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1. Barbosa-Silva A, Soldatos TG, Magalhães IL, Pavlopoulos GA, Fontaine JF, Andrade-Navarro MA, Schneider R, Ortega JM: LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships. BMC Bioinformatics; 2010;11:70
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  • [Source] The source of this record is MEDLINE®, a database of the U.S. National Library of Medicine.
  • [Title] LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships.
  • BACKGROUND: Biological knowledge is represented in scientific literature that often describes the function of genes/proteins (bioentities) in terms of their interactions (biointeractions).
  • Such bioentities are often related to biological concepts of interest that are specific of a determined research field.
  • Therefore, the study of the current literature about a selected topic deposited in public databases, facilitates the generation of novel hypotheses associating a set of bioentities to a common context.
  • RESULTS: We created a text mining system (LAITOR: Literature Assistant for Identification of Terms co-Occurrences and Relationships) that analyses co-occurrences of bioentities, biointeractions, and other biological terms in MEDLINE abstracts.
  • The method accounts for the position of the co-occurring terms within sentences or abstracts.
  • The system detected abstracts mentioning protein-protein interactions in a standard test (BioCreative II IAS test data) with a precision of 0.82-0.89 and a recall of 0.48-0.70.
  • We illustrate the application of LAITOR to the detection of plant response genes in a dataset of 1000 abstracts relevant to the topic.
  • CONCLUSIONS: Text mining tools combining the extraction of interacting bioentities and biological concepts with network displays can be helpful in developing reasonable hypotheses in different scientific backgrounds.
  • [MeSH-major] Data Mining / methods. Information Storage and Retrieval / methods. Software
  • [MeSH-minor] Computational Biology / methods. MEDLINE. Publications. United States

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  • (PMID = 20122157.001).
  • [ISSN] 1471-2105
  • [Journal-full-title] BMC bioinformatics
  • [ISO-abbreviation] BMC Bioinformatics
  • [Language] eng
  • [Publication-type] Journal Article; Research Support, Non-U.S. Gov't
  • [Publication-country] England
  • [Other-IDs] NLM/ PMC3098111
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2. Fontaine JF, Priller F, Barbosa-Silva A, Andrade-Navarro MA: Génie: literature-based gene prioritization at multi genomic scale. Nucleic Acids Res; 2011 Jul;39(Web Server issue):W455-61
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  • [Title] Génie: literature-based gene prioritization at multi genomic scale.
  • Biomedical literature is traditionally used as a way to inform scientists of the relevance of genes in relation to a research topic.
  • However many genes, especially from poorly studied organisms, are not discussed in the literature.
  • Moreover, a manual and comprehensive summarization of the literature attached to the genes of an organism is in general impossible due to the high number of genes and abstracts involved.
  • We introduce the novel Génie algorithm that overcomes these problems by evaluating the literature attached to all genes in a genome and to their orthologs according to a selected topic.
  • Génie showed high precision (up to 100%) and the best performance in comparison to other algorithms in most of the benchmarks, especially when high sensitivity was required.
  • Moreover, the prioritization of zebrafish genes involved in heart development, using human and mouse orthologs, showed high enrichment in differentially expressed genes from microarray experiments.
  • The Génie web server supports hundreds of species, millions of genes and offers novel functionalities.
  • Common run times below a minute, even when analyzing the human genome with hundreds of thousands of literature records, allows the use of Génie in routine lab work.
  • AVAILABILITY: http://cbdm.mdc-berlin.de/tools/genie/.
  • [MeSH-major] Genes. Software
  • [MeSH-minor] Algorithms. Animals. Gene Expression Profiling. Genomics. Heart / embryology. Humans. Internet. MEDLINE. Mice. Models, Animal. Zebrafish / embryology. Zebrafish / genetics

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  • (PMID = 21609954.001).
  • [ISSN] 1362-4962
  • [Journal-full-title] Nucleic acids research
  • [ISO-abbreviation] Nucleic Acids Res.
  • [Language] eng
  • [Publication-type] Journal Article; Research Support, Non-U.S. Gov't
  • [Publication-country] England
  • [Other-IDs] NLM/ PMC3125729
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3. 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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