wesome Scholarly Data Analysis

List of resources on scholarly data analysis ranging from datasets, papers, and code about bibliometrics, citation analysis, and other scholarly commons resources. Available online at https://shubhanshu.com/awesome-scholarly-data-analysis/

Table of Contents

• Awesome Scholarly Data Analysis

• Table of Contents

• Datasets

• Publication and Citation

• Peer Review

• Grants and Funding

• Academic Genealogy

• Author Profiles

• Author name disambiguation

• Thesis datasets

• Information Extraction and NLP

• Networks

• Taxonomies and Ontologies of Research Concepts

• Affiliations

• Altmetrics and Dimensions

• Tools

• User interface to publication datasets and analysis

• Tools for collecting open access papers

• Tools for classifying research papers

• Visualizations

• Language Processing and Information Extraction

• Citation and metadata extraction

• Publication and Publisher Info

• Community

• Journals

• Conferences

• Workshops

• Summer Schools

• Courses

• Associations & Community

• Research Groups

• Blogs

• Contributions

Table of contents generated with markdown-toc

Datasets

Publication and Citation

• Arnet Miner

• Microsoft Academic Graph

• OpenAlex - Replacement for MAG

• Open Academic Graph - MAG + AMiner

• OpenAIRE Research Graph - More info here

• Semantic Scholar Corpus

• CiteSeer

• PubMed

• CORA datasets for citation string parsing

• Humanities and multilingual citation string parsing Flux-CiM and ICONIP see Neural ParsCit paper for details

• Citation string parsing data for social sciences for English and German citations - comparison with Grobid and Cermine

• CrossRef DOI URLs

• DOIboost (Crossres + MAG + ORCID + Unpaywall)

• DBLP Citation dataset

• DBLP XML data

• DBLP Discovery Dataset (D3)

• NBER Patent Citations

• Scopus Citation Database

• Papers, patents, and grants from Indiana University

• Small Network Data - Mark Newman’s Lab

• The Koblenz Network Collection

• Google Scholar citation relations

• Google Scholar Citations data set direct-download

• Open citations project

• Wikicite Project

• Ecnonomic Papers

• ArXiv data dump

• ArXiv data on Kaggle

• EuropePMC

• Complete ACL anthology as bibtex file

• ACL Anthology Reference Corpus

• Astrophysics data system (ADS) - All physics papers

• CORE 37M full text open access papers

• Inspire database for high energy physics articles

• Scholarly Data of workshops and conferences in RDF triplets

• The Collection of Computer Science Bibliographies

• OpenCitations corpus

• COCI Doi-Doi citation data

• DOAJ API (Directory of Open Access Journals)

• ROAD (Directory of Open Access Scholarly Resources)

• Sherpa/Romeo (Publisher copyright policies & self-archiving)

• OpenAPC (fees paid for open access journal articles)

• OSF API (Open Science Framework)

• Digital tools for researchers

• Fatcat - versioned, publicly-editable catalog of research publications

• Microsoft Academic Knowledge Graph - RDF dump

• arXiv CS citation in context

• arXiv fulltext + citations dataset

• Self-citation analysis data based on PubMed Central subset (2002-2005)

• Unpaywalled Corpus - PDF to 23M DOIs Data Schema

• A dataset of publication records for Nobel laureates - paper

• OpenAIRE Scholexplorer - 126+ Million literature-dataset and dataset-dataset links between 12+ Million objects - About the data

• Manually annotated citation data from the ACL Anthology into uses, motivation, future, extends, compare or contrast, and background

• iCite - NIH Open Citation Collection

• MEDLINE/PubMed Baseline Repository (MBR) - All Medline abstracts and paper paper meta-data in XML

• American Physical Society Data Sets for Research

• Co-citation networks of all Nature papers

• Semantic Scholar Graph of References in Context (GORC) dataset

• Multiple journal publication datasets

• Structured citations in the English Wikipedia

• ICSR Lab (free for researchers) for scopus and plumx use

• COVID-19 Open Research Dataset (CORD-19)

