Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results

Smalheiser, Neil R.; Zhou, Wei; Torvik, Vetle I.

doi:10.1186/1747-5333-3-2

Cited by 46 publications

(56 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The user inputs an author name and is shown a list of predicted author-individual clusters ordered by the number of articles in each cluster. Each cluster has a simple summary showing the number of articles, name variants, range of publication dates, affiliation words, email address(es), topics, a link to PubMed, as well as a link to our in-house tool called Anne O’Tate [Smalheiser et al 2008], which allows for more advanced summarization. Alternatively, the complete dataset is available upon request for nonprofit academic research.…”

Section: Discussionmentioning

confidence: 99%

Author name disambiguation in MEDLINE

Torvik

Smalheiser

2009

ACM Trans. Knowl. Discov. Data

246

303

View full text Add to dashboard Cite

Background-We recently described "Author-ity," a model for estimating the probability that two articles in MEDLINE, sharing the same author name, were written by the same individual. Features include shared title words, journal name, coauthors, medical subject headings, language, affiliations, and author name features (middle initial, suffix, and prevalence in MEDLINE). Here we test the hypothesis that the Author-ity model will suffice to disambiguate author names for the vast majority of articles in MEDLINE.Methods-Enhancements include: (a) incorporating first names and their variants, email addresses, and correlations between specific last names and affiliation words; (b) new methods of generating large unbiased training sets; (c) new methods for estimating the prior probability; (d) a weighted least squares algorithm for correcting transitivity violations; and (e) a maximum likelihood based agglomerative algorithm for computing clusters of articles that represent inferred author-individuals.Results-Pairwise comparisons were computed for all author names on all 15.3 million articles in MEDLINE (2006 baseline), that share last name and first initial, to create Author-ity 2006, a database that has each name on each article assigned to one of 6.7 million inferred author-individual clusters. Recall is estimated at ~98.8%. Lumping (putting two different individuals into the same cluster) affects ~0.5% of clusters, whereas splitting (assigning articles written by the same individual to >1 cluster) affects ~2% of articles.Impact-The Author-ity model can be applied generally to other bibliographic databases. Author name disambiguation allows information retrieval and data integration to become person-centered, not just document-centered, setting the stage for new data mining and social network tools that will facilitate the analysis of scholarly publishing and collaboration behavior.Availability-The Author-ity 2006 database is available for nonprofit academic research, and can be freely queried via http://arrowsmith.psych.uic.edu.

show abstract

Section: Discussionmentioning

confidence: 99%

Author name disambiguation in MEDLINE

Torvik

Smalheiser

2009

ACM Trans. Knowl. Discov. Data

246

303

View full text Add to dashboard Cite

show abstract

“…Tyrosine and tryptophan derivatives are known to readily cross the blood-brain barrier and facilitate cellular internalization. 22 On the other hand, Ru(II)-polypyridyl complexes are known to generate reactive oxygen species (ROS) up on irradiation into their MLCT band in the visible region of the spectrum. [23][24][25][26] As outlined above, such ROS species damage biomolecules and are therefore cytotoxic to living cells.…”

Section: Resultsmentioning

confidence: 99%

Photo-induced cytotoxicity and anti-metastatic activity of ruthenium(ii)–polypyridyl complexes functionalized with tyrosine or tryptophan

et al. 2017

View full text Add to dashboard Cite

show abstract

“…In the Anne O'Tate tool [11] that combines PubMed literature retrieval with additional post-retrieval analyses, the set of characteristic terms gives a thumbnail annotation of any retrieved literature. For example, in the case of papers describing diabetes research, the set of characteristic terms (restricted to the semantic category of gene names) gives a thumbnail annotation of the genes that have been studied in this field.…”

Section: Discussionmentioning

confidence: 99%

Distribution of “Characteristic” Terms in MEDLINE Literatures

2011

Self Cite

View full text Add to dashboard Cite

Given the occurrence frequency of any term within any set of articles within MEDLINE, we define -characteristic‖ terms as words and phrases that occur in that literature more frequently than expected by chance (at p < 0.001 or better). In this report, we studied how the cut-off criterion varied as a function of literature size and term frequency in MEDLINE as a whole, and have compared the distribution of characteristic terms within a number of journal-defined, affiliation-defined and random literatures. We also investigated how the characteristic terms were distributed among MEDLINE titles, abstracts, and last sentence of abstracts, including -regularized‖ terms that appear both in the title and abstract of the same paper for at least one paper in the literature. For a set of 10 disciplinary journals, the characteristic terms comprised 18% of the total terms on average. Characteristic terms are utilized in several of our web-based services (Anne O'Tate and Arrowsmith), and should be useful for a variety of other information-processing tasks designed to improve text mining in MEDLINE.

show abstract

Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results

Cited by 46 publications

References 19 publications

Author name disambiguation in MEDLINE

Author name disambiguation in MEDLINE

Photo-induced cytotoxicity and anti-metastatic activity of ruthenium(ii)–polypyridyl complexes functionalized with tyrosine or tryptophan

Distribution of “Characteristic” Terms in MEDLINE Literatures

Contact Info

Product

Resources

About