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Tuesday, 27 October 2015

Advanced keyword and structure searches with SureChEMBL


Previously in the SureChEMBL series, we described how to access SureChEMBL data in bulk, offline and locally. So, you may ask, what is the point in using the SureChEMBL web interface? Well, how about the unprecedented functionality that allows you to submit very granular queries by combining: i) Lucene fields against full-text and bibliographic metadata and ii) advanced structure query features against the annotated compound corpus - at the same time?

Let’s see each one separately first:

Lucene-powered keyword searching

You may use the main text box for simple keyword-based patent searches, such as ‘Apple’, ‘diabetes’ or even 'chocolate cake' (the patent corpus as a recipe book is a new use-case here). You will get a lot of results and probably a lot of noise. With Lucene fields, you can slice and dice a query by indicating specific patent sections and bibliographic metadata, such as date/year of filing or publication, assignee, patent classification code, patent authority, etc. For example, to search for the term ‘diabetes’ only in the abstract of patents, you can search with:
ab:diabetes

where ab is the Lucene query field for abstract. For a full list of Lucene queries, see here. Furthermore, you can combine these fields with boolean operators (AND, OR, NOT - always in UPPER case) and brackets. For example to find US patents published in 2014 which also mention the word ‘diabetes’ in the title or abstract, you could search with:

(ttl:diabetes OR ab:diabetes) AND pdyear:2014 AND pnctry:US

or even limit it to more med-chem relevant patent hits by using the appropriate IPC hierarchical classification codes:

(ttl:diabetes OR ab:diabetes) AND ic:(C07D AND (A61K OR A61P)) AND pdyear:2014 AND pnctry:US

Is that all? No, you could also use wildcards, such as * and ?, as well as proximity searches:

(ttl:diabet* OR ab:diabet*) AND pdyear:2014 AND pnctry:US

A couple of thing worth pointing out here:
1) in the way described above, you may search not only the chemically-annotated (EP, US, WO, JP patents) or chemically-relevant corpus but any patent within SureChEMBL’s broad coverage, such as French, German, British, Chinese, Australian, Canadian, etc., patents about any topic:

pa:"Apple Inc" AND ab:vehicle AND pnctry:CN

for such cases, just remember to check the 'All authorities' box on the right hand side panel.
2) If the Lucene query syntax seems too complicated, almost the same functionality is available via a more user-friendly field-based widget called Fielded Search:
  

ChemAxon-powered structure searching

To begin with, SureChEMBL provides basic substructure and similarity searches against the currently 17 million chemical structures, powered by ChemAxon’s JChem technology. Some of you may have noticed that we have recently done some refurbishment around the sketchers and we now provide the latest MarvinJS sketcher as the sole source of structure input. We also removed the manual entry box, as it is superseded by functionality described below. Behind the scenes, we use the native ChemAxon inter-conversion functionality to ensure maximum compatibility and minimum information loss during structure conversions. The good news is that you can input a structure in several ways (besides sketching it from scratch), e.g. SMILES, SMARTS, CML, InChI, Molfile and IUPAC/trivial name. Just click and paste your string on the MarvinJS sketcher or open the import dialogue to paste it right there - or even upload a file. More importantly, you may now take advantage of more advanced query features, such as (NOT) atom and bond lists, explicit hydrogens, as well as the Markush-friendly position variation and repetition ranges.

For example, this is a query that combines atom, not atom, and bond lists, as well as explicit hydrogens to control substitution:


Or this one, which combines position variation and linker repetition range:


Again, don't forget that you have additional control over the MW range of the search hits, as well as their exact location in the patent document (title, abstract, claims, description, images/molfiles).


Combined keyword and structure searching

Finally, as mentioned in the beginning, you can easily submit combined keyword and structure queries, such as this one:


...to our knowledge, there's no other freely available patent searching resource or interface out there providing this type of functionality but we're happy to stand corrected...

As usual, for any questions or feedback, drop us a line.


George and Nathan

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