• PaperRobot - includes PubMed Paper Reading Dataset

• SciMag - Microsoft Academic Linked to SciMago Journals - WebPage

• SciGraph Springer Nature

• Citations to scholarly data in various language wikipedias Code

• 800K publications matched from CrossRef, CORE, and Mendeley with data on publication and open access dates

• Coronavirus Open Citations Dataset

• Crossref dumps DOI meta-data

• S2ORC: The Semantic Scholar Open Research Corpus - 12.7M full text papers

• Wikipedia Citations: A comprehensive dataset of citations with identifiers extracted from English Wikipedia

• Microsoft Academic Data for conducting covid-19 research

• Initiative for Open Abstracts

• Dataset Search: metadata for datasets - Datasets with DOIs and compact identifiers

• Open Syllabus Project

• Journal Causal effect in Citations

• Sci-Hub Download Logs - Latest

• Sci-Hub databases

• SAGE Rejected article tracker dataset from ArXiv

• The Open Research Knowledge Graph (ORKG)

• ACADEMIA INDUSTRY DYNAMICS

• Test of Time Awards

Peer Review

• PeerRead - paper drafts, reviews, and accept/reject decision

• CiteTracked: A Longitudinal Dataset of Peer Reviews and Citations - Contact Author

• Elsevier’s Peer Review Workbench

• ACL-18 Numerical Peer Review Dataset

• Argument Mining for Understanding Peer Reviews

• APE: Argument Pair Extraction - Annotated ICLR 2013-2020 review-rebuttal argument pair

• Argument Mining Driven Analysis of Peer-Reviews Dataset

• Publons review length dataset with 498K reviews - anonymized

• Peer review analyze: A novel benchmark resource for computational analysis of peer reviews

• Open Editors: data about scholarly journals’ editors and editorial board members - Github

Grants and Funding

• GrantExplorer: a free, open-source tool for examining the phrases funded by U.S. federal agencies

• USASpending.gov: Award Data Archive

• NIH research funding

• Authors linked to PIs in NIH Grants

Academic Genealogy

• Mathematics Genealogy Project

• Academic Tree - Cross discipline academic genealogies

• MPACT project - Library Sciences

• PhDTree

• Chemistry Genealogy - curated at UIUC

• Notre Dame Genealogy Project

• UIUC Chemistry, Chemical Engineering, and Biochemistry

• Software Engineering Academic Genealogy

• Other lists of genealogy projects

• Wikipedia - Computer Science Genealogy

• Wikipedia - Theorecical Physicits Genealogy

• Wikipedia - Chemists Genealogy

• SCIENTIFIC GENEALOGY MASTER LIST - Scientists Associated with Concepts in Chemistry & Physics

• Economic Geneology Text Format

• S2AMP : Semantic Scholar Analysis of Mentorship Dataset

• MENTORSHIP - A dataset of mentorship in science with semantic and demographic estimations - Code

Author Profiles

• Temporal profiles of PubMed authors

• ORCID data dump

• National Library of Medicine Profiles

• UIUC Professors database - Publications, Affiliations

• Author Profiles of scholarly authors in Wikipedia

• Career Transitions of CS students

• Author name gender and ethnicity dataset based on PubMed

• MapAffil 2016 dataset – PubMed author affiliations mapped to cities and their geocodes worldwide

• Conceptual novelty scores for PubMed articles

• 100,000 top-scientists that provides standardized information on citations, h-index, co-authorship adjusted hm-index, citations to papers in different authorship positions and a composite indicator

• Canadian PhD career survey - Science report

• Data from the CVs of over 150 assistant professors in psychology in top-ranked research universities and small liberal art colleges in the US - Used in this blog

• Wikidata Author Disambiguation Dataset

• The 4 Universities Data Set - Web pages of CS departments classified for author role (faculty, student, etc.)

