Anne O'Tate
Encyclopedia
Anne O'Tate is a free, web-based application that analyses sets of records identified on PubMed
, the bibliographic database
of articles from over 5,500 biomedical journals worldwide. While PubMed has its own wide range of search options to identify sets of records relevant to a researchers query it lacks the ability to analyse these sets of records further, a process for which the terms text mining
and drill down
have been used. Anne O'Tate is able to perform such analysis and can process sets of up to 25,000 PubMed records.
(known as MeSH terms, but called ‘Topics’ by Anne O’Tate) for a subject for which no corresponding subject heading or ‘entry term’ (cross-references to preferred MeSH term) exists or where PubMed’s automatic mapping process (identifying a MeSH term and including it in a search formulation) fails.
Searching for instance for articles on ‘“Knowledge Transfer”’ (for which no correspnding MeSH or entry term exists) will retrieve a set of some 530 studies in PubMed (as of August 2011); Anne O’Tate’s analysis suggests that MeSH terms like "Diffusion of Innovation" or "Information Dissemination" may be suitable additional concepts to retrieve a more ‘sensitive’ (comprehensive) set of references. This method of identifying possible MeSH terms is not available on PubMed.
as a whole, thus they distinguish the result subset from the rest of MEDLINE" can be identified and help with further refining a search on PubMed.
. It is part of the Arrowsmith Project, which developed tools such as “Arrowsmith” proper, a text-comparison application, "Adam", a database of medical abbreviations,, and ‘’Author-ity’’ (an author-disambiguation tool), "Compendium", a list of biomedical text mining
tools, and Anne O’Tate. The Project is based on research led by Don R. Swanson
at the University of Chicago
which hosted the original tool.
Further research was led by Neil R. Smalheiser at the University of Illinois at Chicago
, with funding from the National Institutes of Health
.
, ClusterMed, or PubReMiner. Only Anne O’Tate uses PubMed’s standard interface, search syntax, and some of its functionality.
PubMed
PubMed is a free database accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez information retrieval system...
, the bibliographic database
Bibliographic database
A bibliographic database is a database of bibliographic records, an organized digital collection of references to published literature, including journal and newspaper articles, conference proceedings, reports, government and legal publications, patents, books, etc...
of articles from over 5,500 biomedical journals worldwide. While PubMed has its own wide range of search options to identify sets of records relevant to a researchers query it lacks the ability to analyse these sets of records further, a process for which the terms text mining
Text mining
Text mining, sometimes alternately referred to as text data mining, roughly equivalent to text analytics, refers to the process of deriving high-quality information from text. High-quality information is typically derived through the devising of patterns and trends through means such as...
and drill down
Drill down
In information technology, to drill down means to move from summary information to detailed data by focusing in on something. In a GUI-environment, "drilling-down" may involve clicking on some representation in order to reveal more detail....
have been used. Anne O'Tate is able to perform such analysis and can process sets of up to 25,000 PubMed records.
Description
Once a set of articles has been identified using Anne O’Tate with its PubMed-like interface and search syntax, the set can be analysed and words and concepts mentioned in specific 'fields' (sections) of PubMed records can be displayed in order of frequency. ‘Fields’ which Anne O’Tate can display in this manner are:Topics (MeSH)
This option may help to identify possible Medical Subject HeadingsMedical Subject Headings
Medical Subject Headings is a comprehensive controlled vocabulary for the purpose of indexing journal articles and books in the life sciences; it can also serve as a thesaurus that facilitates searching...
(known as MeSH terms, but called ‘Topics’ by Anne O’Tate) for a subject for which no corresponding subject heading or ‘entry term’ (cross-references to preferred MeSH term) exists or where PubMed’s automatic mapping process (identifying a MeSH term and including it in a search formulation) fails.
Searching for instance for articles on ‘“Knowledge Transfer”’ (for which no correspnding MeSH or entry term exists) will retrieve a set of some 530 studies in PubMed (as of August 2011); Anne O’Tate’s analysis suggests that MeSH terms like "Diffusion of Innovation" or "Information Dissemination" may be suitable additional concepts to retrieve a more ‘sensitive’ (comprehensive) set of references. This method of identifying possible MeSH terms is not available on PubMed.
Authors
This option may help with identifying authors who have written frequently about a given subject, or may help with identifying possible experts or peer reviewersJournals
Identifying journals which publish papers on the subject under investigation may assist with selecting suitable journals to consider for manuscripts or for detailed scanning for relevant articles ('hand searching') not found by the search on PubMed.Other fields
Author affiliations (addresses) and the years of publication can also be analysed. ‘Important words’ from titles and abstracts which may "[...] have more frequent occurrences in the result subset than in the MEDLINEMEDLINE
MEDLINE is a bibliographic database of life sciences and biomedical information. It includes bibliographic information for articles from academic journals covering medicine, nursing, pharmacy, dentistry, veterinary medicine, and health care...
as a whole, thus they distinguish the result subset from the rest of MEDLINE" can be identified and help with further refining a search on PubMed.
History
Anne O'Tate (a pun on the word ‘annotate’) was developed by Neil R Smalheiser and a team of researchers from the University of ChicagoUniversity of Chicago
The University of Chicago is a private research university in Chicago, Illinois, USA. It was founded by the American Baptist Education Society with a donation from oil magnate and philanthropist John D. Rockefeller and incorporated in 1890...
. It is part of the Arrowsmith Project, which developed tools such as “Arrowsmith” proper, a text-comparison application, "Adam", a database of medical abbreviations,, and ‘’Author-ity’’ (an author-disambiguation tool), "Compendium", a list of biomedical text mining
Biomedical text mining
Biomedical text mining refers to text mining applied to texts and literature of the biomedical and molecular biology domain...
tools, and Anne O’Tate. The Project is based on research led by Don R. Swanson
Don R. Swanson
Don R. Swanson is an American information scientist, most known for his work in literature-based discovery in the biomedical domain. His particular method has been used as a model for further work, and is often referred to as Swanson linking...
at the University of Chicago
University of Chicago
The University of Chicago is a private research university in Chicago, Illinois, USA. It was founded by the American Baptist Education Society with a donation from oil magnate and philanthropist John D. Rockefeller and incorporated in 1890...
which hosted the original tool.
Further research was led by Neil R. Smalheiser at the University of Illinois at Chicago
University of Illinois at Chicago
The University of Illinois at Chicago, or UIC, is a state-funded public research university located in Chicago, Illinois, United States. Its campus is in the Near West Side community area, near the Chicago Loop...
, with funding from the National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
.
Other PubMed text-mining applications
A wide range of text-mining applications for PubMed have been developed, using their own interface, such as GoPubMedGoPubMed
GoPubMed is a knowledge-based search engine for biomedical texts. TheGene Ontology and Medical Subject Headings serve as "Table of contents" in order to structure the millions of articles of the MEDLINE database. The search engine allows its users to find relevant search results significantly...
, ClusterMed, or PubReMiner. Only Anne O’Tate uses PubMed’s standard interface, search syntax, and some of its functionality.