Scientific Publications

@article{nokey,

title = {Using Machine Learning to Collect and Facilitate Remote Access to Biomedical Databases: Development of the Biomedical Database Inventory},

author = {E Rosado and M Garcia-Remesal and S Paraiso-Medina and A Pazos and V Maojo},

editor = {JMIR Publications Inc., Toronto, Canada},

url = {https://medinform.jmir.org/2021/2/e22976/},

doi = {10.2196/22976 },

issn = {2291-9694},

year  = {2021},

date = {2021-02-25},

journal = {JMIR Medical Informatics},

volume = {9},

number = {2},

abstract = {Background: Currently, existing biomedical literature repositories do not commonly provide users with specific means to locate and remotely access biomedical databases. Objective: To address this issue, we developed the Biomedical Database Inventory (BiDI), a repository linking to biomedical databases automatically extracted from the scientific literature. BiDI provides an index of data resources and a path to access them seamlessly. Methods: We designed an ensemble of deep learning methods to extract database mentions. To train the system, we annotated a set of 1242 articles that included mentions of database publications. Such a data set was used along with transfer learning techniques to train an ensemble of deep learning natural language processing models targeted at database publication detection. Results: The system obtained an F1 score of 0.929 on database detection, showing high precision and recall values. When applying this model to the PubMed and PubMed Central databases, we identified over 10,000 unique databases. The ensemble model also extracted the weblinks to the reported databases and discarded irrelevant links. For the extraction of weblinks, the model achieved a cross-validated F1 score of 0.908. We show two use cases: one  related to ``omics'' and the other related to the COVID-19 pandemic. Conclusions: BiDI enables access to biomedical resources over the internet and facilitates data-driven research and other scientific initiatives. The repository is openly available online and will be regularly updated with an automatic text processing pipeline. The approach can be reused to create repositories of different types (ie, biomedical and others). },

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid28802325b,

title = {SNOMED2HL7: A tool to normalize and bind SNOMED CT concepts to the HL7 Reference Information Model},

author = {D Perez-Rey and R Alonso-Calvo and S Paraiso-Medina and C R Munteanu and M Garcia-Remesal},

url = {https://www.ncbi.nlm.nih.gov/pubmed/28802325},

year  = {2017},

date = {2017-01-01},

journal = {Comput Methods Programs Biomed},

volume = {149},

pages = {1--9},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid26873780,

title = {A method and software framework for enriching private biomedical sources with data from public online repositories},

author = {A Anguita and M Garcia-Remesal and N Graf and V Maojo},

url = {https://www.ncbi.nlm.nih.gov/pubmed/26873780},

year  = {2016},

date = {2016-01-01},

journal = {J Biomed Inform},

volume = {60},

pages = {177--186},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid24777240,

title = {Toward a view-oriented approach for aligning RDF-based biomedical repositories},

author = {A Anguita and M Garcia-Remesal and D de la Iglesia and N Graf and V Maojo},

url = {https://www.ncbi.nlm.nih.gov/pubmed/24777240},

year  = {2015},

date = {2015-01-01},

journal = {Methods Inf Med},

volume = {54},

number = {1},

pages = {50-55},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid25347075,

title = {A machine learning approach to identify clinical trials involving nanodrugs and nanodevices from ClinicalTrials.gov.},

author = {D de la Iglesia and M Garcia-Remesal and A Anguita and M Munoz-Marmol and C Kulikowski and V Maojo},

url = {https://www.ncbi.nlm.nih.gov/pubmed/25347075},

year  = {2014},

date = {2014-01-01},

journal = {PLoS ONE},

volume = {9},

number = {10},

pages = {e110331},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid24932210,

title = {Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research},

author = {D de la Iglesia and R E Cachau and M Garcia-Remesal and V Maojo},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053539/},

year  = {2013},

date = {2013-11-01},

journal = {Comput Sci Discov},

volume = {6},

number = {1},

pages = {014011},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid23669178b,

title = {RDFBuilder: a tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources},

author = {A Anguita and M Garcia-Remesal and V Maojo},

url = {https://www.ncbi.nlm.nih.gov/pubmed/23669178},

year  = {2013},

date = {2013-07-01},

journal = {Comput Methods Programs Biomed},

volume = {111},

number = {1},

pages = {220--227},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid23984425,

