Introducing Gene Retriever

An international collaboration produces the first data mining solution to retrieve all genes associated with a list of articles.

Investigators seeking novel biomarkers and clues to disease mechanisms have asked countless times: “What genes are referenced in the results of my PubMed search?” Gene Retriever, a collaboration between Acumenta Biotech, the builder of Literature Lab™ and Sidra Medicine, answers this critical question by creating gene lists from the results of any PubMed search.

Comprised of software written by the Advanced Application team in Sidra Medicine’s Biomedical Informatics department and the Literature Lab™ database and Gene Thesaurus™, Gene Retriever is an easy-to-use software application for Mac or Windows computers:

Gene Retriever allows users to retrieve all genes associated with a lit of articles.

How it works

GRResultSummary1.PNG

Gene Retriever processes a list of PubMed IDs that you submit, and produces an analysis of the genes mentioned in the title, text and MeSH tags of each record.

Results are ranked and presented in a spreadsheet that enables quick and comprehensive analysis. Hyperlinks are provided for instant review of the genes or PubMed IDs of interest.

GRResultSummary2.PNG

How accurate is Gene Retriever?

Very accurate. At the core of the Literature Lab™ database is the Acumenta Biotech Gene Thesaurus™, a repository of gene, protein and pathway nomenclature gathered from the major genomic databases, and human-curated to produce searches combining high precision and high recall. The Gene Thesaurus™ is unique because it is constantly updated on the Literature™ Lab platform, and human curation resolves ambiguous terminology, alias redundancy and generic terms.

 

APPLICATION

The large number of factors involved in the pathogenesis of certain diseases makes the identification of a targeted, manageable-sized list of genes involved in these interactions extremely difficult. 

Portion of the immune response network in patients with inflammatory bowel diseases.

Portion of the immune response network in patients with inflammatory bowel diseases.

Gene Retriever helps identify genes that are highly associated with a particular disease, allowing construction of gene panels that contain putative disease signatures. These signatures can be used as biological markers of disease to classify patients for personalized care.

 

analyzing your PubMed search with Gene Retriever

GR_PubMed_Window.PNG

Start with a PubMed search specific to your subject of interest.

After running the PubMed search, click on the “Send to” link in the upper right corner of the search results and select “File”. This will expand the window - select “PMID List” in the “Format” drop-down menu and click “Create File”. The file of PubMed IDs will be downloaded to a location that you specify on your computer.

Put this file in the Gene Retriever Input File directory, select it and click “RUN”. The analysis will begin immediately and the results spreadsheet will be placed in the Gene Retriever Output File directory.

The Literature Lab database starts on January 1, 1990. If you want to see the genes in a specific time-frame, you can add date-range controls to your search using the following addition to your search:

Put your search in parentheses and add the syntax as shown in the example below. You can tailor the date range to meet your interest.

( your search ) AND "1980/01/01"[EDAT] : "2019/08/31"[EDAT]


how do I get Gene Retriever?

It’s easy. Gene Retriever is provided with any License of the Literature Lab™ database.

Now you can have something you always wanted but couldn’t get: an easy, thorough and accurate retrieval of the genes in the results of your PubMed searches.

Click here to request more information about Literature Lab!

see pricing and how to get started with with Gene Retriever.