• Journal editors dataset

• Career long various citation metrics for 100,000 top-scientists

• Network-Data-Career-Transitions - two anonymized network datasets of post-PhD career transitions and trajectories in computing research

Author name disambiguation

• INSPIRE dataset

• Lee Giles dataset

• Cleaner version of Lee Giles dataset

• DBLP Korean Authors

• Arnet Miner

• Arnet Miner - Manual Name Disambiguation data 210 authors

• DBLP Name disambiguation dataset - Error corrected version

• rexa-coref-data

• Dedped author names on IEEE Vis papers 1990-2018

• Author-ity dataset for PubMed 2009

• ACL Anthology dataset

• Base data for estimating precision and recall of Author-ity among NIH-funded scientists

• ORCID-Linked Labeled Data for Evaluating Author Name Disambiguation at Scale

• S2AND - Semantic Scholar Author Name Disambiguation Tool and Dataset

• BibTex Dataset for 1M authors

• Ethnicity sensitive author disambiguation from INSPIRE HEP

• Pre-processed PubMed data for a study of coauthorship

Thesis datasets

• Open Access Theses and Dissertations

• The Networked Digital Library of Theses and Dissertations (NDLTD)

• PhD Dissertations in the Area of Software Engineering

• ProQuest Dissertations & Theses Global

• History Dissertation Analysis

• Peer-making: the interconnections between PhD Thesis Committee membership and co-publishing - Zenodo

• DISAPERE: A Dataset for DIscourse Structure in Academic PEer REview

• ETDs: Virginia Tech Electronic Theses and Dissertations

Information Extraction and NLP

• Citation Parsing

• Citation Parsing in humanities

• Sentences tagged for Drug Disease pairs

• Document Summarization and citation span identification

• ACL Anthology human summaries for 1000 papers

• Keyphrase Extraction

• Related Work Summarization

• Biomedical NLP annotated datasets

• Chemical compound and drug name recognition task

• Semantic Scholar Dataset

• ScienceIE

• ACL RD TEC 2.0 also at @CLARIN

• SEPID Corpus - Segmended ACL ARC 1.0

• PubMed Central Open Access - BioC

• PubMed Fulltext - protein-protein and genetic interactions

• BioNLP - Argo

• Biomedical NLP - Stav

• GENIA - BioNLP 2011

• Genia Treebank used for SciSpacy training - SciSpacy link

• Full GENIA corpus

• Anatomical Entity Mention (AnEM) corpus

• CellFinder - Entity detection

• Multi-Level Event Extraction (MLEE)

• Biomedical sentence simplification

• PubMed - Colorado Richly Annotated Full-Text

• Biomedical NER datasets related publication

• BioVerbNet

• Lunar and Planetary Science abstracts for NER and Relations

• ACM data affiliations

• ACM - DBLP database entry matching

• Colorado Richly Annotated Full-Text - PubMed abstract annotated with entities mapped to 10 biomedical ontology terms.

• CLEF datasets for multilingual Biomedical NLP+IE

• MedMentions - UMLS entities in PubMed

• Colright Initiatve - Rich text competition

• SciERC - scientific entities, their relations, and coreference clusters for 500 AI conf abstracts

• PubMed200k_RCT - Label abstract sentences into Objective, Background, Method, Results, Conclusions

• NER, Parsing, Classification datasets from SciBert

• ACA Wiki - Paper summaries of more than 1600 papers

• SemEval-2018 task 7 Semantic Relation Extraction and Classification in Scientific Papers

• A Compendium of Free, Public Biomedical Text Mining Tools Available on the Web

• Medical Information Extraction from PubMed abstracts

• Corpus of 40 scientific papers manually annotated by multiple scientific discourse facets

• PharmaCoNER: Pharmacological Substances, Compounds and proteins and Named Entity Recognition track - Train - Dev - Test - Background Test set

• Bacteria Biotope (BB) Task - NER, NEL, Relation, KB Extraction

• Entity/relation recognition and GOF/LOF mutated gene text identification task based on the Active Gene Annotation Corpus

• The Regulatory Network of Plant Seed Development (SeeDev) Task - NER, Relation

• TalkSumm - Summary of papers via alignment to talks

• SeminalSurveyDBLP - Classification of seminal or survey papers

• Supp.ai - PubMed supplement-drug interactions and supplement-supplement interactions

• GENETAG - More recent versions Publication and Download 2005

• MedTag: A Collection of Biomedical Annotations - Download

• Open Biomedical corpora

• Biomedical Abstract Meaning Representation corpus based on PubMed Fulltext - Also see other NLM curated biomedical resources

