of the available [APIs](https://terminology.nfdi4chem.de/ts/api) in the [Terminology Service](https://terminology.nfdi4chem.de/ts/index), which, along with more general possibilities such as retrieving an entire ontology, enable retrieving a specific term and restricting the search to a list of ontologies. Additionally, they support the suggestion of new terms. For a detailed description of the available endpoints and parameters, please check the [API Documentation](https://terminology.nfdi4chem.de/ts/api).
+
+### Schemas Export with Ontologies
+Metadata describing the submitted projects/studies/datasets can be exported in nmrXiv as files complying with a schema chosen by the user from the [schemas supported in nmrXiv](/introduction/data/data-schema). Many of those schemas support ontologies usage such as [ISA](https://isa-tools.org/) and [Bioschema](https://bioschemas.org/), which will efficiently reflect the use of ontology terms in the exported files by providing links and identifiers to the intended terms.
+
+### Ontologies of Interest in nmrXiv
+Several factors have been considered to pick the ontologies to use in nmrXiv,:
+- Flexibility: A flexible workflow of new terms submission has a high priority for nmrXiv as it will contribute to ontologies curation.
+- Usage in the NMR domain: Ontologies frequently used by other NMR repositories and already known to the chemists have been considred.
+- Specialisation: Specialised ontologies usually provide more extensive coverage of the field with more accurate definitions of terms.
+
+#### Domain-Independent Ontologies:
+The following ontologies provide identifiers, references, formats, and possible operations to define experiments:
+
+* [Bioinformatics operations, data types, formats, identifiers and topics - EDAM](https://terminology.nfdi4chem.de/ts/ontologies/edam)
+* [REPRODUCE-ME Ontology - REPR](https://www.ebi.ac.uk/ols/ontologies/reproduceme)
+* [Medical Subject Headings - MeSH](https://meshb-prev.nlm.nih.gov/treeView)
+* [NCI Thesaurus OBO Edition - NCIt](https://www.ebi.ac.uk/ols/ontologies/ncit)
+
+#### Domain-Specific Ontologies:
+
+* [nuclear magnetic resonance CV - NMR](https://terminology.nfdi4chem.de/ts/ontologies/nmrcv):
+nmrCV is highly relevant for nmrXiv as it covers many aspects of the NMR assay and the resulting spectral data, including the files formats, dimensionality, instruments, used materials, and later data processing.
+
+* [Chemical Methods Ontology - CHMO](https://terminology.nfdi4chem.de/ts/ontologies/chmo):
+ Methods used to collect data in chemical experiments, including NMR spectroscopy, are covered under this ontology.
+
+* [NCBI organismal classification - NCBITAXON](https://www.ebi.ac.uk/ols/ontologies/ncbitaxon):
+ Widely used curated classification for organisms.
+
+* [The BRENDA Tissue Ontology - BTO](https://www.ebi.ac.uk/ols/ontologies/bto):
+ It covers organism parts and variants. Examples include tissues, cell lines, cell types and cell cultures.
+
+* [Experimental Factor Ontology - EFO](https://www.ebi.ac.uk/ols/ontologies/efo):
+ For many experimental variables, which can be used, e.g., to describe the tissue and the organism part.
+
+* [NCI Thesaurus OBO Edition - NCIt](https://www.ebi.ac.uk/ols/ontologies/ncit):
+It includes broad coverage of the cancer domain, including cancer-related diseases, findings and abnormalities.
+
+* [Medical Subject Headings - MeSH](https://meshb-prev.nlm.nih.gov/treeView):
+ Medical Subject Headings is a comprehensive controlled vocabulary for indexing journal articles and books in the life sciences.
+
+* [Ontology for Biomedical Investigations - OBI](https://terminology.nfdi4chem.de/ts/ontologies/obi):
+Ontology for Biomedical Investigations (OBI) serves as a resource for annotating biomedical investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. This ontology arose from the Functional Genomics Investigation Ontology (FuGO) and contains both terms common to all biomedical investigations, including functional genomics investigations and those that are more domain-specific.
+
+* [CHEBI Integrated Role Ontology - CHIRO](https://terminology.nfdi4chem.de/ts/ontologies/chiro):
+CHEBI provides a distinct role hierarchy for chemical entities.
+* [chemical information ontology - CHEMINF](https://terminology.nfdi4chem.de/ts/ontologies/cheminf):
+CHEMINF provides terms for cheminformatics software and algorithms, such as chemical identifiers and others.
+
+* [Units of measurement ontology - UO](https://terminology.nfdi4chem.de/ts/ontologies/uo):
+For metrical units.
+
+
+
+
+
+
+
+
diff --git a/docs/introduction/data/schemas.md b/docs/introduction/data/schemas.md
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+# Data Schemas
+
+Data schemas enable structuring the data in a well-designed form by providing precise definitions of entities with relations among them. Additionally, they enable data indexing and feasible metadata export making those schema a valuable asset to improve data findability on the web, and to enhance machine-readability and data analysis, especially when considering that many of the available schemas support ontologies usage by accepting/requesting values to be provided as ontology terms and providing links and identifiers to the terms.
+
+## nmrXiv Data Model
+nmrXiv uses the ISA [(Investigation, Study, Assay)](https://isa-tools.org/format/specification.html) approach to capture the experimental metadata in a structured format, though it has opted for a different terminology than the one used by ISA:
+- Investigation ⇛ Project
+- Study ⇛ Study
+- Assay ⇛ Experiment
+
+For more details about the objects and relations among them, please check the [Data Model folder](/category/data-model)
+
+## Data Schemas in nmrXiv
+nmrXiv focus on obtaining DOIs for the different entities and describing the data with ontology terms led to prioritizing a list of schemas. Some have been already implemented, and others will be coming soon. Here you can find a list of those schemas:
+
+### Bioschemas (Repository, Project, Studay, Dataset, Sample)
+
+[Bioschemas](https://bioschemas.org/) aims to improve the Findability of life sciences resources (such as datasets) on the Web by using [Schema.org](https://schema.org/) markup in the websites, so that they are indexable by search engines and other services. Bioschemas is making two main contributions:
+- Proposing new [types and properties](https://bioschemas.org/types) to [Schema.org](https://schema.org/) to allow for the description of life science resources.
+- Defining usage [profiles](https://bioschemas.org/profiles) over the [Schema.org](https://schema.org/) types that identify the essential properties to use in describing a resource.[1]
+
+nmrXiv uses Bioschemas profiles to describe both data structuring components (such as datasets) and experiment-related components (such as samples and molecules). Missing profiles will be contributed to Bioschemas and discussion about NMR-specific schemas is going on. Here is a list of the used profiles/types:
+
+#### [DataCatalog](https://bioschemas.org/profiles/DataCatalog/0.3-RELEASE-2019_07_01)
+DataCatalog profile can be used as a guide to describe repositories, and thus, it is used to describe nmrXiv repository.[DataCatalog API endpoint link](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17195598-31c24120-14f0-41c4-b511-292fd310db79)
+
+#### [Project](https://github.com/NFDI4Chem/nmrxiv/blob/main/app/Models/Bioschema/Project.php)
+[Project type](https://schema.org/Project) already exists in [Schema.org](https://schema.org/), but it refers to enterprises rather than a scientific investigation. However, as the project metadata is somehow similar to the study metadata (id, name, URL, etc.), nmrXiv initially defines a new project type similarly to the [study](https://bioschemas.org/types/Study/0.3-DRAFT) provided by [Bioschemas](https://bioschemas.org/). Further enhancements will be applied upon discussion with field experts, and possible submission to [Bioschemas](https://bioschemas.org/) will take place. Project properties allow linking with the included studies and their inner data. [Project API endpoint link](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17195598-d7481762-e431-4975-b786-9cfd7f007d56).
+
+#### [Study](https://bioschemas.org/profiles/Study/0.2-DRAFT)
+Study profile is currently still a draft in Bioschemas. It is used in nmrXiv to describe the study, and its properties are used to link the study to the corresponding sample and the contained datasets, while being a part of a project. [Study API endpoint link](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17195598-910d6c75-2a1d-42ff-9f0d-b669bbfa6db5).
+
+#### [Sample](https://bioschemas.org/profiles/Sample/0.2-RELEASE-2018_11_10)
+Sample profile is used in nmrXiv to describe NMR samples. It is attached to the study as a value of "about" property indicating that the study is about this sample. Furthermore, the molecules existing in the Sample are added to it as a value of the property "additionalProperty". There is no API endpoint for the Sample as it can be found in the Study.
+
+#### [MolecularEntity](https://bioschemas.org/profiles/MolecularEntity/0.5-RELEASE)
+MolecularEntity can be used for any constitutionally or isotopically distinct atom, molecule, ion, etc., identifiable as a separately distinguishable entity. At the moment, it is used in nmrXiv only to describe the molecules in a sample, but further usages such as describing the nucleus or the solvent are possible too. There is no API endpoint for the MolecularEntity as it can be found in the Study ⇛ Sample.
+
+#### [Dataset](https://bioschemas.org/profiles/Dataset/1.0-RELEASE)
+Dataset schema is used in nmrXiv to describe the datasets there. Each dataset is linked to the parent project and study through the property "isPartOf". [Dataset API endpoint link](https://www.postman.com/nmrxiv-jena/workspace/nmrxiv/request/17195598-0408e3df-3c8f-4899-b440-eda6d8f71193).
+
+
+### ISA (Sample, Assay, Ontology)
+
+[ISA is a metadata framework](https://isa-tools.org/) to manage a diverse set of life science, environmental, and biomedical experiments that employ one or a combination of technologies, built around the **I**nvestigation (the project context), **S**tudy (a unit of research), and **A**ssay (analytical measurement) data model and serializations (tabular, JSON and RDF).[2]
+
+nmrXiv will comply with ISA Schema specifications to capture NMR metadata (Assay, Sample, and Ontology) to provide a detailed description of the experimental metadata for both synthetic and biological experiments (i.e., sample characteristics, technology and measurement types, sample-to-data relationships). ISA enables interoperability with other platforms and services while keeping the information in a simplistic and open-text format that is FAIR compliant. nmrXiv back-end will be designed to support ISA for newly entered data. However, ISA still comes with few limitations from the data management (repository) perspective, configurable templates on the go and redundant data being some of them. nmrXiv will contribute to extending the existing ISA models with NMR domain-specific requirements to ensure total flexibility for the end user to define their own templates while still being complaint with ISA Specifications and the minimum information standards.
+
+
+
+#### ISA Sample Schema
+In a Study object, ISA records the provenance of biological [samples](https://github.com/ISA-tools/isa-api/blob/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/sample_schema.json) from [source](https://github.com/ISA-tools/isa-api/blob/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/source_schema.json) material through a collection process to sample material represented with directed acyclic graphs (direct graphs with no loops/cycles). The pattern of nodes is usually formed of a source material node, followed by a sample collection process node, followed by a sample material node.
+
+(source material)->(sample collection)->(sample material)
+
+These study graphs MAY split and pool depending on how the samples are collected.
+
+In a splitting example, multiple samples might be derived from the same source:
+
+(source material 1)->(sample collection)->(sample material 1)
+
+(source material 1)->(sample collection)->(sample material 2)
+
+In a pooling example, multiple sources may be used to create a single sample:
+
+(source material 1)->(sample collection)->(sample material 1)
+
+(source material 2)->(sample collection)->(sample material 1)
+
+However, sample collection applies only to biological samples where the source comes from a certain organism, while with synthetic samples we have a certain compound that gets dissolved in a solvent to create the sample. We are trying to capture this concept in ISA adopting mock-ups derived from actual samples/molecules found in non-biological repositories such as [Chemotion](https://www.chemotion-repository.net/welcome) and [NMRShiftDB](https://nmrshiftdb.nmr.uni-koeln.de/), and compare them with a biological sample coming from the biological repository [MetaboLights](https://www.ebi.ac.uk/metabolights/). Please find the mentioned mock-ups [here](https://github.com/NFDI4Chem/schema/tree/main/ISA). Those mock-ups are still under development, especially due to the absence of the relevant ISA configurations in addition to the continuous update upon discussion.
