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nih-cfde / 2022-feb-hackathon

The CFDE February 2022 Hackathon
https://nih-cfde.github.io/2022-feb-hackathon/
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Metabolomics Workbench Hackathon Session #3

Open raynamharris opened 2 years ago

raynamharris commented 2 years ago

Metabolomics Workbench (MW) is an online resource that houses the NIH Common Fund's National Metabolomics Data Repository (NMDR) as well as related databases and resources. The MW provides a platform to deposit metabolomics data to NMDR by researchers across the world, and provides tools to browse, analyze and visualize such data and the related metabolite structures and annotations. Currently, the NMDR has over 2,000 MS and NMR studies covering over 130 different species. The MW metabolite database currently has more than 164,000 molecular structures with the ability to search by text, substructure and m/z values. Tutorials about various aspects of the MW data are provided here.

The Metabolomics Workbench Hackathon Session will provide an introduction to the data as well as structured and unstructured activities.

mano-at-sdsc commented 2 years ago

@raynamharris Please update the above text with:

Metabolomics Workbench (MW) is the NIH Common Fund's National Metabolomics Data Repository (NMDR). The MW provides a platform to deposit metabolomics data by researchers across the world, and provides tools to browse, analyze and visualize such data and the related metabolite structures and annotations. Currently, the MW has about 1,700 publicly released studies. The MW metabolite database currently has more than 164,000 entries with the ability to search by text, substructure and m/z values. Tutorials about various aspects of the MW data are provided here.

The Metabolomics Workbench Hackathon Session will provide an introduction to the data as well as structured and unstructured activities.

mano-at-sdsc commented 2 years ago

Please update the above text to (we have more studies now):

Metabolomics Workbench (MW) is an online resource that houses the NIH Common Fund's National Metabolomics Data Repository (NMDR) as well as related databases and resources. The MW provides a platform to deposit metabolomics data to NMDR by researchers across the world, and provides tools to browse, analyze and visualize such data and the related metabolite structures and annotations. Currently, the NMDR has over 2,000 MS and NMR studies covering over 130 different species. The MW metabolite database currently has more than 164,000 molecular structures with the ability to search by text, substructure and m/z values. Tutorials about various aspects of the MW data are provided here.

The Metabolomics Workbench Hackathon Session will provide an introduction to the data as well as structured and unstructured activities.

barupal commented 2 years ago

We had to merge mwTAB files from all MW studies for a project. The result is posted on Zenodo https://zenodo.org/record/5860638#.YgvdQDjMKpp .

mano-at-sdsc commented 2 years ago

Great to know. I will let Eoin Fahy at our DCC know.

jessicalumian commented 2 years ago

For reference, here is a link to the Metabolomics Workbench GitHub repository, which features a hosted Jupyter Notebook: https://github.com/metabolomicsworkbench/MetENP

mano-at-sdsc commented 2 years ago

Thanks, Jessica.

The link to working jupyter notebook is:

https://mybinder.org/v2/gh/metabolomicsworkbench/MetENP/test01?filepath=vignettes%2FMetENP_vignette_Jupyter_notebook.ipynb

Mano

From: jessicalumian @.> Sent: Wednesday, February 23, 2022 10:02 AM To: nih-cfde/2022-feb-hackathon @.> Cc: Maurya, Mano @.>; Assign @.> Subject: Re: [nih-cfde/2022-feb-hackathon] Metabolomics Workbench Hackathon Session (Issue #3)

For reference, here is a link to the Metabolomics Workbench GitHub repository, which features a hosted Jupyter Notebook: https://github.com/metabolomicsworkbench/MetENPhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_metabolomicsworkbench_MetENP&d=DwMCaQ&c=-35OiAkTchMrZOngvJPOeA&r=Lhm9JKwr1uCYexC4a9X-3Q&m=4czaR7q-bkLUCZ83IXH-eRiiexmQRA8jfDhsPHmvsNew8DioqDpwBGJvFr9Gue8J&s=YFCNhd65D1elJttML2puOoYWKmCPhEVwZ-UeCH_Xi-E&e=

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