1. Tools For Vertebrate Gene Naming
Bethan Yates – HGNC SAB 2015

2. Key aims of the VGNC project
To coordinate the naming of genes across vertebrate species.
Initial work has focused on identifying a consensus set of 1:1 orthologs between chimpanzee and human that could be named in a semi-automated manner and creating a system to allow this.
To assign gene names within complex gene families across multiple vertebrate species.
We are working on developing a curatorial interface for gene superfamily annotation by expert collaborators, focusing initially on cytochrome P450s and olfactory receptors.

3. 1:1 consensus orthologs in in chimp58
Ensembl
NCBI
Panther
OMA
10,834 96
375 92
545
1153 68
100
4555
5837
296
229
2915

4. Curation Database
A MySQL database schema has been designed to store vertebrate gene symbols and their associated data
This database has been populated with a set of chimp genes provided by identifying consensus 1:1 orthologs with human genes using out HCOP tool.
In this case consensus was based on agreement between OMA, Panther, Ensembl Compara and NCBI’s “ortholog gene group data”.
This seed set of 10,834 chimp genes is being used to test the database schema and curation tools.
Our curators have currently been able to use the system to assign approved gene names and symbols to 6000 chimpanzee genes.

5. Database schema

6. Curation Tools Website
A new website has been developed, this site provides tools for VGNC curators to input, access and edit vertebrate gene nomenclature data.
Access is restricted to people with user accounts.
This website is for internal use only and will not be made accessible to the general public.
New curation tools will be added to this site as needed.

8. Quick curate tool

9. Quick curate user interface

10. Tool to restrict human nomenclature data to human genes only

11. Symbol list

12. Preview Symbol Report

13. Family upload tool – work in progress!

14. VGNC database Database schema is identical to the curation database
Contains vertebrate genes that have had their nomenclature data approved by our curators.
Updated daily
Provides the data that will be displayed at
Used to generate download files for FTP site

15.
This will be the public facing website and will mirror the website for human data,
The site is currently in development, we hope to have a beta site out early in 2016.
Initially the site will be very simple and will host symbol reports and a basic search facility for chimp genes as well as download files for the curated chimp data.

16. Approved symbol list/search

17. Symbol report

18. Statistics and Downloads

19. Future Plans: New Species
We need to identify which species we should be working on next and are happy to take input from the SAB members.
Species :
# of protein coding genes we can name using HCOP:
Total # of protein coding genes (taken from Ensembl)
Chimp
10,834
18,749
Cow
11,574
19,994
Dog
10.748
19,856
Horse
9909
20,449
Macaque
9745
21,905
Chicken
7649
15,508
Opossum
6605
21,327
Zebrafish
4974
25,642
Platypus
1415
21,698

20. Future Plans: New Tools/Features
For herd.genenames.org:
Gene family curation tool
Comprehensive gene curation tool
Gene mapping tool
For vgnc.genenames.org:
SOLR powered search and REST service
BioMart server/Custom downloads tool?
Data Submission tools
Sequence Alignment tool

21. Future Plans: Gene family information
Complete work on the family upload tool to allow data that has been already been curated by our gene family experts to be entered into the VGNC database and website.
Enable display of vertebrate gene family data on the VGNC website, replicating the displays we have for human gene family data on the HGNC site.
Continue working with our family experts to provide tools to enable them to more easily curate gene family data.