+
+nmrXiv approach to represent a synthetic sample is to take the compound found in Chemotion or NMRShiftDB as a source, and apply an NMR sample protocol where a solvent gets added to generate the sample, and where the solvent becomes one of the sample characteristics. This NMR sample undergoes an NMR spectroscopy protocol with parameters such as the instrument, magnetic field strength, pulse sequence name, temperature and others. This protocol will result in a data file, which, in return, undergoes an NMR assay protocol with some NMR processing software. This approach is still under discussion and not confirmed.
+
+However, we are still facing issues regarding:
+* Missing ontology terms to represent the characteristics and factors categories.
+* The limited use of ontologies in both Chemotion and NMRShiftDB, so we picked terms representing the fields and values in the mock-ups despite the frequent use of free text in the actual models.
+* Representing characteristics and factors categories when the category is a combination of two or more ontology terms. e.g., "number of rings", "duration of incubation".
+
+#### ISA Ontology Schema
+[ISA ontology reference schema](https://github.com/ISA-tools/isa-api/blob/master/isatools/resources/schemas/isa_model_version_1_0_schemas/core/ontology_annotation_schema.json) can capture ontology terms where those "annotation_values" are linked to their "term_source" which is the ontology the term comes from, and the "term_accession", which is the link to that term.
+
+#### ISA Converters
+nmrXiv will contribute to developing data converters as independent microservices (python-based applications) to convert data from and to ISA, which enables nmrXiv and other repositories to utilize these converters as plugins to capture and export data. nmrXiv will also leverage the existing tool set in the domain, such as [nmrml2isa](https://github.com/ISA-tools/nmrml2isa) converter, to capture rich metadata from the open nmrML files. **nmrml2isa** is a Python3 program that can be used to generate an ISA-Tab structured investigation out of nmrML files, providing the backbone of a study that can then be edited further to provide additional metadata that cannot be automatically extracted.
+
+### IUPAC - FAIRSpec (Spectra)
+nmrXiv will contribute to and adopt the definition of standardized metadata being developed within IUPAC [Project](https://github.com/IUPAC/IUPAC-FAIRSpec) "Development of a Standard for FAIR Data Management for Spectroscopic Data", which covers spectroscopic data including NMR spectroscopy. But this project is still preliminary and under development.
+
+### DataCite (Data Citation and Discovery)
+
+The [DataCite Metadata Schema](https://schema.datacite.org/) is a list of core metadata properties chosen for accurate and consistent identification of a resource for citation and retrieval purposes, along with recommended use instructions. It primarily supports citation of data rather than discipline-specific metadata.
+
+Complying with the DataCite schema enables the creation of new [Digital Object Identifiers (DOIs)](https://www.doi.org/) and their assignment to content on nmrXiv, which is essential for identifiers' persistence. Only mandatory property values are needed to obtain the DOI, but still, there is the ability of rich citing-metadata description with recommended and optional properties. nmrXiv will mostly treat some recommended fields as mandatory since they are expected to become mandatory in DataCite in the near future and to make sure all essential metadata is captured. Mandatory fields include the DOI, Creator, Title, Publisher, PublicationYear, and ResourceType. Additionally, using DataCite schema will enable easy export of the metadata in XML format.
+
+### OpenAIRE Guidelines (Data Citation and Discovery)
+
+Complying with [OpenAIRE Guidelines for Data Archive Managers](https://guidelines.openaire.eu/en/latest/) ensures compatibility with the OpenAIRE infrastructure, which facilitates interoperability with other repositories already adhering to those guidelines, enhancing data exposure and visibility. OpenAIRE has already adopted the DataCite Metadata Schema, yet with some minor adjustments, such as accepting other persistent identifier schemes rather than the DOI and some changes in the obligations of properties.
+
+ # References
+1- [https://bioschemas.org/](https://bioschemas.org/)
+2- [https://isa-tools.org/](https://isa-tools.org/)
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+# Overview
+
+**[nmrXiv](https://nmrxiv.org)** (pronounced `nm-archive`) is a FAIR and Open, Consensus-Driven Nuclear Magnetic Resonance (NMR) Data Repository and Computational platform. It is currently being developed as a part of [NFDI4Chem](https://www.nfdi4chem.de/) initiative with the ultimate goal of accelerating broader coordination and data sharing among researchers by creating a platform for managing, sharing, and analyzing raw and processed NMR spectral data.
+
+The immediate goal of **[nmrXiv](https://nmrxiv.org)** is to integrate and execute the following objectives by establishing **[nmrXiv](https://nmrxiv.org)** as a consensus-driven resource designed to serve global chemistry research and adjacent natural products / metabolomics communities.
+
+### Software Development
+To develop nmrXiv based on a voluntarily FAIR, cloud-based infrastructure that uses freely shared source code and deployment methods. Apply industry-grade development practices to ensure platform reliability, safety, and efficacy. Use Continuous Improvement principles will ensure an always-on user experience and high reliability. Release the codebase and infrastructure details (including the development, documentation, and usage practices) through [MIT Open Source License](/license.md) for openness.
+
+*More details about the platform architecture and related topics* - [here](/category/developer-guides)
+
+### Submission, Curation, and Analysis
+
+Enable the FAIR (**F**indable · **A**ccessible · **I**nteroperable · **R**eusable) Sharing of raw NMR data to enhance the quality of chemical research and dissemination. Also, to develop non-prescriptivist curation and analysis standards for data and metadata. Build standards with input and contributions from the community and make them compatible with existing and potential newly developed formats and approaches.
+
+*More details about the data standards and related topics* - [here](/category/data)
+
+### Workshops and Training
+To engage analytical chemistry researchers and adjacent communities through webinars, workshops, tutorials, and community calls to ensure that **[nmrXiv](https://nmrxiv.org)** meets the researchers’ needs and implements adequate incentive mechanisms for data contributions and curation.
+
+This documentation site comprises detailed walk-through explanations from basic to more complex functionalities for developers ([Developer Guides](/category/developer-guides)), submitters ([Submission Guides](/category/submission-guides)) and users (Search and [API](/developer-guides/API.md)) of **[nmrXiv](https://nmrxiv.org)**. All the adopted core concepts, such as [Data Schemas](/introduction/data/schemas.md), [NMR File Formats](/introduction/data/formats.md), tools & [Converters](/introduction/data/file-format#nmr-file-formats-converters), [Ontologies](/introduction/data/ontologies.md), FAIR best practices, etc., are documented to ensure a clear scaffolding for developers to revisit previously developed parts and continue building upon them. This documentation-first approach allows developers and users to discuss proposed features and ensure that the implementations reflect the actual use cases.
+
+:::info note
+**Why nmrXiv?**
+Over the past few decades, several attempts have been made to host literature-derived NMR data; however, these databases do not meet the needs of all chemical communities (including natural products & metabolomics) in several ways, including a lack of experimental data, limited search capabilities, and more importantly, they are not FAIR compliant.
+
+**[nmrXiv](https://nmrxiv.org)** is the **first FAIR and Open archive to preserve NMR data in its original instrument format**, and it promotes **Open Data and Open Standards** to maximize long term sustainability of the resource and FAIRness of the archived data.
+:::
+
+
+
+
+
+
+
diff --git a/docs/license.md b/docs/license.md
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+# License
+
+### MIT License (MIT)
+
+Copyright (c) 2022 NFDI4Chem
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/docs/miscellaneous/shortcuts.md b/docs/miscellaneous/shortcuts.md
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+---
+sidebar_position: 2
+title: Shortcuts
+---
+
+Coming soon
\ No newline at end of file
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+---
+sidebar_position: 1
+title: Tour
+---
+
+Coming soon
\ No newline at end of file
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+
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+
diff --git a/docs/submission-guides/data-lifecycle.md b/docs/submission-guides/data-lifecycle.md
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+# Data Life Cycle
+
+Research data passes through many processes from creation to (voluntary or accidental) destruction. While data is generated by our submitters/contributors, nmrXiv aims at supporting all subsequent stages of the data lifecycle, starting with data deposition. Using various sources and community involvement/incentives, we will endeavour to procure and disseminate raw NMR data that is currently not required (e.g., by journals or funding agencies) to be shared.
+
+**Deposition:** User(s) can submit their datasets to the repository using our easy-to-use interface, or an electronic lab notebook such as Chemotion ELN. Using smart lab notebooks enables easy integration with commonly used software. We ensure that the submitted data sets are in accordance with minimum information standards and additional requirements set by the domain experts and funders. The submitter can then enrich their dataset with additional information (taxonomic and genomic information, related publication) according to standards defined by the community, with some metadata and acquisition parameters being pre-populated.
+
+**Processing/Archiving/Distribution:**
+nmrXiv infrastructure will convert the data into the standard formats using workflows over distributed infrastructure. Data and associated metadata will be processed, stored, and archived following the RDM best practises such as [BagIt](https://tools.ietf.org/id/draft-kunze-bagit-16.html).
+
+**Archiving:**
+Once deposited, the users receive a stable identifier, typically a [DOI](https://www.doi.org/) hyperlink that remains unchanged for the resource's lifetime. As nmrXiv will issue [DOI](https://www.doi.org/)s, any deposited data will immediately have a stable identifier that can point to the dataset and allow its re-use or repurposing. This fully accommodates manuscript submission, peer review, and post-acceptance needs. nmrXiv will also develop restricted access models that allow only authorized reviewers to access the author's original NMR data. Upon acceptance, the [DOI](https://www.doi.org/)-labeled datasets will become publicly accessible.
+
+nmrXiv will also support **DOI Versioning**, allowing users to update their data while maintaining modification records. In **DOI Versioning**, the [DOI](https://www.doi.org/) assigned to a dataset will always point to the latest version, while specific [DOI](https://www.doi.org/)s are assigned to specific versions. This will allow nmrXiv to manage data, e.g., structural revisions, without breaking the [DOI](https://www.doi.org/) link in publications.
+
+## Other Sources of Data
+
+nmrXiv will not be limited to publication-related applications. We also envision and make an effort towards characterizing a set of well-known "flagship" **Natural Products (NP)** and deposit these data in nmrXiv.
+
+### Harvard's Dataverse
+
+An existing comprehensive set of publicly available NMR data for +40 of the most well-studied bioactive NPs (already publicly available via Harvard's Dataverse) will be integrated into nmrXiv.
+
+### NMRShiftDB
+
+nmrXiv will strive to make data accessible for machines (making use of ontologies), while ensuring it remains human-readable. The data can be utilized through external tools using the APIs and nmrXiv processing tools. Any data available publicly on the platform will be re-usable under **FAIR** and **Open licenses**. That way, this data can be re-used for incremental or completely new research by any user.
diff --git a/docs/submission-guides/data-model/dataset.md b/docs/submission-guides/data-model/dataset.md
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+# Dataset
+
+The concept of the dataset in **[nmrXiv](https://nmrxiv.org/)** is similar to the one of [assay](https://isa-specs.readthedocs.io/en/latest/isamodel.html#assay) in [ISA model](https://isa-tools.org/format/specification.html) yet broader, as it refers to the files corresponding to experiments along with their metadata. For instance, one dataset could be a Bruker folder with all the underlying files corresponding to a 1H assay. **[nmrXiv](https://nmrxiv.org/)** is capable of detecting datasets automatically and grouping them in studies, which requires the user to ensure submitting their data in a compatible way. For more details, it is highly recommended to check the [folder structuring section](/submission-guides/submission/folder-structure.md) before submitting data.
