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Frequently Asked Questions


Mastermind FAQ


What is the source of articles for Mastermind's database of scientific literature?
PubMed. Mastermind uses PubMed as the source of the articles that are prioritized for full-text download. The content of the Titles and Abstracts are used to prioritize those articles that mention a gene or disease or any synonym of either entity for automatic full-text download and data processing.
How often is the Mastermind database updated?
Weekly. Mastermind performs weekly updates to its database by identifying what new content has been published in the preceding week and prioritizing this content for full-text download and data processing.
Can results change from day-to-day on the same search in Mastermind?
Yes. Because Mastermind data is updated on a weekly basis, as new articles are published, new content is simultaneously being added to Mastermind.
Does Mastermind provide access to articles to users without journal subscriptions?
No. Mastermind does not provide direct, on-line access to articles if those articles are not already available to users – either for free or through an institutional subscription. If a PDF is available to you through the publisher website, the PDF Viewer will allow you to view the full-text publication within Mastermind. If you do not have an institutional subscription to the journal, Mastermind will show you the sentence fragments where the search terms were found in the article and also will direct you to PubMed where you can link to the journal and pay a one-time access fee to obtain the manuscript.
Are genes and variants found in the tables and figures of full-text searches included in the Mastermind database?
Yes. Mastermind scans the entirety of the full-text in its search for gene names or variants including tables and figures.
Is supplemental data from PubMed currently included in the Mastermind database of scientific literature?
No. Mastermind v1.0 has not prioritized Supplemental data for download.
What is the source of the protein domain data shown in the "Protein Diagram" plot in Mastermind?
Protein domain data are obtained from the Universal Protein Resource (UniProt; http://www.uniprot.org/ ), a comprehensive, curated resource for protein sequence and annotation data.

Applications

Does Mastermind differentiate between positive and negative associations for diseases and genes or diseases and variants?
No. Mastermind does not draw conclusion about the nature of the association between the variant and the disease.
Does Mastermind provide variant interpretations or reports?
No. In contrast to knowledge-bases like HGMD, Mastermind does not draw conclusions about the clinical significance of individual variants but rather provides the user with all the evidence necessary to make these conclusions on their own.
How is Mastermind different from HGMD, ClinVar and other genomic knowledge-bases?
Mastermind is a variant curation tool. In contrast to HGMD, Mastermind does not draw conclusions about the clinical significance of individual variants but rather provides the user with all the evidence necessary to make these conclusions on their own.
What does Mastermind offer that differentiates it from PubMed and Google Scholar searches?
Comprehensive, pre-organized full-text searches of relevant literature. Mastermind provides a much greater depth of coverage of full-text articles relative to PubMed and Google Scholar. Mastermind has also indexed every possible genomic permutation (cDNA/protein, expanded/contracted, conventional/non-canonical) to create a comprehensive search environment that yields more results over PubMed and Google Scholar. Mastermind serves as a comprehensive variant curation tool to aggregate the results based on the biomedical literature, whereas PubMed and Google Scholar only catalogue citations.

