DOI: 10.7488/ds/2589
title: SUPERSEDED - Human, yeast and pig genomics: sequence submissions and first sequence descriptions in the literature (1980-2015)

description: ## This item has been replaced by the one which can be found at https://doi.org/10.7488/ds/2718 ## This data collection is derived from two sources: 1) Submissions of DNA sequences of S. cerevisiae (yeast), Sus scrofa (pig) and Homo sapiens (human) to the European Nucleotide Archive, and 2) First description of these sequences in the scientific literature. The time range of the records is 1980-2000 (yeast), 1985-2005 (human) and 1990-2015 (pig). In total, each species has two associated datasets: 1) A .csv file documenting the PubMed ID of each article describing new sequences, all paper authors, all institutional affiliations of each author, country of institution, year of first submission to the European Nucleotide Archive, and the year of article publication, and 2) A .csv file documenting all institutions submitting to the European Nucleotide Archive, number of nucleotides sequenced, number of submissions per institution, and year of submission to the database. The approximate number of records is 28,000 publications and over 13 million sequence submissions. Some data about submitting institutions is not fully cleaned. We also include three files with the software codes that were used to obtain the submission and publication records.
description: This item includes the following data files: pig_publications.csv PubMed ID of each article describing new sequences of Sus scrofa, all paper authors, all institutional affiliations of each author, country of institution, year of first submission to the European Nucleotide Archive, and the year of article publication. Time range: 1990-2015. pig_submissions.csv All institutions submitting sequences of Sus scrofa to the European Nucleotide Archive, number of nucleotides sequenced, number of submissions per institution, and year of submission to the database. Time range: 1990-2015. yeast_publications.csv PubMed ID of each article describing new sequences of S. cerevisiae, all paper authors, all institutional affiliations of each author, country of institution, year of first submission to the European Nucleotide Archive, and the year of article publication. Time range: 1980-2000. yeast_submissions.csv All institutions submitting sequences of S. cerevisiae to the European Nucleotide Archive, number of nucleotides sequenced, number of submissions per institution, and year of submission to the database. Time range: 1980-2000. human_publications.csv PubMed ID of each article describing new sequences of Homo sapiens, all paper authors, all institutional affiliations of each author, country of institution, year of first submission to the European Nucleotide Archive, and the year of article publication. Time range: 1985-2005. human_submissions.csv All institutions submitting sequences of Homo sapiens to the European Nucleotide Archive, number of nucleotides sequenced, number of submissions per institution, and year of submission to the database. Time range: 1985-2005. softwarecode_submissions_ENA_API.R Source code to automatically search the European Nucleotide Archive and retrieve accession numbers documenting sequence submissions. softwarecode_publications_EPMC_API.R Source code to automatically search Europe PubMed Central and retrieve the PMIDs of the publications associated with each sequence submission. softwarecode_publications_SCOPUS_API.R Source code to automatically search SCOPUS and retrieve the institutional affiliation of each publication author. Please, note that the submission data is not fully cleaned.