From bd66b58cded2c2c7e7b7e5d374434d6531dd70de Mon Sep 17 00:00:00 2001
From: Martin Czygan <martin.czygan@gmail.com>
Date: Sun, 8 Aug 2021 15:18:29 +0200
Subject: docs: cleanup and naming

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-\documentclass[hidelinks,10pt,twocolumn]{article}
-\usepackage{simpleConference}
-\usepackage[utf8]{inputenc}
-\usepackage{times}
-\usepackage{graphicx}
-\usepackage{natbib}
-\usepackage{doi}
-\usepackage{amssymb}
-\usepackage{url,hyperref}
-\usepackage{booktabs}       % professional-quality tables
-\usepackage{amsfonts}       % blackboard math symbols
-\usepackage{nicefrac}       % compact symbols for 1/2, etc.
-\usepackage{caption}
-
-\usepackage{datetime}
-\providecommand{\keywords}[1]{\textbf{\textit{Index terms---}} #1}
-\setlength{\parindent}{0pt}
-
-\begin{document}
-
-\title{Fatcat Reference Dataset}
-
-\author{Martin Czygan \\
-	\\
-	Internet Archive \\
-	San Francisco, California, USA \\
-	martin@archive.org  \\
-	\and
-	Bryan Newbold \\
-	\\
-	Internet Archive \\
-	San Francisco, California, USA \\
-	bnewbold@archive.org  \\
-	\\
-}
-
-
-\maketitle
-\thispagestyle{empty}
-
-
-\begin{abstract}
-	As part of its scholarly data efforts, the Internet Archive releases a first version of a citation
-	graph dataset, named \emph{refcat}, derived from scholarly publications and
-	additional data sources. It is composed of data gathered by the fatcat
-	cataloging project\footnote{\url{https://fatcat.wiki}}, related web-scale
-	crawls targeting primary and secondary scholarly outputs, as well as metadata
-	from the Open Library\footnote{\url{https://openlibrary.org}} project and
-	Wikipedia\footnote{\url{https://wikipedia.org}}. This first version of the
-	graph consists of 1,323,423,672 citations. We release this dataset under a CC0
-	Public Domain Dedication, accessible through an archive
-	item\footnote{\url{https://archive.org/details/refcat_2021-07-28}}. All
-	code used in the derivation process is released under an MIT
-	license\footnote{\url{https://gitlab.com/internetarchive/cgraph}}.
-\end{abstract}
-
-\keywords{Citation Graph, Web Archiving}
-
-\section{Introduction}
-
-
-The Internet Archive releases a first version of a citation graph dataset
-derived from a raw corpus of about 2.5B references gathered from metadata and
-data obtained by PDF extraction tools such as
-GROBID\cite{lopez2009grobid}. Additionally, we consider integration with
-metadata from Open Library and Wikipedia.
-The goal of this report is to describe briefly the current contents and the
-derivation of the dataset. We expect
-this dataset to be iterated upon, with changes both in content and processing.
-
-Modern citation indexes can be traced back to the early computing age, when
-projects like the Science Citation Index (1955)\citep{garfield2007evolution}
-were first devised, living on in existing commercial knowledge bases today.
-Open alternatives were started such as the Open Citations Corpus (OCC) in 2010
-- the first version of which contained 6,325,178 individual
-references\citep{shotton2013publishing}. Other notable early projects
-include CiteSeerX\citep{wu2019citeseerx} and CitEc\citep{CitEc}. The last
-decade has seen the emergence of more openly available, large scale
-citation projects like Microsoft Academic\citep{sinha2015overview} or the
-Initiative for Open Citations\citep{i4oc}\citep{shotton2018funders}. In 2021,
-according to \citep{hutchins2021tipping} over 1B citations are publicly
-available, marking a tipping point for this category of data.
