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1. Bedrick SD, Sittig DF: A scientific collaboration tool built on the facebook platform. AMIA Annu Symp Proc; 2008 Nov 06;:41-5
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] A scientific collaboration tool built on the facebook platform.
  • We describe an application ("Medline Publications")written for the Facebook platform that allows users to maintain and publish a list of their own Medline-indexed publications, as well as easily access their contacts lists.
  • The system is semi-automatic in that it interfaces directly with the National Library of Medicine's PubMed database to find and retrieve citation data.
  • Furthermore, the system has the capability to present the user with sets of other users with similar publication profiles.
  • As of July 2008,Medline Publications has attracted approximately 759 users, 624 of which have listed a total of 5,193 unique publications.

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  • (PMID = 18999247.001).
  • [ISSN] 1942-597X
  • [Journal-full-title] AMIA ... Annual Symposium proceedings. AMIA Symposium
  • [ISO-abbreviation] AMIA Annu Symp Proc
  • [Language] ENG
  • [Grant] United States / NLM NIH HHS / LM / T15 LM007088; United States / NLM NIH HHS / LM / T15LM007088
  • [Publication-type] Journal Article; Research Support, N.I.H., Extramural
  • [Publication-country] United States
  • [Other-IDs] NLM/ PMC2656030
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2. Krallinger M, Valencia A, Hirschman L: Linking genes to literature: text mining, information extraction, and retrieval applications for biology. Genome Biol; 2008;9 Suppl 2:S8
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Linking genes to literature: text mining, information extraction, and retrieval applications for biology.
  • Efficient access to information contained in online scientific literature collections is essential for life science research, playing a crucial role from the initial stage of experiment planning to the final interpretation and communication of the results.
  • The biological literature also constitutes the main information source for manual literature curation used by expert-curated databases.
  • Following the increasing popularity of web-based applications for analyzing biological data, new text-mining and information extraction strategies are being implemented.
  • These systems exploit existing regularities in natural language to extract biologically relevant information from electronic texts automatically.
  • The aim of the BioCreative challenge is to promote the development of such tools and to provide insight into their performance.
  • This review presents a general introduction to the main characteristics and applications of currently available text-mining systems for life sciences in terms of the following: the type of biological information demands being addressed; the level of information granularity of both user queries and results; and the features and methods commonly exploited by these applications.
  • The current trend in biomedical text mining points toward an increasing diversification in terms of application types and techniques, together with integration of domain-specific resources such as ontologies.
  • Additional descriptions of some of the systems discussed here are available on the internet http://zope.bioinfo.cnio.es/bionlp_tools/.
  • [MeSH-major] Computational Biology / methods. Databases, Bibliographic. Genes. Information Storage and Retrieval
  • [MeSH-minor] Semantics. Terminology as Topic

  • MedlinePlus Health Information. consumer health - Genes and Gene Therapy.
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  • (PMID = 18834499.001).
  • [ISSN] 1474-760X
  • [Journal-full-title] Genome biology
  • [ISO-abbreviation] Genome Biol.
  • [Language] eng
  • [Publication-type] Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Review
  • [Publication-country] England
  • [Number-of-references] 103
  • [Other-IDs] NLM/ PMC2559992
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3. Smalheiser NR, Torvik VI, Zhou W: Arrowsmith two-node search interface: a tutorial on finding meaningful links between two disparate sets of articles in MEDLINE. Comput Methods Programs Biomed; 2009 May;94(2):190-7
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] Arrowsmith two-node search interface: a tutorial on finding meaningful links between two disparate sets of articles in MEDLINE.
  • The Arrowsmith two-node search is a strategy that is designed to assist biomedical investigators in formulating and assessing scientific hypotheses.
  • More generally, it allows users to identify biologically meaningful links between any two sets of articles A and C in PubMed, even when these share no articles or authors in common and represent disparate topics or disciplines.
  • The key idea is to relate the two sets of articles via title words and phrases (B-terms) that they share.
  • We have created a free, public web-based version of the two-node search tool (http://arrowsmith.psych.uic.edu), have described its development and implementation, and have presented analyses of individual two-node searches.
  • In this paper, we provide an updated tutorial intended for end-users, that covers the use of the tool for a variety of potential scientific use case scenarios.
  • For example, one can assess a recent experimental, clinical or epidemiologic finding that connects two disparate fields of inquiry--identifying likely mechanisms to explain the finding, and choosing promising follow-up lines of investigation.
  • Alternatively, one can assess whether the existing scientific literature lends indirect support to a hypothesis posed by the user that has not yet been investigated.
  • One can also employ two-node searches to search for novel hypotheses.
  • Arrowsmith provides a service that cannot be carried out feasibly via standard PubMed searches or by other available text mining tools.

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  • (PMID = 19185946.001).
  • [ISSN] 1872-7565
  • [Journal-full-title] Computer methods and programs in biomedicine
  • [ISO-abbreviation] Comput Methods Programs Biomed
  • [Language] ENG
  • [Grant] United States / NLM NIH HHS / LM / R01 LM007292; United States / NLM NIH HHS / LM / LM008364; United States / NLM NIH HHS / LM / R21 LM008364; United States / NLM NIH HHS / LM / R01 LM007292-05; United States / NLM NIH HHS / LM / LM008364-02; United States / NLM NIH HHS / LM / R21 LM008364-02; United States / NLM NIH HHS / LM / LM007292
  • [Publication-type] Journal Article; Research Support, N.I.H., Extramural
  • [Publication-country] Ireland
  • [Other-IDs] NLM/ NIHMS105821; NLM/ PMC2693227
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4. Lu Z: PubMed and beyond: a survey of web tools for searching biomedical literature. Database (Oxford); 2011;2011:baq036
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] PubMed and beyond: a survey of web tools for searching biomedical literature.
  • The past decade has witnessed the modern advances of high-throughput technology and rapid growth of research capacity in producing large-scale biological data, both of which were concomitant with an exponential growth of biomedical literature.
  • This wealth of scholarly knowledge is of significant importance for researchers in making scientific discoveries and healthcare professionals in managing health-related matters.
  • However, the acquisition of such information is becoming increasingly difficult due to its large volume and rapid growth.
  • In response, the National Center for Biotechnology Information (NCBI) is continuously making changes to its PubMed Web service for improvement.
  • Meanwhile, different entities have devoted themselves to developing Web tools for helping users quickly and efficiently search and retrieve relevant publications.
  • These practices, together with maturity in the field of text mining, have led to an increase in the number and quality of various Web tools that provide comparable literature search service to PubMed.
  • In this study, we review 28 such tools, highlight their respective innovations, compare them to the PubMed system and one another, and discuss directions for future development.
  • Furthermore, we have built a website dedicated to tracking existing systems and future advances in the field of biomedical literature search.
  • Taken together, our work serves information seekers in choosing tools for their needs and service providers and developers in keeping current in the field.
  • Database URL: http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/search.

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  • (PMID = 21245076.001).
  • [ISSN] 1758-0463
  • [Journal-full-title] Database : the journal of biological databases and curation
  • [ISO-abbreviation] Database (Oxford)
  • [Language] ENG
  • [Grant] United States / Intramural NIH HHS / /
  • [Publication-type] Journal Article; Research Support, N.I.H., Intramural; Review
  • [Publication-country] England
  • [Other-IDs] NLM/ PMC3025693
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