• SciDTB: Discourse Dependency TreeBank for Scientific Abstracts

• SciDTB corpus annotated for argumentation mining - Paper

• Dr. Inventor Multi-layer Scientific Corpus for multiple scientific discourse facets

• ART corpus - 225 papers manually annotated the CISP labels (i.e. “Goal”, “Method”, “Result”).- Browse files - Project details

• Multi-CoreSC CRA corpus (MCCRA) - 50 papers annotated with multiple CoreSC labels per sentence. - Project details

• PubMedQA - Question answering on PubMed

• Corposaurus - Collection of biomedical corpus for NER

• BioNER corpus

• NeuroQuery - 14,000 full-text publications and 400,000 peak activations - NeuroQuery website

• Medical Information Extraction dataset

• A Large Parallel Corpus of Full-Text Scientific Articles

• Annotated Corpus of Scientific Conference’s Homepages for Information Extraction

• Chi QA - Health Question Answering dataset from NLM

• Corpus of Open Access articles from multiple fields in Science, Technology, and Medicine - Includes wikification data

• Grounding Scientific Entity References in STEM Scholarly Content to Authoritative Encyclopedic and Lexicographic Sources

• Open Research Knowledge Graph project - Website

• Academic PhraseBank

• SciKG - Statement extraction datasets

• A Fully Coreference-annotated Corpus of Scholarly Papers from the ACL Anthology

• A manual corpus of annotated main findings of clinical case reports

• TREC Precision Medicine / Clinical Decision Support Track

• Lots of biomedical entity linking and entity identification datasets

• Materials Science Named Entity Recognition: train/development/test sets

• Entities in 3.27 million materials science abstracts

• Normalized entities in material science papers

• Named Entity Recognition for Bacterial Type IV Secretion Systems - Paper

• Annotating and detecting phenotypic information for chronic obstructive pulmonary disease

• MiRoR11 - P2 - Annotated corpus for primary and reported outcomes extraction

• Data from: PGxCorpus, a Manually Annotated Corpus for Pharmacogenomics

• Multiple PUBMED annotated corpora from iProLink project

• Mars Target Encyclopedia - LPSC abstracts labeled data set

• Annotation of phenotypes using ontologies

• The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text - SPECIES Direct Download - ORGANISMS Direct Download

• Entity mention in articles used for benchmark

• RAMBO 800+: A Corpus for the Development of Gene/Protein Recognition from Rare and Ambiguous Abbreviations

• Medical Relation Extraction - CrowdTruth

• KP20k - Kehphrase extraction on 20k abstracts

• Named Entity Recognition: (17.3 MB), 8 datasets on biomedical named entity recognition

• Relation Extraction: (2.5 MB), 2 datasets on biomedical relation extraction

• Question Answering: (5.23 MB), 3 datasets on biomedical question answering task

• SciREX : A Challenge Dataset for Document-Level Information Extraction

• Papers with Code - Links between papers and repositories and extraction of SOTA results

• Citation Context Classification based on purpose

• Citation Context Classification based on influence

• PubMed knowledge graph (PKG) Figshare

• Citation and Header Datasets

• Gobrid-NER data

• Multiple NER and Entity Linking data for science

• Scitation Context Classification

• S2ORC: The Semantic Scholar Open Research Corpus - 12.7M full text papers

• EuropePMC annotations for entities and relationships

• NLPContributionGraph - Structuring Scholarly NLP Contributions in the Open Research Knowledge Graph

• GOBRID NER

• GOBRID Sequence Labeling data

• The General Index - Metadata, Ngrams, and Keyphrases in 107,233,728 journal articles

• Pubtrends Review Dataset

• PubTator Central (PTC) - NLP annotated PMC datasets

• PubMedCentral Author Manuscript Collection

• Paper analyzer pubmed

• NER on Material Science Papers

• SoMeSci - Software Mentions in Science

• NLMChem a new resource for chemical entity recognition in PubMed full-text literature

• Scientific summarization datasets

• PubMed Classification

• Annotated scientific findings with sentence-level and aspect-level certainty

• SoftwareKG_Social and SoftwareKG_PubMed - Software mentions in articles

• Bioinformatics Named Entity Recogniser for Databases and Software

• The CodeMeta Project: preservation, discovery, reuse, and attribution of software

