Showing 11 open source projects for "pubmed"

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  • 1
    GROBID

    GROBID

    A machine learning software for extracting information

    ... here covers the usual bibliographical information (e.g. title, abstract, authors, affiliations, keywords, etc.). References extraction and parsing from articles in PDF format, around .87 F1-score against on an independent PubMed Central set of 1943 PDF containing 90,125 references, and around .89 on a similar bioRxiv set of 2000 PDF (using the Deep Learning citation model). All the usual publication metadata are covered (including DOI, PMID, etc.).
    Downloads: 2 This Week
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  • 2
    JabRef Bibliography Management

    JabRef Bibliography Management

    Graphical Java application for managing BibTeX and biblatex

    JabRef is an open-source, cross-platform citation and reference management tool. Stay on top of your literature: JabRef helps you to collect and organize sources, find the paper you need and discover the latest research. JabRef is available free of charge and is actively developed. It supports you in every step of your research work.
    Downloads: 0 This Week
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  • 3
    CiteSpace

    CiteSpace

    A widely used tool for visual exploration of scientific literature.

    ..., for example, PubMed, CNKI, ProQuest Dissertations and Theses. CiteSpace reveals how a field of research has evolved, what intellectual turning points are evident along a critical path, and what topics have attracted attention. CiteSpace can be applied repeatedly so as to track the development of a field closely and extensively. The e-book How to Use CiteSpace explains the design principles and functions along with illustrative examples in more detail: https://leanpub.com/howtousecitespace
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    Downloads: 7,229 This Week
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  • 4
    Web based cataloging and dedupe application. Highly optimized for processing journal articles. Reads MarcXML and dedupes records using the field 773 combined with a fuzzy search on the title. Written for bibnet.org
    Downloads: 0 This Week
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  • 5
    GNAT

    GNAT

    GNAT recognizes gene names in text and maps them to NCBI Entrez Gene

    GNAT is a BioNLP/text mining tool to recognize and identify gene/protein names in natural language text. It will detect mentions of genes in text, such as PubMed/Medline abstracts, and disambiguate them to remove false positives and map them to the correct entry in the NCBI Entrez Gene database by gene ID. March 2017: We started to upload GNAT output on Medline. See files/results/medline/.
    Downloads: 1 This Week
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  • 6
    Bibi - the Bibtex File Manager
    Bibi - the Bibtex File Manager. Bibi is a graphical, platform-independent editor and manager for .bib files.
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    Downloads: 15 This Week
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  • 7

    TUIT

    Taxonomic Unit Identification Tool

    ...://www.ncbi.nlm.nih.gov/pubmed/24502797 Taxonomic Unit Identification Tool (TUIT) is a free open source platform-independent software, designed specifically to facilitate taxonomic annotation of nucleotide sequences via BLAST homology search against the NCBI databases. TUIT is immediately applicable for both to 16S microboime studies as well as for taxonomic classification of the nucleotide reads. Please see the project's Wiki page.
    Downloads: 0 This Week
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  • 8

    EDNA

    Energy Based Multiple Sequence Alignment (MSA) for Binding Sites

    Multiple Sequence Alignment for Transcription Factor Binding Sites using Di nucleotides dependencies and relying on Free Interaction energies between neighbouring DNA bases to stabilise substitution energy of the alignment. http://www.ncbi.nlm.nih.gov/pubmed/23990411
    Downloads: 0 This Week
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  • 9
    Winnow is a graphical application for importing and organising articles from PubMed. It gives access to abstracts, full text and allows references to be saved. It can also predict what a user will find interesting through adaptive filtering.
    Downloads: 0 This Week
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    Cyber Risk Assessment and Management Platform

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  • 10
    Urbigene contains SciFOAF and MyFOAFExplorer, two tools used to build a scientific FOAF network from NCBI pubmed and to browse it.
    Downloads: 0 This Week
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  • 11
    Manages your bibliographic data and files. Easy to use explorer-like GUI, (pubmed, bibtex,...) import and (bibtex,din,...) export features and a WebService interface to exchange data between multiple instances allow convenient data management.
    Downloads: 0 This Week
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