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Author name disambiguation for PubMed

Wanli Liu, Rezarta Islamaj Doğan, Sun Kim, Donald C. Comeau, Won Kim, Lana Yeganova, Zhiyong Lu, W. John Wilbur
2013 Journal of the Association for Information Science and Technology  
With integration of the author name disambiguation system into the PubMed search engine, the overall click-through-rate of PubMed users on author name query results improved from 34.9% to 36.9%. function  ...  Log analysis shows that PubMed users frequently use author names in queries for retrieving scientific literature. However, author name ambiguity may lead to irrelevant retrieval results.  ...  We thank the anonymous reviewers for valuable suggestions, which improved this paper.  ... 
doi:10.1002/asi.23063 pmid:28758138 pmcid:PMC5530597 fatcat:g4kxd6xd4jcdhd5o4rbbfrxeje

LAGOS-AND-Online-Appendix [article]

Li Zhang
2021 Zenodo  
The most important datasets for author name disambiguation as of March, 2021.  ...  Online Appendix for the paper "LAGOS-AND: A Large, Gold Standard Dataset for Scholarly Author Name Disambiguation" Appendix A.  ...  Author Name, PMID for associating metadata from PubMed, Author Position, ORCID iD/NIH ID, ORCID Name/NIH Name, Authority2009 ID (disambiguated IDs for PubMed2009), Publish Year, Predicted Ethnicity, Predicted  ... 
doi:10.5281/zenodo.4659684 fatcat:bhhufkl775crhfcdgpu3cuhc6i

Author Disambiguation in PubMed: Evidence on the Precision and Recall of Author-ity among NIH-Funded Scientists

Marc J. Lerchenmueller, Olav Sorenson, Lutz Bornmann
2016 PLoS ONE  
We examined the usefulness (precision) and completeness (recall) of the Author-ity author disambiguation for PubMed articles by associating articles with scientists funded by the National Institutes of  ...  of the Author-ity disambiguation.  ...  Author Contributions Analyzed the data: MJL OS. Wrote the paper: MJL OS.  ... 
doi:10.1371/journal.pone.0158731 pmid:27367860 pmcid:PMC4930168 fatcat:o5behvke4fdtxhtx5lftam44v4

Building a PubMed knowledge graph [article]

Jian Xu, Sunkyu Kim, Min Song, Minbyul Jeong, Donghyeon Kim, Jaewoo Kang, Justin F. Rousseau, Xin Li, Weijia Xu, Vetle I. Torvik, Yi Bu, Chongyan Chen (+3 others)
2020 arXiv   pre-print
To address this issue, we constructed a PubMed knowledge graph (PKG) by extracting bio-entities from 29 million PubMed abstracts, disambiguating author names, integrating funding data through the National  ...  Data validation revealed that the BioBERT deep learning method of bio-entity extraction significantly outperformed the state-of-the-art models based on the F1 score (by 0.51%), with the author name disambiguation  ...  Validity of Author Name Disambiguation The validation of author disambiguation remains a challenge because there is a lack of abundant validation sets.  ... 
arXiv:2005.04308v2 fatcat:257dnmd4xrgzfmj5ftk4myhaxm

GeneE: Gene and protein query expansion with disambiguation

M. J. Schuemie, N. Kang, M. L. Hekkelman, J. A. Kors
2009 Bioinformatics  
for ambiguous terms, before forwarding the query to either PubMed, Google or Jane.  ...  When referring to genes, authors often use synonyms instead of the official gene symbols.  ...  ., 2007) , in which ambiguous gene names are identified and combined with disambiguation information derived from a gene dictionary.  ... 
doi:10.1093/bioinformatics/btp597 pmid:19837720 fatcat:nsekyujdtffplmn5n2jcpugoom

Pubmed Parser: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset XML Dataset

Titipat Achakulvisut, Daniel Acuna, Konrad Kording
2020 Journal of Open Source Software  
Parser has already been used in published work for several different purposes, including author name disambiguation (Tang et al., 2019) , information extraction and summarization (Abdeddaım, Vimard,  ...  For example, Pubmed Parser's capabilities were used in Tang et al. (2019) to parse authorship lists, affiliations, and MeSH terms as part of a large-scale name disambiguation pipeline.  ... 
doi:10.21105/joss.01979 fatcat:7o2eolnk3jf25da4kctpyi4qpi

Integrating the ReCiter author disambiguation engine with a faculty information system [article]

Paul Albert, Michael Bales, Jie Lin
2017 Figshare  
name disambiguation using records harvested from PubMed.  ...  ReCiter employs 15 separate strategies for disambiguation including department name, known co-investigators, and year of degree.Fundamentally speaking, ReCiter is a publication suggestion engine.  ...  -a fancy word for requirements Integrating the ReCiter author disambiguation engine with a faculty information system Problem Manual entry of publications is unsustainable.  ... 
doi:10.6084/m9.figshare.5303299.v1 fatcat:3eeaggia2zbjhjxskmwoblkpge

NEMO: Extraction and normalization of organization names from PubMed affiliations

Siddhartha Reddy Jonnalagadda, Philip Topham
2010 Journal of Biomedical Discovery and Collaboration  
network of authors, augmenting NLM's MARS system for correcting errors in OCR output of affiliation field, and automatically indexing the PubMed citations with the normalized organization name and country  ...  This research could potentially help in analyzing large social networks of organizations for landscaping a particular topic, improving performance of author disambiguation, adding weak links in the co-author  ...  Background In recent years, many systems have been developed for disambiguating author names from PubMed abstracts (1; 2). Torvik et al.  ... 
pmid:20922666 pmcid:PMC2990275 fatcat:ta54k6kqjra2neu2gaefnvdpxe