• Social Science Software Citation Dataset

• SoMeSci - A 5 Star Open Data Gold Standard Knowledge Graph of Software Mentions in Scientific Articles

• Softcite dataset: A gold-standard dataset of software mentions in research publications for supervised learning based named entity recognition

• SoftwareKG-PMC:a Knowledge Graph of Software mentions extracted from articles of the PMC Open Access Dataset

• DEAL: Detecting Entities in the Astrophysics Literature

• COMPUTER SCIENCE KNOWLEDGE GRAPH

• SCIERC: Multi-Task Identification of Entities, Relations, and Coreferencefor Scientific Knowledge Graph Construction - Code

• University of Washington BIO NLP datasets

• multimodal_summ: Multimodal summarization of research papers

• ACL Anthology Corpus - Full Text

• Entity Linking of Crossref Funding Orgs in Acknowledgements - paper

• Microsoft Academic Knowledge Graph (MAKG) - Zenodo ComplEx entity embeddings (120 GB) for all 243 million authors, 239 publications, 49,000 journals, and 16,000 conferences

• Wikidata:WikiProject Clinical Trials

• A Dataset of Alt Texts from HCI Publications

• PubMed-OA-Extraction-dataset

Networks

• ACL Anthology Network

• I3 Open Innovation Dataset Index - Multiple datasets related to patent networks, inventor careers, etc.

• Science4cast Competition - capture the evolution of scientific concepts and predict which research topics will emerge in the coming years

Taxonomies and Ontologies of Research Concepts

• SciGraph Springer Nature

• Medical Subject Headings maintained by the National Library of Medicine of the United States

• Computer Science Ontology maintained by Scholarly Knowledge: Modeling, Mining and Sense Making

• Physics Subject Headings (PhySH) maintained by American Physical Society (APS) GitHub

• Open Biological and Biomedical Ontology (OBO) maintained by the OBO Foundry

• ACM Computing Classification System maintained by the Association for Computing Machinery

• Physics and Astronomy Classification Scheme (PACS) maintained by American Institute of Physics (AIP) discontinued in 2010 and replaced by Physics Subject Headings

• Mathematics Subject Classification (MSC) mantained by Mathematical Reviews and zbMATH

• Journal of Economic Literature (JEL) maintained by the American Economic Association

• STW Thesaurus for Economics maintained by ZBW - Leibniz Information Centre for Economics

• Australian and New Zealand Standard Research Classification (ANZSRC) maintained by Australian Bureau of Statistics, it consists of 3 sub-classification schemes:

• Fields of Research (FoR) classification

• Research Fields, Courses and Disciplines (RFCD) classification

• Socio-Economic Objective (SEO) classification

• Library of Congress Classification (LCC) maintained by Library of Congress

• Fields of Study (FoS) maintained by Microsoft Academic

• CrossRef Open Funder’s Registry

• Scientific Keyphrase Extraction Datasets - KP20k, NUS, MAG_KP

• Grounding Scientific Entity References in STEM Scholarly Content to Authoritative Encyclopedic and Lexicographic Sources

• XL-BEL is a benchmark for cross-lingual biomedical entity linking (XL-BEL). The benchmark spans 10 typologically diverse languages

• IteraTeR: Understanding Iterative Revision from Human-Written Text based on ArXiv abstract edit versions

• CiteSum: Citation Text-guided Scientific Extreme Summarization and Low-resource Domain Adaptation

Affiliations

• Global Research Identifier Database (GRID)

• CS Rankings with people linked to institutes

Altmetrics and Dimensions

• Altmetrics API

• Dimensions.ai API - documentation, example

• Core Conference Rankings

• China Computer Federation Conference Rankings

Tools

User interface to publication datasets and analysis

• Google Scholar

• Semantic Scholar

• Microsoft Academic Graph

• OpenAIRE Explore

• AceMap

• GitXiv

• ACL Anthology

• NIPS papers

• Abel tools for PubMed data

• infolis: linking research data and publications

• Metrics toolkit

• Rcrossref (R library)