-
-\section{Related Work}
-
-There are a few large scale citation dataset available today. COCI, the
-``OpenCitations Index of Crossref open DOI-to-DOI citations'' was first
-released 2018-07-29. As of its most recent release\footnote{\url{https://opencitations.net/download}}, on
-2021-07-29, it contains
-1,094,394,688 citations across 65,835,422 bibliographic
-resources\citep{peroni2020opencitations}.
-
-The WikiCite\footnote{\url{https://meta.wikimedia.org/wiki/WikiCite}} project,
-``a Wikimedia initiative to develop open citations and linked bibliographic
-data to serve free knowledge'' continously adds citations to its database and
-as of 2021-06-28 tracks 253,719,394 citations across 39,994,937
-publications\footnote{\url{http://wikicite.org/statistics.html}}.
-
-Microsoft Academic Graph\citep{sinha2015overview} is comprised of a number of
-entities\footnote{\url{https://docs.microsoft.com/en-us/academic-services/graph/reference-data-schema}}
-with \emph{PaperReferences} being one relation among many others. As of 2021-06-07\footnote{A recent copy has been preserved at
-	\url{https://archive.org/details/mag-2021-06-07}}  the
-\emph{PaperReferences} relation contains 1,832,226,781 rows (edges) across 123,923,466
-bibliographic entities.
-
-Numerous other projects have been or are concerned with various aspects of
-citation discovery and curation as part their feature set, among them Semantic
-Scholar\citep{fricke2018semantic}, CiteSeerX\citep{li2006citeseerx} or Aminer\citep{tang2016aminer}.
-
-As mentioned in \citep{hutchins2021tipping}, the number of openly available
-citations is not expected to shrink in the future.
-
-
-\section{Dataset}
-
-We release the first version of the \emph{refcat} dataset in an format used
-internally for storage and to serve queries (and which we call \emph{biblioref}
-or \emph{bref} for short). The dataset includes metadata from fatcat, the
-Open Library Project and inbound links from the English Wikipedia. The fatcat
-project itself aggregates data from variety of open data sources, such as
-Crossref\citep{crossref}, PubMed\citep{canese2013pubmed},
-DataCite\citep{brase2009datacite}, DOAJ\citep{doaj}, dblp\citep{ley2002dblp} and others,
-as well as metadata generated from analysis of data preserved at the Internet
-Archive and active crawls of publication sites on the web.
-
-The dataset is
-integrated into the \href{https://fatcat.wiki}{fatcat website} and allows users
-to explore inbound and outbound references\cite{fatcatguidereferencegraph}.
-
-The format records source and target (fatcat release and work) identifiers, a
-few attributes from the metadata (such as year or release stage) as well as
-information about the match status and provanance.
-
-The dataset currently contains 1,323,423,672 citations across 76,327,662
-entities (55,123,635 unique source and 60,244,206 unique target work
-identifiers; for 1,303,424,212 - or 98.49\% of all citations - we do have a DOI
-for both source and target).
-The majority of matches - 1,250,523,321 - are established through identifier
-based matching (DOI, PMIC, PMCID, ARXIV, ISBN). 72,900,351 citations are
-established through fuzzy matching techniques.
-
-The majority of citations between \emph{refcat} and COCI overlap, as can be
-seen in~Table~\ref{table:cocicmp}.
