Genenames.org: the HGNC resources in 2015

Abstract

The HUGO Gene Nomenclature Committee (HGNC) based at the European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. To date the HGNC have assigned over 39,000 gene names and, representing an increase of over 5000 entries in the past two years. As well as increasing the size of our database, we have continued redesigning our website http://www.genenames.org and have modified, updated and improved many aspects of the site including a faster and more powerful search, a vastly improved HCOP tool and a REST service to increase the number of ways users can retrieve our data. This article provides an overview of our current online data and resources, and highlights the changes we have made in recent years.

Figure 1.

The new search box located within the masthead activates the search and returns the results as seen above in section ‘a’. The results are faceted as seen on the left allowing the user to filter the returned results by locus type and group. The results display some of the core HGNC data such as symbol, name and ID. Each result also highlights the field(s) the term matches. Section ‘b’ displays a typical symbol report showing the HGNC core data fields within the shaded box. New additions to the core data are the HCOP and gene families links that have migrated from the external links section below. A slightly changed format to the external links section can be seen including our improved references section. The first reference is the default view while the second displays the full author list and abstract as would be displayed once the plus sign is clicked. Clicking on the minus will return the reference back to the default. Another addition is the support for multiple mouse and rat homologs per human gene within our symbol reports as seen above.

Figure 2.

Section ‘a’ shows the updated HCOP search form. Users select a primary species and one or more species that they wish to identify orthologs in. They then select the ortholog resources they wish to include in the search, and the type of search term, e.g. approved symbol, or database identifier, that they are providing. A single search term or list of search terms may be pasted into a text box, or uploaded as a file to be used to run the search. Users can optionally see the results in HTML or plain text format. Section ‘b’ displays an example result panel from HCOP. In this case orthologs between the human gene CSF2RB in chimp and mouse were requested. Information about the query gene appears in the blue section at the top of the results panel, with each ortholog identified having its own section below this. For both the query and ortholog genes we provide basic information about the gene as well as links to the gene in other resources. Each ortholog section has an additional column labelled ‘Assertion derived from’ that contains a set of icons that represent the orthology sources that support this assignment. Section ‘c’ is the bulk downloads section of the HCOP form. This allows users to download pre-computed files of HCOP data from our FTP site, providing fast access to all the data stored in HCOP.