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Wikidata and the bibliography of life

Page, R. D. M.

2021-05-04 bioinformatics
10.1101/2021.05.04.442638 bioRxiv
Show abstract

Biological taxonomy rests on a long tail of publications spanning nearly three centuries. Not only is this literature vital to resolving disputes about taxonomy and nomenclature, for many species it represents a key source - indeed sometimes the only source - of information about that species. Unlike other disciplines such as biomedicine, the taxonomic community lacks a centralised, curated literature database (the "bibliography of life"). This paper argues that Wikidata can be that database as it has flexible and sophisticated models of bibliographic information, and an active community of people and programs ("bots") adding, editing, and curating that information. The paper also describes a tool to visualise and explore bibliography information in Wikidata and how it links to both taxa and taxonomists.

Matching journals

The top 7 journals account for 50% of the predicted probability mass.

1
PeerJ
◐ 308 papers in training set
Top 0.1%
15.4%
Similar papers in this journal
2
Bioinformatics
◐ 1204 papers in training set
Top 2%
13.2%
Similar papers in this journal
3
Applications in Plant Sciences
○ 23 papers in training set
Top 0.1%
6.9%
Similar papers in this journal
4
PLOS ONE
● 5266 papers in training set
Top 26%
5.6%
Similar papers in this journal
5
Frontiers in Bioinformatics
○ 49 papers in training set
Top 0.1%
3.6%
Similar papers in this journal
6
GigaScience
◐ 212 papers in training set
Top 1%
3.3%
7
Ecology and Evolution
○ 267 papers in training set
Top 2%
3.3%
50% of probability mass above
8
F1000Research
○ 88 papers in training set
Top 0.5%
3.3%
9
Bioinformatics Advances
◐ 203 papers in training set
Top 2%
3.3%
10
Methods in Ecology and Evolution
○ 176 papers in training set
Top 0.7%
3.2%
11
Ecological Informatics
○ 33 papers in training set
Top 0.3%
2.2%
12
Journal of Open Source Software
● 25 papers in training set
Top 0.2%
2.2%
13
Peer Community Journal
● 281 papers in training set
Top 2%
2.2%
14
Neuroinformatics
○ 46 papers in training set
Top 0.4%
2.0%
15
Database
◐ 61 papers in training set
Top 0.4%
2.0%
16
Scientific Data
○ 209 papers in training set
Top 1%
1.8%
17
BMC Bioinformatics
○ 457 papers in training set
Top 4%
1.8%
18
Systematic Entomology
○ 14 papers in training set
Top 0.2%
1.4%
19
Gigabyte
● 62 papers in training set
Top 0.8%
1.2%
20
Royal Society Open Science
● 214 papers in training set
Top 4%
1.2%
21
Frontiers in Neuroinformatics
○ 41 papers in training set
Top 0.6%
1.0%
22
BMC Research Notes
○ 33 papers in training set
Top 1%
0.9%
23
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 4%
0.9%
24
Molecular Ecology Resources
○ 171 papers in training set
Top 2%
0.9%
25
Systematic Biology
◐ 144 papers in training set
Top 0.7%
0.9%
26
Biosystems
○ 31 papers in training set
Top 0.6%
0.6%
27
PLOS Computational Biology
● 1863 papers in training set
Top 21%
0.6%
28
Frontiers in Plant Science
○ 256 papers in training set
Top 4%
0.6%
29
Frontiers in Genetics
○ 230 papers in training set
Top 6%
0.6%
30
eLife
● 5828 papers in training set
Top 69%
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.