+
+## Dataset View
+
+
+
+Dataset view
+
+
+The view of a public dataset is similar to the private's one. In fact, it is just a tab from the [study view](/submission-guides/data-model/study/#study-view), and it is similar to the [Step 2](/submission-guides/submission/upload#assignement--meta-data---step-2) Experiments (Spectra) tab of the [Data Submission Pipeline](/submission-guides/submission/upload). At the top, there is a drop-down menu to select an experiment (within a study, thus, sample).
+
+
+
+Select experiment menu
+
+
+The selected experiment will be viewed in the embedded NMRium. For more details about [NMRium](https://www.nmrium.org/), please visit our [NMRium documentation page](/advanced-guides/nmrium/) and [NMRium official documentation](https://docs.nmrium.org/).
+
+Next to the `Select Experiment` menu, there is a `Manage Datasets` button, which enables adding datasets or deleting them to and from a study through the [submission pipeline](/submission-guides/submission/upload.md).
+
+Directly above the NMRium window, you can see a gray message on the left that informs the user about the current status of the spectra (being uploaded, saved, etc.). On the right side, there exist three buttons. `Reset` will reset all the edits done on the spectra, getting it back to its original status when uploaded. Resetting is an edit that is saved along with other edits in the history, which can be viewed by clicking `Edit History`, which opens a side menu to show the editors, and the dates of edits.
+
+
+
+
+
+Below, there is [NMRium](https://www.nmrium.org/) window. Clicking on the `User manual` leads to [NMRium Documentation page](https://docs.nmrium.org/). You can control the panels and tools you have by default in [NMRium](https://www.nmrium.org/) from `General settings`. You can also click `Full screen` to enable that mode.
+
+If any structure is added to `Chemical structures` field in NMRium, it appears directly below NMRium. Then there is the metadata of the experiment:
+
+- **Info** includes all the information extracted by [NMRium](https://www.nmrium.org/) about the NMR experiment.
+
+- **Meta** is the second table coming after **Info**. It includes the metadata from the instrument file.
+
+## Create
+
+There are two ways to create datasets. First is through the [submission pipeline](/submission-guides/submission/upload.md), where the datasets will be automatically detected. The second is after submission from the `Datasets` tab within a study by clicking on [`Manage Datasets` button](#manage-datasets) and dragging and dropping files or folders to the opened [submission pipeline](/submission-guides/submission/upload.md), but the second option is possible only for private ones. Please pay attention to dragging the datasets to the right study folder.
+
+## Access
+
+You can access your created datasets and the ones shared with you by [entering their parent studies](/submission-guides/data-model/study/#access) and going to the `Datasets` or `Files` tabs. All the public datasets on **[nmrXiv](https://nmrxiv.org/)** are in the `Datasets` folder.
+
+## Edit
+
+To edit a dataset, you should have **editing** access to it, which is the case when you are its creator or when it is shared with you as an owner or a collaborator. The dataset should also still be private. You can edit the dataset through NMRium, and a history of changes is kept.
+
+### Manage Datasets
+
+From the `Datasets` tab within a study, you can add more datasets by dragging and dropping files or folders to the opened [submission pipeline](/submission-guides/submission/upload.md). Please pay attention to dragging the datasets to the right study folder. Or you can delete them by selecting a dataset **in the left panel** and pressing `Delete`.
+
+## Validation
+
+To publish a dataset, i.e., to make it public, you need to publish its parent project, which must comply with community standards. At the moment, we are checking for [DataCite](https://datacite.org/) mandatory metadata needed to receive a [DOI](https://www.doi.org/) in addition to requesting an image for the project. If any piece of metadata is missing, you will see a **Why can't I publish?** link message at the top of the project view.
+
+
+
+
+
+Clicking on **Why can't I publish?** leads to a new page similar to the [step-3 of the submission pipeline](/submission-guides/submission/upload#complete---step-3). Here you can find either red x, or a green ✓ to indicate the existence or absence of the mandatory metadata respectively. A yellow ⚠ indicates the absence of recommended (not mandatory) metadata. Whenever the red x or the yellow ⚠ exist, they are accompanied by an `Edit` button to facilitate providing the missing data. Here are more details about why a certain dataset validation fails:
+
+- Files: This field checks whether there are spectral NMR data files. Since the [project submission](/submission-guides/submission/upload.md) (not publishing) is not possible without spectral files, this field always passes the validation before submission ✓.
+- NMRium info: This field is about whether the dataset was processed completely by NMRium, where its metadata gets parsed and the spectrum gets viewed. If this field doesn't pass the validation x, please go to the respective dataset (with the edit button), and there click on `Preview`, which will update the preview and save it. You can make sure that the metadata is generated by checking the existence of the `Info` table below NMRium ✓.
+- Assay (Metadata): This feature is in development and, at the moment, the corresponding field will always pass the validation ✓.
+- Assignments: The molecular assignment with NMRium is recommended by **[nmrXiv](https://nmrxiv.org/)**. Therefore, whenever it is not provided, the field gets marked with a yellow ⚠, but it is still possible to publish without it. To provide the molecular assignment, please refer to [NMRium documentation](https://docs.nmrium.org/structure_assignment/assign/add).
+
+
+
+Validation Checklist of the Dataset (within a study)
+
+
+## Share
+
+[Sharing a study](/submission-guides/data-model/study#share) results in sharing all the underlying datasets. There is no way to share individual datasets.
+
+## Delete and Archive
+
+Only private datasets can be deleted, while public ones can be archived. The reason is that once a dataset is public, it can be referenced somewhere else, which requires the repository to keep an active link to this dataset. Therefore, when the creators of a public dataset decide that it is no longer maintained, or that the data provided is not accurate, they can only archive it instead of deleting it, while deletion is always an option for private datasets.
+
+Deleting/Archiving a [project](/submission-guides/data-model/project#delete-and-archive) or a [study](/submission-guides/data-model/study#delete-and-archive) will delete/archive all the underlying datasets. In the case of project deletion, this action is reversible for 30 days as the deleted project will be stored in the **Trash** folder, where the user can find the project and restore it from the `Project Settings`. After 30 days, deletion leads to permanently deleting the project and all of its content data. In the case of archiving, the user can unarchive the project anytime from the `Project Settings`. Archived projects are not moved to the trash.
+
+However, there is another way to delete datasets, which is from the [`Manage Datasets` button](#manage-datasets) in the [dataset view](#dataset-view).
diff --git a/docs/submission-guides/data-model/project.md b/docs/submission-guides/data-model/project.md
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+# Project
+
+The concept of project in **[nmrXiv](https://nmrxiv.org/)** is similar to the [Investigation](https://isa-specs.readthedocs.io/en/latest/isamodel.html#investigation) one in [ISA model](https://isa-tools.org/format/specification.html). Therefore, the project helps to group related studies and describe their collective metadata. How those studies are related is up to the user. They can be a collection of studies used for teaching or in a thesis. They can also be a part of one [Investigation](https://isa-specs.readthedocs.io/en/latest/isamodel.html#investigation) (several samples from one source). In other words, the relation can be based on the domain of the studies, their usage, or any other basis, as long the user is aware that all the data submitted to **[nmrXiv](https://nmrxiv.org/)** in [one process](/submission-guides/submission/upload.md) are grouped as one project.
+
+## Project View
+
+### Private Project View
+
+
+
+Private project view
+
+
+Starting with **private** projects, from the top, one can see the project **name** (FSU NMR Platform Samples), which must be unique within the workspace. Next to the name is a star to indicate whether the project is starred and to enable starring/de-starring, which helps to bookmark projects. Below, one can see the avatars of the users with whom the project is shared as circles with either the users' images or names' first letters. Clicking on those avatars enables sharing control (more on that in [Share](#share)). One can also click on `View details` to view and edit the project details (more on that in [Edit](#edit)), and to see the project's privacy and the user's ownership. Both those last two are not clickable, but they are editable from `View details` and `Share`. And finally, there are details about when the project was last updated.
+
+
+
+
+
+To the right, there is the `Project Settings` (more on that in [Delete](#delete)), and the `Publish` button. This button remains inactive as long as the data validation fails. To get more details on the failing validation and to fix it, the user can click on **Why can't I publish?**, which leads to the validation page (more on that in [Validation](#validation)).
+
+Moving down, the view of the **private** project differs from the **public** one by having the `Edit` buttons next to the fields in the earlier one. Those fields include the project's `Description`, which must be at least 20 characters describing its content and/or its purpose, while the `Keywords` are tags used to search for the project and increase its findability. Then comes the `License` with an `i`nformation sign. When hovering over the `i`, a brief description of the license appears. More about **[nmrXiv](https://nmrxiv.org/)** licenses can be found [here](/submission-guides/licenses.md)
+
+
+
+
+
+The `Citation` field contains the article to which the submitted data is attached, and the `Author` is the creator(s) of the data.
+
+
+
+
+
+At the bottom are the studies included in the project supported by the `Search` bar. At the moment, only the search "by the name" is supported. To search for a study, you need to provide at least a few consecutive letters of its name. The search is case-insensitive. Pressing `GO` takes you to the search results, while `Reset` will takes you back to a view of all the studies. To the right, there is a `Manage Studies` button, which enables adding and deleting studies to and from the project. For more details, please check [Manage Studies](#manage-studies).
+
+
+
+
+
+### Public Project View
+
+
+
+Public project view
+
+
+The public project view is similar to the [private's](#private-project-view), but still, there are some differences. Once a project is public, a green bar appears at the top informing the user that no more edits are possible, and any needed changes can be made as a new version.
+Moving down, a blue bar contains the citation details which can be adjusted according to the citation system (can be picked from the drop-down menu on the right). The citation includes a DOI to the project, which contains the project identifier (P7 in the image). This identifier always has the structure of "P", which stands for the project, and a number. Projects identifiers are [**Persistent Identifiers (PID)**](https://en.wikipedia.org/wiki/Persistent_identifier) within the repository. Additionally, all the `Edit` buttons disappear in public projects as no more editing is allowed after publishing.
+
+## Create
+
+The only way to create projects is through the [Data Submission](/submission-guides/submission/upload.md).
+
+## Access
+
+You can find your created projects in the `Dashboard` (or in the [team](/submission-guides/data-model/team) dashboard), while you can find the ones shared with you by others in the `Shared with me` folder. All the public projects on **[nmrXiv](https://nmrxiv.org/)** are in the `Projects` folder, and the projects you viewed recently are in the `Recent` folder. Projects that you have starred (along with starred studies) can be found in the `Starred` folder. In the `Trash` you can find the projects you have deleted within the last 30 days. Please note that t the end of the 30 days, the project and all its resources will be deleted and they cannot be recovered. You can restore a deleted project within the 30-day recovery period.
+
+
+
+User dashboard
+
+
+In the `Dashboard`, you can see a quick view of the project, including its **name**, **privacy**, and dates of **creating and updating**. You can also see if the project is **starred**.
+
+## Edit
+
+To edit a project, you should have **editing** access to it, which is the case when you are its creator or when it is shared with you as an owner or a collaborator. The project should also still be private.
+
+Enter the chosen project by clicking anywhere on its card from the `Dashboard` or [the other folders](#access), which leads to the project view. Within the project view, you can edit the project from `View details` at the top or from any `Edit` button found next to the fields. Additionally, you can edit the files in the project by adding or deleting them with the `Manage Studies` button at the bottom.
