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dbPTB and Curating Guidelines (click on the image to download the PDF file)

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What is dbPTB? The Database for Preterm Birth (dbPTB) is a web-based aggregation tool developed to create a database for the genes, genetic variations and pathways involved in preterm birth. What is the current content of dbPTB? dbPTB contains a well supported collection of genes and SNPs related to preterm birth, their chromosomal location and information on the articles, databases and pathways supporting their relationship to preterm birth. How was dbPTB created? From the 31,018 articles dealing with preterm birth in PubMed, SciMiner extracted a ‘filtered set’ which included 980 articles for which there was likely information about genes and genetic variants related to preterm birth. These articles contained information on more than 1200 putatively related genes. From among these articles, with over 5,000 associated MeSH terms, we ‘accepted’ 142 articles described by a total of 960 unique MeSH terms. These articles provided statistically valid associations of 185 genes with preterm birth. We further identified and imported 213 genes from published and public databases containing array data and data from other proteomic analyses. We included an additional 218 genes based on the interpolation from pathway analysis. These genes were contained in 173 unique pathways. What do you mean by curation team? The team consisted of researchers and medical students formally trained in the molecular and cell biology of preterm birth. Each article was carefully read. Attention was devoted in particular to study design, relevance of the article to preterm birth per se and not issues related to prematurity but distinct from preterm delivery. Inter-rater reliability was assessed and kappa scores were measured after training. Inter-rater reliability was maintained by formal, weekly "curation meetings" where difficult publications, or any publication a curation team member felt would be useful for discussion and comparison, were reviewed conjointly. What did the curators enter into the database? Articles that were considered relevant were “accepted” and deposited into the database with their unique PMID. Also entered into the database from each article were the genes, genetic variants, SNPs, rs numbers (when available) and annotations describing gene-gene interactions shown to be statistically significantly related to an increased risk for preterm birth. We accepted in all cases the authors’ criteria for statistical significance. All genes and genetic variants entered into the database were entered using their unique Hugo Gene Nomenclature (HGNC) numbers for identification. SNPs were entered into the database and recorded with their appropriate rs number using HapMap Data Release 27. Where specific haplotypes were shown to confer significant risk for preterm birth, all the individual SNPs within the haplotype were entered into the database. This was true even if by univariate analysis an individual SNP was not statistically associated with increased risk for preterm birth. What is dbPTB’s primary source of information? dbPTB currently consists of genes, SNPs and articles which carry information about Preterm Birth (PTB). NCBI PubMed is the main source of articles. Gene information is based on HGNC (Human Gene Nomenclature Committee) as well as NCBI Entrez Genes. Disease related information is provided by OMIM. dbSNP built 126 is used in collection of SNPs and All abstracts and related information about the articles also stored in dbPTB. What kind of searches can be performed in dbPTB? Users can search for genes, SNPs, articles, or chromosomes that are related to preterm birth. Keyword searches are available for all the curated abstracts of the articles in the database. Searches can be performed by author’s last name. All of the content depends on a demonstrated relationship to PTB. If a gene of interest is related to PTB, then information on that gene is listed in several tables with supported links. What is the search query for “article” vs. “gene” used for? Articles can be searched for their inclusion in dbPTB by PMID number. If an article has been entered into dbPTB, The search will show the journal name, the title, the PMID number, the abstract and the genes verified by this article. Genes for their inclusion in dbPTB. The search requires the gene name from HGNC. Aliases will also retrieve the gene information. The search will show the HGNC id, the gene name, the aliases, the gene family name, OMIM number, the chromosome number and location, the articles supporting inclusion in dbPTB, the pathway names and SNP information. Where did the articles come from? SciMiner extracted the “filtered set” from PubMed. Out of 980 extracted articles 142 gave evidence for PTB related genes, SNPs or gene-gene interactions. All of these articles can be reviewed. What does PMID stand for? Each published article was assigned a unique identifier by NCBI called the PubMed IDentifier or PubMed unique Identifier. What search results are displayed on the web browser? Depending on the query; gene, SNP, pathway and article information are listed with their live links. Is dbPTB content updated regularly? Yes, the content is updated bimonthly. For the best visualization, do you recommend any web browsers? At present**, Mozilla Firefox, Google Chrome, and Safari are the best options. Microsoft Internet Explorer in some versions may not be as effective.

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