Text Mining for Search Strategy Development
Text Mining
What is Text Mining?
Text Mining with PubMed
Text Mining - User Input Tools
Other tools and packages
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PubVenn
PubVenn allows you to explore PubMed visually by generating Venn diagrams. You can enter
any multi-term search to generate a Venn diagram that allows you to view the size of the citation
set for each term as well as how those sets interact.
Availability: Free online
Data Source: PubMed
Tool Type: Visualisation tool
Features: Provides example PubMed search strategy and links to relevant publications.
Selecting the 'Expanded subjects' checkbox will include other relevant terms from PubMed.
Import Formats: Free text
Export Formats: Save as .png
Known Limitations: PubMed data only
URL: [Link]
Also try Search Workbench: [Link]
Images:
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PubMed PubReMiner
Enter a free text search into the PubReMiner tool and it will query PubMed for relevant results.
The tool analyses these results and provides tables that rank the frequency of words in the title
and abstract of the articles and also relevant MeSH headings. Other ranked tables include
journals in which your query is published the most and authors which are most active in related
fields.
Availability: Free online
Data Source: PubMed
Tool Type: Text frequency
Features: Self selection of elements to display in the results. Direct connection to PubMed
Import Formats: Free text
Export Formats: Save results as a .txt file
Known Limitations: Limited to PubMed
URL: [Link]
Images:
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Coremine
Coremine Medical is a product of the PubGene Company designed to be used by anyone
seeking information on health, medicine and biology. It is ideal for those seeking an overview of a
complex subject while allowing the possibility to "drill down" to specific details. Search results are
presented in a dashboard format comprised of panels containing various categories of
information ranging from introductory sources to the latest scientific articles. Coremine presents
search results as a graphic network that describes relationships discovered through text-mining.
Availability: Register for free account
Data Source: PubMed
Tool Type: Visualisation, clustering, text frequency, relationship networks
Features: File upload, Hyperbrowser, search history, alerts
Import Formats: Free text, tab delimited file can be uploaded
Export Formats: None
URL: [Link]
Instructions: [Link]
Images:
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MeSH on Demand
The MeSH on Demand tool uses the NLM Medical Text Indexer to identifiy MeSH vocabulary in
submitted text (paste up to five pages). The results are displayed in a list as well as highlighted in
the pasted text (also defines term frequency within the text). Links to similar PubMed related
citations are included.
Availability: Free online
Data Source: PubMed
Tool Type: Text analyser
Features: Suggests MeSH vocabulary found in similar, related citations as well as the submitted
text.
Import Formats: Free text
Export Formats: Text file
Known Limitations: Non English text needs to be translated first
URL: [Link]
Images:
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Yale MeSH Analyser
Availability: Free online
Data Source: PubMed
Tool Type: Comparison
Features: Easy to view comparison of article indexing
Import Formats: Free text (type or paste)
Export Formats: Excel, HTML table
Known Limitations: Query with PubMed IDs only - maximum 20
URL: [Link]
Images:
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HelioBLAST
HelioBLAST is a free service provided by HelioText. The HelioBLAST text similarity engine finds
text records that are similar to the submitted query. Your query is searched against the citations
(abstract and titles) in Medline/PubMed and the top matching articles are returned in the results
Availability: Free online
Data Source: PubMed
Tool Type: Word analysis
Features: 'Implicit keywords' - additional word frequency analysis tool
Import Formats: Free text - copy and paste
Export Formats: No export function but links to article records in PubMed
URL: [Link]
Images:
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Carrot2
Carrot2 is an Open Source Results Clustering Engine that can automatically organise search
results into topics. Carrot2 can query PubMed and allows boolean searching.
Availability: Free online, download
Data Source: PubMed
Tool Type: Clustering
Features: Simple online interface
Import Formats: Free text
Export Formats: View on screen
Known Limitations: No export options
URL: [Link]
Images:
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