+
+### View Details
+
+Clicking on `View details` opens a side menu.
+
+
+
+View details side menu
+
+
+In the side menu, the user can edit the project's name, description, keywords, and license. If you are not sure which license to use, please check the link [How to choose the right license?](/submission-guides/licenses.md) provided next to the `License` field. The user can also view the privacy, and add a photo to the project which can be seen in its public view or replace an existing one. At the bottom, there is a [link to learn more about sharing](#share), and an `activity` button, which opens a new side menu to show the updates history of the project.
+
+
+
+Project activity log
+
+
+### Edit Button
+
+For the `Description`, `Keywords`, and `License` fields, the `Edit` button will open the same side menu as with `View details`, while it has a different function for other fields.
+
+`Edit` the **Citation** will pop up a new window **Manage Citation**.
+
+
+
+Project Manage Citation window
+
+
+**Manage Citation** window enables adding/editing the citation by either importing from a DOI or manually filling the fields, where all the fields marked with a red asterisk are mandatory. If the user is satisfied with the article imported from the DOI, or when they finish filling in the fields, they need to press `ADD`, which then shows an overview of the entered information. If the user is satisfied with it, they press `SAVE`. Otherwise, they can `delete` the citation or `CLOSE` without saving. This window also enables deleting previously entered citations.
+
+`Edit` the **Author** will also pop up a window **Manage Author** where the user can use an article DOI to import its authors or enter the ORCID to fetch the corresponding author. By clicking `IMPORT`, a list of authors appears so that the user can select out of it with checkboxes. An alternative would be to enter the authors manually, where all the fields marked with a red asterisk are mandatory. If the user is satisfied with the article imported from the DOI, or when they finish filling in the fields, they need to press `ADD`, which then shows an overview of the entered information. If the user is satisfied with it, they press `SAVE`. Otherwise, they can `delete` the author data or `CLOSE` without saving. This window also enables deleting previously entered authors' details.
+
+
+
+Project Manage Author window
+
+
+### Manage Studies
+
+Files and folders stored under the project can be managed (by adding more or deleting some out of them) with the button `Manage Studies`, which leads you back to the [upload](/submission-guides/submission/upload#files-upload---step-1) window, where you can add more files by dragging and dropping to the project folder, or delete existing ones by selecting them in the **left panel** and clicking `Delete` button. Once the editing is done, you can click `Proceed` to continue normally with the submission pipeline.
+
+:::caution Folder Structure
+Please pay attention to preserving your project folder structure when adding more studies. This means that the new study should be added to the same level as the rest of the existing ones. The recommended structuring is to group all the studies in one folder and then upload this folder. Thus, when adding a new study, it should be added to the same folder and not the root. In the following image, the study should be added to the **data** folder. Please find more in [Folder Structure documentation](/submission-guides/submission/folder-structure.md)
+:::
+
+
+
+
+
+## Validation
+
+To publish a project, i.e., to make it public, it must comply with community standards. At the moment we are checking for [DataCite](https://datacite.org/) mandatory metadata needed to receive a [DOI](https://www.doi.org/) in addition to requesting an image for the project. If any piece of metadata is missing, you will see a **Why can't I publish?** link message at the top of the project view.
+
+
+
+
+
+Clicking on **Why can't I publish?** leads to a new page similar to the [step-3 of the submission pipeline](/submission-guides/submission/upload#complete---step-3). Here you can find either red x or green ✓ to indicate the existence or absence of the metadata respectively. Whenever the red x exists, it is accompanied by an `Edit` button to facilitate providing the missing data. Missing metadata at the level of the study can be inferred from the red highlighting of its name. More on validating studies in the [study page](/submission-guides/data-model/study#validation)
+
+
+
+Validation Checklist of the Project
+
+
+## Share
+
+When generating a project, it is shared by default with its creator. When it is generated in a team, then it is shared with the team members. At the top of the project view, there are avatars of the users with whom the project is shared as circles with either their images or names' first letters. Clicking on those avatars enables modifying the sharing settings by first opening a window that shows with whom the project is already shared along with the roles.
+
+
+
+Project sharing status
+
+
+Then the user can click on the button `Share`, which will open another window to share the project with other users.
+
+
+
+ Share with users window
+
+
+In the opened window, the user needs to fill in the email and select the role of the user to share with, and they can optionally add a message. There are three roles for sharing:
+
+- **Owner**: read/update/delete the project/studies/datasets.
+- **Collaborator**: read/update the project/studies/datasets. A collaborator cannot delete any of the project content.
+- **Viewer**: read the project/studies/datasets. A viewer cannot update or delete any of the project content.
+
+When the user is satisfied with their entries, they can click `SEND` to send an email to the other user. Then the window gets refreshed to enable entering details of other users to share with them. When all the invitations are sent, the user can click the back arrow to go back to the project sharing-status window, which will be updated to show the status of the new invitations. Sharing can be canceled as long the invitation is still pending (not accepted or rejected by the receivers).
+
+
+
+Updated project sharing status
+
+
+After an invitation is accepted, the creator can still remove any of the members, while the owners can remove any of them but the creator.
+
+
+
+Project sharing status with the option to remove a collaborator
+
+
+## Project Up
+
+After projects are published, they can be found in the **Projects** folder in the left panel.
+
+
+
+Projects folder view
+
+
+**[nmrXiv](https://nmrxiv.org/)** users can use the up arrow, which can be found at the top right corner of each project, to give it an "up", increasing the number next to the arrow by one. If the user finds a project interesting, if they have used the provided data there, or if they are aware of similar confirming work, they can press the "up" arrow, and based on the number of users who decided to move a project upward, the project will move up in the view of public projects.
+
+:::caution
+Sorting projects by the number of ups is not provided yet, but it is coming soon.
+:::
+
+## Delete and Archive
+
+Only private projects can be deleted, while public ones can be archived. The reason is that once a project is public, it can be referenced somewhere else, which requires the repository to keep an active link to this project. Therefore, when the creators of a public project decide that it is no longer maintained, or that the data provided is not accurate, they can only archive it instead of deleting it, while deletion is always an option for private projects.
+
+To delete/archive a project, click on `Project Settings` at the top right of the project view. It will lead to a new window where you can click on `DELETE PROJECT`/ `ARCHIVE PROJECT`.
+
+
+
+Private project settings
+
+
+To avoid accidental deleting/ archiving, the user has to confirm their choice again and enter their password.
+
+
+
+Project delete confirmation
+
+
+:::caution
+In the case of deletion, this action is reversible for 30 days as the deleted project will be stored in the **Trash** folder, where the user can find the project and restore it from the `Project Settings`. After 30 days, deletion leads to permanently deleting the project and all of its content data. In the case of archiving, the user can unarchive the project anytime from the `Project Settings`. Archived projects are not moved to the trash.
+:::
diff --git a/docs/submission-guides/data-model/sharing.md b/docs/submission-guides/data-model/sharing.md
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+# Sharing Projects
+
+**[nmrXiv](https://nmrxiv.org/)** projects and associated studies can be shared with others through email or teams. Teams feature allows you to share projects with multiple people with out having to issue explicit access. If you would like to explicitly give access to a project or study you can use the sharing via email option.
+
+In both cases i.e sharing via email or teams, the access can further be controlled by assigning the right roles to the users.
+
+:::info Info
+There are three roles for sharing:
+
+- **Owner**: read/update/delete the project/studies/datasets.
+- **Collaborator**: read/update the project/studies/datasets. A collaborator cannot delete any of the project content.
+- **Viewer**: read the project/studies/datasets. A viewer cannot update or delete any of the project content.
+ :::
+
+## Sharing via Email
+
+Projects and studies can be shared explicitly with a user through email. To share a project or study click on the avatar(s) at the top left of the project or study page. This will open a share with users dialogue. This dialogue gives you an overview of the users and/or team with whom the project or study is already shared along with the associated roles.
+
+
+
+Project sharing status
+
+
+To share the project/study with a new user
+
+1. click on the share button.
+1. Enter the email id of the user.
+1. Select the right role you would like to issue the new user.
+1. Message to describe the user about the project (optional)
+
+Once you filled in the details click on the send button and the user will receive an invitation
+
+
+
+Share with users window
+
+
+
+
+## Teams Sharing
+
+Teams enable sharing bulks of projects with a group of people (with associated roles) while providing the flexibility to add or remove members or change their roles. For more details on how to create teams and add members, please check [Team page](/submission-guides/data-model/team.md).
diff --git a/docs/submission-guides/data-model/study.md b/docs/submission-guides/data-model/study.md
new file mode 100644
index 00000000..2c35a60b
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+++ b/docs/submission-guides/data-model/study.md
@@ -0,0 +1,167 @@
+# Study
+
+The concept of study in **[nmrXiv](https://nmrxiv.org/)** is similar to the one of [Study](https://isa-specs.readthedocs.io/en/latest/isamodel.html#study) in [ISA model](https://isa-tools.org/format/specification.html). Therefore, the study helps group related datasets and describe their collective metadata. Those datasets are related as they correspond to experiments applied to the same sample. Therefore, one study corresponds to one sample in **[nmrXiv](https://nmrxiv.org/)**. **[nmrXiv](https://nmrxiv.org/)** is capable of detecting datasets automatically and grouping them in studies, which requires the user to make sure that they submit their data in a compatible way. For more details, it is highly recommended to check the [folder structuring section](/submission-guides/submission/folder-structure.md) before submitting data.
+
+## Study View
+
+### Private Study View
+
+
+
+Private study view
+
+
+As with the project, the study's public view differs from the private one. Starting with the private one, at the top, there is the path to the study (Dashboard > CENAPTnmr), followed by a somehow similar view to the project. Below is the study **name** (Eugenol 400 MHz CDCl3 NMR data), which in contrast to the project, doesn't have to be unique within the project namespace. Next to the name is a star to indicate whether the study is starred and to enable starring/de-starring, which helps to bookmark studies. Starring a project doesn't propagate to the underlying studies. Starred studies can all be found in the `Starred` folder in the left panel. Below, one can see the avatars of the users with whom the study is shared as circles with either their images or names' first letters. Clicking on those avatars enables sharing control (more on that in [Share](#share)). One can also click on `View details` to view and edit the study details (more on that in [Edit](#edit)), and see the privacy of the study, when it was last updated, and the ownership by the user. Those three are not clickable but editable from `View details` and `Share`.
+
+
+
+The top of study view
+
+
+Moving down, there are three tabs: `About`, `Datasets`, and `Files`, with `About` being the one shown by default when entering a study, and the one similar to the project view. Its view differs in the private study from the public's one by having `edit` buttons next to the fields in the private one. Those fields include the study `Description` must be at least 20 characters describing its content and/or its purpose, while the `Keywords` are tags used to search for the study and increase its findability. Then comes the `License` with an `i`nformation sign. When hovering over the `i`, a brief description of the license appears. More about **[nmrXiv](https://nmrxiv.org/)** licenses can be found [here](/submission-guides/licenses.md)
+
+
+
+
+
+At the bottom is the **Sample chemical composition**, which also differs between private and public studies. This section is similar to the [**Sample Info**](/submission-guides/submission/upload#assignement--meta-data---step-2) tab during the [submission upload](/submission-guides/submission/upload.md). More on how to edit this section in [Sample chemical composition section](#sample-chemical-composition). More on how to use the structure editor in [Structure Editor Page](/submission-guides/submission/editor.md).
+
+:::caution
+The purpose of the **Sample chemical composition** section is to enable the user to add the molecules they are aware of their existence in the sample **before the NMR spectroscopy** along with their percentages. Molecules identified through the NMR analysis are located at the dataset level.
