4 ms·

There's a mapping of various chemical identifiers/name to PubChem compound id at ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/ . Quoting Quoting README-E

by dalke 4y ago

There's a mapping of various chemical identifiers/name to PubChem compound id at ftp://ftp.ncbi.nlm.nih.gov/pubchem/Compound/Extras/ . Quoting Quoting README-Extras in the that directory there are three files you might look at: SID-Synonym.gz: This is a listing of all (live) SIDs with their depositor provided synonyms (one per line). It is a gzipped text file with SID, tab, synonym on each line. CID-Synonym-filtered.gz: CID-Synonym-unfiltered.gz: These are listings of all names associated with a CID. The unfiltered list are names aggregated from all SIDs whose standardized form is that CID, sorted by weight with the "best" names first. The filtered list has some names removed that are considered inconsistent with the structure. Both are gzipped text files with CID, tab, and name on each line. Note that the names may be composed of more than one word, separated by spaces. A similar list may be available from ChemSpider or eMolecules - I don't know. https://wikipedia.cheminfo.org/smiles.txt https://wikipedia.cheminfo.org/smiles.txt is a mapping from Wikipedia title to SMILES, done using the chemical infobox. > We can all manage it as an open source governing community and use tools to declare whether these chemicals are safe or not for general use. Yeah, that's not going to happen. You're in for a world of hurt if you try to crowdsource this list and find lots of contributors. As the old phrase goes, "The dose makes the poison". Oxygen can be toxic - https://en.wikipedia.org/wiki/Oxygen_toxicity https://en.wikipedia.org/wiki/Oxygen_toxicity . The California Prop 65 list ("Safe Drinking Water and Toxic Enforcement Act of 1986") includes "Ethyl alcohol in alcoholic beverages" as a chemical "known to cause cancer, birth defects or other reproductive harm" - https://oehha.ca.gov/proposition-65/chemicals/ethyl-alcohol-alcoholic-beverages https://oehha.ca.gov/proposition-65/chemicals/ethyl-alcohol-... Opinions vary, sometimes with strong emotions. In this project, who has the final say on if thiomersal is safe or not for general use? (For the matter, what does "general use" mean?)

Sulstice 4y ago
I guess that's something I am really trying to figure out. The project is moving into the Linux Foundation on Non-Profit Community Platform. Contributors have so far been from a variety of universities across the world and have been contributing in. I am still trying to figure out the mechanisms as to how to create this type of government mechanisms. I have a couple of advantages over the other platforms I think. Mine is organized in such a way data can be found easily and categorized. My lists are abstracted from expertise who and what resource so folk can trace easily. I also wrote a lot of tooling for analysis and other things you can use to analyze the data yourself to get an idea of the functional groups and diversity. Things that relate to your compound. I didn't see the Prop 65 list and that's very cool.I think that is something I need to keep watch of as well.
- dalke 4y ago
  > Mine is organized in such a way data can be found easily and categorized. I do not know what this means. It's very easy to find compounds in PubChem or ChemSpider. I didn't see how to find, say, 1,3,7-Trimethylxanthine in your system. As far as I can tell, it requires using the no-cost version of ChemDraw to convert the name into a structure and then ... do what? > My lists are abstracted from expertise who and what resource so folk can trace easily. How is this different than what ChemSpider does? They also offer "Manual comment and correction tools offer crowdsourced curation with expert review" and "You are invited to help build this community for chemists by contributing your structures, spectra, or syntheses. You can also actively participate in the curation of the data; registration enables you to become a depositor or curator." (quoting https://www.chemspider.com/AboutUs.aspx https://www.chemspider.com/AboutUs.aspx ). Is the main difference that you organize things by lists? In that case, couldn't you save a lot of effort by being an overlay into ChemSpider? Let them handle the chemical entry, name validation, property prediction, and so on. > I also wrote a lot of tooling for analysis and other things you can use to analyze the data yourself to get an idea of the functional groups and diversity. I didn't see any of that tooling from your site. What is your measure of "diversity"? Could you elaborate on your internal naming scheme for compounds? For example, https://github.com/Sulstice/global-chem/blob/ec4a5cb28a6360c9c1dc0c393357d8c9f36df840/global_chem/global_chem/medicinal_chemistry/warheads/common_warheads_covalent_inhibitors.py#L23 https://github.com/Sulstice/global-chem/blob/ec4a5cb28a6360c... has: 'haloalkane': 'CBr', That should be bromomethane, yes? "Halo" is any halogen, and "alkane" is any alkane, so "haloalkane" should refer to a class of compound, yes? And a few lines down, 'nitrile': 'N#CC', Here again, "nitrile" is a class of compounds - the specific compound is acetonitrile. Picking another data set, https://github.com/Sulstice/global-chem/blob/ec4a5cb28a6360c9c1dc0c393357d8c9f36df840/global_chem/global_chem/medicinal_chemistry/cannabinoids/constituents_of_cannabis_sativa.py#L57 https://github.com/Sulstice/global-chem/blob/ec4a5cb28a6360c... has: 'detla-9 tetrahvdrocannabinolic acid c': 'CCCCC1=CC2=C(C3C=C(CCC3C(O2)(C)C)C)C(=C1C(=O)O)O', That should almost certainly be "delta" and "hydro", yes? And line 427 of that file has: 'zanthophylls': 'CC1=C(C(CC(C1)O)(C)C) ... when I think that's 1) supposed to be "xanthophyll", which 2) is a class of compounds, and 3) PubChem tells me the compound is "beta,epsilon-Carotene-3,3'-diol, (3R,3'R,6'R)-", see https://pubchem.ncbi.nlm.nih.gov/compound/181579 https://pubchem.ncbi.nlm.nih.gov/compound/181579 . Also, it appears "constituents_of_cannabis_sativa" is a subset of what's available from https://pubchem.ncbi.nlm.nih.gov/taxonomy/3483#section=Natural-Products&fullscreen=true https://pubchem.ncbi.nlm.nih.gov/taxonomy/3483#section=Natur...

