Retrieving MeSH Pharmacological Classification for Compounds in pubChem

Question

[mattia.cordioli01]

I would like to extract, together with the other properties, the MeSH pharmacological classification for any compound in pubchem. For example, for Aspirin I'd like to retrieve "Analgesics, Non-Narcotic" and "Antipyretics".

It seems this is not possible using PUG REST like for retrieving other compound's properties, like this https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/1/property/MolecularFormula,MolecularWeight,InChIKey/CSV beacuse there's no reference to MeSH terms in Compound Property Table.

Does anyone have any idea on how to do it? Thank you so much

Answer 1

[Wolf Ihlenfeldt]

You cannot do this via PUG alone. You need to perform some multi-level Entrez EUtils wrangling for this.

Two possibilities:

a) Learn and understand EUtils and the relationships between the various NCBI databases to some depth

b) Use our Cheminformatics toolkit www.xemistry.com/academic for free academic versions)

Example: Get the full MeSH term tree for Aspirin in JSON form with a Python statement:

cspy
pycactvs>Ens('name:aspirin').jget('E_MESH_TERMS')
'[{"id":68001241,"terms":["Aspirin","Acetylsalicylic Acid","Acid, Acetylsalicylic","2-(Acetyloxy)benzoic Acid","Acylpyrin","Aloxiprimum","Colfarit","Dispril","Easprin","Ecotrin","Endosprin","Magnecyl","Micristin","Polopirin","Polopiryna","Solprin","Solupsan","Zorprin","Acetysal"],"url":"https://www.ncbi.nlm.nih.gov/sites/entrez?Db=mesh&Cmd=ShowDetailView&TermToSearch=68001241","ontotree":{"name":"68001241","type":"data","values":["Aspirin"],"children":[]}},{"id":68058633,"terms":["Antipyretics","Antipyretic Agents","Agents, Antipyretic","Antifebrile Agents","Agents, Antifebrile","Antipyretic Effect","Effect, Antipyretic","Antipyretic Effects","Effects, Antipyretic"],"url":"https://www.ncbi.nlm.nih.gov/sites/entrez?Db=mesh&Cmd=ShowDetailView&TermToSearch=68058633","ontotree":{"name":"68058633","type":"data","values":["Antipyretics"],"children":[]}},{"id":68016861,"terms":["Cyclooxygenase Inhibitors","Inhibitors, Cyclo-Oxygenase","Inhibitors, Cyclo Oxygenase","Inhibitors, Cyclooxygenase","Prostaglandin Synthesis Antagonists","Antagonists, Prostaglandin Synthesis","Inhibitors, Prostaglandin-Endoperoxide Synthase","Inhibitors, Prostaglandin Endoperoxide Synthase","Prostaglandin Endoperoxide Synthase Inhibitors",... (shortened)

Example: Get the full MeSH term tree in nested list/dict form in Tcl:

csts
cactvs>ens get name:aspirin E_MESH_TERMS
{68001241 {Aspirin {Acetylsalicylic Acid} {Acid, Acetylsalicylic} {2-(Acetyloxy)benzoic Acid} Acylpyrin Aloxiprimum Colfarit Dispril Easprin Ecotrin Endosprin Magnecyl Micristin Polopirin Polopiryna Solprin Solupsan Zorprin Acetysal} https://www.ncbi.nlm.nih.gov/sites/entrez?Db=mesh&Cmd=ShowDetailView&TermToSearch=68001241 {68001241 Aspirin}} {68058633 {Antipyretics {Antipyretic Agents} {Agents, Antipyretic} {Antifebrile Agents} {Agents, Antifebrile} {Antipyretic Effect} {Effect, Antipyretic} {Antipyretic Effects} {Effects, Antipyretic}} https://www.ncbi.nlm.nih.gov/sites/entrez?Db=mesh&Cmd=ShowDetailView&TermToSearch=68058633 {68058633 Antipyretics}} {68016861 {{Cyclooxygenase Inhibitors} {Inhibitors, Cyclo-Oxygenase} {Inhibitors, Cyclo Oxygenase} {Inhibitors, Cyclooxygenase} {Prostaglandin Synthesis Antagonists} {Antagonists, Prostaglandin Synthesis} {Inhibitors, Prostaglandin-Endoperoxide Synthase} {Inhibitors, Prostaglandin Endoperoxide Synthase} {Prostaglandin Endoperoxide Synthase Inhibitors} {Prostaglandin Synthase Inhibitors} {Cyclo-Oxygenase Inhibitors} {Cyclo Oxygenase Inhibitors} {Inhibitors, Prostaglandin Synthase}} https://www.ncbi.nlm.nih.gov/sites/entrez?Db=mesh&Cmd=ShowDetailView&TermToSearch=68016861 {68016861 {{Cyclooxygenase Inhibitors}} {68000894 {Anti-Inflammatory Agents, Non-Steroidal} {68000893 {Anti-Inflammatory Agents}} {68018501 {Antirheumatic Agents}}} {68000894 {Anti-Inflammatory Agents, Non-Steroidal} {68000893 {Anti-Inflammatory Agents}} {68018501 ... (shortened)

You can then dig deeper into the MeSH data with script commands isolating the desired nodes from the tree. You data is in there:

...ontotree":{"name":"68058633","type":"data","values":["Antipyretics"],"children":[]}},{"id":68016861,"terms":["Cyclooxygenase Inhibi...