+:::
+
+The `Datasets` tab has a dropdown menu with all the datasets within the study. This tab will be covered in [Dataset page](/submission-guides/data-model/dataset.md).
+
+
+
+Study Datasets tab
+
+
+The `Files` tab view is similar in both private and public studies where the user can select folders on the left side to show an overview of their content on the right side. They can also navigate the folders with arrows. Within the folder, they can select files to show their metadata on the right side. For both selected folders and files there is a `Download` button.
+
+
+
+Study Files tab
+
+
+### Public Study View
+
+
+
+Public study view
+
+
+The public study view is similar to the [private's](#private-project-view), but still, there are some differences. Once a project is public, a green bar appears at the top informing the user that no more edits are possible, and any needed changes can be made as a new version.
+Moving down, a blue bar contains the citation details which can be adjusted according to the citation system (can be picked from the drop-down menu on the right). The citation includes a DOI to the study, which contains the study identifier (S46 in the image). This identifier always has the structure of "S", which stands for the study, and a number. Studies identifiers are [**Persistent Identifiers (PID)**](https://en.wikipedia.org/wiki/Persistent_identifier) within the repository. Additionally, all the `Edit` buttons disappear in public study as no more editing is allowed after publishing.
+
+With public studies, the option of adding more structures disappears, removing the entire right side of the section, including the structure editor with the [SMILES](https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html) field and the percentage bar. On the left side, one can see all the added molecules with their percentage and [INChI](https://iupac.org/who-we-are/divisions/division-details/inchi/) in the molecules list.
+
+## Create
+
+There are two ways to create studies. First is through the [submission pipeline](/submission-guides/submission/upload.md) where the studies will be created within the submitted project. Second is after submission from within the project view using [`Manage Studies` button](/submission-guides/data-model/project#manage-studies), which leads back to the [submission pipeline](/submission-guides/submission/upload.md).
+
+## Access
+
+You can access your created studies by [entering their parent projects](/submission-guides/data-model/project/#access) and scrolling down to **Studies**. You can also find the ones shared with you by others in the `Shared with me` folder directly if the parent project is not shared with you. Studies that you have starred can be found in the `Starred` folder. Other folders, such as `Recent` and `Trash`, can include projects only. Lists of studies show a quick view of them, including their **name**, **privacy**, and **last updating date**.
+
+
+
+Studies within a project
+
+
+## Edit
+
+To edit a study, you should have **editing** access to it, which is the case when you are its creator or when it is shared with you as an owner or a collaborator. The study should also still be private.
+
+You can edit the study from `View details` at the top of the study view or from any `Edit` buttons found next to the fields, while you can edit the sample in the **Sample chemical composition** section at the bottom.
+
+### View Details
+
+Clicking on `View details` opens a side menu where the user can edit the study name, description, keywords, color, and license, and they can view the privacy.
+
+
+
+View details side menu
+
+
+At the bottom, there is a link to the [Share](#share) section and an `activity` button, which opens a new side menu to show the updates history of the study.
+
+
+
+Study activity log
+
+
+### Edit Button
+
+For all the fields `Description`, `Keywords`, and the `License`, the `Edit` button will open the same side menu as with `View details`.
+
+### Sample chemical composition
+
+In the private mode, you can load structures by adding **SMILES** to the corresponding field and pressing `Load Structure`. It will view the structure in the [structure editor](/submission-guides/submission/editor.md), where you can apply any needed changes. Alternatively, you can draw the structure in the editor from scratch. Here are more [details on how to use the structure editor](/submission-guides/submission/editor.md). When you feel satisfied with the structure, set its percentage using the bar and press `ADD`. The molecule with its percentage and INChI will appear in the molecules list on the left side. Added structures can be `Edit`ed and `Delete`d using the corresponding buttons.
+
+:::caution
+The purpose of the **Sample chemical composition** section is to enable the user to add the molecules they are aware of their existence in the sample **before the NMR spectroscopy** along with their percentages. Molecules identified through the NMR analysis are located at the dataset level.
+:::
+
+:::caution
+If you don't know the percentage of a molecule in your sample, you have to set it to **zero**.
+:::
+
+
+
+Sample chemical composition section of a private study
+
+
+## Validation
+
+To publish a study, i.e., to make it public, you need to publish its parent project, which must comply with community standards. At the moment, we are checking for [DataCite](https://datacite.org/) mandatory metadata needed to receive a [DOI](https://www.doi.org/) in addition to requesting an image for the project. If any piece of metadata is missing, you will see a **Why can't I publish?** link message at the top of the project view.
+
+
+
+
+
+Clicking on **Why can't I publish?** leads to a new page similar to the [step-3 of the submission pipeline](/submission-guides/submission/upload#complete---step-3). Here you can find either red x or green ✓ to indicate the existence or absence of the metadata respectively. Whenever the red x exists, it is accompanied by an `Edit` button to facilitate providing the missing data. If the datasets validation fails, the study validation fails too as a parent, which can be inferred from the red highlighting of its name. More on validating datasets in the [dataset page](/submission-guides/data-model/dataset#validation)
+
+
+
+Validation Checklist of the Study
+
+
+## Share
+
+Studies are shared by default with the members of the parent project. At the top of the study view, there are avatars of the users with whom the study is shared as circles with either their images or names' first letters. Clicking on those avatars enables modifying the sharing settings by first opening a window that shows with whom the study is already shared along with the roles.
+
+
+
+Study sharing status
+
+
+Then the user can click on the button `Share`, which will open another window to share the study with other users.
+
+
+
+Share with users window
+
+
+In the opened window, the user needs to fill in the email and select the role of the user to share with, and they can optionally add a message. There are three roles for sharing:
+
+- **Owner**: read/update/delete the study/datasets.
+- **Collaborator**: read/update the study/datasets. A collaborator cannot delete any of the study content.
+- **Viewer**: read the study/datasets. A viewer cannot update or delete any of the study content.
+
+When the user is satisfied with their entries, they can click `SEND` to send an email to the other user. Then the window gets refreshed to enable entering details of other users to share with them. When all the invitations are sent, the user can click the back arrow to go back to the project-sharing status window, which will be updated to show the status of the new invitations. Sharing can be canceled as long the invitation is still pending (not accepted or rejected by the receivers).
+
+
+
+Updated project sharing status
+
+
+After an invitation is accepted, the creator can still remove any of the members, while the owners can remove any of them but the creator.
+
+## Delete and Archive
+
+Only private studies can be deleted, while public ones can be archived. The reason is that once a study is public, it can be referenced somewhere else, which requires the repository to keep an active link to this study. Therefore, when the creators of a public study decide that it is no longer maintained, or that the data provided is not accurate, they can only archive it instead of deleting it, while deletion is always an option for private studies.
+
+[Deleting/Archiving](/submission-guides/data-model/project#delete-and-archive) will delete/archive all the underlying studies. In the case of project deletion, this action is reversible for 30 days as the deleted project will be stored in the **Trash** folder, where the user can find the project and restore it from the `Project Settings`. After 30 days, deletion leads to permanently deleting the project and all of its content data. In the case of archiving, the user can unarchive the project anytime from the `Project Settings`. Archived projects are not moved to the trash.
+
+However, there is another way to delete studies, which is from the [`Manage Studies` button](/submission-guides/data-model/project#manage-studies) in the [project view](/submission-guides/data-model/project#project-view).
diff --git a/docs/submission-guides/data-model/team.md b/docs/submission-guides/data-model/team.md
new file mode 100644
index 00000000..d29db824
--- /dev/null
+++ b/docs/submission-guides/data-model/team.md
@@ -0,0 +1,120 @@
+# Team
+
+**Teams** facilitate collaboration with others on projects by simplifying sharing options. Any user in **[nmrXiv](https://nmrxiv.org/)** can create or join teams.
+
+## Team View
+
+Teams have their own **Dashboards** that look like the main user **Dashboard**, but still, there are a few differences.
+
+
+
+Shared team view
+
+
+Starting from the top left, one can see the team **name** (DOCS), which appears instead of (YOUR DASHBOARD) that is shown in the main user's dashboard, along with avatars of the users who are members of the team as circles with either their images or names' first letters. Going to the left, there are the `TEAM SETTINGS`, which will be explored more in [Edit section](#edit). Moving down, you can see a list of all the teams' projects with a quick view of the project's **name**, **privacy**, and dates of **creating and updating**. You can also see if the project is **starred**.
+
+:::info
+There is a difference between the team creator's dashboard view and the members', as members will have a greenly-highlighted text mentioning by whom the projects were shared, which is always the team creator, **regardless of who created the project**.
+:::
+
+## Create
+
+You can create as many teams as you need by clicking on the user's name at the top right corner to open a menu and click `Create New Team`.
+
+
+
+Creating a new team from user's menu
+
+
+It will lead to a new page that confirms your team ownership and requests a name for it. Then you click `CREATE`, and it is done. Then you get forwarded to the team dashboard. However, you still need to [Edit](#edit) the team to add members.
+
+
+
+Create new team page
+
+
+## Edit - Team Settings
+
+Once created, you can control the **Team** through **Team Settings**, which can be found at the top right of the page. The **Team** creator is the only one who can change the team settings., although the rest of the members can view the settings.
+
+### Team Name
+
+This section includes details on **The Team's Name and Owner Information**.
+The **Team** creator is the only person who can change the **Team**'s name in the field **Team Name**, and then they press `SAVE`. The email of the **Team** creator is also shown here, but it can't be modified.
+
+
+
+ Team Name section in the Team Settings
+
+
+### Add Team Member
+
+If you are the creator of the **Team**, you can invite people to join the **Team** and grant them specific roles. You have to enter the invitee's email and pick their role from the provided list, and press `ADD`. The possible roles are:
+
+1. **Owner**: Provides full control of the projects. They can read and/or update, including deleting, the project, study, and dataset.
+1. **Collaborator**: They can read and/or update the project, study, and dataset.
+1. **Reviewer**: They can only read the project, study, and dataset.
+
+:::info
+Please note that one **Team** can have many owners with the same permissions to control **Projects** and **Studies**. However, only the **Team** creator has the right to change the settings of the **Team**.
+
+**Team** creator is a **Team** owner by default.
+:::
+
+
+
+Add Team Member section in the Team Settings
+
+
+### Pending Team Invitations
+
+This section appears only when there are pending invitations and only to the **Team** creator. It enables them to `Cancel` invitations before they are accepted.
+
+
+
+Pending Team Invitations section in the Team Settings
+
+
+The invitee will receive the invitation via email. The invitation has two buttons, one to `Accept Invitation` and another to `Create Account` if the invitee doesn't have one already. In this second case, the invitee can go back to the invitation to accept it after creating the account.
+
+
+
+Invitation email to join team on nmrXiv
+
+
+### Team Members
+
+This section shows a list of all the **Team** members (except the creator). Each member is present with the following details:
+
+- Member's name: As provided to **[nmrXiv](https://nmrxiv.org/)**.
+- Member's role: The **Team** creator can manage the members' roles here by clicking on the shown role and picking another one, and then either `SAVE` the changes or `CANCEL` them.
+- Remove: So that the **Team** creator can `Remove` members from the **Team**.
+
+
+
+Team Members section in the Team Settings
+
+
+This section appears to the rest of the team members too, but with a different view. All the entries are not editable, and the `Remove` option is replaced by `Leave`.
+
+
+
+Team Settings view for teams members
+
+
+## Delete and Archive
+
+This option permanently deletes the **Team** with all its data and private resources. We recommend downloading the data before deleting it. However, if the team has some public resources, they get archived instead of deleted.
+
+
+
+Delete Team section in the Team Settings
+
+
+## More on Ownerships
+
+Ownership can get complicated within a team. Here are some cases you might want to be aware of:
+
+- Team **creator** is also assigned a **creator** ownership of all the team resources, regardless of who actually uploaded the data.
