Paper Tables in Postgres
Contents
List of Paper Tables in Postgres (Alphabetical)
pap_affiliation
Contains the affiliation (location) of one or more authors of the paper, meeting abstract, or gazette article
For papers, this table mostly contains legacy information that was imported from the CGC when WormBase starting curating paper data, as PubMed currently does not curate all author affiliations for papers.
For meeting abstracts and gazette articles, this table contains the full list of affiliations, but the affiliations are not mapped to specific individuals.
pap_author
Contains the author_id
pap_author_index
author_id as joinkey
pap_author_possible
author_id as joinkey
pap_author_sent
author_id as joinkey
pap_author_verified
author_id as joinkey
pap_contained_in
Contains the WBPaper IDs for books in which book chapters are found.
pap_contains
Currently empty. May be able to delete.
Information is already found in the pap_contained_in table.
pap_curation_flags
Contains one of five values for information on how the paper should be treated in subsequent pipelines, RNAi data, and the status of the gene-paper associations.
functional_annotation - this tag is placed on papers that are used to compose concise descriptions, but for which there is no curatable C. elegans data.
genestudied_done - this tag is placed on papers when the gene-paper associations are complete.
Phenotype2GO - this tag is placed on papers that will be used to create Phenotype2GO annotations.
rnai_curation -
rnai_int_done -
pap_day
The day the paper is published. Note that not all papers have an associated publication day, some just have month and year, or just year.
If a PubMed-indexed paper, the day is taken from the day tag in the corresponding paper XML:
<PubDate> <Year>2011</Year> <Month>Feb</Month> <Day>4</Day> </PubDate>
pap_editor
This table holds the information on editors of paper objects, mostly books. The current ACeDB
PubMed has recently started indexing book chapters and differentiating between authors of the chapter and editors of the book. This is done in the XML by designating and Author Type:
<AuthorList Type="editors"> <Author> <LastName>Riddle</LastName> <ForeName>Donald L</ForeName> <Initials>DL</Initials> </Author> <Author> <LastName>Blumenthal</LastName> <ForeName>Thomas</ForeName> <Initials>T</Initials> </Author> <Author> <LastName>Meyer</LastName> <ForeName>Barbara J</ForeName> <Initials>BJ</Initials> </Author> <Author> <LastName>Priess</LastName> <ForeName>James R</ForeName> <Initials>JR</Initials> </Author> </AuthorList>
<AuthorList Type="authors"> <Author> <LastName>Ambros</LastName> <ForeName>Victor</ForeName> <Initials>V</Initials> </Author> </AuthorList>
History Tables
All paper history tables are in the format h_pap_X where X is the name of the corresponding table above.
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