Preliminary Ideas for Use Cases

Note - See the Use Cases Project for an overview of use cases and activities.

Also tracked in GitHub - https://github.com/covidgraph/documentation/issues/35

As a researcher, I would like to...

• Get a list of gene symbols, ordered by number of publications and/or patents that mention it. Synonyms should be grouped together.
• Get a list of all publications and/or patents that mention a selected gene symbol or one of its synonyms.
• 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

Also tracked in GitHub - https://github.com/covidgraph/documentation/issues/37

As patent lawyer, I would like to know:

• Get a list of publications that are cited in a patent
  • select the publication dates of the publications
• Get the priority date for each patent
• Get a list of applicants and inventors given a patent / patent family
• Get the list of countries the patent or other family members are filed
  • get the status in each patent application
• Get a list of genes/proteins mentioned in the claims
  • Sub-claims
• Get the list of cited patents
• Given a patent, get the list of:
  • bib data
  • divisional patent applications
  • descriptions
• Get the list of publications from the list of inventors on the patent
  • get the list of genes/proteins that are mentioned in these publications
• Get the list of publications where a gene or protein or drug is mentioned
• Get a list of clinical trials given a company
  • in what phase is the specific clinical study
• Given a company:
  • what are there patents
  • what is the status of each patent
  • when do they expire
• Get a list of drugs, compounds, gene symbols, proteins ordered by number of publications and/or patents that mention it. Synonyms should be grouped together.