DOI: 10.7488/ds/2718
title: Human, yeast and pig genomics: sequence submissions and first sequence descriptions in the literature (1980-2015)

description: 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 (ENA), 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 (PMID) of each article describing new sequences, all paper authors, all institutional affiliations of each author, country of institution, year of first submission to the ENA (when available) and year of article publication; 2) A .csv file documenting all institutions submitting to the ENA, number of nucleotides sequenced and year of submission to the database. While the data about yeast submissions is provided sequence per sequence with full dates and information about both submitting individuals and institutions, the pig and human submission datasets offer aggregate figures per institution and per year. Some submission data is not fully clean. The approximate number of records is 29,500 publications and 13.5 million sequence submissions. The software codes that were used to obtain the submission and publication records can be found at https://github.com/UofGMarkWong/TRANSGENE. A publication describing the data collection and cleaning protocol is available at https://f1000research.com/articles/8-1200. Further information about the project within which this collection was generated: https://transgene.sps.ed.ac.uk/ and https://online.ucpress.edu/hsns/issue/52/3.
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 (only partially available), and the year of article publication. Time range: 1980-2000. yeast_submissions.csv All sequence submissions of S. cerevisiae to the European Nucleotide Archive (accession numbers), year of first submission, sequence length, submitting scientists (when available), submitting institutions (when available) and authors of associated publication (when available). 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. Please, note that the submission data is not fully cleaned.