Functionality

Can I see all the articles for a variant or gene that I search on – even if the variant or gene is not in the title or abstract of PubMed?
Yes. Mastermind displays the ALL variants found whether they were present in the Title and/or Abstract only or otherwise somewhere within the full-text.
How can you search for variants across the protein structure in Mastermind?
The protein diagram. Once you have searched for the gene of interest, the protein diagram in the association page displays all the variants along the linear axis of the protein.
Which types of variants can be searched in Mastermind?
Mastermind can be used to search for coding mutations, insertion and deletions (indels), non-sense mutations, and frameshift mutations. Mastermind will also search for non-coding variants affecting 5’- and 3’-untranslated regions (UTRs) and splice donor/acceptor sites.
How can I search for coding mutations in Mastermind?
Entering a gene name in the “Gene” search box on the Mastermind home page will evoke the “Mutation” search box. Coding mutations can be found by typing the one letter code of the original amino acid residue, followed by the position in the protein, and ending with the one letter code of the resulting amino acid. For example, V600E, refers to the change from valine to glutamic acid at position 600 in the protein. Coding variants can also be selected from the auto-fill drop down menu.
How are insertions and deletions, non-sense, frameshift, and non-coding variants displayed in Mastermind?
The “FILTER BY MUTATION” feature in the "Mutations" section of the Mastermind report can be used to find such mutations. For example, “INS” or “DEL” will filter the results for insertions and deletions. Typing “X” will filter for all non-sense mutations. Frameshift mutations can be found by typing “FS”. Typing “UTR” will filter the results for variants in untranslated regions of the protein. The abbreviations “SD” or “SA” can be used to filter the results for all splice donor or splice acceptor sites, respectively.
What gene formats and nomenclatures are supported in Mastermind?
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).
What variant formats & nomenclatures are supported in Mastermind?
HGVS and others. Mastermind searches the literature for any one of dozens of different variant nomenclature – standardized (e.g. HGVS; http://www.hgvs.org/) or not. For data display, the protein co-ordinates of the variants are used preferentially.
Can we search variants on genomic positions in Mastermind?
No. Mastermind v1.0 currently does not permit searches by genomic co-ordinate. However, this function has been added to our list of features to be considered for future Mastermind software releases.
What kind of queries does Mastermind support?
Diseases, genes, variants and keywords. Mastermind supports searches by disease name or gene name queries. You can also search by variants after a gene name is provided. The Advanced Search capabilities of Mastermind will support user-defined text-based queries in combination with disease, gene or variant searches.
How can I use the Advanced Search capabilities of Mastermind?
The Advanced Search capabilities of Mastermind can be used to search for user-defined, free-text terms in the title or abstract of any publication. This features allows you to quickly filter publication by keyword and also find publications where non-standard terminologies may be have been used by the corresponding author of the publication.
What is the association strength and how can I use it to qualify my results?
The association strength is a measure of 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. It 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 association strength in the Articles List.
What is the impact factor/impact plot and how can I use it to qualify or guide my results?
The impact factor (IF) or Journal impact factor (JIF) 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.
What are the Categories in Mastermind and how can they be used?
The default categories in Mastermind include: Diagnosis (Dx); Prognosis (Px); Treatment (Rx); Function (Fx); Inheritance (Ix); Mechanism (Mx); SNP or variation (SNP); Goldmine (GM); Case Report (CR); CM and Custom Match (CM). 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. Case Reports identify articles that are case reports as defined in PubMed. Goldmine articles include those articles that describe large-scale studies of cohorts where sequencing was performed (e.g. exome sequencing). The Custom Match identifies key words 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 orders the terms by their frequency of occurrence in the content of interest. As an example, for the disease-gene association Melanoma-BRAF, the Custom Match category comprises anti-BRAF inhibitors like Vemurafenib and Imatinib as well as other genes such as GNAQ and ancillary disease terms like uveal.
How can I see all articles for a given variant if the variant does not appear in the Title of Abstract of the paper?
In many instances, reported variants will not appear in the Title or Abstract of a paper, but may be mentioned in the body of the text. The Mutations section of Mastermind separately displays the number of variants identified in the full-text and Title or Abstract. Clicking on the “Full-text” link will display those papers where the variant was identified somewhere in the full-text. Note that the number of citations will be considerably larger than that for the Title/Abstract, and may need to be filtered further using other keyword or categories.
Can I input a VCF file into Mastermind?
No. Mastermind v1.0 currently does not support batch upload of VCF files. However, this function has been added to our list of features to be considered for future Mastermind software releases.

Implementation

What browsers are currently supported by Mastermind?
Google Chrome is the preferred browser. For instance, to view the articles as PDFs in Mastermind, you will need to use Google Chrome. Additionally, you will need to have the Mastermind extension for the Google Chrome Browser, which can be installed locally on your own computer:

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

If you do not have Google Chrome installed yet on your computer, you can download it from https://www.google.com/chrome/ and follow the download instructions for your computer platform.
Is Mastermind a desktop application or cloud-based?
Mastermind is a cloud-based software application.
Is Mastermind available through API access?
No. Mastermind v1.0 currently does not support API access. However user APIs are being developed for a future release to integrate Mastermind queries directly into your workflow. Please contact us if you would like to discuss your integration needs.