New features and changes

New Features

New HGNC BioMart server has been released

Since 2008 we have provided a BioMart service to allow our users to query and download the data that they want easily and quickly. Due to infrastructure and data changes it has become necessary to close this service, but fear not, as the old BioMart service has been replaced by a new BioMart server using the latest BioMart (0.9.0) code. Despite looking very different the new service retains an easy to use interface, include our gene family data in addition to the gene symbol report dataset, and allow our users to access and query a lot more of the HGNC data than was previously possible. Bioinformaticians and web developers can also interact with our BioMart server via REST/SOAP, SPARQL and a Java BioMart API available from the BioMart project website. Check out the BioMart help page for an overview of what the new BioMart offers.

Changes

URL change for BioMart

The old HGNC BioMart URL (www.genenames.org/biomart/) has changed to biomart.genenames.org. A redirect for the old URL is now in place.

Previous introduced features and changes

The new look gene families has been released - 2015-04-13

The beta release of our new gene families is now live and is the default version of our gene families across the site. Our new gene family pages include family aliases, a family hierarchy map, a family text description and a graphical representation of protein domains for an example family member. Improvements include a searchable gene family index, the ability to browse through and download gene family hierarchies, and a unique numerical ID for each gene family. For a full description of the new gene family pages, please visit the Gene families help page. This has ushered in many changes within the site which can be seen below in the "Changes" section. The older gene families can still be found here.

New search - search enerything with one search request - 2015-04-13

We have improved the search application on our site so that you can now search all aspects of our site through one search. The search will now search the gene symbol reports, our new gene families and all of our other pages by default. If however you only want to search our gene symbol reports, our gene families or pages not associated with either, you can use the drop down box to specify the type of search you would like to carry out ignoring the other sections of the site. For more information please vist our search help.

New gene families are now within our gene symbol reports - 2015-04-13

Links to our gene families within our symbol reports now point to our new gene families.

Custom downloads tool has new gene family columns - 2015-04-13

The custom downloads tool now has our "Gene family name" and "Gene family ID" as selectable columns. These columns replace the old gene family columns and provides the user with our new families. See our custom downloads help for more information.

Download files are in a new format - 2015-04-13

The downloadable files found within the Statistics & Downloads page now have a new format and are also now available in JSON format as well as text. The files now contain all the information we have from our gene symbol reports rather than just the HGNC core data. The old file format can still be found on our FTP site and will continue to be updated in the short term. If you use the old file format please be aware that these files will report on the previous version of our gene families data and are not comparable to the new families. See the statistics & downloads help for more information.

REST service now contains new gene family information- 2015-04-13

The REST service now returns "gene_family" and "gene_family_id" fields which represents our new gene family data for the gene.

New gene families release (beta) - 2015-01-28

We have released a beta version of new, improved gene family pages. Our new gene family pages include family aliases, a family hierarchy map, a family text description and a graphical representation of protein domains for an example family member. Improvements include a searchable gene family index, the ability to browse through and download gene family hierarchies, and a unique numerical ID for each gene family. For a full description of the new gene family pages, please visit the Gene families (beta) help page. Please send us your feedback on these pages.

New look search results - 2014-07-31

We changed our search results to include not only the matching field type, but also the field itself with the query string highlighted within. We hope this makes the search result more understandable and clearer.

REST service: entrez_id and hgnc_id are now strings - 2014-07-31

In order to make it clear that the HGNC ID is officially HGNC:# rather than just number, we have changed the type associated with the hgnc_id field from int to string and the resulting hgnc_id will have the "HGNC:" prefix. The entrez_id field has also changed to a string due to backend code reasons. We hope that this has not caused too much disruption to anyone using our REST service. 

New HCOP Orthology Predictions Search Tool released! - 2014-07-21

A new and improved version of our HCOP tool has been released. This updated version of HCOP includes ortholog data from eggNOG, Ensembl Compara, HGNC, HomoloGene, Inparanoid, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, TreeFam and ZFIN. The new HCOP also features a revamped, more user-friendly interface and ortholog data for three new species, with pig, xenopus and anole lizard being the first new species to be added. For more information about the new HCOP please visit the HCOP help page. Due to this new version of HCOP we have frozen the data in the archived version of HCOP as it stood on December 1st 2014. We will remove the HCOP (archive) page from this website at the end of February 2015. Please contact us if this is likely to cause problems for you.

