Dictyostelium discoideum (Retired)
We do basically the same as SGD.
L - Total Publications
For this metric, we count the total number of articles of any kind, including both research articles and reviews, associated with a gene in dictyBase.
There are two scripts that run to identify relevant papers. Then genes are associated with papers in two ways: 1) via a script that automatically associates the papers with the genes mentioned in the title or abstract, and 2) via manual association as part of our first-pass paper curation.
1. The PubMed script searches all of PubMed, weekly, for citations containing 'dictyostelium' in the title or abstract. It compares the references in the search with those currently in the database and adds new references to the database, unless the corresponding PubMed ID has been previously marked as inapproriate for dictyBase.
This script also makes automated links between references and the genes mentioned in each. For newly added papers, the genes mentioned within are automatically linked to the paper in dictyBase. It also compares the genes mentioned in each reference with those currently linked in the database and will add new links between a gene and a reference, unless the link has been previously marked as inapproriate. New links between genes and references are assigned the 'Not yet curated' topic.
In subsequent curation, curators may add links that were missed and will remove any inappropriate links that were made automatically.
2. Because the PubMed script misses some references, we also do a broader search on a weekly basis ('dictyostelium') of the references added to PubMed each week. This script runs automatically, immediately after the PubMed script runs on Friday nights. The script compares its list of hits to the references already in the dictyBase database, removes any that are already present, and loads the remainder automatically into a temporary location. Because this broader search contains a high proportion of irrelevant hits, the references must be reviewed to select the relevant ones. Links between these papers and any relevant genes are made manually by curators during the curation process.
Note that this second script was only begun in 2005. Prior to that time, our coverage of references relevant to D. discoideum will be less complete.
In addition to references added by scripts, curators will occasionally come across a paper that should be linked but is not, or a book chapter that is relevant to that gene. These references are added directly by curators.
M - Triaged papers
dictyBase does not do any triage to target papers for GO, so this column will contain 'n/a' for dictyBase.
N - Number of papers read
This is the number of papers read or checked for possible GO annotations by the curator who was responsible for the Reference Genome curation of that gene. This number is manually tracked by the curator during the curation process for reference genome genes. We don't track this number as a part of standard curation, just when genes are designated for the Reference Genomes project.
O - Number of papers producing GO annotations
This is the number of papers from which we actually made GO annotations.