title = {NCBI2RDF: enabling full RDF-based access to NCBI databases},

author = {A Anguita and M Garcia-Remesal and D de la Iglesia and V Maojo},

url = {https://www.hindawi.com/journals/bmri/2013/983805/},

year  = {2013},

date = {2013-01-01},

journal = {Biomed Res Int},

volume = {2013},

pages = {983805},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid23548020b,

title = {The impact of computer science in molecular medicine: enabling high-throughput research},

author = {D de la Iglesia and M Garcia-Remesal and G de la Calle and C Kulikowski and F Sanz and V Maojo},

url = {https://www.ncbi.nlm.nih.gov/pubmed/23548020},

year  = {2013},

date = {2013-01-01},

journal = {Curr Top Med Chem},

volume = {13},

number = {5},

pages = {526--575},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid23509721b,

title = {Using nanoinformatics methods for automatically identifying relevant nanotoxicology entities from the literature},

author = {M Garcia-Remesal and A Garcia-Ruiz and D Perez-Rey and D de la Iglesia and V Maojo},

url = {https://www.ncbi.nlm.nih.gov/pubmed/23509721},

year  = {2013},

date = {2013-01-01},

journal = {Biomed Res Int},

volume = {2013},

pages = {410294},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid22942787b,

title = {Nanoinformatics: developing new computing applications for nanomedicine},

author = {V Maojo and M Fritts and F Martin-Sanchez and D De la Iglesia and R E Cachau and M Garcia-Remesal and J Crespo and J A Mitchell and A Anguita and N Baker and J M Barreiro and S E Benitez and G De la Calle and J C Facelli and P Ghazal and A Geissbuhler and F Gonzalez-Nilo and N Graf and P Grangeat and I Hermosilla and R Hussein and J Kern and S Koch and Y Legre and V Lopez-Alonso and G Lopez-Campos and L Milanesi and V Moustakis and C Munteanu and P Otero and A Pazos and D Perez-Rey and G Potamias and F Sanz and C Kulikowski},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3430140/},

year  = {2012},

date = {2012-06-01},

journal = {Comput Sci Eng},

volume = {94},

number = {6},

pages = {521--539},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid22183800b,

title = {Biomedical informatics publications: a global perspective: part I: conferences},

author = {V Maojo and M Garcia-Remesal and C Bielza and J Crespo and D Perez-Rey and C Kulikowski},

url = {https://www.ncbi.nlm.nih.gov/pubmed/22183800},

year  = {2012},

date = {2012-01-01},

journal = {Methods Inf Med},

volume = {51},

number = {1},

pages = {82--90},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid22311187b,

title = {Biomedical informatics publications: a global perspective. Part II: Journals},

author = {V Maojo and M Garcia-Remesal and C Bielza and J Crespo and D Perez-Rey and C Kulikowski},

url = {https://www.ncbi.nlm.nih.gov/pubmed/22311187},

year  = {2012},

date = {2012-01-01},

journal = {Methods Inf Med},

volume = {51},

number = {2},

pages = {131--137},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid22480327b,

title = {CDAPubMed: a browser extension to retrieve EHR-based biomedical literature},

author = {D Perez-Rey and A Jimenez-Castellanos and M Garcia-Remesal and J Crespo and V Maojo},

url = {https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/1472-6947-12-29},

year  = {2012},

date = {2012-01-01},

journal = {BMC Med Inform Decis Mak},

volume = {12},

pages = {29},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid22857741b,

title = {e-MIR2: a public online inventory of medical informatics resources},

author = {G de la Calle and M Garcia-Remesal and N Nkumu-Mbomio and C Kulikowski and V Maojo},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3441434/},

year  = {2012},

date = {2012-01-01},

journal = {BMC Med Inform Decis Mak},

volume = {12},

pages = {82},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid22866003b,

title = {Nanoinformatics: a new area of research in nanomedicine},

author = {V Maojo and M Fritts and D de la Iglesia and R E Cachau and M Garcia-Remesal and J A Mitchell and C Kulikowski},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3410693/},

year  = {2012},

date = {2012-01-01},

journal = {Int J Nanomedicine},

volume = {7},

pages = {3867--3890},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid21431244b,

title = {Biomedical ontologies: toward scientific debate},

author = {V Maojo and J Crespo and M Garcia-Remesal and D de la Iglesia and D Perez-Rey and C Kulikowski},

url = {https://www.ncbi.nlm.nih.gov/pubmed/21431244},

year  = {2011},

date = {2011-01-01},

journal = {Methods Inf Med},

volume = {50},

number = {3},

pages = {203--216},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid21085742b,

