add drug description to mychem.info from PubChem

newgene commented 1 year ago

PubChem looks like has informative description from their website:

https://pubchem.ncbi.nlm.nih.gov/compound/16051951

Description
Clindamycin hydrochloride is a S-glycosyl compound. ChEBI Clindamycin Hydrochloride is the hydrochloride salt form of clindamycin, a semi-synthetic, chlorinated broad spectrum antibiotic produced by chemical modification of lincomycin. Clindamycin hydrochloride is used as a solid in capsules. NCI Thesaurus (NCIt) An antibacterial agent that is a semisynthetic analog of LINCOMYCIN. Medical Subject Headings (MeSH)

Let's see if we can include these descriptions (or one of them) from PubChem or other sources in MyChem.info.

https://mychem.info/v1/query?q=16051951

colleenXu commented 1 year ago

perhaps related to the annotation service effort? https://github.com/biothings/biothings_explorer/issues/344#issuecomment-1583034829

erikyao commented 1 year ago

Description Text

The description text shown in the Title and Summary section of a Compound Summary page is actually the description of the mapped entities.

E.g. on the CID:16051951 page, the description Clindamycin hydrochloride is a S-glycosyl compound., is actually from its mapped CHEBI:176915 page.

The same pattern applies to mapped NCIt and MeSH.

Mapping

Therefore if we can find all the CID-ChEBI, CID-NCIt, and CID-MeSH mappings, we can fetch all the description texts.

Currently our plugin uses the XML files from pubchem/Compound/CURRENT-Full/XML folder; however, those XML files do not contain the mappings.

In the pubchem/Compound/Extras folder, there SHOULD be a SID-Map.gz file. According to the README:

This is a listing of all (live) SIDs with their source names and registry identifiers, and the standardized CID if present. It is a gzipped text file where each line contains at least three columns: SID, tab, source name, tab, registry identifier; then a fourth column of tab, CID if there is a standardized CID for the given SID.

However, this file is missing in the folder. Maybe we can ask NIH to provide it.

Also note that the CID-MeSH file does not provide MeSH IDs.

Source XML data for CID:16051951

Just FYI:

Click me

```xml

16051951

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4.4837

0

9.6799

7.9478

6.2158

7.9478

9.6799

4.4837

4.5407

6.2158

5.8497

5.3497

6.1588

4.8497

7.0818

6.2158

7.0818

6.4375

7.9478

5.3497

8.8138

5.3497

3.5896

6.0308

5.3497

6.6186

9.6799

6.4621

4.7973

6.4688

6.7251

4.9145

4.2433

7.8179

6.7527

6.5448

6.8682

6.9515

7.4109

8.8138

6.7527

8.8138

4.8128

3.3981

3

3.7812

5.6001

5.5168

4.7297

5.3497

5.9697

6.2158

8.4847

7.1202

6.983

6.117

10.2168

10.2999

9.6799

9.0599

1

3.31

4.941

3.31

1.31

0.31

1.31

4.31

6.3978

4.31

7.3488

5.81

6.3978

7.3488

2.81

3.31

1.81

8.1579

1.31

4.81

1.81

2.81

6.0888

9.0714

1.81

9.8804

4.31

7.2518

5.5285

5.8608

6.65

7.9654

7.4778

2.385

3.62

2.12

7.7119

8.5046

1

1.19

4.62

3.43

2.5

6.6784

5.8972

5.4991

9.5174

8.7247

1.81

1.19

1.81

0.69

0

9.516

10.382

10.2448

1.62

4.31

4.93

4.31

4.941

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0

Compound

Canonicalized

5

2021.05.07

1

Compound Complexity

7

E_COMPLEXITY

3.4.8.18

Cactvs

Xemistry GmbH

2021.05.07

502

Count

Hydrogen Bond Acceptor

5

E_NHACCEPTORS

3.4.8.18

Cactvs

Xemistry GmbH

2021.05.07

7

Count

Hydrogen Bond Donor

5

E_NHDONORS

3.4.8.18

Cactvs

Xemistry GmbH

2021.05.07

5

Count

Rotatable Bond

5

E_NROTBONDS

3.4.8.18

Cactvs

Xemistry GmbH

2021.05.07

7

Fingerprint

SubStructure Keys

16

extended 2

E_SCREEN

3.4.8.18

Cactvs

Xemistry GmbH

2021.05.07

00000371F07B3800460000000000000000000000000160000000240000000000000000000000001E06100800000D3FE5C046820003C00608080001101000000000000010000081880200035012218020574000071600930001F8D9A38E00000000000000000000000000000000000000000000

IUPAC Name

Allowed

1

2.7.0

Lexichem TK

OpenEye Scientific Software

2021.05.07

(2S,4R)-N-[(1S,2S)-2-chloro-1-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-methylsulfanyl-tetrahydropyran-2-yl]propyl]-1-methyl-4-propyl-pyrrolidine-2-carboxamide;hydrochloride

IUPAC Name

CAS-like Style

1

2.7.0

Lexichem TK

OpenEye Scientific Software

2021.05.07

(2S,4R)-N-[(1S,2S)-2-chloro-1-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(methylthio)-2-oxanyl]propyl]-1-methyl-4-propyl-2-pyrrolidinecarboxamide;hydrochloride

IUPAC Name

Markup

1

2.7.0

Lexichem TK

OpenEye Scientific Software

2021.05.07

(2S,4R)-N-[(1S,2S)-2-chloro-1-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-methylsulfanyloxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboxamide;hydrochloride

IUPAC Name

Preferred

1

2.7.0

Lexichem TK

OpenEye Scientific Software

2021.05.07

(2S,4R)-N-[(1S,2S)-2-chloro-1-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-methylsulfanyloxan-2-yl]propyl]-1-methyl-4-propylpyrrolidine-2-carboxamide;hydrochloride

IUPAC Name

Systematic

1

2.7.0

Lexichem TK

OpenEye Scientific Software

2021.05.07

(2S,4R)-N-[(1S,2S)-2-chloranyl-1-[(2R,3R,4S,5R,6R)-6-methylsulfanyl-3,4,5-tris(oxidanyl)oxan-2-yl]propyl]-1-methyl-4-propyl-pyrrolidine-2-carboxamide;hydrochloride

IUPAC Name

Traditional

1

2.7.0

Lexichem TK

OpenEye Scientific Software

2021.05.07

(2S,4R)-N-[(1S,2S)-2-chloro-1-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(methylthio)tetrahydropyran-2-yl]propyl]-1-methyl-4-propyl-pyrrolidine-2-carboxamide;hydrochloride

InChI

Standard

1

1.0.6

InChI

iupac.org

2021.05.07

InChI=1S/C18H33ClN2O5S.ClH/c1-5-6-10-7-11(21(3)8-10)17(25)20-12(9(2)19)16-14(23)13(22)15(24)18(26-16)27-4;/h9-16,18,22-24H,5-8H2,1-4H3,(H,20,25);1H/t9-,10+,11-,12+,13-,14+,15+,16+,18+;/m0./s1

InChIKey

Standard

1

1.0.6

InChI

iupac.org

2021.05.07

AUODDLQVRAJAJM-XJQDNNTCSA-N

Mass

Exact

1

2.1

PubChem

ncbi.nlm.nih.gov

2021.05.07

460.1565488

Molecular Formula

1

2.1

PubChem

ncbi.nlm.nih.gov

2021.05.07

C18H34Cl2N2O5S

Molecular Weight

1

2.1

PubChem

ncbi.nlm.nih.gov

2021.05.07

461.4

SMILES

Canonical

1

2.3.0

OEChem

OpenEye Scientific Software

2021.05.07

CCCC1CC(N(C1)C)C(=O)NC(C2C(C(C(C(O2)SC)O)O)O)C(C)Cl.Cl

SMILES

Isomeric

1

2.3.0

OEChem

OpenEye Scientific Software

2021.05.07

CCC[C@@H]1C[C@H](N(C1)C)C(=O)N[C@@H]([C@@H]2[C@@H]([C@@H]([C@H]([C@H](O2)SC)O)O)O)[C@H](C)Cl.Cl

Topological

Polar Surface Area

7

E_TPSA

3.4.8.18

Cactvs

Xemistry GmbH

2021.05.07

128

Weight

MonoIsotopic

1

2.1

PubChem

ncbi.nlm.nih.gov

2021.05.07

460.1565488

28

9

0

2

-1

