This guide is based on a Welch Medical Library class on finding gene-based information using the web interface of the National Center for Biotechnology Information (NCBI).
It situates the Gene database in the broader context of NCBI's mission and NCBI's suite of related databases. It then summarizes Gene's content, scope, and searching features. Finally, the guide walks users step-by-step through a use case on finding genes by gene ontology.
Far from an exhaustive look at Gene, this guide nevertheless provides an excellent starting point for understanding its scope and effectively searching its content.
After reading through this guide, users will be able to do the following in NCBI Gene:
Use a concept-based approach to searching
Use trusted sources for finding gene names and gene ontology terms when constructing searches
Use advanced searching tools, such as fields tags, truncation, quotation marks, Boolean operators, and index lists
Navigate and export search results
A hands-on companion class from the Welch Medical Library called "NCBI Nucleotide, Gene, and dbSNP Databases" exists for this guide. It is currently offered a few times a year. Check the Welch Classes calendar for the next offering of the class.
The Nucleotide, Gene, and dbSNP databases from the National Center for Biotechnology Information (NCBI) provide a wealth of gene-based information. Nucleotide organizes and makes searchable sequence data from multiple sources, including GenBank and RefSeq. Gene provides detailed information, including gene ontology and genomic context, for known and predicted genes from all major taxonomic groups. And dbSNP archives human single nucleotide variations, microsatellites, and small-scale insertions and deletions.
This class outlines the content, scope, and searching features of NCBI’s Nucleotide, Gene, and dbSNP databases. Real-world searching scenarios are presented for finding sequence, gene ontology, and variants. Participants are guided live through hands-on searching workflows using the web interfaces of each database. Participants learn how to:
A guide called "Finding Sequence Using NCBI Nucleotide" was developed based on this class. This guide is structured just like the guide you are using now and presents similar information.
It situates the Nucleotide database in the broader context of NCBI's mission and NCBI's suite of related databases. It then summarizes Nucleotide's content, scope, and searching features. Finally, the guide walks users step-by-step through a use case on finding sequences for a family of genes.
If you have questions about searching Gene, other NCBI databases, EMBL-EBI databases, or web-based bioinformatics databases from other sources, please contact:
Rob Wright, Basic Science Informationist, rwrigh32@jhmi.edu.