From c6b7c264d4f01e466405115da020c160e77157cc Mon Sep 17 00:00:00 2001 From: Madina Bekbergenova <140626371+madina1203@users.noreply.github.com> Date: Fri, 1 Aug 2025 11:24:30 +0200 Subject: [PATCH 1/3] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b3e136a..181444d 100644 --- a/README.md +++ b/README.md @@ -129,7 +129,7 @@ It should also work on other Unix-based systems. For more details on compatibili LANGCHAIN_ENDPOINT=https://api.smith.langchain.com LANGCHAIN_PROJECT=metabot_project ``` - **Note:** The system can also be used with other LLM models, namely: Meta-Llama-3_1-70B-Instruct and deepseek-reasoner. For Meta-Llama-3_1-70B-Instruct (which runs on OVH Cloud – see [OVH Cloud](https://www.ovh.com/)), add the API key OVHCLOUD_API_KEY to your `.env` file; for deepseek-reasoner, add DEEPSEEK_API_KEY. Currently, all agents use the OpenAI model gpt-4o (including the SPARQL generation chain). Furthermore, if the initial query yields no results, a SPARQL improvement chain using the OpenAI o3-mini model is activated. + **Note:** The system can also be used with other LLM models, namely: Meta-Llama-3_1-70B-Instruct and deepseek-reasoner. For Meta-Llama-3_1-70B-Instruct (which runs on OVH Cloud – see [OVH Cloud](https://www.ovh.com/)), add the API key OVHCLOUD_API_KEY to your `.env` file; for deepseek-reasoner, add DEEPSEEK_API_KEY. Detailed information on how to configure other LLM models is available [here](https://holobiomicslab.github.io/MetaboT/getting-started/installation/#adding-new-models). Currently, all agents use the OpenAI model gpt-4o (including the SPARQL generation chain). Furthermore, if the initial query yields no results, a SPARQL improvement chain using the OpenAI o3-mini model is activated. ### Installation Steps From c2e0761987d84714ebe59b30a71dd4b647e6bf16 Mon Sep 17 00:00:00 2001 From: Madina Bekbergenova <140626371+madina1203@users.noreply.github.com> Date: Mon, 8 Sep 2025 16:54:53 +0200 Subject: [PATCH 2/3] Fix demo instance URL in README.md Updated the link to the demo instance of MetaboT in the README. --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 181444d..4f1f5f5 100644 --- a/README.md +++ b/README.md @@ -13,7 +13,7 @@ Take a break, brew a cup of tea while 🧪 MetaboT 🍵 digs into mass spec data! -🧪 MetaboT 🍵 is an AI system that accelerates mass spectrometry-based metabolomics data mining. Leveraging advanced large language models and knowledge graph technologies, 🧪 MetaboT 🍵 translates natural language queries into SPARQL requests—enabling researchers to explore and interpret complex metabolomics datasets. Built in Python and powered by state-of-the-art libraries, 🧪 MetaboT 🍵 offers an intuitive chat interface that bridges the gap between data complexity and user-friendly access. 🧪 MetaboT 🍵 can be installed locally and you can try our demo instance on an open [1,600 plant extract dataset](https://doi.org/10.1093/gigascience/giac124) available at [https://metabot.holobiomicslab.cnrs.fr](https://metabot.holobiomicslab.cnrs.fr). +🧪 MetaboT 🍵 is an AI system that accelerates mass spectrometry-based metabolomics data mining. Leveraging advanced large language models and knowledge graph technologies, 🧪 MetaboT 🍵 translates natural language queries into SPARQL requests—enabling researchers to explore and interpret complex metabolomics datasets. Built in Python and powered by state-of-the-art libraries, 🧪 MetaboT 🍵 offers an intuitive chat interface that bridges the gap between data complexity and user-friendly access. 🧪 MetaboT 🍵 can be installed locally and you can try our demo instance on an open [1,600 plant extract dataset](https://doi.org/10.1093/gigascience/giac124) available at [ https://metabot.holobiomicslab.eu]( https://metabot.holobiomicslab.eu). Take a break, brew a cup of tea 🍵, and have some fun with words while 🧪 MetaboT 🍵 digs into mass spec data! Enjoy your brew and happy puzzling! From 92dddc8a9392f64870781f8c36db87a3a3b0c809 Mon Sep 17 00:00:00 2001 From: Madina Bekbergenova <140626371+madina1203@users.noreply.github.com> Date: Mon, 8 Sep 2025 17:12:17 +0200 Subject: [PATCH 3/3] Fix demo link in Quick Start Guide Updated the demo link in the Quick Start Guide to remove the trailing slash. --- docs/getting-started/quickstart.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/getting-started/quickstart.md b/docs/getting-started/quickstart.md index 36759e8..27a1ec8 100644 --- a/docs/getting-started/quickstart.md +++ b/docs/getting-started/quickstart.md @@ -2,7 +2,7 @@ Welcome to the Quick Start Guide for 🧪 MetaboT 🍵. This guide will help you quickly run and test the application. -👉 **Try the MetaboT Web App Demo**: [https://metabot.holobiomicslab.eu/](https://metabot.holobiomicslab.eu/) — no installation needed! +👉 **Try the MetaboT Web App Demo**: [https://metabot.holobiomicslab.eu](https://metabot.holobiomicslab.eu) — no installation needed! The demo provides access to an open [dataset of 1,600 plant extracts](https://doi.org/10.1093/gigascience/giac124). You can explore metabolomics data and ask questions about the dataset directly through the web interface.