+- Members who submit projects are **owners** of those projects.
+- If a member is **collaborator** or a **reviewer** in a team and they submit a project there, they become an **owner** of the project, even if they have a lower role in the team.
diff --git a/docs/submission-guides/licenses.md b/docs/submission-guides/licenses.md
new file mode 100644
index 00000000..48332225
--- /dev/null
+++ b/docs/submission-guides/licenses.md
@@ -0,0 +1,64 @@
+# License
+
+Users have the option to provide a license for their privately submitted data. However, the license is mandatory for making the data public. In [step-3 of the submission](/submission-guides/submission/upload#complete---step-3), the user can see that the license field in the project is marked with red as it is required for publishing. By clicking `Edit`, they can provide one. Alternatively, after submission, the user can provide a license to the project from [View details](/submission-guides/data-model/project#view-details) or [Edit button](/submission-guides/data-model/project#edit-button) found next to the license field.
+
+Licensing propagates from parent objects to their children, meaning that licensing a project will reflect in its studies and datasets. However, the user can selectively give the studies different licenses, which propagate again to the datasets. At the dataset level, the user cannot provide licenses, which means that the dataset will always inherit its parent study license. Licensing a study can be done from the [View details](/submission-guides/data-model/study#view-details) or [Edit button](/submission-guides/data-model/study#edit-button) found next to the license field in the `About` tab of the [study view](/submission-guides/data-model/study#study-view). The user can edit the licenses as long as the project is private.
+
+
+
+License editing
+
+
+## Licenses in nmrXiv
+
+Data producers might have different wishes on how their shared data can be used in the sense of modifications, resharing, citing, etc. Thus, **[nmrXiv](https://nmrxiv.org/)** aims at using as many relevant licenses as possible, and providing the user with the required knowledge to pick the right license. Here we provide a list of all licenses available in **[nmrXiv](https://nmrxiv.org/)**. Please reach out to us if you believe any relevant license is missing.
+
+:::caution Our recommendations
+As we promote open data, we encourage you to use [Attribution 4.0 International (CC BY 4.0)](https://creativecommons.org/licenses/by/4.0/), which allows the users to modify and share your material while crediting you for it.
+:::
+
+### [Creative Commons](https://creativecommons.org/about/cclicenses/)
+
+[Creative Commons licenses](https://creativecommons.org/about/cclicenses/) give everyone from individual creators to large institutions a standardized way to grant the public permission to use their creative work under copyright law. There are different license types, listed from most to least permissive here:
+
+- [CC0](https://creativecommons.org/publicdomain/zero/1.0/)
+ CC0 (aka CC Zero) is a public dedication tool, which allows creators to give up their copyright and put their works into the worldwide public domain. CC0 allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, with no conditions.
+
+- [CC BY](https://creativecommons.org/licenses/by/4.0/)
+ This license allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
+
+ In **[nmrXiv](https://nmrxiv.org/)**, version 4 ([Attribution 4.0 International (CC BY 4.0)](https://creativecommons.org/licenses/by/4.0/)) can be used.
+
+- [CC BY-SA](https://creativecommons.org/licenses/by-sa/4.0/)
+ This license allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use. If you remix, adapt, or build upon the material, you must license the modified material under identical terms.
+
+ In **[nmrXiv](https://nmrxiv.org/)**, version 4 ([Attribution-ShareAlike 4.0 International (CC BY-SA 4.0)](https://creativecommons.org/licenses/by-sa/4.0/)) can be used.
+
+- [CC BY-NC](https://creativecommons.org/licenses/by-nc/4.0/)
+ This license allows reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator.
+
+ In **[nmrXiv](https://nmrxiv.org/)**, version 4 ([Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)](https://creativecommons.org/licenses/by-nc/4.0/)) can be used.
+
+- [CC BY-NC-SA](https://creativecommons.org/licenses/by-nc-sa/4.0/)
+ This license allows reusers to distribute, remix, adapt, and build upon the material in any medium or format for noncommercial purposes only, and only so long as attribution is given to the creator. If you remix, adapt, or build upon the material, you must license the modified material under identical terms.
+
+ In **[nmrXiv](https://nmrxiv.org/)**, [Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)](https://creativecommons.org/licenses/by-nc-sa/4.0/)
+
+- [CC BY-ND](https://creativecommons.org/licenses/by-nd/4.0/)
+ This license allows reusers to copy and distribute the material in any medium or format in unadapted form only, and only so long as attribution is given to the creator. The license allows for commercial use.
+
+ In **[nmrXiv](https://nmrxiv.org/)**, version 4 ([Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)](https://creativecommons.org/licenses/by-nd/4.0/))
+
+- [CC BY-NC-ND](https://creativecommons.org/licenses/by-nc-nd/4.0/)
+ This license allows reusers to copy and distribute the material in any medium or format in unadapted form only, for noncommercial purposes only, and only so long as attribution is given to the creator.
+
+ In **[nmrXiv](https://nmrxiv.org/)**, version 4 ([Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)](https://creativecommons.org/licenses/by-nc-nd/4.0/))
+
+### [Open Data Commons](https://opendatacommons.org/)
+
+- [Open Data Commons Public Domain Dedication and License (PDDL) v1.0](https://opendatacommons.org/licenses/pddl/1-0/) is a document intended to allow you to freely share, modify, and use this work for any purpose and without any restrictions. This license is intended for use on databases or their contents (“data”), either together or individually.
+
+### [Community Data License Agreement](https://cdla.dev/)
+
+- [Community Data License Agreement – Permissive – Version 1.0](https://cdla.dev/permissive-1-0/)
+- [Community Data License Agreement – Sharing – Version 1.0](https://cdla.dev/sharing-1-0/)
diff --git a/docs/submission-guides/registration.md b/docs/submission-guides/registration.md
new file mode 100644
index 00000000..79e32de0
--- /dev/null
+++ b/docs/submission-guides/registration.md
@@ -0,0 +1,27 @@
+# Registration in nmrXiv
+
+Before submitting data to nmrXiv, users need to have nmrXiv accounts. Although they can log in using their GitHub or Twitter accounts, this logging will result in registering them on nmrXiv.
+
+To create a new nmrXiv account:
+
+- Head to [nmrXiv website](https://nmrxiv.org/)
+- Click on register on the top right side.
+- Fill in the fields in the registration form.
+
+
+
+
+
+- You need to agree to the [Terms of Service](https://nmrxiv.org/terms-of-service), and [Privacy Policy](https://nmrxiv.org/privacy-policy) to register.
+- If you agree to the [Terms of Service](https://nmrxiv.org/terms-of-service), and [Privacy Policy](https://nmrxiv.org/privacy-policy), please press `REGISTER`.
+- A new window will open asking for email verification.
+
+
+
+
+- Check your email for verification. If you haven't received an email, click on `RESEND VERIFICATION EMAIL`.
+- In the received email, click on `Verify Email Address` and confirm the link.
+
+
+
+- Welcome to nmrXiv.
diff --git a/docs/submission-guides/spectra.md b/docs/submission-guides/spectra.md
new file mode 100644
index 00000000..515d82f7
--- /dev/null
+++ b/docs/submission-guides/spectra.md
@@ -0,0 +1,5 @@
+# Spectra Viewing and Processing
+
+**[nmrXiv](https://nmrxiv.org/)** uses [NMRium](https://www.nmrium.org/) as its spectra viewer and editor. [NMRium](https://www.nmrium.org/) shows up in two places within **[nmrXiv](https://nmrxiv.org/)**: in [Step 2 of the Submission Pipeline](/submission-guides/submission/upload#assignement--meta-data---step-2) and in the [Datasets tab of the studies](/submission-guides/data-model/dataset) after submission.
+
+We recommend checking [NMRium Documentation](https://docs.nmrium.org/) when using **[nmrXiv](https://nmrxiv.org/)**, which includes a Quick Start Guide ([English](https://docs.nmrium.org/) and [German](https://docs.nmrium.org/quickstart/quickstart_de/quickstart_de)), along with details on [General Tools](https://docs.nmrium.org/general/basic/basic_toolbar), processing [1D](https://docs.nmrium.org/20_1d-spectra/loading_a_spectrum/loading_a_spectrum) and [2D](https://docs.nmrium.org/30_2d-spectra/select/select/) spectra, reaching to the [Molecular Assignments](https://docs.nmrium.org/structure_assignment/assign/add).
diff --git a/docs/submission-guides/submission/editor.md b/docs/submission-guides/submission/editor.md
new file mode 100644
index 00000000..ebe79c90
--- /dev/null
+++ b/docs/submission-guides/submission/editor.md
@@ -0,0 +1,120 @@
+______________________________________________________________________
+
+## sidebar_position: 3 title: Structure Editor
+
+# Structure Editor
+
+**[nmrXiv](https://nmrxiv.org)** uses [OpenChemLib](https://github.com/Actelion/openchemlib) as its structure editor, which is presented to the user during the [submission](/submission-guides/submission/upload.md) and, after submission, on the [study](/submission-guides/data-model/study#edit) level, and on the [dataset](/submission-guides/data-model/dataset#edit) level within NMRium as, in the Chemical structures section, the user can press **+** to open the editor. The editor allows drawing up structures from scratch, and it also accepts structures loaded from [SMILES](https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html). Above the editor, there is a link to this documentation that you can always access by clicking `Need help?`.
+
+Here we provide an overview of the tools available in the editor:
+
+
+
+
Tool image
+
Usage
+
Tool image
+
Usage
+
+
+
+
Clean canvas: it deletes everything resulting in an empty canvas.
+
+
Undo: it undoes the last change made.
+
+
+
+
Tidy up canvas: it changes the coordinates of the molecules and the bonds to provide a better view of the structure in terms of bond lengths and angles.
+
+
Zoom and Rotate: by clicking anywhere in the space and scrolling up and down, it enables zooming out and in, while scrolling right and left, it rotates clock-wise and counter-clock.
+
+
+
+
Lasso select: it enables the lasso selection of atoms and bonds to apply bulk actions, such as with the eraser.
+
+
Mapping: This tool is only for reactions and not applicable in nmrXiv
+
+
+
+
Stereo configuration unknown: it enables adding question marks on chiral centers with unknown stereo configuration.
+
+
Enantiomere: this tool extends to three tools: **Abs**, which indicates that the provided enantiomer is the one intended. **Or** indicates that the intended structure is either this one or the other enantiomer. **And** indicates that the intended structure is both this enantiomer and the other one, with equal quantities, which means having a racemic mixture.
+
+
+
+
Eraser: it deletes atoms and bonds. When applied to atoms, it deletes the adjacent bonds, while when applied to bonds, it only deletes the adjacent atoms having no more bonds. Bulk erasing can be done by selecting a set of atoms and bonds. Please note that erasing a double bond will result in the full deletion and not in reducing the bond to a single one.
+
+
Text: not applicable in nmrXiv.
+
+
+
+
When applied in empty space, it draws a bond between two carbon atoms, while when applied on an atom, it draws a bond between that atom and a carbon atom. Additionally, it can link two already existing atoms. It can also increase the bond order (e.g., single bond to double bond).
+
+
Chain: it enables drawing saturated aliphatic chains.
+
+
+
+
Wedge bond: it indicates that the chiral bond is above the ring. It can be used similarly to the bond tool, or to change the bond type.
+
+
Hatched bond: it indicates that the chiral bond is below the ring. It can be used similarly to the bond tool, or to change the bond type.
+
+
+
+
Triangle: it enables drawing a triangle of carbons.
+
+
Square: it enables drawing a square of carbons.
