Archives February 2020

Notes on Nomenclature

At the Gene Mapping Workshop held during the 22nd Conference of the International Society for Animal Genetics (ISAG) held in East Lansing, Michigan, USA it was resolved unanimously that animal gene nomenclature should “follow the rules for human gene nomenclature, including the use of identical symbols for homologous genes and the reservation of human symbols for yet unidentified animals genes”. [Animal Genetics (1991) 22, 97-99] The report from the workshop cited the human gene nomenclature rules and lists of mapped genes as published in Cytogenetics and Cell Genetics proceedings of the Human Gene Mapping Workshops. Approved human gene symbols and nomenclature rules can now be accessed through the Web site maintained by the HUGO Gene Nomenclature Committee

The HUGO Gene Nomenclature Committee is responsible for approving and implementing unique human gene symbols and names, and works closely with the Mouse Genome Database and other organism databases. Considerable efforts are made to approve symbols acceptable to workers in the field, but sometimes it is not possible to use exactly what has previously appeared in the literature. In such cases the previously used symbols are listed as aliases for the approved nomenclature in the Human Gene Nomenclature Database (Genew) and LocusLink, to allow retrieval of all the information available for each gene.


Using ARKdb

ARKdb can be queried in a number of ways. The main ways of querying are by locus/marker, by published reference or by map. You can also query by clone or library, although these tend to be less well-used areas of the system. Each species database is accessed in the same way. Brief details of the options available are given below. A more detailed guide to the text-based interfaces (locus and reference queries) can be found using the help links in the relevant query pages..

You can query for a locus based on its symbol, its description (name), chromosome position or marker type. You can also limit the search to markers mapped on a specific mapping population and further refine this search by limiting the search to a particular mapping cross sex. However, you should be aware that it is possible to generate queries that return no markers simply by choosing the incorrect sex in this form, so the option should only be used if you really know what you are doing. You can also partially customise the report format by choosing to display primer details (in which case the query will return symbol, primer sequences and EMBL accession numbers) and sort criteria.
You can look for specific references by full or partial title, author, journal name or publication year. Alternatively you can use the internal database identifier unique to each reference (accession number).
You can query for maps using either the “advanced” or the “simpler” interface. Maps are selected by species, chromosome and published map name – you can alternatively use your own data to generate maps.
You can query the database for details of clones used in mapping experiments. The searchable fields are Clone Name, Vector and Cloning Sites.
You can query the database for details of libraries from which clones used in mapping experiments were derived. The searchable fields are Library Name, Vector and Host.

History of ARKdb

ARKdb arose initially from the needs of a project co-ordinated at Roslin Institute to map the pig genome. The original intention was to utilise the Jackson Laboratory’s then current mouseGBASE database design, and this was actually implemented for pigs, chickens and sheep. However, it soon became clear that the nature of genome mapping in farmed animal species differed significantly from the methods and population types employed in mouse genetics. These differences meant that the schema we had didn’t fit our data requirements and the decision was taken to develop our own database system.

Because we needed a system that would work for all of the species that we work with at Roslin, we tried to make the design as generic as possible. We hope that we have managed to strike a balance between generalisation and utility. In any case, the number of species that have adopted the ARKdb database system for their genome mapping informatics needs extends considerably beyond those initially in mind when we established the schema.

ARKdb species databases at this site