Germline sets, or additional data for existing sets, is provided in two CSV files which are uploaded to the site. This repo documents file formats and the process to follow in creating them. It also provides a number of utilities which are designed to simplify data creation and to check the data before upload.
Category: OGRDB_News
Contributing germline sets to OGRB
We welcome submissions of germline sets for new species, and new sequences for existing species. Under our overall policy, expressed in the name of the site, contributions must be free for anyone to use. OGRDB is structured to allow individuals or groups to manage the sets that they provide, and we hope that they will… Continue reading Contributing germline sets to OGRB
Gene Tables and Alignments!
This month we’ve added gene tables and alignments to OGRDB. Both can be reached from the Sequences dropdown at the top of every page. Gene Tables list all the sequences in a locus, organised by gene. You can click on the sequence name to see full details of the sequence, including the support we have… Continue reading Gene Tables and Alignments!
Website updated
We have redesigned the front page and added a new help page which brings together all information on how to use OGRDB. Other pages have been restyled to make them simpler and easier to use. We hope you will enjoy the new site. If there are any problems, please let us know by using the… Continue reading Website updated
OGRDB API v2
The OGRDB API has been upgraded to provide new features: This guide describes the new API. The old API is still available for compatibility with existing scripts.
Additional support for germline sets
We have created step-by-step walk-throughs showing how to use the AIRR-C germline sets with local installations of IgBLAST and MiXCR. These tools make use of download_germline_set, which is a powerful command-line utility which can be used to download sets in various formats, and explore the sets and versions available in OGRDB. It can even create… Continue reading Additional support for germline sets
Mouse IG Reference Sets Updated
Fixes have been made to two mouse reference sets. In C57BL/6 IGH, a stray character in the coding sequence for IGHV-KAOG has been removed. There are no other changes to this set. In PWD/PhJ IGH, the delineation j_cdr3_end has been corrected. There are no other changes in this set, and coding sequences are unchanged.
Human IG Reference Sets Updated
The human IG reference sets on OGRDB have been updated and carry new versions, but no coding sequences are affected. The updates add longer gene sequences for many light-chain alleles, allowing better characterisation of leader and RSS. Delineations of CDRs and other features have been reviewed and fixed in some cases. The changes made are… Continue reading Human IG Reference Sets Updated
OGRDB Updated
OGRDB has been updated to use binomial (latin) species names instead of colloquial names. The former names can still be used in calls to fetch germline sets, which I hope will prevent automated scripts from breaking, but if you do have problems please try substituting, for example, “Homo sapiens” for “Human”. This turned out to… Continue reading OGRDB Updated
Collaboration Opportunities
OGRDB and VDJbase are part of the AIRR Knowledge Commons project – bringing together immune repertoires from the AIRR Data Commons, epitopes from IEDB, receptor germline analysis from OGRDB and VDJbase with other emerging datasets. We are actively seeking collaborators whose projects will drive use cases and demonstrate the utility of bringing these various sources… Continue reading Collaboration Opportunities