# 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

![](static/approach.png)

## 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)