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Anne O'Tate

February 15, 2024

Anne O'Tate is a free, web-based application [1] 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.[1]

Description edit

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.[2] ‘Fields’ which Anne O’Tate can display in this manner are:

Topics (MeSH) edit

This option may help to identify possible Medical Subject Headings (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 corresponding 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 edit

This option may help with identifying authors who have written frequently about a given subject, or may help with identifying possible experts or peer reviewers

Journals edit

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'[3]) not found by the search on PubMed.

Other fields edit

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 MEDLINE as a whole, thus they distinguish the result subset from the rest of MEDLINE" [4] can be identified and help with further refining a search on PubMed.[5][6][7]

History edit

Anne O'Tate (a pun on the word ‘annotate’) was developed by Neil R Smalheiser and a team of researchers from the University of Chicago. It is part of the Arrowsmith Project, which developed tools such as “Arrowsmith” proper, a text-comparison application,[8] "Adam", a database of medical abbreviations,[9] and ‘’Author-ity’’ (an author-disambiguation tool),[10] "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[11] which hosted the original tool.[12] Further research was led by Neil R. Smalheiser at the University of Illinois at Chicago, with funding from the National Institutes of Health.[13]

Other PubMed text-mining applications edit

A wide range of text-mining applications for PubMed have been developed,[4] using their own interface, such as GoPubMed, ClusterMed, or PubReMiner. Only Anne O’Tate uses PubMed’s standard interface, search syntax, and some of its functionality.

References edit

  1. ^ a b Smalheiser, N. R.; Zhou, W.; Torvik, V. I. (2008). "Anne O'Tate: A tool to support user-driven summarization, drill-down and browsing of PubMed search results". Journal of Biomedical Discovery and Collaboration. 3: 2. doi:10.1186/1747-5333-3-2. PMC 2276193. PMID 18279519.
  2. ^ Palidwor, G. A.; Andrade-Navarro, M. A. (2010). "MLTrends: Graphing MEDLINE term usage over time". Journal of Biomedical Discovery and Collaboration. 5: 1–6. doi:10.5210/disco.v5i0.2680. PMC 2990277. PMID 20333611.
  3. ^ Langham, J.; Thompson, E.; Rowan, K. (1999). "Identification of randomized controlled trials from the emergency medicine literature: Comparison of hand searching versus MEDLINE searching". Annals of Emergency Medicine. 34 (1): 25–34. doi:10.1016/s0196-0644(99)70268-4. PMID 10381991.
  4. ^ a b Lu, Z. (2011). "PubMed and beyond: A survey of web tools for searching biomedical literature". Database. 2011: baq036. doi:10.1093/database/baq036. PMC 3025693. PMID 21245076.
  5. ^ Wilczynski, N. L.; Walker, C. J.; McKibbon, K. A.; Haynes, R. B. (1995). "Reasons for the loss of sensitivity and specificity of methodologic MeSH terms and textwords in MEDLINE". Proceedings. Symposium on Computer Applications in Medical Care: 436–440. PMC 2579130. PMID 8563319.
  6. ^ Greenhalgh, T. (1997). "How to read a paper. The Medline database". BMJ (Clinical Research Ed.). 315 (7101): 180–183. doi:10.1136/bmj.315.7101.180. PMC 2127107. PMID 9251552.
  7. ^ Smalheiser, N. R.; Zhou, W.; Torvik, V. I. (2011). "Distribution of "Characteristic" Terms in MEDLINE Literatures". Information. 2 (4): 266–276. doi:10.3390/info2020266.
  8. ^ Smalheiser, N. R.; Torvik, V. I.; Zhou, W. (2009). "Arrowsmith two-node search interface: A tutorial on finding meaningful links between two disparate sets of articles in MEDLINE". Computer Methods and Programs in Biomedicine. 94 (2): 190–197. doi:10.1016/j.cmpb.2008.12.006. PMC 2693227. PMID 19185946.
  9. ^ Zhou, W.; Torvik, V. I.; Smalheiser, N. R. (2006). "ADAM: Another database of abbreviations in MEDLINE". Bioinformatics. 22 (22): 2813–2818. doi:10.1093/bioinformatics/btl480. PMID 16982707.
  10. ^ Torvik, V. I.; Smalheiser, N. R. (2009). "Author Name Disambiguation in MEDLINE". ACM Transactions on Knowledge Discovery from Data. 3 (3): 1–29. doi:10.1145/1552303.1552304. PMC 2805000. PMID 20072710.
  11. ^ Swanson, D.R.; Smalheiser, N.R. (Summer 1999). "Implicit Text Linkages between Medline Records: Using Arrowsmith as an Aid to Scientific Discovery" (PDF). Library Trends. 48 (1): 48–59. Retrieved July 4, 2011.
  12. ^ . The University of Chicago. Archived from the original on June 18, 2009. Retrieved July 4, 2011.
  13. ^ Smalheiser, N.R. (October 2005). "The Arrowsmith Project: 2005 Status Report". Discovery Science. 8th international conference on discovery science. Lecture Notes in Computer Science. Vol. 3735. pp. 26–43. doi:10.1007/11563983_5. ISBN 978-3-540-29230-2.

