OBI term for Metabolomics (Mano Maurya's group)

nsuvarnaiari commented 3 years ago

From Mano @mano-at-sdsc:

For the upcoming submission, for assay_type, e.g., for GC-MS, are we using terms like OBI:0000470" or we can now use "OBO:CHMO_0000497". The page https://docs.nih-cfde.org/en/latest/c2m2/draft-C2M2_specification/#c2m2-technical-specification

Thanks, Suvvi

nsuvarnaiari commented 3 years ago

Hi @mano-at-sdsc

Michelle reserved an OBI id for "gas chromatography- mass spectrometry assay" after discussing with OBI folks. You can start using the id for CFDE portal submissions. It's not in the ontology yet but should be available in the next OBI release.

OBI:0003110 | gas chromatography mass spectrometry assay

Thanks, Suvvi

mano-at-sdsc commented 3 years ago

Hi @nsuvarnaiari:

Thanks. Will use this for GC-MS. Other assay_type for which we will need OBI ID at finer level, for which currently I am just using OBI:0000470, are:

In case there are already OBI code for some of these and I may have missed them, please let me know.

Mano @mano-at-sdsc

nsuvarnaiari commented 3 years ago

Hi @mano-at-sdsc

Thanks for sharing the list of terms for which you need OBI ids. We will try to register ids for these terms with OBI soon so that you can start using them.

Please take a look at the actual names of the assay_type acronyms from your list and let us know if they are incorrect for the ones I was able to find a name. For the ones with a question mark, please tell us the name of the assay. We would really appreciate if you provide us definitions for these assays or a pubmed paper / some documentation / links that can help us define the terms.

LC-MS : liquid chromatography mass spectrometry MALDI : matrix-assisted laser desorption ionization time-of-flight mass-spectrometry or an other variant of MALDI? API-MS : atmospheric pressure ionization mass spectrometry APCI-MS : atmospheric pressure chemical ionization mass spectrometry ESI : electrospray ionization mass spectrometry IR MS : ?

Thanks, Suvvi

mano-at-sdsc commented 3 years ago

Hi @nsuvarnaiari ,

Thanks, and sorry about the delay in response; sorry to make you search for these terms. We have decided to only use the terms "MS", "NMR", GC-MS" and "LC-MS". These already cover > 90% of the studies. For all others, we will use "MS". So, we request a OBI ID only for "LC-MS": liquid chromatography mass spectrometry. We already have one for MS, NMR and GC-MS.

Thanks. Mano

nsuvarnaiari commented 3 years ago

Hi Mano,

We have registered an OBI id for "liquid chromatography mass spectrometry assay" for HuBMAP . You can start using this id in your metadata files.

Thanks, Suvvi

mano-at-sdsc commented 3 years ago

Thanks, Suvvi.

Please share the OBI ID for "liquid chromatography mass spectrometry", or let me know if it is listed in one of the resource files here: https://github.com/hubmapconsortium/hubmap-ontology/tree/master/source_ontologies or elsewhere.

Mano

nsuvarnaiari commented 3 years ago

Oh sorry @mano-at-sdsc, forgot to paste OBI id for "liquid chromatography mass spectrometry assay". It's OBI:0003097.

Thanks, Suvvi

mano-at-sdsc commented 3 years ago

Thanks, @nsuvarnaiari . No worries.

Mano

mgiglio99 commented 2 years ago

This work was finished a while ago - term has been live in OBI for a long time. Closing....

nih-cfde / ontologyWG

OBI term for Metabolomics (Mano Maurya's group) #3