+
+
+
+
Pentagon: it enables drawing a pentagon of carbons.
+
+
Hexagon: it enables drawing a hexagon of carbons.
+
+
+
+
Heptagon: it enables drawing a heptagon of carbons.
+
+
Benzene: it enables drawing a Benzene molecules.
+
+
+
+
Charge plus: it increases the positive charge of atoms.
+
+
Charge minus: it decreases the positive charge of atoms (increases the negative one).
+
+
+
+
Carbon atom: it creates a carbon atom, along with hydrogen atoms bonded to it, to reach the carbon's four bonds. So if clicked in space, it creates a Methane molecule. It can also replace an existing atom with a carbon one.
+
+
Silicon atom: it creates a silicon atom, along with hydrogen atoms bonded to it to reach the silicon's four bonds. So if clicked in space, it creates a Silane molecule. It can also replace an existing atom with a silicon one.
+
+
+
+
Nitrogen atom: it creates a nitrogen atom, along with hydrogen atoms bonded to it to reach the nitrogen's three bonds. So if clicked in space, it creates an Ammonia molecule. It can also replace an existing atom with a nitrogen one.
+
+
Phosphorus atom: it creates a phosphorus atom, along with hydrogen atoms bonded to it to reach the phosphorus' three bonds. So if clicked in space, it creates a Phosphine molecule. It can also replace an existing atom with a phosphorus one.
+
+
+
+
Oxygen atom: it creates an oxygen atom, along with hydrogen atoms bonded to it to reach the oxygen's two bonds. So if clicked in space, it creates a water molecule. It can also replace an existing atom with an oxygen one.
+
+
Sulfur atom: it creates a sulfur atom along with hydrogen atoms bonded to it to reach the sulfur's two bonds. So if clicked in space, it creates a Hydrogen sulfide molecule. It can also replace an existing atom with a sulfur one.
+
+
+
+
Fluorine atom: it creates a fluorine atom, along with a hydrogen atom bonded to it, to reach the fluorine's one bond. So if clicked in space, it creates a hydrogen fluoride molecule. It can also replace an existing atom with a fluorine one.
+
+
Chlorine atom: it creates a chlorine atom, along with a hydrogen atom bonded to it, to reach the chlorine's one bond. So if clicked in space, it creates a hydrogen chloride molecule. It can also replace an existing atom with a chlorine one.
+
+
+
+
Bromine atom: it creates a bromine atom, along with a hydrogen atom bonded to it to reach the bromine's one bond. So if clicked in space, it creates a hydrogen bromide molecule. It can also replace an existing atom with a bromine one.
+
+
Iodine atom: it creates an iodine atom, along with a hydrogen atom bonded to it, to reach the iodine one bond. So if clicked in space, it creates a hydrogen iodide molecule. It can also replace an existing atom with an iodine one.
+
+
+
+
Hydrogen atom: it creates a hydrogen atom, along with a hydrogen atom bonded to it, to reach the hydrogen's one bond. So if clicked in space, it creates a hydrogen molecule. It can also replace an existing atom with a hydrogen one.
+
+
Atom properties: when applied to an atom, it displays its properties, including the label, mass, valence, and radical state, where the user can edit all of these values. It is mostly useful for isotope and radicals
+
+
diff --git a/docs/submission-guides/submission/folder-structure.md b/docs/submission-guides/submission/folder-structure.md
new file mode 100644
index 00000000..6fa0bf85
--- /dev/null
+++ b/docs/submission-guides/submission/folder-structure.md
@@ -0,0 +1,59 @@
+# Folder Structure Before Submission
+
+Folders structuring means how data should ideally be structured in folders before submission. Even that **[nmrXiv](https://nmrxiv.org/)** has the capability to detect all the formats supported by NMRium in the submitted data, which enables it to structure the data into datasets/studies/projects, there is still no way to guarantee that the automatically generated structure is what the user was hoping to get. Therefore, it is recommended to have a look at this section before submitting data.
+
+## nmrXiv Automated Structuring
+
+**[nmrXiv](https://nmrxiv.org/)** can detect the formats supported by [NMRium](https://www.nmrium.org/). In some cases, as with Bruker files, spectrum gets generated using a folder of files. Whatever generates spectra (one .jdx file, one .jdf file, or one entire Bruker folder) is considered a dataset. The direct parent folder to the dataset (or multiple datasets) is the study. It can be noticed during the submission pipeline as a folder marked with a blue dot.
+
+
+
+In the above image, Bruker folder (named Bruker dataset) was detected by **[nmrXiv](https://nmrxiv.org/)**, hence the blue dot on the parent folder Bruker study. The group of JCAMP files were detected too, and the parent folder received a blue dot.
+
+## Sources of Misleading Structuring
+
+Considering that **[nmrXiv](https://nmrxiv.org/)** has specific definitions of what projects, studies, and datasets are, wrong structuring will lead to the wrong interpretation of the data (especially when read by machines). Study in **[nmrXiv](https://nmrxiv.org/)** is not only the folder containing datasets, but it is basically the folder containing all the datasets **of one sample**. Therefore, separating two datasets belonging to one sample into two different folders will lead to having two studies instead of the intended one study. To make this clearer, please check the following image:
+
+
+
+In this case, the user has a 13 Carbon dataset that belongs with the other JCAMP files in the **JCAMP study** folder. As the user had separated this file (which corresponds to one dataset), **[nmrXiv](https://nmrxiv.org/)** recognized its parent folder as a new study (note the blue dot), resulting in two studies for one sample instead of one.
+
+## Ideal Folders Structuring
+
+What is considered a dataset in **[nmrXiv](https://nmrxiv.org/)** depends on the format used. Here you can find the ideal structuring you need to apply.
+
+### Identify your datasets
+
+- Bruker: The dataset is the entire Bruker **folder**. Many NMR experiments (1H, 13C, etc.) will lead to many Bruker **folders**, with each being a dataset.
+
+- JCAMP-DX: The dataset is one jcamp-dx **file**. Many NMR experiments (1H, 13C, etc.) will lead to many jcamp-dx **files**, with each being a dataset.
+
+- JEOL: The dataset is one jeol **file**. Many NMR experiments (1H, 13C, etc.) will lead to many jeol **files**, with each being a dataset.
+
+
+
+
+
+
+
+### Group Datasets per Studies
+
+All experiments (datasets) belonging to one sample should go to one folder. It means one study can contain several Bruker folders. Alternatively, one study can contain several JCAMP files and so. In the below image, you can see two studies (Bruker study and JCMAP study). Bruker study has two datasets, while the JCAMP study has five datasets (the mol file isn't a dataset).
+
+
+
+
+
+
+
+#### Mixing Formats in One Study
+
+The sample rules apply when the user needs, for example, to add an exported JCAMP file to their Bruker data. The JCAMP file should added to the level of study it represents as it is one dataset. Same goes for other formats such as **.nmrium**, or **.nmredata**. It means in one study folder you can find JCAMP files and NMReData files at the same level next to Bruker folders (as long all of them belong to the same sample).
+
+### Group Studies per Project
+
+All the data submitted to **[nmrXiv](https://nmrxiv.org/)** in one process is grouped as a project. Therefore, make sure that you group related studies together in one folder. How those studies are related is up to the user. They can be a collection of studies used for teaching, or a collection used in a thesis. They can also be a part of one investigation (several samples from one source).
+
+## Final Step
+
+Make sure to give your folders and datasets proper names. in **[nmrXiv](https://nmrxiv.org/)** you can rename projects and studies, but you can't rename the folders they came from or the datasets. After this step you are ready for [Data Submission](/submission-guides/submission/upload.md)
diff --git a/docs/submission-guides/submission/upload.md b/docs/submission-guides/submission/upload.md
new file mode 100644
index 00000000..a6254373
--- /dev/null
+++ b/docs/submission-guides/submission/upload.md
@@ -0,0 +1,118 @@
+# Data Submission
+
+## Before You start
+
+Before you start submitting your data, you need to:
+
+- First, [register](/submission-guides/registration.md) to create an account in **[nmrXiv](https://www.nmrxiv.org)**, or login to **[nmrXiv](https://www.nmrxiv.org)** via single sign-on with your GitHub or Twitter ID. Please be aware that the single sign-on will result in registering you on **[nmrXiv](https://www.nmrxiv.org)**.
+- Make sure to structure your folder in the way described [here](/submission-guides/submission/folder-structure).
+- Make sure to include at least one [file format supported by NMRium](https://docs.nmrium.org/#2-open-spectra) in your folder to generate spectra.
+
+### What You Need to Know
+
+- Keep in mind that your submission will be structured as a **Project**.
+- If you submit more than one folder at once, they will still be one **Project**, and the underlying folders with datasets will be studies.
+
+## The Submission Pipeline
+
+### Files Upload - Step 1
+
+- Click on the `UPLOAD` button in your Dashboard or the [team Dahsboard](/submission-guides/data-model/team.md) to start the submission pipeline.
+
+
+
+
+- The window **Files Upload** will open.
+
+
+
+- Provide details about your **Project**. Every field marked with a red asterisk is **mandatory**.
+ - **Project Name** must be unique within the workspace (personal workspace or team).
+ - **Project Description** must be at least 20 characters.
+ - **Keywords** can be added singly by typing the keyword and pressing "enter", or in bulk by typing a list of keywords separated by commas and pressing enter. Keywords increase the visibility of the **Project**.
+- Drag and drop your folder to the dedicated field.
+- The loading bar will get green as the upload progresses.
+- Wait until the upload has ended.
+- Your folders are now added to the root folder "\".
+- Clicking on any folder on the left side will show an overview of its content on the right side. You can also navigate the folders with the arrows.
+
+
+
+- At this step, you can delete any unwanted folders or files by selecting them from the panel on the left side and pressing the `Delete` button on the right side.
+
+
+
+### Assignement & Meta data - Step 2
+
+Within this step, you can use [NMRium](https://www.nmrium.org/) to edit your spectra and assign peaks to the corresponding chemical groups. Additionally, you can provide the metadata of the studies and samples within the project.
+
+- **STUDY** can be seen as a title at the top left side of the panel with the total number of studies within the project. In this panel, you can switch between studies and see the names of the underlying datasets. The dataset will have one of three colors:
+ - **Green**: When the dataset is successfully viewed.
+ - **Gray**: If there were no attempts to view the dataset yet, such as when you first open the study before you start viewing the datasets.
+ - **Red**: When the attempt to view the dataset fails.
+
+
+
+
+
+- **Experiments (Spectra)** is the first tab shown by default under the study name on the left side. Here you can navigate between different datasets (experiments) from the dropdown **Select Experiment**, which enables you to visualize and edit the corresponding spectra in the NMRium window in the middle. For more details on how to use NMRium, please check its [documentation](https://docs.nmrium.org/).
+
+
+
+
+
+Directly above the NMRium window, you can see a gray message on the left that informs the user about the current status of the spectra (being uploaded, saved, etc.). On the right side, there exist three buttons. `Reset` will reset all the edits done on the spectra, getting it back to its original status when uploaded. Resetting is an edit that is saved along with other edits in the history. To view the history, click `Edit History`, which opens a side menu to show the editors, and the dates of edits.
+
+
+
+
+
+The last button `Preview` helps is to refresh the spectra when you face any issues viewing your edits.
+
+Below, there is [NMRium](https://www.nmrium.org/) window. Clicking on the `User manual` leads to [NMRium Documentation page](https://docs.nmrium.org/). You can control the panels and tools you have by default in [NMRium](https://www.nmrium.org/) from `General settings`. You can also click `Full screen` to enable that mode.