Social Network: a Cytoscape app for visualizing co-authorship networks

Victor Kofia, Ruth Isserlin, Alison M.J. Buchan, Gary D. Bader
2015 F1000Research  
The app focuses on creating visual summaries of individuals connected by co-authorship links in academia, created from bibliographic databases like PubMed, Scopus and InCites.  ...  Acknowledgements We thank the authors of the Hughes et al. paper for sharing their social network data for analysis.  ...  These profiles are helpful when disambiguating authors with very similar or identical names.  ... 
doi:10.12688/f1000research.6804.2 pmid:26949516 pmcid:PMC4760270 fatcat:vozrfa2fejb4fligdqciayuoxu

LAGOS-AND: A Large Gold Standard Dataset for Scholarly Author Name Disambiguation [article]

Li Zhang, Wei Lu, Jinqing Yang
2022 arXiv   pre-print
Using the method, we built LAGOS-AND, two large, gold-standard datasets for author name disambiguation (AND), of which LAGOS-AND-BLOCK is created for clustering-based AND research and LAGOS-AND-PAIRWISE  ...  In building the datasets, we reveal the variation degrees of last names in three literature databases, PubMed, MAG, and Semantic Scholar, by comparing author names hosted to the authors' official last  ...  89.59 81.16 Table 5 . 5 A list of datasets for author name disambiguation research Author Name, PMID for associating metadata from PubMed, Author Position, ORCID iD/NIH ID, ORCID Name/NIH Name, Authority2009  ... 
arXiv:2104.01821v2 fatcat:jszqwvseazg4vpt3wsoexzw7wq

Disambiguate: An open-source application for disambiguating two species in next generation sequencing data from grafted samples

Miika J. Ahdesmäki, Simon R. Gray, Justin H. Johnson, Zhongwu Lai
2017 F1000Research  
Disambiguate is open source and is freely available at https://github.com/AstraZeneca-NGS/disambiguate. Miika J. Ahdesmäki ( ) PubMed Abstract | Publisher Full Text | Free Full Text 2.  ...  Disambiguate is a program for computationally separating the sequencing reads of two species derived from grafted samples.  ...  Acknowledgments The authors wish to thank Brad Chapman, Rory Kirchner and Eric Schelhorn for feedback and fixes on Disambiguate.  ... 
doi:10.12688/f1000research.10082.2 pmid:27990269 pmcid:PMC5130069 fatcat:awfjatnw4fdo5pazrf75mpirxa

Grant proposal: Open, complete, disambiguated database of authorship metadata in biomedicine

Impactstory Team
2018 Figshare  
We will assign an author cluster (named by an ORCID whenever possible) to each author position for each paper in PubMed.  ...  This means that for a given author we have a list of everything they've published that has been indexed by PubMed. Institutional information is a useful attribute in author disambiguation.  ... 
doi:10.6084/m9.figshare.6942872.v1 fatcat:bfqaybedmjakxpqcuedmnzlwda

Building a PubMed knowledge graph

Jian Xu, Sunkyu Kim, Min Song, Minbyul Jeong, Donghyeon Kim, Jaewoo Kang, Justin F. Rousseau, Xin Li, Weijia Xu, Vetle I. Torvik, Yi Bu, Chongyan Chen (+3 others)
2020 Scientific Data  
To address this issue, we constructed a PubMed knowledge graph (PKG) by extracting bio-entities from 29 million PubMed abstracts, disambiguating author names, integrating funding data through the National  ...  Data validation revealed that the BioBERT deep learning method of bio-entity extraction significantly outperformed the state-of-the-art models based on the F1 score (by 0.51%), with the author name disambiguation  ...  Code availability We have made the pre-trained weights of BioBERT freely available at https://github.com/naver/biobertpretrained, and the source code for fine-tuning BioBERT available at https://github.com  ... 
doi:10.1038/s41597-020-0543-2 pmid:32591513 fatcat:puaf2zqqrzgipdjit5zermlrze

Social Network: a Cytoscape app for visualizing co-authorship networks

Victor Kofia, Ruth Isserlin, Alison M.J. Buchan, Gary D. Bader
2015 F1000Research  
PubMed Abstract | Publisher Full Text | Free Full Text 7. Merico D, Isserlin R, Stueker O, et al.: Enrichment map: a network-based method for gene-set enrichment visualization and interpretation.  ...  Morris JH, Apeltsin L, Newman AM, et al.: clusterMaker: a multi-algorithm clustering plugin for Cytoscape. BMC Bioinformatics. 2011; 12(1): 436.  ...  Acknowledgements We thank the authors of the Hughes et al. paper for sharing their social network data for analysis.  ... 
doi:10.12688/f1000research.6804.3 pmid:26949516 pmcid:PMC4760270 fatcat:odrjmng6f5anxlzxjjwco3lkiq

The effect of mentee and mentor gender on scientific productivity of applicants for NIH training fellowships [article]

Hao Yu, Kristine A. Willis, Aviva Litovitz, Robert M. Harriman, Matthew T. Davis, Payam Meyer, Brad Busse, Rebecca A. Meseroll, Hashanthi D. Wijayatilake, Matthew J. Perkins, James M. Anderson, George M. Santangelo
2021 bioRxiv   pre-print
Here we use our novel author disambiguation solution to investigate the role of self-identified gender in mentorship of 12,932 trainees who either successfully or unsuccessfully applied to the National  ...  Institutes of Health for research fellowships between fiscal years 2011 and 2017, applying a multi-dimensional framework to assess productivity.  ...  specific linkages 232 to a person's publications and NIH funding. 233 234 PubMed author disambiguation: PubMed author disambiguation was performed in a similar fashion as 235 described previously [14-  ... 
doi:10.1101/2021.02.02.429450 fatcat:5uy35npapjds3p657mpuhp5bdi
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