Data schema

This repository contains a description of the data schema using for the cheminfo ELN. It is also the place where changes to the schema are discussed.

Table of contents

• reaction

  • reaction
  • products
  • reagents

• sample

  • general
  • identifier
  • image
  • misc
  • physical
  • safety
  • stock

  • video

  • spectra

    • chromatogram
    • cyclicVoltammetry
    • dynamicAdsorptionAnalysis
    • differentialCentrifugalSedimentation
    • differentialScanningCalorimetry
    • elementalAnalysis
    • hgPorosimetry
    • ir
    • isotherm
    • iv
    • mass
    • nmr
    • raman
    • thermogravimetricAnalysis
    • uv
    • xps
    • xrd
    • xrf
    • xray

  • biology

    • antibody
    • cellLine
    • nucleic
    • peptidic

Conventions

• Entries typically have the following format: name (type, unit): Description.
• For objects or array of objects the format is as follows

- arrayOfObjectExample (array<object>):
  - key1 (string): Description of key1
  - key2 (number, K): This is temperature

• For categorical variables, specify the allowed categories instead of the type, e.g. kind ("a,b,c"): compound class
• For many values, unit objects of the following form are used:

unitObject:
  - SI (number): value in SI units
  - unit (string): default unit that is shown to the user

• For instruments, the metadata is recorded in an object of the following form

instrumentObject:
    - model (string)
    - manufacturer (string)
    - software (string)
    - serialNumber (string)

• For spectra, there is also the source which can be specified with

source (object):
    - type (experiment|simulation|literature)
    - name (str): e.g., aiidalab.materialscloud.org
    - uuid (str): e.g., the UUID of the node of the object in AiiDAlab or the UUID of the data in some other database
    - doi (str)
    - url (str)

• In some cases, there might be derived properties. Those should be grouped under derivedProperties

• Any new markdown page must be added to the README.md file

Spectra

Spectra are typically converted into JCAMP-DX files. We store all user metadata using ##$ labels. That is, even though there is a global, IUPAC defined, label for TEMPERATURE we will store the temperature using a ##$ to keep all metadata consistent.

package metadata

To be able to automatically curate an overview of all the tools we add standardized metadata to the package.json file under the info key. We use the following keys:

• logo (string): link to an image, ideally from the cheminfo/font repository
• domain (array<string>): array of “tags” to allow for easy filtering. We currently use “Materials Science”, “Physical Chemistry”, “Organic Chemistry”, “Machine Learning”, “Data Processing”
• technique (object): we use this to clarify what experimental technique the package is built for. For this, we reference the Chemical Methods Ontology and the IUPAC gold book
  • name (string): name of the technique
  • chmo (string): identifier in the chemical methods ontology
  • iupac (string): doi link to the entry in the IUPAC gold book
• functionality (object): We use this to describe the functionality of the package. That is, the file types it can deal with or tags for the analysis techniques it can perform:
  • fileType (array
    • extension (str): extension without dot
    • manufacturer (str): the maintainer/developer/supplier of the file. For chemical data that usually is an instrument manufacturer
    • example (str): link to an example of the file so users can compare this with their own file
• techniques (array): List of analysis/processing techniques the package supports

If there is a filetype for which multiple extension are used, then use multiple objects (for example, jdx, dx, jcamp).

An example is:

"version" : "",
"name": "",
"description": "",
"info": {
    "logo": "https://raw.githubusercontent.com/cheminfo/font/master/src/tga/assignment.svg",
    "domain": [
      "Physical Chemistry",
      "Materials Science"
    ],
    "technique": {
      "name": "TGA",
      "chmo": "0000690",
      "iupac": "https://doi.org/10.1351/goldbook.T06324"
    },
    "functionality": {
      "fileTypes": [
        {
          "extension": "txt",
          "manufacturer": "TA Instruments",
          "example": "https://raw.githubusercontent.com/cheminfo/tga-spectrum/master/testFiles/TAInstruments.txt"
        },
        {
          "extension": "csv",
          "manufacturer": "Perkin Elmer",
          "example": "https://raw.githubusercontent.com/cheminfo/tga-spectrum/master/testFiles/perkinElmer.csv"
        },
        {
          "extension": "txt",
          "manufacturer": "Perkin Elmer",
          "example": "https://raw.githubusercontent.com/cheminfo/tga-spectrum/master/testFiles/perkinElmer_tga4000.txt"
        },
        {
          "extension": "jcamp",
          "manufacturer": "cheminfo",
          "example": "https://raw.githubusercontent.com/cheminfo/tga-spectrum/master/testFiles/ntuples.jdx"
        }
      ]
    }
  }