by dalke 4y ago

Sulstice 4y ago

I guess that's something I am really trying to figure out. The project is moving into the Linux Foundation on Non-Profit Community Platform. Contributors have so far been from a variety of universities across the world and have been contributing in. I am still trying to figure out the mechanisms as to how to create this type of government mechanisms. I have a couple of advantages over the other platforms I think. Mine is organized in such a way data can be found easily and categorized. My lists are abstracted from expertise who and what resource so folk can trace easily. I also wrote a lot of tooling for analysis and other things you can use to analyze the data yourself to get an idea of the functional groups and diversity. Things that relate to your compound. I didn't see the Prop 65 list and that's very cool.I think that is something I need to keep watch of as well.

dalke 4y ago
> Mine is organized in such a way data can be found easily and categorized. I do not know what this means. It's very easy to find compounds in PubChem or ChemSpider. I didn't see how to find, say, 1,3,7-Trimethylxanthine in your system. As far as I can tell, it requires using the no-cost version of ChemDraw to convert the name into a structure and then ... do what? > My lists are abstracted from expertise who and what resource so folk can trace easily. How is this different than what ChemSpider does? They also offer "Manual comment and correction tools offer crowdsourced curation with expert review" and "You are invited to help build this community for chemists by contributing your structures, spectra, or syntheses. You can also actively participate in the curation of the data; registration enables you to become a depositor or curator." (quoting https://www.chemspider.com/AboutUs.aspx https://www.chemspider.com/AboutUs.aspx ). Is the main difference that you organize things by lists? In that case, couldn't you save a lot of effort by being an overlay into ChemSpider? Let them handle the chemical entry, name validation, property prediction, and so on. > I also wrote a lot of tooling for analysis and other things you can use to analyze the data yourself to get an idea of the functional groups and diversity. I didn't see any of that tooling from your site. What is your measure of "diversity"? Could you elaborate on your internal naming scheme for compounds? For example, https://github.com/Sulstice/global-chem/blob/ec4a5cb28a6360c9c1dc0c393357d8c9f36df840/global_chem/global_chem/medicinal_chemistry/warheads/common_warheads_covalent_inhibitors.py#L23 https://github.com/Sulstice/global-chem/blob/ec4a5cb28a6360c... has: 'haloalkane': 'CBr', That should be bromomethane, yes? "Halo" is any halogen, and "alkane" is any alkane, so "haloalkane" should refer to a class of compound, yes? And a few lines down, 'nitrile': 'N#CC', Here again, "nitrile" is a class of compounds - the specific compound is acetonitrile. Picking another data set, https://github.com/Sulstice/global-chem/blob/ec4a5cb28a6360c9c1dc0c393357d8c9f36df840/global_chem/global_chem/medicinal_chemistry/cannabinoids/constituents_of_cannabis_sativa.py#L57 https://github.com/Sulstice/global-chem/blob/ec4a5cb28a6360c... has: 'detla-9 tetrahvdrocannabinolic acid c': 'CCCCC1=CC2=C(C3C=C(CCC3C(O2)(C)C)C)C(=C1C(=O)O)O', That should almost certainly be "delta" and "hydro", yes? And line 427 of that file has: 'zanthophylls': 'CC1=C(C(CC(C1)O)(C)C) ... when I think that's 1) supposed to be "xanthophyll", which 2) is a class of compounds, and 3) PubChem tells me the compound is "beta,epsilon-Carotene-3,3'-diol, (3R,3'R,6'R)-", see https://pubchem.ncbi.nlm.nih.gov/compound/181579 https://pubchem.ncbi.nlm.nih.gov/compound/181579 . Also, it appears "constituents_of_cannabis_sativa" is a subset of what's available from https://pubchem.ncbi.nlm.nih.gov/taxonomy/3483#section=Natural-Products&fullscreen=true https://pubchem.ncbi.nlm.nih.gov/taxonomy/3483#section=Natur...