1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
|
# fuzzycat (wip)
Fuzzy matching publications for [fatcat](https://fatcat.wiki).
* [fuzzycat](https://pypi.org/project/fuzzycat/)
## Motivation
Most of the results on sites like [Google
Scholar](https://scholar.google.com/scholar?q=fuzzy+matching) group
publications into clusters. Each cluster represents one publication, abstracted
from its concrete representation as a link to a PDF.
We call the abstract publication *work* and the concrete instance a *release*.
The goal is to group releases under works and to implement a versions feature.
This repository contains both generic code for matching as well as fatcat
specific code using the fatcat openapi client.
## Approach
There are probably a few assumption we can make:
* If two strings are given, an exact string match does not mean equality (at
all), e.g. "Acta geographica" has currently eight associated ISSN, and a
title like "Buchbesprechungen" appears many hundreds of times.
* ...
* ...
## Datasets
* release and container metadata from: [https://archive.org/details/fatcat_bulk_exports_2020-08-05](https://archive.org/details/fatcat_bulk_exports_2020-08-05).
* issn journal level data, via [issnlister](https://github.com/miku/issnlister)
* abbreviation lists
## Matching approaches
## Performance data point
Candidate generation via elasticsearch, 40 parallel queries, sustained speed at
about 17857 queries per hour, that is around 5 queries/s.
```
$ time cat ~/data/researchgate/x04 | \
parallel -j40 --pipe -N 1 ./fatcatx_rg_unmatched.py - \
> ~/data/researchgate/x04_results.ndj
...
real 3409m16.442s
user 29177m5.516s
sys 4927m3.277s
```
## Data issues
### A republished article
* [https://fatcat.wiki/release/search?q=%22The+doctor+with+seven+billion+patients%22](https://fatcat.wiki/release/search?q=%22The+doctor+with+seven+billion+patients%22)
There is "student BMJ" and "BMJ" - this (html) article (interview) has been
first published on "sbmj" (Published 07 July 2011), then "bmj" (Published 10
August 2011).
> Notes; Originally published as: Student BMJ 2011;19:d3983
* https://www.bmj.com/content/343/sbmj.d3983
* https://www.bmj.com/content/343/bmj.d4964
It is essentially the same text, same title, author, just different DOI and
probably a different recorded date.
Generic pattern "republication" duplicate:
* metadata mostly same, except date and doi
### Common title
Probably a few thousand very common short titles.
* [https://fatcat.wiki/release/search?q=%22Book+Reviews%22](https://fatcat.wiki/release/search?q=%22Book+Reviews%22) (238852)
Some authors do this regularly:
* [https://fatcat.wiki/release/search?q=%22Book+Reviews%22+%22william%22+%22michael%22](https://fatcat.wiki/release/search?q=%22Book+Reviews%22+%22william%22+%22michael%22) (398)
Different DOI, so we know it is different.
More examples:
* [https://fatcat.wiki/release/search?q=%22errata%22](https://fatcat.wiki/release/search?q=%22errata%22) (37680)
* [https://fatcat.wiki/release/search?q=%22Einleitung%22](https://fatcat.wiki/release/search?q=%22Einleitung%22) (68005)
* [https://fatcat.wiki/release/search?q=%22Notes%22](https://fatcat.wiki/release/search?q=%22Notes%22) (1507705)
* [https://fatcat.wiki/release/search?q=%22Letters+to+the+Editor%22](https://fatcat.wiki/release/search?q=%22Letters+to+the+Editor%22) (30976)
### Title with extra data
* like ISBN, ISSN, price and all kind of extra metadata
* [https://fatcat.wiki/release/search?q=title%3A%22ISBN%22](https://fatcat.wiki/release/search?q=title%3A%22ISBN%22)
* titles typically get longer: [https://fatcat.wiki/release/olxswrilxfci3ibb3bg5xhstr4](https://fatcat.wiki/release/olxswrilxfci3ibb3bg5xhstr4)
* some of these are actually "reviews", e.g. [https://fatcat.wiki/release/4blc5mfc5bfaxkofuletqxuzp4](https://fatcat.wiki/release/4blc5mfc5bfaxkofuletqxuzp4)
Another example:
* too [long](https://fatcat.wiki/release/hewmq4afvnew7pwttvulzguubu), original suggested citation seems to be:
> Parker, S. and Kerrod, R. (2002), "Children’s) Space Busters (1st) Looking at Stars (2nd)", Reference Reviews, Vol. 16 No. 5, pp. 26-27. https://doi.org/10.1108/rr.2002.16.5.26.252
### Sometimes a title will be ambiguous
For example given a title "Shakespeare in Tokyo" we would have to always return "ambiguous", as there are at least two separate publication with that name:
* [https://fatcat.wiki/release/search?q=%22Shakespeare+in+Tokyo%22](https://fatcat.wiki/release/search?q=%22Shakespeare+in+Tokyo%22)
This is similar to journal names, where some journal names will always be ambiguous.