• Rscopus (R library)

• Scholar (R library)

• Bibliometrix (R library)

• CITAN (R library)

• BibeR (BibeR: A Web-based tool for bibliometric analysis in scientific literature)

• scihub.py (Python library)

• SoPaper (Python library)

• CiteSeer tools

• Novelty quantification in PubMed articles

• TidyPMC - R based PMC XML parser

• PublicationHarvester - Download PubMed publications of an author

• Publish or Perish - retrieves and analyzes academic citations from MS Academic and Scholar

• Affiliation string parser

• CiteSeerX

• Data Set Knowledge Graph (DSKG) - a RDF data set about data sets

• Citation Gecko - Find related papers

• pySciSci - Python tool for working with MAG, PubMed, etc.

Tools for collecting open access papers

• ContentMine - getpapers

• rcoreoa - CORE API R client

• metaknowledge - A Python library for doing bibliometric and network analysis in science and health policy research

• PubMedPortable - PubMed to Postgres

• medic - Parsing MEDLINE and storing into a DB

Tools for classifying research papers

• CSO-Classifier

• WikiCSSH

• SAGE Rejected Article Tracker

Visualizations

• Rexplore

• VOSviewer

• CitNetExplorer

• CiteSpace

• Nobel nominations and recipients

• WOS2Pajek

Language Processing and Information Extraction

• Biomedical - BioSentVec Embeddings

• Biomedical embeddings - CambridgeLTL

• NIH scientific paper pre-processing

• SciSpacy - Spacy models for Biomedical NLP from AllenAI

• Multitask Biomedical NER

• SciBERT - Bert LM for Biomedical and CS papers

Citation and metadata extraction

• CERMINE

• Grobid

• EXCITE (Extraction of Citations from PDF Documents)

• Science-Parse

• unarXiv (Citation in context from arXiv)

• Biblio-Glutton

• PDF/LaTeX to JSON

• CrossRef Reference Matching code and evaluation data

• Citation style classifier and evaluation data

• refextract - extracting references used in scholarly communication

Publication and Publisher Info

• Interactive sheet for deciding publication strategy and open science - Tweet

Author Name Disambiguation

• Bibliographic Entity Automatic Recognition and Disambiguation - paper

Community

Journals

• Frontiers in Research Metrics and Analytics

• Scientometrics

• Journal of Informetrics

• Quantitative Science Studies (Open Access)

• Science, technology and human values

• Social Studies of Science

• Science and Public Policy

Conferences

• Joint Conference on Digital Libraries (JCDL)

• International Conference on Theory and Practice of Digital Libraries (TPDL)

• European Semantic Web Conference (ESWC), Research of Research Track

• STI Conference series (Science and Technology indicators, e.g., 2018)

• ISSI Conference series (INTERNATIONAL CONFERENCE ON SCIENTOMETRICS & INFORMETRICS, e.g., 2019)

Workshops

• SIGMET - Metrics workshop

• International Workshop on Mining Scientific Publications

• Semantics, Analytics, Visualisation: Enhancing Scholarly Dissemination (SAVE-SD)

• Workshop on Reframing Research (RefResh)

• Enabling Open Semantic Science (SemSci)

• Workshop on Scholarly Document Processing

Summer Schools

• CWTS Scientometrics Spring School (CS3)

• European Summer School of Scientometrics (ESSS)

Courses

• SI 710: Science of Science - University of Michigan School of Information

Associations & Community

• International Society for Informetrics and Scientometrics (ISSI)

• European Network of Indicator Designers (ENID)

• 4S (Society for Social Studies of Science)

• SIG/MET - Special Interest Group for the measurement of information production and use

Research Groups

• Science of Science and Computational Discovery Lab - Colorado University, Boulder

Blogs

• Clarivate Blog

• Elsevier Connect

• The Scholarly Kitchen

Contributions

The following people have contributed to the items on this list.

• Shubhanshu Mishra - Maintainer of the list.

• Angelo Antonio Salatino

• Philipp Zumstein

• Ali (Aliakbar Akbaritabar)

• Andrea Mannocci

http://shubhanshu.com/awesome-scholarly-data-analysis/