research use case

As a researcher I would like to...

• Get a list of gene symbols that are mentioned in CORD-19 papers and active in kidney (background: Covid19 patients often have severe problems with kidney function
• Get a list of gene symbols, ordered by number of publications and/or patents that mention it. Synonyms should be grouped together.
  • select these genes and their synonyms ( +transcripts&synonyms ) and list the coding proteins with their gene function (GO-term)
• Get a list of all publications and/or patents that mention a selected gene symbol or one of its synonyms.
• Get the set of overlapping genes that are mentioned in Paper "with diabetes" and genes that are mentioned in Papers "with Covid19"
• Select a gene symbol, and get a list of other genes that are often mentioned in the same/related publications (gene clustering).
• Select a gene symbol and get the protein it transcribes for and all the publictaions/patents that mention that protein (or vice versa - select a protein and get gene/s).
• Select a virus type (H1N1, Mers-COV,...) from an ordered list and get all the publications/patents that mention it.
• Select a cell line or organism
• Select a drug
• Combine the mentioned search criteria: e. g.
• select an organism and get a list of genes or proteins that are mentioned most frequently together with it
  • select a gene and get a list of organisms mentioned together with it
  • select an organism and get a list of genes that the organism has
  • select a tissue (cell line) and get a list of genes that are expressed and vice versa
  • select a virus type and get a list of other organisms or cell lines that are mentioned together with it
• Have a visual representation of the number of mentions of genes, virus types etc
• Be able to access full text of publications or patents via a link

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• Be able to receive alerts when new information (based on criteria I select) is added into CovidGraph (e.g. new paper about a specific Therapeutic Indicator)
• Be able to create a long-list of useful nodes and be able to bookmark, tag or annotate results to narrow down to a short-list
• Be able to quickly review abstracts to help short-list
• Be able to focus search filters on abstracts to help short-list
• Be able to get a snap-shot of the state of the art in a specific area / topic.
• Be able to see what others are working on in the same area
• In certain cases share any annotations, bookmarks, tags etc with everyone (e.g. I work in Academia and want to share my findings)
• In certain cases keep any annotations, bookmarks, tags etc private (e.g. I work for a Pharma company that is concerned about IP)
• Be able to export results

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Given that medical domains are deeply divided, locating collaborators across domains is arduous. For instance, if a researcher wants to study ACE2 gene related to COVID-19, he or she would like to know the following: which researchers are currently actively studying ACE2 gene, what are the related genes, diseases, or drugs discussed in these articles related to ACE2 gene, and with whom could the researcher collaborate? This is a strenuous position to be in, and the aforementioned problems diminish the curiosity directed at the topic. From https://www.nature.com/articles/s41597-020-0543-2