Chemical mixtures: File format, open source tools, example data, and mixtures InChI derivative
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This document discusses representing chemical mixtures using an open format called Mixfile. It proposes Mixfile as a standard format for mixtures, analogous to Molfile for individual molecules. Tools were created to edit and manipulate Mixfiles. Over 5,600 real-world mixture examples were extracted from text and represented in the Mixfile format. A MInChI notation was also defined as a condensed representation of mixtures. Future work is proposed to integrate mixture definitions and lookups into electronic lab notebooks and improve automated extraction of mixture information from text.
![COLLABORATIVE DRUG DISCOVERY - MIXTURES
Representation
◈ Serialised using JSON: natural datastructure, human
readable, concise, easy to code on any platform
7
{
"mixfileVersion": 0.01,
"name": "Lithium diisopropylamide solution",
"contents":
[
{
"name": "Lithium diisopropylamide",
"molfile": "nGenerated by WebMolKitnn 8 6 0 0 0 0 0 0 0 0999 V2000n 0.2500 1.5000 0.0000 N 0 5 0 0 0 0 0 0 0
0 0 0n -1.0490 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n -2.3481 1.5000 0.0000 C 0 0 0 0 0
0 0 0 0 0 0 0n -1.0490 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n 1.5490 0.7500 0.0000 C 0
0 0 0 0 0 0 0 0 0 0 0n 2.8481 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n 1.5490 -0.7500
0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n 0.2500 3.0000 0.0000 Li 0 3 0 0 0 0 0 0 0 0 0 0n 1 2 1
0 0 0 0n 2 3 1 0 0 0 0n 2 4 1 0 0 0 0n 1 5 1 0 0 0 0n 5 6 1 0 0 0 0n 5 7 1 0 0 0 0nM
CHG 2 1 -1 8 1nM END",
"quantity": 1,
"units": "mol/L",
"inchi": "InChI=1S/C6H14N.Li/c1-5(2)7-6(3)4;/h5-6H,1-4H3;/q-1;+1",
"inchiKey": "InChIKey=ZCSHNCUQKCANBX-UHFFFAOYSA-N"
},
{
"contents":
[
{
"name": "THF",
"molfile": "nGenerated by WebMolKitnn 5 5 0 0 0 0 0 0 0 0999 V2000n -0.2500 3.7500 0.0000 O 0 0 0 0 0 0
0 0 0 0 0 0n -1.4600 2.8700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n -1.0000 1.4400 0.0000 C 0 0
0 0 0 0 0 0 0 0 0 0n 0.9600 2.8700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n 0.5000 1.4400
0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n 3 2 1 0 0 0 0n 2 1 1 0 0 0 0n 1 4 1 0 0 0 0n 4 5 1 0
0 0 0n 5 3 1 0 0 0 0nM END",
"ratio":
[
1,
8
],
"inchi": "InChI=1S/C4H8O/c1-2-4-5-3-1/h1-4H2",
"inchiKey": "InChIKey=WYURNTSHIVDZCO-UHFFFAOYSA-N"
},](https://image.slidesharecdn.com/acstalkmixtures-190826232001/85/Chemical-mixtures-File-format-open-source-tools-example-data-and-mixtures-InChI-derivative-7-320.jpg)
![COLLABORATIVE DRUG DISCOVERY - MIXTURES
Brute Force
◈ Compose a set of regular expression rules
◈ Remove brand names:
11
{"effect": "remove", "regex": "(.*)A[cC][rR][oO][sS] Organics?™?(.*?)$"},
{"effect": "remove", "regex": "(.*)AcroSeal™?(.*?)$"},
{"effect": "remove", "regex": "(.*)Alfa Aesar™?(.*?)$"},
{"effect": "remove", "regex": "(.*)BioReagents™?(.*?)$"},
{"effect": "remove", "regex": "(.*)Burdick & Jackson™?(.*?)$"},
{"effect": "remove", "regex": "(.*)(Technical)$"},
{"effect": "remove", "regex": "(.*)(Certified)$"},
{"effect": "remove", "regex": "(.*), pure$"},
{"effect": "remove", "regex": "(.*), for analysis$"},
{"effect": "remove", "regex": "(.*), extra pure$"},
◈ Remove suffixes:](https://image.slidesharecdn.com/acstalkmixtures-190826232001/85/Chemical-mixtures-File-format-open-source-tools-example-data-and-mixtures-InChI-derivative-11-320.jpg)
![COLLABORATIVE DRUG DISCOVERY - MIXTURES
Brute Force (ctd)
◈ Identify branches (with quantities):
12
{"effect": "branch", "regex":
"(.*) (over (molecular sieve .*))", "substance": "$2"},