```

This section can be pulled with the following command:

zcat Compound_016000001_016500000.xml.gz | sed -n '49819264,49820357p;49820358q'

newgene commented 12 months ago

We might end up don't have to do extra ID mappings, since we already have the mappings to CHEBI, NCIT and UMLS.

For the particular case above:

https://mychem.info/v1/chem/AUODDLQVRAJAJM-XJQDNNTCSA-N?fields=unii.ncit,chebi.id,umls.mesh

We don't have mesh ID for this drug/chemical, but some objects do have like "Hydromorphone":

https://mychem.info/v1/chem/WVLOADHCBXTIJK-YNHQPCIGSA-N?fields=unii.ncit,chebi.id,umls.mesh

Then we can get their descriptions from our CHEBI and NCIT APIs:

https://biothings.ncats.io/chebi/chemical/CHEBI:176915?fields=def (checked that don't have def field in the latest CHEBI obo file) https://biothings.ncats.io/chebi/chemical/CHEBI:5790?fields=def (this one does have the def field)

https://biothings.ncats.io/ncit/node/NCIT:C47977?fields=def https://biothings.ncats.io/ncit/node/NCIT:C62034?fields=def

Not sure if we can get mesh description easily based on the MESH id, but we can go with CHEBI and NCIT first.

newgene commented 12 months ago

This mychem query can be useful to list all hits contains all three IDs:

https://mychem.info/v1/query?q=_exists_:umls.mesh%20AND%20_exists_:chebi.id%20AND%20_exists_:unii.ncit&fields=umls,chebi,unii

newgene commented 12 months ago

As the next step, we probably don't need to do anything yet at MyChem.info side. We can implement the logic at the Translator Annotator Service side, using the existing mapped CHEBI and NCIT IDs to retrieve their descriptions. We will then evaluate how good they are, if we need to improve the mapping at MyChem.info (e.g. using PubChem's extra mapping file) and also how we can get the MESH description.

Later, it will still be good to include these descriptions directly in MyChem.info.

newgene commented 10 months ago

Drug/Chemical description:

from CHEBI: MyChem.info also has the chebi.definition field available, we don't need to do anything
from NCIT: MyChem.info currently has the mapping from chemical/drug to NCIT term ID via unii.ncit field. The description/definition value can be then retrieved from our NCIT biothings API at https://biothings.ncats.io/ncit.

Here are a few examples from the Translator Annotator service, which uses multiple BioThings APIs, including MyChem.info, to annotate chemicals/drugs:

Closing this issue now, since we don't need to include additional chemical/drug description fields for now.

biothings / mychem.info