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Bibliome Variant Database: Automated Identification and Annotation of Genetic Variants in Primary Literature

Baker, S. W.; Ganguly, A.

2020-07-17 bioinformatics
10.1101/2020.07.16.207688 bioRxiv
Show abstract

The Bibliome Variant Database (BVdb) is a freely available reference database containing over 1 million human genetic variants mapped to the human genome that have been mined from primary literature. The BVdb is designed to facilitate variant interpretation in clinical and research contexts by reducing or eliminating the time required to search for literature describing a given variant. Users can search the database using gene symbols, HGVS variant nomenclature, genomic positions, or rsIDs. Each variant page lists references in the database that describe the variant, as well as the exact gene symbol and variant text description identified in each reference. AVAILABILITY AND IMPLEMENTATIONThe BVdb is freely available at http://bibliome.ai

Matching journals

The top 3 journals account for 50% of the predicted probability mass.

1
Bioinformatics
◐ 1204 papers in training set
Top 0.9%
22.5%
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2
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○ 34 papers in training set
Top 0.1%
22.5%
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3
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◐ 61 papers in training set
Top 0.1%
8.1%
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50% of probability mass above
4
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Top 2%
5.3%
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5
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Top 1%
4.4%
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6
BMC Medical Genomics
○ 50 papers in training set
Top 0.1%
4.1%
7
Nucleic Acids Research
◐ 1281 papers in training set
Top 5%
3.6%
8
Frontiers in Genetics
○ 230 papers in training set
Top 2%
2.2%
9
BMC Genomics
○ 406 papers in training set
Top 3%
2.2%
10
G3: Genes, Genomes, Genetics
◐ 252 papers in training set
Top 2%
1.8%
11
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 2%
1.8%
12
Genes
○ 144 papers in training set
Top 2%
1.4%
13
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 4%
1.2%
14
Journal of Medical Genetics
● 29 papers in training set
Top 0.4%
1.2%
15
PeerJ
◐ 308 papers in training set
Top 7%
1.2%
16
BioData Mining
○ 22 papers in training set
Top 0.4%
1.1%
17
Journal of Bioinformatics and Systems Biology
○ 15 papers in training set
Top 0.1%
1.1%
18
G3 Genes|Genomes|Genetics
◐ 351 papers in training set
Top 4%
1.0%
19
European Journal of Human Genetics
○ 58 papers in training set
Top 1%
0.6%
20
Genetic Epidemiology
○ 55 papers in training set
Top 0.7%
0.6%
21
F1000Research
○ 88 papers in training set
Top 4%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.