Citations and literature
This ticket adds support for citations and literature to Genesys.
What does this mean?
Researchers often use data from Genesys and refer to Genesys as the source of the data. Genebanks often maintain the list of citations referencing specific accessions in their collections. Either way, there is a paper published somewhere (with a URL) and a citation record. It is these citation records that we wish to include in Genesys.
A Citation
includes:
- title (text)
- author names (text)
- year of publication (number)
- journal (text)
- type (one of
enum
: Journal article, Book, Book section, Conference proceedings, Preprint, Report, Other) - article DOI (text, doi, must be unique in the database)
- download URL, if available (text, URL)
- abstract (long text)
- source of citation (one of:
enum
Google Scholar, bioRxiv, genebank, user submission) - relevance (one or more of:
enum
Genesys cited, Genesys used, Accession referenced, Genesys discussed, Genesys mentioned) - owner (SID) - user or
Partner
(like in datasets?) - status (one of
enum
: SUBMITTED, PUBLISHED, DUPLICATE, REJECTED) - statusText (text) - explanation why submission is not published
- link to valid
Citation
- used for duplicates, otherwisenull
Extra properties (next version)
Additionally we may consider including:
- author OrcIDs and countries/territories/islands of affiliation
- is paper peer reviewed?
- is paper open access?
- subject of research
- source of funding
- countries/territories/islands covered in research
Detecting duplicates
We'll use our Similarity method to detect similar/duplicate submissions. We'll compare the title, journal, year of publication, author names and abstract.
Linking to Citations
A Citation
may refer to Genesys in general (Genesys used, discussed, mentioned) or link to specific Accessions, Datasets, or Subsets. These "links" will then be rendered on corresponding details pages in Genesys.
Other text-based categories could include crops and species names.
User submissions
Users (any role) will be able to use a form in Genesys to submit a new citation. Genesys will first search for duplicates and present the matches to the user. If the user still wants to submit their citation, they'll need to include submitAnyway=true
in the API request.
New submissions will have status = SUBMITTED
until reviewed and handled by the Genesys team.
Users will be able to see their submitted citations (and their status) in their Dashboard.
Genebank submissions
In the future, genebanks will be able to push citations related to Accessions
(with GGCE).
Managing citations
Users with CITATION_MANAGER
or ADMINISTRATOR
role can modify and publish individual citations. The corresponding UI will be in their Dashboard.
They are able to add links to specific Accessions, Datasets, or Subsets.
Inspired by https://www.gbif.org/literature-tracking