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THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 13, 2026. Server that allows you to explore a set of abstracts derived from a MEDLINE search. The system gives you the main associations between the words in groups of abstracts. Then, you can select a subset of your abstracts based on selected groups of related words and iterate your analysis on them. The only input needed is a set of abstracts (in one of the currently accepted input formats) or a definition of how to obtain them. XplorMed is recommended for cases in which you do not know exactly what are you expecting to find. Your interests may be modified by the results obtained, or you may want to inquire new questions as the analysis develops. Also, the results may suggest you additional words that should be used to expand your query in MEDLINE (e.g., unexpected abbreviations of a protein name, or synonyms of a disease).
Proper citation: XplorMed (RRID:SCR_002549) Copy
http://www.ncbi.nlm.nih.gov/pubmedcommons/
A forum where authors who have published in PubMed may comment on any publication in PubMed. Members of PubMed Commons are not anonymous and must agree to certain terms and guidelines concerning appropriate and inapproriate comments.
Proper citation: Pubmed Commons (RRID:SCR_014021) Copy
A comprehensive index for locating and compiling bioinformatics and online science tools. Users can browse, rate, share and save various tools listed in the LabWorm repository. Resources contain a short description, a list of related sites, comments, a list of users who have shared and rated the resource, and the main site URL. Resources may be saved to a personal toolbox collection. User news feeds can be customized to include new scientific literature from journals of choice. Users who want to utilize LabWorm tools to improve their own website can access the alternate Developer site.
Proper citation: LabWorm (RRID:SCR_014079) Copy
https://cran.r-project.org/web/packages/rentrez/index.html
Software package provides R interface to NCBI EUtils API, to search databases like GenBank and PubMed, process of those searches. Provides functions that work with NCBI Eutils API to search, download data from, and otherwise interact with NCBI databases.
Proper citation: rentrez (RRID:SCR_021062) Copy
http://www.chibi.ubc.ca/WhiteText/
Freely available corpus of manually annotated brain region mentions created to facilitate text mining of neuroscience literature. The corpus contains 1,377 abstracts with 18,242 brain region annotations. Interannotator agreement was evaluated for a subset of the documents, and was 90.7% and 96.7% for strict and lenient matching respectively. We observed a large vocabulary of over 6,000 unique brain region terms and 17,000 words. For automatic extraction of brain region mentions we evaluated simple dictionary methods and complex natural language processing techniques. The dictionary methods based on neuroanatomical lexicons recalled 36% of the mentions with 57% precision. The best performance was achieved using a conditional random field (CRF) with a rich feature set. Features were based on morphological, lexical, syntactic and contextual information. The CRF recalled 76% of mentions at 81% precision, by counting partial matches recall and precision increase to 86% and 92% respectively. We suspect a large amount of error is due to coordinating conjunctions, previously unseen words and brain regions of less commonly studied organisms. We found context windows, lemmatization and abbreviation expansion to be the most informative techniques. We encourage you to test new methods and applications of the dataset. Please contact us if you do, we would like to hear about and link to your work. The abstracts are from PubMed/Medline, specifically The Journal of Comparative Neurology.
Proper citation: Automated recognition of brain region mentions in neuroscience literature. (RRID:SCR_002731) Copy
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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