Literature

Textpresso for Echinoidea

Published and publicly available sea urchin research papers are regularly collected for updating the literature links and the reagent data in SpBase. The literature date including title, abstracts, full length text, etc. are also used for updating our literature database "Textpresso for sea urchin". First, all the sea urchin research papers are fetched from PubMed. We use a scripts adapted from get_PMID.pl written by Textpresso developing team and keyword phrases shown below to exhaustively search PubMed literature database for sea urchin related papers. Any paper that contains one of the keywords in the title or abstract would be selected. In this beginning step, PMID numbers of the papers related to sea urchin and echinoderms are collected.
Collected PMID numbers are used to fetch items such as abstract, author, journal, publication date, etc for each of the papers using get_bib_info.pl scripts which were also written by Textpresso team. Only a small fraction of the full length papers in PDF can be automatically fetched by downloadPDF.pl script. Therefore, it is necessary to download PDF files manually from PubMed and other online resources. Finally, each paper is examined for relevance to sea urchin research by the content of the abstract, and true sea urchin (Echinoidea) papers are selected. Research papers for Echinodermata are selected in the same manner.