Multiple homologs per species - 2014-07-17

We have recently updated the HOMOLOGS section of our symbol reports to show multiple mouse and rat homologs for each human gene, where applicable. This also means that there will be multiple MGI or RGD IDs within the download files, which are comma space (ie ', ') separated within the tab separated output. The REST API output has also changed for RGD and MGD data as they are now within an array named mgd_id and rgd_id (see REST web-service help).

New "REFERENCES" section with the Symbol reports - 2014-03-13

We have improved the REFERENCES section within the Symbol Report pages to display the title, authors and citation of the publications as well as providing links out to Europe PMC and Pubmed. Next to the links you will find a '+' icon and clicking on this icon will additionally reveal the abstract and full author list for the publication.

Multiple OMIM IDs - 2014-02-07

Since some of our symbols can link to more than one OMIM entry, you may find that some symbol reports now have multiple OMIM cross reference (i.e IGH) when in the past we displayed one. This change has also affected the "Complete HGNC Dataset" download file (available on our Statistics & Downloads page) in that the omim_id column in the tab separated file may have multiple OMIM IDs separated by a comma and space (i.e ', '). This is also applicable to the data downloaded from our Custom Downloads application when returning OMIM IDs.

New solr search - 2014-01-08

New solr search allowing for better and more relevant search results. The new search also introduces facetted searching allowing the user to filter down the results by locus type and locus group. For more information view our search help page.

REST web service - 2014-01-08

A new REST web service is a quick way and easy way of searching and fetching data from our database within a script/program. Users may request results as either XML or JSON making our data easier to parse.For more information view our REST web-service help page.

Root symbol word cloud - 2014-01-08

The karyotypes image on the front page is replaced by a word cloud of the most common root symbols. Each root symbol links to a search based on that particular root symbol (ie ZNF activates a search for ZNF*).

Application changes - 2014-01-08

The tool "list search" has been renamed "Symbol checker" and the interface to the application has been revamped for clarity and ease of use. The application itself will work in a similar manner to the original tool. As well as a change in name, the URL has changed from http://www.genenames.org/cgi-bin/hgnc_bulkcheck.pl to http://www.genenames.org/cgi-bin/symbol_checker. For more information about our new "Symbol checker" visit our Symbol checker help page.

The karyotype image for linking to statistics for a particular chromosome has moved to the "Statistics & Downloads" page to control the statistics shown within the page by filtering the statistics by chromosome.

The "Symbol Report" pages have been changed slightly to make it easier to read the data shown within and to clearly define which data is novel to the HGNC and which are external links to other resources.To learn more about our Symbol reports visit our Symbol report help page

Because we have released our new solr based search, which is more powerful and easier to use, we have retired the "advanced gene search" (i.e http://www.genenames.org/cgi-bin/advanced_search.pl). The new solr search should be able to do all that was possible with the old application. If this isn't so please email us and we shall endevour to add the missing functionality to the solr search. To learn more about our new search visit our search help page.

The site search that was present within the front page has now been incorporated into the search within the mast head of the page. By default the search box will use our solr gene search however you can select the site search by clicking on the drop down box.

URL changes - 2014-01-08

As mentioned above the URL for the "list search" has changed to http://www.genenames.org/cgi-bin/symbol_checker. There are other changes to the URLs within the site which are listed below:

Update to displaying genes annotated on alternate reference loci - 2014-01-08

We are making a slight change to the way genes annotated on alternate reference loci are displayed within Symbol Reports. The Chromosomal Location field will now display the location plus the term "alternate reference locus" instead of the assembly unit name. For a full description of how we name genes on alternate loci, please see our recent publication "Vive la difference: naming structural variants in the human reference genome." PMCID: PMC3648363.

New "Specialist Database" link for solute carrier (SLC) genes - 2013-05-22

We have added a new "Specialist Database" link for all genes within the solute carrier (SLC) gene family. The link will take the format "BioParadigms: <Symbol>" and will link to the BioParadigms SLC tables which provide up-to-date information on the SLC families and their members, as well as relevant links to gene databases and reviews in the literature (see Symbol Report Documentation). The "Specialist Database IDs" and "Specialist Database Links" within the "Custom Downloads" will now include the BioParadigms symbol/link at the end of the comma delimited list, which brings the total number of elements to 18 (see Downloads Documentation for more information).