### Versions
* same title, same authors, "vX" doi
* [https://fatcat.wiki/release/search?q=%22Self-similarity+analysis+of+the+non-linear%22](https://fatcat.wiki/release/search?q=%22Self-similarity+analysis+of+the+non-linear%22)
Sometimes, we have a couple of preprint versions, plus a published version (with a slightly different title):
* [https://fatcat.wiki/release/search?q=%22Time-periodic+solutions+of+massive%22](https://fatcat.wiki/release/search?q=%22Time-periodic+solutions+of+massive%22)
### Almost same
* same author, maybe year
* different DOI
* title almost the same, e.g. [MassIVE MSV000085583 - Aedes aegypti protein profile and proteome analysis](https://fatcat.wiki/release/search?q=%22Aedes+aegypti+protein+profile+and+proteome+analysis%22)
### Duplication by different granularity
* [https://fatcat.wiki/release/search?q=%22Volkshochschule+Leipzig%22](https://fatcat.wiki/release/search?q=%22Volkshochschule+Leipzig%22) (20308)
* contains both yearly entries, as well as "DOI per page",
[https://fatcat.wiki/release/r734v367nza4tl37j6d74rfqo4](https://fatcat.wiki/release/r734v367nza4tl37j6d74rfqo4);
could group pages under "container" of yearly release?
* We have [one container](https://github.com/internetarchive/fatcat/blob/4f80b87722d64f27c985f0040ea177269b6e028b/fatcat-openapi2.yml#L704-L709) per release, currently.
### Partial titles
A metadata title might differ from the full title.
* [https://fatcat.wiki/release/search?q=%22Brain-derived+neurotrophic+factor%22](https://fatcat.wiki/release/search?q=%22Brain-derived+neurotrophic+factor%22)
Here, the [release](https://fatcat.wiki/release/2vi655gcejffhnzzbkkcnjpscm) points to two PDFs, one is an article, the other a weekly report (summary).
### Exact duplicates
* [https://fatcat.wiki/release/search?q=%22WEIGHTED+LIPSCHITZ+ESTIMATES+FOR+COMMUTATORS+ON+WEIGHTED+MORREY-HERZ+SPACES%22](https://fatcat.wiki/release/search?q=%22WEIGHTED+LIPSCHITZ+ESTIMATES+FOR+COMMUTATORS+ON+WEIGHTED+MORREY-HERZ+SPACES%22)
### Difference in Subtitle (invisible)
Subtitle is not visible metadata, all same, except for the DOI and the page number. Different.
* [https://fatcat.wiki/release/search?q=%22Slip+in+tungsten+monocarbide%22](https://fatcat.wiki/release/search?q=%22Slip+in+tungsten+monocarbide%22)
### The "what a difference a char makes" case
Typically a yearly report, or "part 1", "part 2", like this:
* [https://fatcat.wiki/release/search?q=%22The+Use+of+Bone+Age+in+Clinical+Practice+%22](https://fatcat.wiki/release/search?q=%22The+Use+of+Bone+Age+in+Clinical+Practice+%22)
DOI differs and could hard code some patterns.
### Published to two sites
An article can have multiple DOI, e.g. when republished by a site that gives out DOI, e.g. researchgate. Example:
* [Effect of Chlorophyll and Anthocyanin on the Secondary Bonds of Poly Vinyl Chloride](https://fatcat.wiki/release/search?q=%22Effect+of+Chlorophyll+and+Anthocyanin+on+the+Secondary+Bonds+of+Poly+Vinyl+Chloride+%22)
> https://doi.org/10.11648/j.ijmsa.s.2015040201.15, https://doi.org/10.13140/rg.2.1.2398.3606
Probably many "10.13140" prefixed DOI has at least another DOI.
Some might be "rg-only", like this: [https://fatcat.wiki/release/search?q=%22Marco+de+trabajo+basado+en+los+datos+enlazados+para%22](https://fatcat.wiki/release/search?q=%22Marco+de+trabajo+basado+en+los+datos+enlazados+para%22)
|