-
-\begin{table}[]
-	\begin{center}
-		\begin{tabular}{ll}
-			\toprule
-			\bf{Set}              & \bf{Count}    \\
-
-			\midrule
-			COCI (C)              & 1,094,394,688 \\
-			\emph{refcat-doi} (R) & 1,303,424,212 \\ % zstdcat -T0 /magna/refcat/2021-07-28/BrefDOITable/date-2021-07-28.tsv.zst | pv -l | LC_ALL=C sort -T /sandcrawler-db/tmp-refcat/ -S70% -k3,4 -u | zstd -c -T0 > uniq_34.tsv.zst
-			C $\cap$ R            & 1,007,539,966 \\
-			C $\setminus$ R       & 86,854,309    \\
-			R $\setminus$ C       & 295,884,246
-		\end{tabular}
-		\vspace*{2mm}
-		\caption{Comparison between COCI and \emph{refcat-doi}, a subset of
-			\emph{refcat} where entities have a known DOI. At least 50\% of the
-			295,884,246 references only in \emph{refcat-doi} come from links
-			recorded within a specific dataset provider (GBIF, DOI prefix:
-			10.15468).}
-		\label{table:cocicmp}
-	\end{center}
-\end{table}
-
-% zstdcat -T0 /magna/refcat/2021-07-28/BrefDOITable/date-2021-07-28.tsv.zst | pv -l | LC_ALL=C sort -T /sandcrawler-db/tmp-refcat/ -S70% -k3,4 -u | zstd -c -T0 > uniq_34.tsv.zst
-% zstdcat -T0 uniq_34.tsv.zst | pv -l | LC_ALL=C cut -f3,4 | zstd -c -T0 > uniq_34_doi.tsv.zst
-% find . -name "*.csv" | parallel -j 16 "LC_ALL=C grep -v ^oci, {} | LC_ALL=C cut -d, -f2,3" | pv -l | zstd -c -T0 > ../6741422v10_doi_only.csv.zst
-
-
-\section{System Design}
-
-The constraints for the systems design are informed by the volume and the
-variety of the data. The capability to run the whole graph derivation on a
-single machine was a minor goal as well. In total, the raw inputs amount to a
-few terabytes of textual content, mostly newline delimited JSON. More
-importantly, while the number of data fields is low, certain schemas are very
-partial with hundreds of different combinations of available field values found
-in the raw reference data. This is most likely caused by aggregators passing on
-reference data coming from hundreds of sources, each of which not necessarily
-agreeing on a common granularity for citation data and from artifacts of
-machine learning based structured data extraction tools.
-
-Each combination of fields may require a slightly different processing path.
-For example, references with an Arxiv identifier can be processed differently
-from references with only a title. Over 50\% of the raw reference data comes
-from a set of eight field set manifestations, as listed in
-Table~\ref{table:fields}.
-
-\begin{table}[]
-	\begin{center}
-		\begin{tabular}{ll}
-			\toprule
-			\bf{Fields}                                                                                     & \bf{Percentage} \\
-			\midrule
-			\multicolumn{1}{l}{CN $\cdot$ RN $\cdot$ P $\cdot$ T $\cdot$  U $\cdot$  V $\cdot$ Y}           & 14\%            \\
-			\multicolumn{1}{l}{\textbf{DOI}}                                                                & 14\%            \\
-			\multicolumn{1}{l}{CN $\cdot$ CRN $\cdot$ IS $\cdot$ P $\cdot$ T $\cdot$ U $\cdot$ V $\cdot$ Y} & 5\%             \\
-			\multicolumn{1}{l}{CN $\cdot$ CRN $\cdot$ \textbf{DOI} $\cdot$ U $\cdot$ V $\cdot$ Y}           & 4\%             \\
-			\multicolumn{1}{l}{\textbf{PMID} $\cdot$ U}                                                     & 4\%             \\
-			\multicolumn{1}{l}{CN $\cdot$ CRN $\cdot$ \textbf{DOI} $\cdot$ T $\cdot$ V $\cdot$ Y}           & 4\%             \\
-			\multicolumn{1}{l}{CN $\cdot$ CRN $\cdot$ Y}                                                    & 4\%             \\
-			\multicolumn{1}{l}{CN $\cdot$ CRN $\cdot$ \textbf{DOI} $\cdot$ V $\cdot$ Y}                     & 4\%             \\
-		\end{tabular}
-		\vspace*{2mm}
-		\caption{Top 8 combinations of available fields in raw reference data
-			accounting for about 53\% of the total data (CN = container name, CRN =
-			contrib raw name, P = pages, T = title, U = unstructured, V = volume, IS =
-			issue, Y = year, DOI = doi, PMID = pmid). Unstructured fields may contain any value. Identifiers emphasized.}
-		\label{table:fields}
-	\end{center}
-\end{table}
-
-Overall, a map-reduce style\citep{dean2010mapreduce} approach is
-followed\footnote{While the operations are similar, the processing is not
-	distributed but runs on a single machine. For space efficiency, zstd\citep{collet2018zstandard} is used to compress raw data and derivations.}, which allows
-for some
-uniformity in the overall processing. We extract (key, document) tuples (as
-TSV) from the raw JSON data and sort by key. We then group documents with the
-same key and apply a function on each group in order to generate
-our target schema or perform
-additional operations such as deduplication or fusion of matched and unmatched references.
