How to search molecules with keywords only

Modified on Wed, 13 Nov at 11:24 AM

How to easily search a molecule from any written form (with Orbit Chemistry optional module)

TABLE OF CONTENT

Preliminary advice
Search engine behaviour and tips
Detailed example
Further tips

Preliminary advice

In order to carry out your search and query optimisation attempts, you should consider the TI/AB or BI/SA fields so as not to saturate the search engine and to obtain results within a reasonable time.

Search engine behaviour and tips

If middle or internal word(s) are 1 character, they will be suppressed and replaced by the nW proximity operator (n equalling the number of words suppressed).

If you enter e.g. amino 3 hydroxylpyridine, Orbit will search AMINO 1W HYDROXYLPYRIDINE. If you use operators to link your terms, middle/internal words will not be suppressed and replaced.

Hyphens separating two terms are deleted for searching and replaced by the implicit adjacency (see the joint operator _ ). Generally, non-alphanumerical characters (hyphens, parentheses, commas, etc.) are not considered characters and are treated as spaces.

The use of quote marks should be reserved for putting around digits ("5") and words that could be interpreted as operators ("AND").

Greek characters should be spelled out in searches: beta, alpha, etc. For example, β could be searched by (“B” OR BETA)

Detailed example

Searching 2-amino-3-hydroxipyridine

The first step is to list synonyms for the substance being searched:

3-Pyridinol, 2-amino
2-Amino-3-hydroxypyridine

2-Amino-3-hydroxylpyridine
2-Amino-3-pyridinol

2-Amino-3-pyridol

Amino-3-hydroxypyridine
3-Hydroxy-2-aminopyridine
3-Hydroxy-2-pyridinamine
2-Amino pyridin-3-ol

NSC 136806
CAS number : 16867-03-1

The second step is to rewrite each synonym in Questel language:

3-Pyridinol, 2-amino:

"3" W pyridinol W "2" W amino?

2-Amino-3-hydroxypyridine/ 2-Amino-3-hydroxylpyridine:

"2" W amino W "3" W hydroxy?_pyridin?

2-Amino-3-pyridinol/2-Amino-3-pyridol:

 "2" W amino W "3" W pyrid??ol

Amino-3-hydroxypyridine:

amino W "3" W hydroxy?_pyridin?

3-Hydroxy-2-aminopyridine:

"3" W hydroxy W "2" W amino_pyridin?

3-Hydroxy-2-pyridinamine:

"3" W hydroxy W "2" W pyridin_amin?

2-Aminopyridin-3-ol:

 "2" W amino_pyridin? W "3" W ol

NSC 136806:

NSC W 136806

CAS number:

16867 W "03" W "1"

Single digits must be enclosed in double quotes to avoid any confusion with search query set numbers. If there are single letters that might be read by the system as operators such as AND, OR, NOT, S, P, etc. enclose those in quotes as well.

The third step is to run the various queries and combine the results via your session search history:

("3" W pyridinol W "2" W amino?)/BI/TX -> 3 results
("2" W amino W "3" W hydroxy?_pyridin?)/BI/TX -> 2783 results
("2" W amino W "3" W pyrid??ol)/BI/TX -> 47 results
(amino W "3" W hydroxy?_pyridin?)/BI/TX -> 2810 results
("3" W hydroxy W "2" W amino_pyridin?)/BI/TX -> 17 results
("3" W hydroxy W "2" W pyridin_amin?)/BI/TX -> 2 results
("2" W amino_pyridin? W "3" W ol)/BI/TX -> 183 results
(NSC W 136806?)/BI/TX -> 0 result
(16867 W "03" W "1")/BI/TX -> 3 results
1:9 -> 2980 results

Further tips

To have a comprehensive search, you can if necessary adjust the proximity allowed by the W operator (1W, 2W, etc.) as well as selecting different fields to search. You can also add limited truncation (?) to be more flexible on the names of the compounds as well as using one or more joint operators _ (up to five). Please note that + must be avoided around one or two characters.

Using the KWIC tab when viewing your search results is recommended for this type of search. This will allow you to quickly determine whether the compounds found are consistent with those you are looking for.