title = {International efforts in nanoinformatics research applied to nanomedicine},

author = {D de la Iglesia and V Maojo and S Chiesa and F Martin-Sanchez and J Kern and G Potamias and J Crespo and M Garcia-Remesal and S Keuchkerian and C Kulikowski and J A Mitchell},

url = {https://www.ncbi.nlm.nih.gov/pubmed/21085742},

year  = {2011},

date = {2011-01-01},

journal = {Methods Inf Med},

volume = {50},

number = {1},

pages = {84--95},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Garcia-Remesal2009,

title = {Integration of relational and textual biomedical sources. A pilot experiment using a semi-automated method for logical schema acquisition.},

author = {M Garcia-Remesal and V Maojo and H Billhardt and J Crespo},

url = {https://www.ncbi.nlm.nih.gov/pubmed/19936436},

year  = {2010},

date = {2010-11-12},

journal = {Methods of Information in Medicine},

volume = {49},

number = {4},

pages = {337-348},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid20829445b,

title = {PubDNA Finder: a web database linking full-text articles to sequences of nucleic acids},

author = {M Garcia-Remesal and A Cuevas and D Perez-Rey and L Martin and A Anguita and D de la Iglesia and G de la Calle and J Crespo and V Maojo},

url = {https://www.ncbi.nlm.nih.gov/pubmed/20829445},

year  = {2010},

date = {2010-11-01},

journal = {Bioinformatics},

volume = {26},

number = {21},

pages = {2801-2802},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid20682041b,

title = {A method for automatically extracting infectious disease-related primers and probes from the literature},

author = {M Garcia-Remesal and A Cuevas and V Lopez-Alonso and G Lopez-Campos and G de la Calle and D de la Iglesia and D Perez-Rey and J Crespo and F Martin-Sanchez and V Maojo},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923139/},

year  = {2010},

date = {2010-08-03},

journal = {BMC Bioinformatics},

volume = {11},

pages = {410},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid21096556b,

title = {A knowledge engineering approach to recognizing and extracting sequences of nucleic acids from scientific literature},

author = {M Garcia-Remesal and V Maojo and J Crespo},

url = {https://www.ncbi.nlm.nih.gov/pubmed/21096556},

year  = {2010},

date = {2010-01-01},

journal = {Conf Proc IEEE Eng Med Biol Soc},

volume = {2010},

pages = {1081--1084},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid19811635b,

title = {BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature},

author = {G de la Calle and M Garcia-Remesal and S Chiesa and D de la Iglesia and V Maojo},

url = {https://www.ncbi.nlm.nih.gov/pubmed/19811635},

year  = {2009},

date = {2009-10-07},

journal = {BMC Bioinformatics},

volume = {10},

pages = {320},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid18987716b,

title = {Detectors could spot plagiarism in research proposals},

author = {V Maojo and M Garcia-Remesal and J Crespo},

url = {http://www.nature.com/nature/journal/v456/n7218/full/456030c.html},

year  = {2008},

date = {2008-11-01},

journal = {Nature},

volume = {456},

number = {7218},

pages = {30},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid17694245b,

title = {Using web services for linking genomic data to medical information systems},

author = {V Maojo and J Crespo and G de la Calle and J M Barreiro and M Garcia-Remesal},

url = {https://www.ncbi.nlm.nih.gov/pubmed/17694245},

year  = {2007},

date = {2007-01-01},

journal = {Methods Inf Med},

volume = {46},

number = {4},

pages = {484--492},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16144697b,

title = {ONTOFUSION: ontology-based integration of genomic and clinical databases},

author = {D Perez-Rey and V Maojo and M Garcia-Remesal and R Alonso-Calvo and H Billhardt and F Martin-Sanchez and A Sousa},

url = {https://www.ncbi.nlm.nih.gov/pubmed/16144697},

year  = {2006},

date = {2006-01-01},

journal = {Comput. Biol. Med.},

volume = {36},

number = {7-8},

pages = {712--730},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pmid16538285b,

title = {Designing new methodologies for integrating biomedical information in clinical trials},

author = {V Maojo and M Garcia-Remesal and H Billhardt and R Alonso-Calvo and D Perez-Rey and F Martin-Sanchez},

url = {https://www.ncbi.nlm.nih.gov/pubmed/16538285},

year  = {2006},

date = {2006-01-01},

journal = {Methods Inf Med},

volume = {45},

number = {2},

pages = {180--185},

keywords = {},

pubstate = {published},

tppubtype = {article}

}