-
-The key derivation can be exact (via an identifier like DOI, PMID, etc) or
-based on a value normalization, like slugifying a title string. For identifier
-based matches we can generate the target schema directly.  For fuzzy matching
-candidates, we pass possible match pairs through a verification procedure,
-which is implemented for \emph{release entity}\footnote{\url{https://guide.fatcat.wiki/entity_release.html}.} pairs. This procedure is a
-domain dependent rule based verification, able to identify different versions
-of a publication, preprint-published pairs and documents, which are
-are similar by various metrics calculated over title and author fields. The fuzzy matching
-approach is applied on all reference documents without identifier (a title is
-currently required).
-
-With a few schema conversions, fuzzy matching can be applied to Wikipedia
-articles and Open Library (edition) records as well. The aspect of precision
-and recall are represented by the two stages: we are generous in the match
-candidate generation phase in order to improve recall, but we are strict during
-verification, in order to control precision. Quality assurance for verification is
-implemented through a growing list of test cases of real examples from the catalog and
-their expected or desired match status\footnote{The list can be found under:
-	\url{https://gitlab.com/internetarchive/cgraph/-/blob/master/skate/testdata/verify.csv}.
-	It is helpful to keep this test suite independent of any specific programming language.}.
-
-
-\section{Limitations and Future Work}
-
-As other dataset in this field we expect this dataset to be iterated upon.
-
-\begin{itemize}
-	\item The fatcat catalog updates its metadata
-	      continously\footnote{A changelog can currenly be followed here:
-		      \url{https://fatcat.wiki/changelog}} and web crawls are conducted
-	      regularly.  Current processing pipelines cover raw reference snapshot
-	      creation and derivation of the graph structure, which allows to rerun
-	      processing based on updated data as it becomes available.
-
-	\item Metadata extraction from PDFs depends on supervised machine learning
-	      models, which in turn depend on available training datasets. With additional crawls and
-	      metadata available we hope to improve models used for metadata
-	      extraction, improving yield and reducing data extraction artifacts in
-	      the process.
-
-	\item As of this version, a number of raw reference
-	      docs remain unmatched, which means that neither exact nor fuzzy matching
-	      has detected a link to a known entity. On the one
-	      hand, this can hint at missing metadata. However, parts of the data
-	      will contain a reference to a catalogued entity, but in a specific,
-	      dense and harder to recover form.
-	      This also include improvements to the fuzzy matching approach.
-	\item The reference dataset contains millions of URLs and their integration
-	      into the graph has been implemented as prototype. A full implementation
-	      requires a few data cleanup and normalization steps.
-\end{itemize}
-
-\section{Acknowledgements}
-
-This work is partially supported by a grant from the \emph{Andrew W. Mellon
-	Foundation}.
-
-
-\section{Appendix A}
-
-
-A note on data quality: While we implement various data quality measures,
-real-world data, especially coming from many different sources will contain
-issues. Among other measures, we keep track of match reasons,
-especially for fuzzy matching to be able to zoom in on systematic errors
-more easily (see~Table~\ref{table:matches}).
