Frequently Asked Questions

Diseases, genes, variants, and keywords. Mastermind supports searches by disease or gene. Searching by disease allows you to see all the genes and variants associated with that disease. You can also search by variants. Searching by gene or variant allows you to see all the diseases that involve the gene or variant. Each of these searches allow users to see and interact with all articles associated with these search terms. The Advanced Search capabilities of Mastermind Professional Edition support user-defined text-based queries in combination with multiparameter disease, gene, variant or keyword searches.

The Advanced Search capabilities are part of Mastermind Professional Edition and can be used to search for user-defined, free-text terms in the title or abstract of any publication in addition to performing multi-parametric searches for multiple disease, gene, or variant combinations using AND or OR operators.

Many. While the data content remains the same between Mastermind Free and Mastermind Professional, there are several differences between the two versions. High-volume users with more specific analytic needs would benefit from use of the Professional Edition. The key differences are outlined here in our feature comparison.

HGNC and others. Mastermind uses Hugo Gene Nomenclature Committee (HGNC; http://www.genenames.org/ ) nomenclature for gene symbol display. Additional synonyms are drawn from multiple other sources including UniProt ( http://www.uniprot.org/help/gene_name).

Yes. Mastermind displays all the variants found whether they were present in the title, abstract, PubMed metadata, or anywhere in the full text. Mastermind Professional Edition has an advanced search function that allows users to switch between displaying results specifically from PubMed only versus displaying results from full-text articles.

Pretty sure. No search engine will ever have 100% sensitivity, but we believe that Mastermind is much more sensitive than any other method or variant database software available. We have done promising benchmarks in the past:

Google Scholar vs. Mastermind

COSMIC vs. Mastermind

…and making improvements to Mastermind to address this issue:

Machine Learning Enhancements in Mastermind

…and are assembling additional data now that speaks to the statistical confidence users can expect of a null result when using Mastermind.

If an article is found to be missing or information was from the article was misinterpreted by Mastermind, feel free to reach out to us through the “Contact Us” link within Mastermind or otherwise email us at support@genomenon.com.

HGVS and others. Mastermind searches the literature for any one of dozens of different variant nomenclatures – standardized (e.g. HGVS; http://www.hgvs.org/) or not. For data display, the protein co-ordinates of the variants are used preferentially to make it easier to find and interact with relevant articles, irrespective of nomenclature used by each author.

Entering a gene name in the “Gene” search box on the Mastermind home page will enable the “Variant” search box. Variants can be entered by typing the variant name using HGVS (or any other valid variant nomenclatures) either in cDNA or protein co-ordinates or by rsID.

Mastermind can be used to search for coding variants including missense variants; insertion, deletion, and indel variants; nonsense variants; and frameshift variants. Mastermind will also search for non-coding variants affecting 5’- and 3’-untranslated regions (UTRs), splice donor/acceptor sites, and introns as well as intergenic variants up- and down-stream of neighboring genes.

Mastermind uses shorthand identifiers to represent each type of variant in the protein space. The shorthands used by Mastermind are as follows:

• • Insertions: “ins” — e.g. V600ins
  • Deletions: “del” — e.g. V600del
  • Indels: “delins” — e.g. V600delins
  • Nonsense: “X” — e.g. V600X
  • Frameshift: “fs” — e.g. V600fs
  • Untranslated regions: “UTR” — e.g. 5’UTR
  • Splice donor: “sd” — e.g. V168sd
  • Splice acceptor: “sa” — e.g. N581sa
  • Intronic: “int” — e.g. E46int
  • Upstream genetic variant: “ugv” — only ugv
  • Downstream genetic variant: “dgv” — only dgv

The “Filter by” input in the “Variants” section of the Mastermind results page can be used to find such variants. For example, typing “ins” or “del” will filter the results for all insertions and deletions cited in that gene. Other shorthands can be used in the same way.

Not yet. Mastermind does not currently enable searches by genomic coordinate. However, genomic variants within VCF files are properly annotated, and searching by genomic coordinates in the user interface has been added to our list of features to be considered for future Mastermind software releases. Want to move this feature request up in the queue? Contact us.

The Relevance of an article is a measure of both clinical relevance of the article and contextual relevance to your search query. Clinical relevance is informed by the content of the article, as well as the journal’s impact score, recency of the publication, and other metadata about the article. Contextual relevance includes considerations including how frequently the selected search terms are mentioned in the text of the article, how close together they appear, and where they appear in the article. Relevance is intended to be a relative and not an absolute estimation of the relevance of the content to your search queries. This ranking is depicted in the impact plot – the size of each circle represents the relevance of the article to the selected key terms, the larger the circle, the greater the relevance. By default, Mastermind will order the publications by their relevance in the Articles List.

The impact factor (IF) of an academic journal is a measure of the average number of citations for articles published in that journal. It is frequently used as an estimate of the relative importance of a journal within its field. The impact factor plot shows each article by publication date along the x-axis and impact factor along the y-axis, with the relevance of the article represented by the size of the bubble.

Categories are part of Mastermind Professional Edition. The default keyword categories in Mastermind Professional include: ACMG Interpretation, Clinical Significance, Genetic Mechanism and Significant Terms in Abstract. Each of these categories allows the user to display only those articles that contain content that is relevant to each individual category based on the appearance of any of the given category’s key terms. The ACMG Interpretation category contains a number of subcategories, such as Functional Studies and Segregation Information, that facilitate identification of articles useful for ACMG/AMP interpretation. The Significant Terms in Abstract category identifies keywords that are specifically associated with the content for the disease and gene in the original search. Mastermind produces this list of custom key terms by aggregating the content of each of these articles, performing a word frequency calculation, normalizing this list against the rest of scientific literature, and then ordering the terms by their frequency of occurrence in the content of interest. As an example, for the disease-gene association Melanoma-BRAF, this category includes anti-BRAF inhibitors like Vemurafenib and Imatinib, other genes such as GNAQ, and ancillary disease terms like uveal.

No. However, Mastermind has a partnership with Saphetor to provide link-outs to VarSome, which aggregates much of this publicly available data. Additionally, Mastermind links out to Google Scholar for additional information from patents and conference abstracts. We have a number of partnerships that will be announced in the coming months as well.

Yes. Genomenon offers gene panel design and variant database assembly, in addition to custom services in clinical NGS experimental design and drug discovery or repurposing projects.

Yes. Mastermind supports batch upload of VCF files. To learn more visit: https://mastermind.genomenon.com/vcf

Google Chrome is the preferred browser. For instance, to view the articles as PDFs in Mastermind, you will need to use Google Chrome and have the Mastermind extension installed from the Google Chrome Webstore:

https://chrome.google.com/webstore/detail/mastermind-extension/afjaifocdahgfpfgepaniahacjjoeeli?hl=en-US

If you do not have Google Chrome installed, you can download it from https://www.google.com/chrome/ and follow the download instructions for your computer platform.

Mastermind is also accessible in Firefox, Safari, and Internet Explorer 11, though some features may be limited.

Yes. There is a Mastermind API to access some data programmatically. You will need a separate license key to use the Mastermind API. To learn more visit: https://mastermind.genomenon.com/api

In addition to the published API, custom APIs are available upon request.