[CONTENT] Mus Musculus TCRs

Description

We've added a large dataset of paired alpha-beta TCR sequences from mouse and human subjects. The database now contains more than a thousand records for Mus Musculus, a species that was nearly absent in previous versions.

Current statistics

species	gene	records	paired.records	epitopes
HomoSapiens	TRA	1372	608	78
HomoSapiens	TRB	4991	590	117
MacacaMulatta	TRA	74	0	1
MacacaMulatta	TRB	1313	0	3
MusMusculus	TRA	1286	1286	22
MusMusculus	TRB	1309	1309	22

[INFRASTRUCTURE] [CONTENT] Getting doi from Zenodo

• First DOI release
• Add datasets submitted by Sewell et al (2k+ sequences)
• Minor change to scoring (lower frequency thresholds)

[INFRASTRUCTURE] [PROOFREADING] Minor fixes & info added

• Proofreading fixes
• Fixed V/J mapping report messages
• Added info on number of samples/papers a given TCR:pMHC was found

[INFRASTRUCTURE] [PROOFREADING] VDJdb web interface compatibility

• Some modifications to database output files added for better interoperability with VDJdb-server
• Several chunks fixed (removed trailing residues after conserved Phe, etc)

[INFRASTRUCTURE] V/J re-mapping

A better algorithm for CDR3AA markup, V/J segment mapping and V/J segment deduction (in case segment was not provided).

[CONTENT] Winter release

Papers added

PMID:15753288 #144
PMID:16982909 #166
PMID:17121793 #152
PMID:18802118 #156
PMID:19349463 #140
PMID:21135165 #142
PMID:21752903 #138
PMID:22278241 #134
PMID:24600035 #146
PMID:27111229 #150
PMID:27645996 #148

Current statistics

species	gene	records	paired.records	epitopes
HomoSapiens	TRA	619	327	77
HomoSapiens	TRB	3452	325	113
MacacaMulatta	TRA	74	0	1
MacacaMulatta	TRB	1313	0	3
MusMusculus	TRA	16	16	16
MusMusculus	TRB	17	17	16

[CONTENT] Monthly release

Papers added

PMID_23521884 #132
PMID_25801351 #130
PMID_17893201 #128
PMID_25911754 #122

[INFRASTRUCTURE] Updated VDJdb confidence scoring system

Improvements

• Completely reworked VDJdb confidence scoring (a more transparent record confidence system)
  • Four confidence levels: 0 (no data), 1 (moderate), 2 (high) and 3 (very high confidence)
  • Now accounts for both sequencing and specificity
  • Changed how identification and in-vitro validation methodology is score, extensively validated records have the highest score
• Added several new method annotations
• More flexible parsing of method.frequency (x/X is now optional)
• Small update to patches (replacement of typos and formatting issues in gene and species naming)

See README for more details and additional guidelines.

[CONTENT] [INFRASTRUCTURE] Another five papers added, some additions to infrastructure

Papers added:

PMID_10756006 #23
PMID_10925283 #22
PMID_11756174 #27
PMID_22314361 #75
PMID_24069285 #20

Papers withheld:

PMID_7964506 #4

Infrastructure

• Added "correct" step to correct ambiguous antigen species/gene naming
• Basic database summary generation
• A draft of algorithm to optimize VDJdb search scoring system

[CONTENT] [INFRASTRUCTURE] Five more papers & db management fixes/modifications

Papers added

PMID_12504586.txt
PMID_16326979.txt
PMID_24512815.txt
PMID_27252176.txt
PMID_7964506.txt

Minor

• Additional keyword for "direct validation" records, i.e. single cell affinity measurement & sequencing
• Also fixed a bug that resulted in single-chain records having a non-zero complex id in flattened database