Chemical structure classifiers

[oolonek]

NPClassifier

• Code : https://npclassifier.ucsd.edu/
• paper: https://chemrxiv.org/engage/chemrxiv/article-details/60c74f58702a9ba8dc18bb6b

Pro ✅	Con ❌
published	Machine learning
already used within the NP community	Only 3 levels
...	...

yaccl

https://github.com/rwst/yaccl
https://www.wikidata.org/wiki/Wikidata:WikiProject_Chemistry/Chemical_classification

Pro ✅	Con ❌
SMARTS based	not published
multiple levels	levels not standardized
often linked to biosynthetic pathways	...

[Adafede]

Also have a look at https://scholia.toolforge.org/chemical-class/Q41581 for an example of the wiki based hierarchy

[oolonek]

How many levels are in yaccl exactly ?
Having a look at https://www.wikidata.org/wiki/Wikidata:WikiProject_Chemistry/Chemical_classification I see this as a very (too ?) dense and detailed taxonomy and I am not sure that compared to the 3 defined levels of NPClassifier it stands as an advantage (at least at the moment and in the frame of the anticipated-lotus project)

[Adafede]

I see it as the more levels the better?

It follows subclass of starting from chemical entity so of course quite broad... but why would it be a limitation? It is the same as the multiple nodes in OTL allowing to mimick a phylogeny?

So maybe we will only be able to input organic compound or acyclic compound or terpene or isoflavonoid but at a much wider range than only 3 levels.

I like the fact that isoflavonoids are linked to biosynthetic processes and much more...

Of course, it comes with multiple complications as having multiple parents, etc.

My initial thought was that having trees that have a similar shape on both sides would help, I might be completely wrong. Having something very fine on the biological side and quite rough on 3 levels on the chemical one did not appear suitable to me, gut feeling

[oolonek]

Yep I get it. But as a finer (way finer) tree we have the ones we can build from the fingerprint (TMAP or whatever fp comparison).

Regarding the multiple parents issue I think we also have it on the NPClassifier side right ?

[Adafede]

Multiple parents: yes and no... very very often on WD, almost never on NPC.

[Adafede]

Shall we maybe try to contact Ralf on the topic? As the author, he will probably answer at best some of our questions.

[Adafede]

So I contacted him and sadly he has no availability for now...

[Adafede]

I will nevertheless try classifying as much as possible with yaccl...running now... should take some days!

for i in `cat ../../elotus-trees/data/smiles4yaccl.txt`; do python3 classify.py -d ./ -j -m "$i">~/Downloads/tmp/lotus/yaccl/$i.txt; done

[Adafede]

So, I just wanted to have a look after 10,000 classified entries (it is slower than NPC) and @oolonek was right: coverage is indeed smaller than NPC at the moment. We have 2,938/10,000 that are not classified.

I do not know how random my 10,000 sampling is... just documenting a bit.

When the whole batch will finish we might be able to check the NPC class of the yaccl-unclassified compounds to see if targeting a few SMARTS could hep maybe classifying a lot more.

[oolonek]

Great. Anyway it will be a good thing to have "yet another chemical classification" on the lotus set ! It was named for this !

[Adafede]

Brief update: it is now 17,773/60,996...so the first ones were representative 😄

[Adafede]

To give an idea of the type of results we get:

yaccl:

{"molecule": "O=C1C(C2CC34c5ccccc5N5C(=O)CC6OCC=C7CN2C3CC7C6C54)=CC2C3CC4N(CCC45c4ccccc4N1C25)CC3=CCO", "ikey": "MMKIAHOGFMPKCT-UHFFFAOYSA-N", "hits": [{"classification_names": ["alkaloid", "indole alkaloid", "terpenoid indole alkaloid", "monoterpenoid indole alkaloid", "strychnidine alkaloid", "24-[14-(2-hydroxyethylidene)-9-oxo-8,16-diazahexacyclo[11.5.2.1\u00b9,\u2078.0\u00b2,\u2077.0\u00b9\u2076,\u00b9\u2079.0\u00b9\u00b2,\u00b2\u00b9]henicosa-2,4,6,10-tetraen-10-yl]-12-oxa-8,17-diazaheptacyclo[15.5.2.0\u00b9,\u00b9\u2078.0\u00b2,\u2077.0\u2078,\u00b2\u00b2.0\u00b9\u00b9,\u00b2\u00b9.0\u00b9\u2075,\u00b2\u2070]tetracosa-2,4,6,14-tetraen-9-one"], "biological_process": ["terpenoid indole alkaloid biosynthetic process", "GO:0009709"]}, {"classification_names": ["alkaloid", "indole alkaloid", "terpenoid indole alkaloid", "monoterpenoid indole alkaloid", "akuammicine alkaloid"], "biological_process": ["terpenoid indole alkaloid biosynthetic process", "GO:0009709"]}]}

NPC:

{"class_results": ["Strychnos type"], "superclass_results": ["Tryptophan alkaloids"], "pathway_results": ["Alkaloids"], "isglycoside": false, "fp1": [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 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[Adafede]

So, hereafter the result of yaccl classification:

101,975/145,422 2D smiles classified.

The yaccl taxonomy encompasses 87,099 nodes. The output I generated has some issues (see rwst/yaccl#10 for a possible explanation on the rest)

The distribution of the depth of the obtained trees is as follows:

number of parents	count
1	13,139
2	844
3	290
4	245
5	3,062
6	2,327
7	9,357
8	32,958
9	13,714
10	4,624
11	5,410
12	703
13	203
14	194
15	24
16	3
17	2

[Adafede]

After further investigation, it appears that for example 12,973/13,139 over the yaccl nodes with only 1 parent miss their label, therefore are not linked to their taxonomies as long as the mentioned issue is not solved.

[Adafede]

One of the ids with only one parent is for example Q188152. I already had the same issue with biological taxa on WD. They are isolated children which usually miss just a single link to be then connected to the whole taxonomy. The curation potential is big.