Given a biological term(s) of interest (e.g. G-quadruplex: MeSH Unique ID: D054856), I am looking for a robust tool to extract all known human gene names (e.g. TP53, P53) found to co-occur in proximity to my query biological term in the entire body of abstracts / freely available main texts in the whole of PubMed.
On the basis of a previous post, the most useful tool that I have tested so far is PolySearch2. You can type a query keyword after selecting Given:Text and marking Find ALL associated: e.g. Genes/proteins. In the end of the day, you can get a result table like the following and download all associations in .json format.
However I can think of two drawbacks though:
(1) Although it returns an Entity id that can be later searched for the corresponding gene name in the thesauri provided in the Downloads, it does not return any standard Ensembl gene ids or UniprotKB accessions.
(2) I could not find a way to extract results from a given species only e.g. Homo sapiens
Are you aware of any other tool that would allow me to find similar associations between biological terms in general and gene names?