{"effect": "branch", "regex": "(.*) (d[d.]*) ? mM in (.*)",
"quantity": "$2", "units": "mmol/L", "substance": "$3"},
{"effect": "branch", "regex":
"(.*) ~?d[d.]*s?% in (.*) ((~?)(d[d.]*) M)$",
"quantity": "$4", "units": "mol/L", "relation": "$3", "substance": "$2"},
{"effect": "branch", "regex":
"(.*), (d[d.]*)s?M [Ss]olution in (.*)",
"quantity": "$2", "units": "mol/L", "substance": "$3"},
{"effect": "conc", "regex": "(.*) (d[d.]*)%, ee d[d.]*.%$",
"quantity": "$2","units": "%", "relation": ""},
{"effect": "conc", "regex": "(.*) ≥ ?(d[d.]*)%$",
"quantity": "$2","units": "%", "relation": ">="},
{"effect": "conc", "regex": "(.*) [Ss]olution (d[d.]*) ?M$",
"quantity": "$2", "units": "mol/L"},
◈ Concentration suffixes:](https://image.slidesharecdn.com/acstalkmixtures-190826232001/85/Chemical-mixtures-File-format-open-source-tools-example-data-and-mixtures-InChI-derivative-12-320.jpg)
![COLLABORATIVE DRUG DISCOVERY - MIXTURES
Future Work: Text Extraction
◈ Initial proof of concept is effective but crude
◈ Planning a much more sophisticated iterative-learning
strategy: start by formulating input for recurrent deep
neural network
18
Trimethyl(trifluoromethyl)silane solution 2 M in THF
■ component ■ quantity ■ branch ■ superfluous
... -5 -4 -3 -2 -1 0 +1 +2 +3 +4 +5 ...
[... *, *, *, *, *, T, r, i, m, e, t ...] = ■ component
[... *, *, *, *, T, r, i, m, e, t, h ...] = ■ component
[... *, *, *, T, r, i, m, e, t, h, y ...] = ■ component
[... *, *, T, r, i, m, e, t, h, y, l ...] = ■ component
...
[... l, u, t, i, o, n, , 2, M, , i ...] = ■ superfluous
[... u, t, i, o, n, , 2, M, , i, n ...] = ■ superfluous
[... t, i, o, n, , 2, M, , i, n, ...] = ■ quantity
[... i, o, n, , 2, M, , i, n, , T ...] = ■ quantity
... etc. ...
◈ Learning from input/
output data rather than
curated rules: more
scalable](https://image.slidesharecdn.com/acstalkmixtures-190826232001/85/Chemical-mixtures-File-format-open-source-tools-example-data-and-mixtures-InChI-derivative-18-320.jpg)
Chemical mixtures: File format, open source tools, example data, and mixtures InChI derivative
- 1. Chemical mixtures: File format, open source tools, example data, and mixtures InChI derivative Alex M. Clark
- 2. COLLABORATIVE DRUG DISCOVERY - MIXTURES Premise ◈ Representing specific chemicals routine since 1980s ▷ e.g. the MDL Molfile CTAB for organics ◈ Most real world encounters are mixtures ◈ No industry standard format... ▷ ... even though it's rather easy ▷ interchange is done with text 2
- 3. COLLABORATIVE DRUG DISCOVERY - MIXTURES Goal ◈ Grant-supported project to: ▷ define a simple format (Mixfile) ▷ create open source tools for editing & manipulating ▷ bootstrap content via text mining ▷ work with IUPAC for interoperability (MInChI) ◈ Results pubished in Journal of Cheminformatics 11:33 3
- 4. COLLABORATIVE DRUG DISCOVERY - MIXTURES Common Lab Mixtures 4 impurity isomers simple solution multisolvent solution
- 5. COLLABORATIVE DRUG DISCOVERY - MIXTURES Real World Mixtures 5 drug tablet toothpaste
- 6. COLLABORATIVE DRUG DISCOVERY - MIXTURES File Format ◈ Mixfile is to mixtures as Molfile is to molecules ◈ Components: ▷ structure & name ▷ concentration ▷ identifiers ◈ Hierarchy ▷ captures nuances of mixing ▷ relative concentrations/uncertainty 6