-
-\begin{table}[]
-	\footnotesize
-	\captionsetup{font=normalsize}
-	\begin{center}
-		\begin{tabular}{@{}rlll@{}}
-			\toprule
-			\textbf{Count} & \textbf{Provenance} & \textbf{Status} & \textbf{Reason}      \\ \midrule
-			934932865      & crossref            & exact           & doi                  \\
-			151366108      & fatcat-datacite     & exact           & doi                  \\
-			65345275       & fatcat-pubmed       & exact           & pmid                 \\
-			48778607       & fuzzy               & strong          & jaccardauthors       \\
-			42465250       & grobid              & exact           & doi                  \\
-			29197902       & fatcat-pubmed       & exact           & doi                  \\
-			19996327       & fatcat-crossref     & exact           & doi                  \\
-			11996694       & fuzzy               & strong          & slugtitleauthormatch \\
-			9157498        & fuzzy               & strong          & tokenizedauthors     \\
-			3547594        & grobid              & exact           & arxiv                \\
-			2310025        & fuzzy               & exact           & titleauthormatch     \\
-			1496515        & grobid              & exact           & pmid                 \\
-			680722         & crossref            & strong          & jaccardauthors       \\
-			476331         & fuzzy               & strong          & versioneddoi         \\
-			449271         & grobid              & exact           & isbn                 \\
-			230645         & fatcat-crossref     & strong          & jaccardauthors       \\
-			190578         & grobid              & strong          & jaccardauthors       \\
-			156657         & crossref            & exact           & isbn                 \\
-			123681         & fatcat-pubmed       & strong          & jaccardauthors       \\
-			79328          & crossref            & exact           & arxiv                \\
-			57414          & crossref            & strong          & tokenizedauthors     \\
-			53480          & fuzzy               & strong          & pmiddoipair          \\
-			52453          & fuzzy               & strong          & dataciterelatedid    \\
-			47119          & grobid              & strong          & slugtitleauthormatch \\
-			36774          & fuzzy               & strong          & arxivversion         \\
-			% 35311          & fuzzy               & strong          & customieeearxiv      \\
-			% 33863          & grobid              & exact           & pmcid                \\
-			% 23504          & crossref            & strong          & slugtitleauthormatch \\
-			% 22753          & fatcat-crossref     & strong          & tokenizedauthors     \\
-			% 17720          & grobid              & exact           & titleauthormatch     \\
-			% 14656          & crossref            & exact           & titleauthormatch     \\
-			% 14438          & grobid              & strong          & tokenizedauthors     \\
-			% 7682           & fatcat-crossref     & exact           & arxiv                \\
-			% 5972           & fatcat-crossref     & exact           & isbn                 \\
-			% 5525           & fatcat-pubmed       & exact           & arxiv                \\
-			% 4290           & fatcat-pubmed       & strong          & tokenizedauthors     \\
-			% 2745           & fatcat-pubmed       & exact           & isbn                 \\
-			% 2342           & fatcat-pubmed       & strong          & slugtitleauthormatch \\
-			% 2273           & fatcat-crossref     & strong          & slugtitleauthormatch \\
-			% 1960           & fuzzy               & exact           & workid               \\
-			% 1150           & fatcat-crossref     & exact           & titleauthormatch     \\
-			% 1041           & fatcat-pubmed       & exact           & titleauthormatch     \\
-			% 895            & fuzzy               & strong          & figshareversion      \\
-			% 317            & fuzzy               & strong          & titleartifact        \\
-			% 82             & grobid              & strong          & titleartifact        \\
-			% 33             & crossref            & strong          & titleartifact        \\
-			% 5              & fuzzy               & strong          & custombsiundated     \\
-			% 1              & fuzzy               & strong          & custombsisubdoc      \\
-			% 1              & fatcat              & exact           & doi                  \\ \bottomrule
-		\end{tabular}
-		\vspace*{2mm}
-		\caption{Table of match counts (top 25), reference provenance, match status and
-			match reason. The match reason identifier encode a specific rule in the domain
-			dependent verification process and are included for completeness - we do not
-			include the details of each rule in this report.}
-		\label{table:matches}
-	\end{center}
-\end{table}
-
-\bibliographystyle{abbrv}
-% \bibliographystyle{plainnat}
-\bibliography{refs}
-\end{document}
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