+
+
+
+
+
+Below the [NMRium](https://www.nmrium.org/) window there are two tables:
+
+- **Info** includes all the information extracted by [NMRium](https://www.nmrium.org/) about the NMR experiment.
+
+- **Meta** is the second table coming after **Info**. It includes the metadata from the instrument file.
+
+
+
+- **Sample Info** tab shows details about the chemical composition of the sample (available molecules and their percentages). You can load structures by adding **SMILES** to the corresponding field and pressing `Load Structure`. It will view the structure in the [structure editor](/submission-guides/submission/editor.md), where you can apply any needed changes. Alternatively, you can draw the structure in the [editor](/submission-guides/submission/editor.md) from scratch. When you feel satisfied with the structure, set its percentage using the bar and press `ADD`. The molecule with its percentage and INChI will appear in the molecules list on the left side. Added structures can be `Edit`ed and `Delete`d using the corresponding buttons. For more details about the structure editor, please [visit its documentation](/submission-guides/submission/editor.md).
+
+:::caution
+The purpose of the **Sample chemical composition** section is to enable the user to add the molecules they are aware of their existence in the sample **before the NMR spectroscopy** along with their percentages. Molecules identified through the NMR analysis are located at the dataset level.
+:::
+
+:::caution Please note
+If you don't know the percentage of a molecule in your sample, you have to set it to **zero**.
+:::
+
+
+
+
+
+- **Meta Data** tab shows an overview of the selected study's metadata. You can edit this metadata at this level or after submission as long your study is private. You can press on **Auto generate** to auto-generate the study description. Please don't forget to press `SAVE` before you proceed.
+
+After providing all the details in this tab, you can go back to step 1 with the button `BACK`, you can `CANCEL` the submission, or you can `PROCEED` to step 3.
+
+
+
+
+
+### Complete - Step 3
+
+In step 3, you can find how your project compares to [recommended community standards](https://nfdi4chem.github.io/workshops/). Whenever a piece of information is missing, you will have it marked in red with an `Edit` button for a quick update. You can press `FINISH` to end the submission process even while having red marks, but your project will remain private, and complying with the standards is a prerequisite for publishing. Here are more details about the validation of [projects](/submission-guides/data-model/project#validation), [studies](/submission-guides/data-model/study#validation), and [datasets](/submission-guides/data-model/dataset#validation)
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+It provides a bundle of handy features, such as:
+* Open various vendors and open file formats (JCAMP-DX file, a zipped Bruker folder, or a JEOL file).
+* It accepts 1D (FID and FT) and 2D spectra (FT only).
+* Advanced peak picking detection for 1D and 2D NMR spectra. Also, it can generate the NMR string required for publication or patent.
+* All the processing and assignment can be stored as a “.nmrium” file. This file contains the original data as well as all the processing that was applied on the spectrum. Assignments of the molecule are also saved in the file. Additionally, export in NMReData is possible as well.
+
+## Demo
+
+
+
+
+
+
+
+
+
diff --git a/docs/developer-guides/code-contribution-guidelines.md b/docs/developer-guides/code-contribution-guidelines.md
new file mode 100644
index 00000000..a813f64c
--- /dev/null
+++ b/docs/developer-guides/code-contribution-guidelines.md
@@ -0,0 +1,104 @@
+# Code Contribution Guidelines
+
+Thank you for investing your time in contributing to our project! Any contribution you make will be reflected on [nmrxiv.org](https://nmrxiv.org) after it has passed all the test cases on [dev.nmrxiv.org](https://dev.nmrxiv.org).
+In this guide you will get an overview of the contribution workflow from opening an issue, creating a PR, reviewing, and merging the PR.
+
+### Getting started
+
+Before you start contributing, make sure:
+
+- You have a GitHub account, for information on how to create an account, see [Signing up for GitHub.](https://docs.github.com/en/get-started/signing-up-for-github).
+- You have proper access to the [repo](https://github.com/NFDI4Chem/nmrxiv) for your GitHub account, for which you can contact repository owners.
+- You have a code editor installed in your local system, we recommend using [Visual Studio Code](https://code.visualstudio.com/).
+- You have cloned the code and have nmrXiv running locally, for which you can follow the steps provided [here](https://docs.nmrxiv.org/developer-guides/installation/development).
+
+#### Create a new issue
+
+If you spot a problem with the application, [search if an issue already exists](https://github.com/NFDI4Chem/nmrxiv/issues). If a related issue doesn't exist, you can open a [new issue](https://github.com/NFDI4Chem/nmrxiv/issues/new/choose) with the appropriate form.
+[Click here](/FAQs#how-to-report-a-bug) to learn more about how to create an issue or report a bug.
+
+#### Solve an issue
+
+Scan through our [existing issues](https://github.com/NFDI4Chem/nmrxiv/issues) to find one that interests you. You can narrow down the search using `labels` as filters.
+
+### Workflow
+
+#### Create a branch
+
+Never push your code directly to the `development` or `main` branch. Switch to the `development` branch and create a new branch in your repository. A short, descriptive branch name enables your collaborators to see ongoing work at a glance. The branch name should be all small with words separated by a hyphen, [click here](https://github.com/NFDI4Chem/nmrxiv/branches) to follow some examples.
+
+#### Make Changes
+
+On your branch, make the desired changes to the repository. Your branch is a safe place to make changes. If you make a mistake, you can revert your changes or push additional changes to fix the mistake. Your changes will not end up on the default branch until you merge your branch. Commit and push your changes to your branch. Once your changes are ready, don't forget to self-review to speed up the review process. Also, you have proper comments all over your code so that it's easy and clean to understand.
+
+#### Format
+
+For formatting, you can simply run below command which will help saving your time in code formatting and makes it simple to ensure that your code style stays clean, consistent and properly indented.
+
+```bash
+npm run format
+./vendor/bin/sail pint
+```
+
+#### Commit
+
+To facilitate auto CHANGELOG generation, creation of GitHub releases, and version bumps(as per [Semantic Versioning](https://semver.org/)), please follow the structure of [Conventional Commit](https://www.conventionalcommits.org/en/v1.0.0/) for your commit messages.
+Each commit should also be descriptive enough to help you and future contributors to understand what changes the commit contains.
+
+```bash
+
+
+#### Address review comments
+
+Reviewers can leave questions, comments, and suggestions. Reviewers can comment on the whole pull request or add comments to specific lines. You and reviewers can insert images or code suggestions to clarify comments.
+You can continue to commit and push changes in response to the reviews. Your pull request will update automatically.
+
+#### Merge your pull request
+
+Your pull request can be merged once it is approved by the reviewer. The primary merge should always be made to the `development` branch, from where your code will be deployed to the [dev environment](https://dev.nmrxiv.org) via our [CI/CD pipeline](https://docs.nmrxiv.org/developer-guides/ci-cd). The [dev environment](https://dev.nmrxiv.org) provides the room to test your feature or code changes. Once it has passed all the test cases, your code changes will now be included as part of a release and be deployed finally to the [production environment](https://nmrxiv.org). These actions are restrictive and should only be performed by our repo admins and owners.
+
+#### Delete your branch
+
+After your branch is merged and the pull request is closed please don't forget to delete your stale branch. This indicates that the work on the branch is complete and prevents you or others from accidentally using old branches. For more information, see [Deleting and restoring branches in a pull request](https://docs.github.com/en/repositories/configuring-branches-and-merges-in-your-repository/managing-branches-in-your-repository/deleting-and-restoring-branches-in-a-pull-request).
+
+
+:::info Info
+
+- Never leak your secrets or commit local config files(.env) into source control.
+- Follow the link to learn more about [Laravel](https://laravel.com/9.x/readme) and [Inertia.js](https://inertiajs.com/) best practices.
+ :::
diff --git a/docs/developer-guides/configurations/_category_.json b/docs/developer-guides/configurations/_category_.json
new file mode 100644
index 00000000..64ff4fc7
--- /dev/null
+++ b/docs/developer-guides/configurations/_category_.json
@@ -0,0 +1,7 @@
+{
+ "label": "Configurations",
+ "position": 2,
+ "link": {
+ "type": "generated-index"
+ }
+}
\ No newline at end of file
diff --git a/docs/developer-guides/configurations/oauth.md b/docs/developer-guides/configurations/oauth.md
new file mode 100644
index 00000000..01bcbc47
--- /dev/null
+++ b/docs/developer-guides/configurations/oauth.md
@@ -0,0 +1,36 @@
+______________________________________________________________________
+
+## sidebar_position: 2 id: oauth title: OAuth
+
+In addition to basic username/password authentication, nmrXiv also supports authentication via [OAuth 2.0](https://www.digitalocean.com/community/tutorials/an-introduction-to-oauth-2), which is an authorization framework that enables third party clients to obtain limited access to user accounts on an HTTP service.
+Currently nmrXiv supports login via below three clients:
+
+- [Twitter](https://twitter.com/)
+- [GitHub](https://github.com/)
+- [ORCID](https://orcid.org/)
+
+In order to get this feature available in your application, you need to register your application with the service. This is done through a registration form in the **developer** or **API** portion of the service's website, where you will provide following information (and probably details about your application):
+
+- Application Name
+- Application Website
+- Redirect URI or Callback URL
+
+Once your application is registered, the service will issue client credentials in the form of a *Client Id* and *Client Secret*. These details should be added to the .env file against the below values.
+
+```
+GITHUB_CLIENT_ID=
+GITHUB_CLIENT_SECRET=
+GITHUB_REDIRECT_URL=
+
+ORCID_CLIENT_ID=
+ORCID_CLIENT_SECRET=
+ORCID_REDIRECT_URL=
+
+TWITTER_CLIENT_ID=
+TWITTER_CLIENT_SECRET=
+TWITTER_REDIRECT_URL=
+```
+
+Once done restart or refresh your application and you would be able to find the single sign-on section added in the Login page.
+
+To know more about how nmrXiv works with OAuth visit the official site of [Laravel](https://laravel.com/8.x/socialite) for more details.
diff --git a/docs/developer-guides/configurations/storage.md b/docs/developer-guides/configurations/storage.md
new file mode 100644
index 00000000..17f1756b
--- /dev/null
+++ b/docs/developer-guides/configurations/storage.md
@@ -0,0 +1,34 @@
+______________________________________________________________________
+
+## sidebar_position: 3 id: storage title: Storage
+
+Files in [nmrxiv](https://nmrxiv.org) are stored as [objects](https://en.wikipedia.org/wiki/Object_storage) and are [S3](https://en.wikipedia.org/wiki/Amazon_S3) compatible which provides below three big benefits.
+
+- **Backup/redundancy** - S3 and similar have built-in backups and redundancy
+- **Scaling** - Savings files off-server becomes necessary in modern hosting, such as serverless or containerized environments, as well as in traditional load-balanced environments
+- **Disk usage** - You won't need as much disk space when storing files in the cloud
+- **Features** - S3 (and other clouds) have some great features, such as versioning support for files, lifecycle rules for deleting old files (or storing them in a cheaper way), deletion protection, and more
+
+#### Configuration
+
+There are just two place where the configuration needs to be done.
+
+- Within your Object Storage or Amazon S3 you need to.
+
+ - Create the bucket.
+ - Create a service account to get Key/Secret Key.
+
+- Within the [nmrxiv](https://nmrxiv.org) you just need to configure below values in the `.env` file.
+
+```
+FILESYSTEM_DRIVER=
+
+AWS_ACCESS_KEY_ID=xxxxxx
+AWS_SECRET_ACCESS_KEY=xxxxxxs
+AWS_DEFAULT_REGION=us-east-1
+AWS_BUCKET=nmrxiv
+AWS_BUCKET_PUBLIC=nmrxiv-public
+AWS_ENDPOINT=
+
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