Dictyostelium discoideum (Retired): Difference between revisions

Revision as of 12:16, 8 June 2007

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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.

We run a weekly script that searches all of PubMed for citations containing 'Dictyostelium' or 'D. discoideum' 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. If a puplication that the curators find has been missed by the automatic script, programmers run a small script to import the missing reference.

Curators link the new papers manually to genes.

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 and 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.

@@ Line 5: / Line 5: @@
 ----------------------
-We do basically the same as SGD.
 ==== L - Total Publications ====
@@ Line 13: / Line 12: @@
 in dictyBase.
-There are two scripts that run to identify relevant papers.   Then
+We run a weekly script that searches all of PubMed for  citations containing 'Dictyostelium' or 'D. discoideum' 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. If a puplication that the curators find has been missed by the automatic script, programmers run a small script to import the missing reference.
-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.
-. The PubMed script searches all of PubMed, weekly, for  citations containing 'dictyostelium' or 'D. discoideum' 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.
+Curators link the new papers manually to genes.
-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.
-. 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 ====
@@ Line 41: / Line 23: @@
 ==== 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.
+This is the number of papers read and 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 ====