Entering New Paper Objects
Approving Papers through the Paper Editor
Sources and types of papers that get entered
Papers and abstracts from different sources and containing a variety of content are entered into postgres and included in WormBase. The protocol for entering a specific paper depends upon the type and subject matter of the paper, and whether or not the paper is indexed by PubMed. For the purposes of this documentation, the type refers to type as specified by PubMed or as specified in the ?Paper model in WormBase.
C. elegans Papers Indexed by PubMed
Every day, a script sends a query to PubMed using the keyword 'elegans'. New papers are entered into PubMed Tuesday thru Saturday.
The keyword search will retrieve new, unindexed papers for which the term 'elegans' exists in either the title or the abstract. The search will also return indexed papers for which there was no mention of 'elegans' in the title or abstract but through which subsequent MeSH indexing the paper is now associated with 'elegans'.
Since 'elegans' can refer to species other than Caenorhabditis elegans and since there are papers that mention C. elegans in the abstract yet don't report any experiments using C. elegans, a curator reviews the papers daily to select those that should be included in the curation pipeline and WormBase bibliography.
There are three mutually exclusive options (decisions) for a paper:
Select 'approve' from the drop-down menu if the paper should be added to the WormBase bibliography.
Select 'reject' if the paper should not be included in the WormBase bibliography.
Select 'remove' if the paper is about C. elegans but will not be entered through the paper editor. Why does this ever happen? PubMed does not index corrections or errata, but publishers will still sometimes erroneously send these journal entries to PubMed. When that happens, the correction or errata initially gets a PMID and appears in PubMed, but is then later removed from PubMed, and the PMID made invalid, during the indexing process. If we approve corrections and errata through the form, we will have papers with invalid PMIDs.
C. elegans Papers not Indexed by PubMed