Anne O’Tate

Engwall, Keith

doi:10.5195/jmla.2017.92

Cited by 2 publications

(7 citation statements)

References 2 publications

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“…Many of the methods were discussed in detail in the original publications [1,22,29]. As one of the reviewers of Anne O'Tate pointed out [8], in the past Anne O'Tate tended to be slow in processing large queries. We therefore devoted considerable effort to optimizing the data PLOS ONE retrieval techniques used for passing information between entities Anne O'Tate and PubMed.…”

Section: Methodsmentioning

confidence: 99%

“…users the most [8], since the chunks are displayed in order of document frequency, rather than in a hierarchy (e.g., institution-city-state-country). Because of the simple text processing that is carried out, different chunks may be semantically redundant (e.g., NY and New York are treated separately), and an entity followed by a comma is displayed separately than the same entity followed by a period.…”

Section: Plos Onementioning

confidence: 99%

“…Its data mining tools provide a variety of dynamic content analysis that can be of great use in identifying relevant search terms and bibliometrics." [8].…”

Section: Introductionmentioning

confidence: 99%

“…To date, the original Anne O’Tate paper [ 1 ] has been cited 57 times according to Google Scholar (excluding self-citations) and 16 times in PubMed Central. In 2017, Engwall reviewed Anne O’Tate from the standpoint of users, especially librarians [ 8 ]. He critiqued its slow performance for large queries (which we have since fixed by moving to a different server and adding memory) and its bare-bones interface (which we deliberately prefer as a design choice), but concluded that “Anne O’Tate provides an excellent tool set for searching PubMed.…”

Section: Introductionmentioning

confidence: 99%

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Anne O’Tate: Value-added PubMed search engine for analysis and text mining

Smalheiser

Fragnito²,

Tirk³

2021

PLoS ONE

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Over a decade ago, we introduced Anne O’Tate, a free, public web-based tool http://arrowsmith.psych.uic.edu/cgi-bin/arrowsmith_uic/AnneOTate.cgi to support user-driven summarization, drill-down and mining of search results from PubMed, the leading search engine for biomedical literature. A set of hotlinked buttons allows the user to sort and rank retrieved articles according to important words in titles and abstracts; topics; author names; affiliations; journal names; publication year; and clustered by topic. Any result can be further mined by choosing any other button, and small search results can be expanded to include related articles. It has been deployed continuously, serving a wide range of biomedical users and needs, and over time has also served as a platform to support the creation of new tools that address additional needs. Here we describe the current, greatly expanded implementation of Anne O’Tate, which has added additional buttons to provide new functionalities: We now allow users to sort and rank search results by important phrases contained in titles and abstracts; the number of authors listed on the article; and pairs of topics that co-occur significantly more than chance. We also display articles according to NLM-indexed publication types, as well as according to 50 different publication types and study designs as predicted by a novel machine learning-based model. Furthermore, users can import search results into two new tools: e) Mine the Gap!, which identifies pairs of topics that are under-represented within set of the search results, and f) Citation Cloud, which for any given article, allows users to visualize the set of articles that cite it; that are cited by it; that are co-cited with it; and that are bibliographically coupled to it. We invite the scientific community to explore how Anne O’Tate can assist in analyzing biomedical literature, in a variety of use cases.

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Section: Methodsmentioning

confidence: 99%

Section: Plos Onementioning

confidence: 99%

“…Its data mining tools provide a variety of dynamic content analysis that can be of great use in identifying relevant search terms and bibliometrics." [8].…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Anne O’Tate: Value-added PubMed search engine for analysis and text mining

Smalheiser

Fragnito²,

Tirk³

2021

PLoS ONE

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“…the systematic download of abstracts from Pub-Med, or text mining. Without the need for programming, different web tools and databases provide summary statistics and annotations for results of a single search term (Engwall, 2017;Garcia-Pelaez et al, 2019;Wei et al, 2013) or associations and relationships among biomedical entities in the literature (Kilicoglu, 2018;Bhasuran and Natarajan, 2018;Szklarczyk et al, 2019;Ren et al, 2018).…”

Section: Introductionmentioning

confidence: 99%

SimText: A text mining framework for interactive analysis and visualization of similarities among biomedical entities

Macnee

Pérez‐Palma

Schumacher-Bass

et al. 2020

Preprint

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AbstractLiterature exploration in PubMed on a large number of biomedical entities (e.g., genes, diseases, experiments) can be time consuming and challenging comparing many entities to one other. Here, we describe SimText, a user-friendly toolset that provides customizable and systematic workflows for the analysis of similarities among a set of entities based on words from abstracts and/or other text. SimText can be used for (i) data generation: text collection from PubMed and extraction of words with different text mining approaches, and (ii) interactive analysis of data using unsupervised learning techniques and visualization in a Shiny web application.Availability and ImplementationWe developed SimText as an open-source R software and integrated it into Galaxy, an online data analysis platform. A command line version of the toolset is available for download from GitHub at https://github.com/mgramm1/simtext.

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Anne O’Tate

Abstract: Anne O’Tate is an alternative interface for searching PubMed developed by the University of Illinois at Chicago (UIC).

Cited by 2 publications

References 2 publications

Anne O’Tate: Value-added PubMed search engine for analysis and text mining

Anne O’Tate: Value-added PubMed search engine for analysis and text mining

SimText: A text mining framework for interactive analysis and visualization of similarities among biomedical entities

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