VarSome Search

beta release

We are proud to release our first complete search feature for VarSome. This expands the existing search functionality of VarSome, enabling you to search not only for variants, but also to  perform word searches over the entire contents of VarSome: articles, diseases, phenotypes, genes, ClinVar & UniProt variants. Importantly this includes content provided by our user community.

Examples

  • shox: finds all the genes, disease, articles etc. that mention the SHOX gene.

  • royal disease: will return the disease, phenotypes & PubMed articles related to Haemophilia, including some ClinVar variants.

  • gene lung cancer: will return all genes associated to lung cancer.

  • disease emphizema: will list all diseases related to emphysema. Note that the search engine will suggest correct spellings or alternative spellings that would yield more results.

  • short stature syndrome: will list all results referring to short stature, you can then navigate the various landing pages to find associated phenotypes, diseases, publications and genes. Alternatively, searching forgene short statureimmediately returns the SHOX and SHOX2 genes.

  • “short stature”: the quotes mean that this phrase, with exactly this spelling, must be found in the results.

  • clinvar "likely pathogenic" renal failure: returns all variants classified in ClinVar as "Likely Pathogenic" and associated with renal failure. 

  • uniprot "pathogenic" "Q9UMX9": returns all variants classified by UniProt as pathogenic within protein Q9UMX9.

Results

Results are automatically ranked by relevance: this includes the words found, how often an article has been referenced in the VarSome database and the impact factor of the journal it is published in. Preference is given to genes, diseases and phenotypes.

You can narrow down the search results to a given result type by clicking on the corresponding link.

Clicking on a result will either take you to the standard VarSome page for a gene, or to a new dedicated page giving you all the available information for that result. This includes a list of all the items that refer to this result. For example, if you find a PubMed article, you can see genes, variants, diseases etc. that may refer to that article.

Advanced Search

As mentioned above, clicking on a type will refine the ranked results to only objects of that type, for example only genes or publications.

  • Alternatively you can narrow the result type by starting your query by one of the following keywords: “gene”, “disease”, “phenotype”, “article”, “clinvar” or “uniprot”. For example gene IVF.

  • Quoting words: adding quotes around a word tells the search engine to discard any entries that don’t contain exactly that word. This helps narrow a search if there are too many results.

In Conclusion

We hope you find this search feature useful. The results are specific to the contents of the VarSome database, including entries submitted by our user community, and are generally very different from what you would get from a generic web search. We have included a link to google so you can always try VarSome first.

This is very much a work in progress, so do please send us feedback and let us have your suggestions.

 

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