[BlueObelisk-discuss] List of chemical names and identifiers

[Peter Murray-Rust]

I am now enhancing contentmine.org to search the daily literature and need
dictionaries to match names. I don't mind false negatives so am simply
matching names, but they should have identifiers.

The format would simply be:
name="ethyl acetate" id="a123"

Peter Ertl has supplied a list of > 10000 wikipedia entries + Inchis
(thanks).

I would ideally like classifications such as:
drugs (INNs)
pesticides
herbicides
etc.
as that will help to get non chemists interested.

The size of dictionaries can be between 100 and 100K approx.

Is there a simple way to get such a list out of ChEBI?

P.

[Zaharevitz, Daniel (NIH/NCI) [E]]

I should be able to give you our list of approved (U.S.) oncology agents. I think I can also give you our list of oncology investigational agents.

DanZ


/***************************************
* Daniel Zaharevitz, PhD
* Chief, Information Technology Branch
* Developmental Therapeutics Program
* DCTD, NCI
* ***@mail.nih.gov
***************************************/


From: Peter Murray-Rust <***@cam.ac.uk<mailto:***@cam.ac.uk>>
Date: Tuesday, March 8, 2016 at 1:43 PM
To: BlueObelisk-Discuss <blueobelisk-***@lists.sourceforge.net<mailto:blueobelisk-***@lists.sourceforge.net>>
Subject: [BlueObelisk-discuss] List of chemical names and identifiers

I am now enhancing contentmine.org<http://contentmine.org> to search the daily literature and need dictionaries to match names. I don't mind false negatives so am simply matching names, but they should have identifiers.

The format would simply be:
name="ethyl acetate" id="a123"

Peter Ertl has supplied a list of > 10000 wikipedia entries + Inchis (thanks).

I would ideally like classifications such as:
drugs (INNs)
pesticides
herbicides
etc.
as that will help to get non chemists interested.

The size of dictionaries can be between 100 and 100K approx.

Is there a simple way to get such a list out of ChEBI?

P.


--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
[phone]

[Peter Murray-Rust]

That's great. And in return we should be able to tell you papers in which
they appear on the day they are published.


On Tue, Mar 8, 2016 at 6:47 PM, Zaharevitz, Daniel (NIH/NCI) [E] <

Post by Zaharevitz, Daniel (NIH/NCI) [E]
I should be able to give you our list of approved (U.S.) oncology agents.
I think I can also give you our list of oncology investigational agents.
DanZ
/***************************************
* Daniel Zaharevitz, PhD
* Chief, Information Technology Branch
* Developmental Therapeutics Program
* DCTD, NCI
***************************************/
Date: Tuesday, March 8, 2016 at 1:43 PM
Subject: [BlueObelisk-discuss] List of chemical names and identifiers
I am now enhancing contentmine.org to search the daily literature and
need dictionaries to match names. I don't mind false negatives so am simply
matching names, but they should have identifiers.
name="ethyl acetate" id="a123"
Peter Ertl has supplied a list of > 10000 wikipedia entries + Inchis (thanks).
drugs (INNs)
pesticides
herbicides
etc.
as that will help to get non chemists interested.
The size of dictionaries can be between 100 and 100K approx.
Is there a simple way to get such a list out of ChEBI?
P.
--
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
[phone]

[Geoffrey Hutchison]

Post by Zaharevitz, Daniel (NIH/NCI) [E]
I should be able to give you our list of approved (U.S.) oncology agents. I think I can also give you our list of oncology investigational agents.

Aren't most of these in the MESH database? (https://www.nlm.nih.gov/mesh/)

-Geoff

[Peter Murray-Rust]

Post by Zaharevitz, Daniel (NIH/NCI) [E]
I should be able to give you our list of approved (U.S.) oncology agents.
I think I can also give you our list of oncology investigational agents.
Aren't most of these in the MESH database? (https://www.nlm.nih.gov/mesh/)

Sure - I was wanting a simple linear list of chemicals. would there be a
simple way of extracting these?

[Egon Willighagen]

Peter,

Post by Peter Murray-Rust
I am now enhancing contentmine.org to search the daily literature and need
dictionaries to match names. I don't mind false negatives so am simply
matching names, but they should have identifiers.
name="ethyl acetate" id="a123"

For WikiPathways were use BridgeDb, and I take care of the metabolite
identifier mapping database, which includes names and synonyms. The
latest BridgeDb file is at Figshare [0], but I guess you want to above
format, right?

But which identifier do you want? Any? Does the name come from the
database matching the identifier?

I have been using HMDB, ChEBI, and since almost a year Wikidata...

Egon

0.https://figshare.com/articles/Metabolite_BridgeDb_ID_Mapping_Database_20160113_/3083842/1
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/EgonWillighagen

[Egon Willighagen]

On Wed, Mar 9, 2016 at 3:39 PM, Egon Willighagen

Post by Egon Willighagen
I have been using HMDB, ChEBI, and since almost a year Wikidata...

So, awaiting some context for the identifier, this is the SPARQL to
get English labels:

PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
SELECT ?compound ?label WHERE {
?compound wdt:P31 wd:Q11173 ;
rdfs:label ?label .
FILTER (lang(?label) = "en")
} LIMIT 5

At https://query.wikidata.org/ and you can save as in several formats...

P31 is "instance of" and Q11173 is "chemical compound".

Egon
--
E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
LinkedIn: http://se.linkedin.com/in/egonw
Blog: http://chem-bla-ics.blogspot.com/
PubList: http://www.citeulike.org/user/egonw/tag/papers
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/EgonWillighagen