- 7. COLLABORATIVE DRUG DISCOVERY - MIXTURES Representation ◈ Serialised using JSON: natural datastructure, human readable, concise, easy to code on any platform 7 { "mixfileVersion": 0.01, "name": "Lithium diisopropylamide solution", "contents": [ { "name": "Lithium diisopropylamide", "molfile": "nGenerated by WebMolKitnn 8 6 0 0 0 0 0 0 0 0999 V2000n 0.2500 1.5000 0.0000 N 0 5 0 0 0 0 0 0 0 0 0 0n -1.0490 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n -2.3481 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n -1.0490 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n 1.5490 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n 2.8481 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n 1.5490 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n 0.2500 3.0000 0.0000 Li 0 3 0 0 0 0 0 0 0 0 0 0n 1 2 1 0 0 0 0n 2 3 1 0 0 0 0n 2 4 1 0 0 0 0n 1 5 1 0 0 0 0n 5 6 1 0 0 0 0n 5 7 1 0 0 0 0nM CHG 2 1 -1 8 1nM END", "quantity": 1, "units": "mol/L", "inchi": "InChI=1S/C6H14N.Li/c1-5(2)7-6(3)4;/h5-6H,1-4H3;/q-1;+1", "inchiKey": "InChIKey=ZCSHNCUQKCANBX-UHFFFAOYSA-N" }, { "contents": [ { "name": "THF", "molfile": "nGenerated by WebMolKitnn 5 5 0 0 0 0 0 0 0 0999 V2000n -0.2500 3.7500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0n -1.4600 2.8700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n -1.0000 1.4400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n 0.9600 2.8700 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n 0.5000 1.4400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0n 3 2 1 0 0 0 0n 2 1 1 0 0 0 0n 1 4 1 0 0 0 0n 4 5 1 0 0 0 0n 5 3 1 0 0 0 0nM END", "ratio": [ 1, 8 ], "inchi": "InChI=1S/C4H8O/c1-2-4-5-3-1/h1-4H2", "inchiKey": "InChIKey=WYURNTSHIVDZCO-UHFFFAOYSA-N" },
- 8. COLLABORATIVE DRUG DISCOVERY - MIXTURES Tooling ◈ Editor & libraries written in TypeScript, cheminformatics library: WebMolKit ◈ Create, modify, view & render Mixfiles ◈ Open source https://github.com/cdd/mixtures 8 (a) (b) (c)
- 9. COLLABORATIVE DRUG DISCOVERY - MIXTURES Mixture Data ◈ Lots of mixtures, but mostly text ◈ Active ingredient often separated ▷ purity ▷ solvent/conc. ◈ Semi-structured databases also 9
- 10. COLLABORATIVE DRUG DISCOVERY - MIXTURES Text Extraction ◈ Many common patterns in text descriptions 10 1-Aza-12-crown-4 ≥97.0% Trimethyl(trifluoromethyl)silane solution 2 M in THF
- 11. COLLABORATIVE DRUG DISCOVERY - MIXTURES Brute Force ◈ Compose a set of regular expression rules ◈ Remove brand names: 11 {"effect": "remove", "regex": "(.*)A[cC][rR][oO][sS] Organics?™?(.*?)$"}, {"effect": "remove", "regex": "(.*)AcroSeal™?(.*?)$"}, {"effect": "remove", "regex": "(.*)Alfa Aesar™?(.*?)$"}, {"effect": "remove", "regex": "(.*)BioReagents™?(.*?)$"}, {"effect": "remove", "regex": "(.*)Burdick & Jackson™?(.*?)$"}, {"effect": "remove", "regex": "(.*)(Technical)$"}, {"effect": "remove", "regex": "(.*)(Certified)$"}, {"effect": "remove", "regex": "(.*), pure$"}, {"effect": "remove", "regex": "(.*), for analysis$"}, {"effect": "remove", "regex": "(.*), extra pure$"}, ◈ Remove suffixes:
- 12. COLLABORATIVE DRUG DISCOVERY - MIXTURES Brute Force (ctd) ◈ Identify branches (with quantities): 12 {"effect": "branch", "regex": "(.*) (over (molecular sieve .*))", "substance": "$2"}, {"effect": "branch", "regex": "(.*) (d[d.]*) ? mM in (.*)", "quantity": "$2", "units": "mmol/L", "substance": "$3"}, {"effect": "branch", "regex": "(.*) ~?d[d.]*s?% in (.*) ((~?)(d[d.]*) M)$", "quantity": "$4", "units": "mol/L", "relation": "$3", "substance": "$2"}, {"effect": "branch", "regex": "(.*), (d[d.]*)s?M [Ss]olution in (.*)", "quantity": "$2", "units": "mol/L", "substance": "$3"}, {"effect": "conc", "regex": "(.*) (d[d.]*)%, ee d[d.]*.%$", "quantity": "$2","units": "%", "relation": ""}, {"effect": "conc", "regex": "(.*) ≥ ?(d[d.]*)%$", "quantity": "$2","units": "%", "relation": ">="}, {"effect": "conc", "regex": "(.*) [Ss]olution (d[d.]*) ?M$", "quantity": "$2", "units": "mol/L"}, ◈ Concentration suffixes:
- 13. COLLABORATIVE DRUG DISCOVERY - MIXTURES Implementation ◈ Apply regular expression rules greedily/recursively ▷ package up into hierarchical components ▷ substances referenced by name ◈ Use OPSIN for name-to-SMILES, RDKit to depict ◈ Use lookup database for: ▷ common exceptions (e.g. trivial names) ▷ named mixtures (e.g. hexanes) 13
- 14. COLLABORATIVE DRUG DISCOVERY - MIXTURES Results ◈ Aggregated thousands of single-line text entries, mostly from online catalogs ◈ 5600 mixtures verified & included on GitHub using the Mixfile format ◈ Success rate ~95% with: ▷ 250 regular expression based rules ▷ 280 name lookup mappings ◈ All of them with calculated MInChI strings... 14
- 15. COLLABORATIVE DRUG DISCOVERY - MIXTURES MInChI ◈ Mixtures InChI is a composite notation... ▷ Mixfile encapsulates Molfiles + extra metadata ▷ MInChI encapsulates InChI + extra metadata ◈ Distilled down to the basics: ▷ canonical structures ▷ simplified concentration ▷ nesting hierarchy ◈ Useful to accompany primary originated data 15
- 16. COLLABORATIVE DRUG DISCOVERY - MIXTURES Dissection ◈ Mixfile to MInChI: designed for one way conversion (verbose-to-concise) ◈ Reduced information content of MInChI adds value for certain use cases ◈ Proof of concept implemented 16 (a) MInChI=0.00.1S/C7H8N4O2/c1-10-3-8-5-4(10)6(12)11(2)7(13)9-5/h3H,1-2H3,(H,9,13)/n1/g99pp0 header structure identifier indexing concentration MInChI=0.00.1S/BBr3/c2-1(3)4&CH2Cl2/c2-1-3/h1H2/n{1&2}/g{1mr0&}(b) (c) MInChI=0.00.1S/C4H8O/c1-2-4-5-3-1/h1-4H2&C6H12/c1-6-4-2-3-5-6/h6H,2-5H2,1H3 &C6H14/c1-3-5-6-4-2/h3-6H2,1-2H3&C6H14/c1-4-5-6(2)3/h6H,4-5H2,1-3H3 &C6H14/c1-4-6(3)5-2/h6H,4-5H2,1-3H3&C6H14N.Li/c1-5(2)7-6(3)4;/h5-6H,1-4H3;/q-1;+1 /n{6&{1&{3&2&4&5}}}/g{1mr0&{1vp0&{5:7vf-1&1:2vf-1&1:5vf-2&1:5vf-2}7vp0}}
- 17. COLLABORATIVE DRUG DISCOVERY - MIXTURES Future Work: ELNs ◈ Embed convenient UI within web ELN ▷ sketch out mixture definitions for procedure writeup ▷ quick lookup databases of known mixtures ▷ search content using precise mixture-aware queries ◈ Vendor integration ▷ work with vendors to markup their products ▷ scientists can use product code to embed mixture 17
- 18. COLLABORATIVE DRUG DISCOVERY - MIXTURES Future Work: Text Extraction ◈ Initial proof of concept is effective but crude ◈ Planning a much more sophisticated iterative-learning strategy: start by formulating input for recurrent deep neural network 18 Trimethyl(trifluoromethyl)silane solution 2 M in THF ■ component ■ quantity ■ branch ■ superfluous ... -5 -4 -3 -2 -1 0 +1 +2 +3 +4 +5 ... [... *, *, *, *, *, T, r, i, m, e, t ...] = ■ component [... *, *, *, *, T, r, i, m, e, t, h ...] = ■ component [... *, *, *, T, r, i, m, e, t, h, y ...] = ■ component [... *, *, T, r, i, m, e, t, h, y, l ...] = ■ component ... [... l, u, t, i, o, n, , 2, M, , i ...] = ■ superfluous [... u, t, i, o, n, , 2, M, , i, n ...] = ■ superfluous [... t, i, o, n, , 2, M, , i, n, ...] = ■ quantity [... i, o, n, , 2, M, , i, n, , T ...] = ■ quantity ... etc. ... ◈ Learning from input/ output data rather than curated rules: more scalable
- 19. COLLABORATIVE DRUG DISCOVERY - MIXTURES Future Work: Molecules ◈ Structures currently limited to ≈ Molfile/InChI subset ◈ Want to extend to: ▷ inorganics (non-integral bond orders) ▷ polymers (repeat units & distributions) ▷ variations (Markush structures, partially definitions) ▷ large molecules (proteins, DNA) ▷ pseudomolecules (ceramics, alloys) ◈ More formal definition of ID codes (CAS, PubChem, etc.) 19
- 20. COLLABORATIVE DRUG DISCOVERY - MIXTURES Acknowledgments 20 ◈ Leah McEwen ▷ and the rest of the IUPAC/InChI working group ◈ Hande Küçük McGinty (and iCorps) ▷ Collaborative Drug Discovery Funding NIH SBIR