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eln-chemotion

Manage compounds and reactions in Chemotion via its API.

6|2|Updated Jun 11, 2026
Search Tags:#eln#electronic lab notebook#reaction tracking#chemotion#compound management
One-click install
npx skills add https://github.com/pradyumnasagar/open-research-skills --skill eln-chemotion
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: eln-chemotion
Source: https://github.com/pradyumnasagar/open-research-skills/tree/main/skills/lab-automation/eln-chemotion
Command: npx skills add https://github.com/pradyumnasagar/open-research-skills --skill eln-chemotion

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, pandas, rdkit, and includes scripts (resource) components.

What problem does it solve?

This Skill streamlines chemical research workflows by providing an interface to integrate with Chemotion, an open-source electronic lab notebook, to manage compounds, reactions, and data in your research projects.

Core Features & Use Cases

  • Electronic Lab Notebook Integration: Store and manage your compound data, reaction details, and analytical spectra.
  • Automated Sample and Reaction Management: Programmatically create samples and reactions in your lab notebook, along with relevant information like SMILES, yield, and spectra.
  • Use Case: Quickly record a reaction from scratch by creating a new sample, defining reactants and products, adding conditions, and importing NMR data, all through the Skill's interface.

Quick Start

Use the 'eln-chemotion' skill to create a new sample in your Chemotion instance, named 'Sample_A', with a SMILES string and add it to your inventory.

Frequently Asked Questions about eln-chemotion

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I automate compound management and reaction tracking in an electronic lab notebook?▼

You can create new samples in Chemotion by defining a name and SMILES string, then adding the compound to your inventory. The Skill automates this process programmatically through the Chemotion API.

Can I upload NMR, IR, MS, and HPLC data directly to Chemotion?▼

Yes, NMR, IR, MS, and HPLC data can be uploaded directly. The Skill automates attaching these analytical spectra to your samples and reactions within the Chemotion electronic lab notebook via API.

Do I need rdkit and pandas to manage reactions in Chemotion?▼

Yes, rdkit and pandas are required dependencies. RDKit processes chemical structures like SMILES strings, while pandas manages tabular data for compounds and reactions integrated into the Chemotion ELN.

What is the best way to record a synthetic reaction from scratch in Chemotion?▼

The best way is to create a new sample, define reactants and products using SMILES strings, add reaction conditions, and import analytical spectra like NMR data, all automated through the Chemotion API.

Does the Chemotion API support automated inventory management for analytical chemistry?▼

Yes, the Chemotion API supports automated inventory management for analytical chemistry. The Skill programmatically handles sample creation and inventory updates, streamlining lab workflow automation.

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