External links edit

  • Anne O'Tate
  • PubMed Home Page
  • Medical Subject Headings Fact Sheet
  • "The Arrowsmith Project Homepage". University of Illinois at Chicago, Department of Psychiatry. December 20, 2007. Retrieved July 4, 2011.

February 15, 2024
anne, tate, free, based, application, that, analyses, sets, records, identified, pubmed, bibliographic, database, articles, from, over, biomedical, journals, worldwide, while, pubmed, wide, range, search, options, identify, sets, records, relevant, researchers. Anne O Tate is a free web based application 1 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 1 Contents 1 Description 1 1 Topics MeSH 1 2 Authors 1 3 Journals 1 4 Other fields 2 History 3 Other PubMed text mining applications 4 References 5 External linksDescription editOnce 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 2 Fields which Anne O Tate can display in this manner are Topics MeSH edit This option may help to identify possible Medical Subject Headings 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 corresponding 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 edit This option may help with identifying authors who have written frequently about a given subject or may help with identifying possible experts or peer reviewers Journals edit 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 3 not found by the search on PubMed Other fields edit 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 MEDLINE as a whole thus they distinguish the result subset from the rest of MEDLINE 4 can be identified and help with further refining a search on PubMed 5 6 7 History editAnne O Tate a pun on the word annotate was developed by Neil R Smalheiser and a team of researchers from the University of Chicago It is part of the Arrowsmith Project which developed tools such as Arrowsmith proper a text comparison application 8 Adam a database of medical abbreviations 9 and Author ity an author disambiguation tool 10 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 11 which hosted the original tool 12 Further research was led by Neil R Smalheiser at the University of Illinois at Chicago with funding from the National Institutes of Health 13 Other PubMed text mining applications editA wide range of text mining applications for PubMed have been developed 4 using their own interface such as GoPubMed ClusterMed or PubReMiner Only Anne O Tate uses PubMed s standard interface search syntax and some of its functionality References edit a b Smalheiser N R Zhou W Torvik V I 2008 Anne O Tate A tool to support user driven summarization drill down and browsing of PubMed search results Journal of Biomedical Discovery and Collaboration 3 2 doi 10 1186 1747 5333 3 2 PMC 2276193 PMID 18279519 Palidwor G A Andrade Navarro M A 2010 MLTrends Graphing MEDLINE term usage over time Journal of Biomedical Discovery and Collaboration 5 1 6 doi 10 5210 disco v5i0 2680 PMC 2990277 PMID 20333611 Langham J Thompson E Rowan K 1999 Identification of randomized controlled trials from the emergency medicine literature Comparison of hand searching versus MEDLINE searching Annals of Emergency Medicine 34 1 25 34 doi 10 1016 s0196 0644 99 70268 4 PMID 10381991 a b Lu Z 2011 PubMed and beyond A survey of web tools for searching biomedical literature Database 2011 baq036 doi 10 1093 database baq036 PMC 3025693 PMID 21245076 Wilczynski N L Walker C J McKibbon K A Haynes R B 1995 Reasons for the loss of sensitivity and specificity of methodologic MeSH terms and textwords in MEDLINE Proceedings Symposium on Computer Applications in Medical Care 436 440 PMC 2579130 PMID 8563319 Greenhalgh T 1997 How to read a paper The Medline database BMJ Clinical Research Ed 315 7101 180 183 doi 10 1136 bmj 315 7101 180 PMC 2127107 PMID 9251552 Smalheiser N R Zhou W Torvik V I 2011 Distribution of Characteristic Terms in MEDLINE Literatures Information 2 4 266 276 doi 10 3390 info2020266 Smalheiser N R Torvik V I Zhou W 2009 Arrowsmith two node search interface A tutorial on finding meaningful links between two disparate sets of articles in MEDLINE Computer Methods and Programs in Biomedicine 94 2 190 197 doi 10 1016 j cmpb 2008 12 006 PMC 2693227 PMID 19185946 Zhou W Torvik V I Smalheiser N R 2006 ADAM Another database of abbreviations in MEDLINE Bioinformatics 22 22 2813 2818 doi 10 1093 bioinformatics btl480 PMID 16982707 Torvik V I Smalheiser N R 2009 Author Name Disambiguation in MEDLINE ACM Transactions on Knowledge Discovery from Data 3 3 1 29 doi 10 1145 1552303 1552304 PMC 2805000 PMID 20072710 Swanson D R Smalheiser N R Summer 1999 Implicit Text Linkages between Medline Records Using Arrowsmith as an Aid to Scientific Discovery PDF Library Trends 48 1 48 59 Retrieved July 4 2011 Arrowsmith 2 on Linux The University of Chicago Archived from the original on June 18 2009 Retrieved July 4 2011 Smalheiser N R October 2005 The Arrowsmith Project 2005 Status Report Discovery Science 8th international conference on discovery science Lecture Notes in Computer Science Vol 3735 pp 26 43 doi 10 1007 11563983 5 ISBN 978 3 540 29230 2 External links editAnne O Tate PubMed Home Page Medical Subject Headings Fact Sheet The Arrowsmith Project Homepage University of Illinois at Chicago Department of Psychiatry December 20 2007 Retrieved July 4 2011 Retrieved from https en wikipedia org w index php title Anne O 27Tate amp oldid 1187841615, wikipedia, wiki, book, books, library,

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