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1.
Nucleic Acids Res ; 51(D1): D29-D38, 2023 01 06.
Artigo em Inglês | MEDLINE | ID: mdl-36370100

RESUMO

The National Center for Biotechnology Information (NCBI) provides online information resources for biology, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for most of these databases. New resources include the Comparative Genome Resource (CGR) and the BLAST ClusteredNR database. Resources receiving significant updates in the past year include PubMed, PMC, Bookshelf, IgBLAST, GDV, RefSeq, NCBI Virus, GenBank type assemblies, iCn3D, ClinVar, GTR, dbGaP, ALFA, ClinicalTrials.gov, Pathogen Detection, antimicrobial resistance resources, and PubChem. These resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.


Assuntos
Bases de Dados Genéticas , Bases de Dados de Ácidos Nucleicos , Estados Unidos , National Library of Medicine (U.S.) , Alinhamento de Sequência , Biotecnologia , Internet
2.
Nucleic Acids Res ; 50(D1): D20-D26, 2022 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-34850941

RESUMO

The National Center for Biotechnology Information (NCBI) produces a variety of online information resources for biology, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the most of these databases. Resources receiving significant updates in the past year include PubMed, PMC, Bookshelf, RefSeq, SRA, Virus, dbSNP, dbVar, ClinicalTrials.gov, MMDB, iCn3D and PubChem. These resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.


Assuntos
Biotecnologia/tendências , Bases de Dados Genéticas/tendências , Bases de Dados de Compostos Químicos , Bases de Dados de Ácidos Nucleicos , Bases de Dados de Proteínas , Humanos , Internet , National Library of Medicine (U.S.) , PubMed , Estados Unidos
3.
Nucleic Acids Res ; 49(D1): D10-D17, 2021 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-33095870

RESUMO

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 34 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Custom implementations of the BLAST program provide sequence-based searching of many specialized datasets. New resources released in the past year include a new PubMed interface and NCBI datasets. Additional resources that were updated in the past year include PMC, Bookshelf, Genome Data Viewer, SRA, ClinVar, dbSNP, dbVar, Pathogen Detection, BLAST, Primer-BLAST, IgBLAST, iCn3D and PubChem. All of these resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.


Assuntos
Bases de Dados Genéticas , National Library of Medicine (U.S.) , Biologia Computacional/métodos , Bases de Dados de Compostos Químicos , Bases de Dados de Ácidos Nucleicos , Bases de Dados de Proteínas , Genômica/métodos , Humanos , PubMed , Estados Unidos
4.
Nucleic Acids Res ; 48(D1): D9-D16, 2020 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-31602479

RESUMO

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Custom implementations of the BLAST program provide sequence-based searching of many specialized datasets. New resources released in the past year include a new PubMed interface, a sequence database search and a gene orthologs page. Additional resources that were updated in the past year include PMC, Bookshelf, My Bibliography, Assembly, RefSeq, viral genomes, the prokaryotic genome annotation pipeline, Genome Workbench, dbSNP, BLAST, Primer-BLAST, IgBLAST and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.


Assuntos
Biologia Computacional/métodos , Biologia Computacional/organização & administração , Bases de Dados Genéticas , National Library of Medicine (U.S.) , Bases de Dados de Ácidos Nucleicos , Genômica/métodos , Humanos , PubMed , Estados Unidos , Navegador
5.
PLoS Biol ; 16(8): e2005343, 2018 08.
Artigo em Inglês | MEDLINE | ID: mdl-30153250

RESUMO

PubMed is a free search engine for biomedical literature accessed by millions of users from around the world each day. With the rapid growth of biomedical literature-about two articles are added every minute on average-finding and retrieving the most relevant papers for a given query is increasingly challenging. We present Best Match, a new relevance search algorithm for PubMed that leverages the intelligence of our users and cutting-edge machine-learning technology as an alternative to the traditional date sort order. The Best Match algorithm is trained with past user searches with dozens of relevance-ranking signals (factors), the most important being the past usage of an article, publication date, relevance score, and type of article. This new algorithm demonstrates state-of-the-art retrieval performance in benchmarking experiments as well as an improved user experience in real-world testing (over 20% increase in user click-through rate). Since its deployment in June 2017, we have observed a significant increase (60%) in PubMed searches with relevance sort order: it now assists millions of PubMed searches each week. In this work, we hope to increase the awareness and transparency of this new relevance sort option for PubMed users, enabling them to retrieve information more effectively.


Assuntos
Mineração de Dados/métodos , Armazenamento e Recuperação da Informação/métodos , Algoritmos , Humanos , MEDLINE , Aprendizado de Máquina , PubMed , Publicações , Ferramenta de Busca
6.
Nucleic Acids Res ; 47(D1): D23-D28, 2019 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-30395293

RESUMO

The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts published in life science journals. The Entrez system provides search and retrieval operations for most of these data from 38 distinct databases. The E-utilities serve as the programming interface for the Entrez system. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. New resources released in the past year include PubMed Labs and a new sequence database search. Resources that were updated in the past year include PubMed, PMC, Bookshelf, genome data viewer, Assembly, prokaryotic genomes, Genome, BioProject, dbSNP, dbVar, BLAST databases, igBLAST, iCn3D and PubChem. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.


Assuntos
Biotecnologia/organização & administração , Bases de Dados Genéticas , Animais , Biotecnologia/métodos , Bases de Dados de Compostos Químicos , Humanos , Software , Estados Unidos/epidemiologia , Navegador
7.
Nucleic Acids Res ; 40(Database issue): D13-25, 2012 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-22140104

RESUMO

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Website. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Genome and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, BioProject, BioSample, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Probe, Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), Biosystems, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.


Assuntos
Bases de Dados como Assunto , Bases de Dados Genéticas , Bases de Dados de Proteínas , Expressão Gênica , Genômica , Internet , Modelos Moleculares , National Library of Medicine (U.S.) , Publicações Periódicas como Assunto , PubMed , Alinhamento de Sequência , Análise de Sequência de DNA , Análise de Sequência de Proteína , Análise de Sequência de RNA , Bibliotecas de Moléculas Pequenas , Estados Unidos
8.
Nucleic Acids Res ; 39(Database issue): D38-51, 2011 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-21097890

RESUMO

In addition to maintaining the GenBank® nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central (PMC), Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Primer-BLAST, COBALT, Electronic PCR, OrfFinder, Splign, ProSplign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, dbVar, Epigenomics, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART), IBIS, Biosystems, Peptidome, OMSSA, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.


Assuntos
Bases de Dados Genéticas , Bases de Dados de Proteínas , Expressão Gênica , Genômica , National Library of Medicine (U.S.) , Estrutura Terciária de Proteína , PubMed , Alinhamento de Sequência , Análise de Sequência de DNA , Análise de Sequência de RNA , Software , Integração de Sistemas , Estados Unidos
9.
Nucleic Acids Res ; 38(Database issue): D5-16, 2010 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-19910364

RESUMO

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, Reference Sequence, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Trace Archive, Sequence Read Archive, Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool, Biosystems, Peptidome, Protein Clusters and the PubChem suite of small molecule databases. Augmenting many of the web applications are custom implementations of the BLAST program optimized to search specialized data sets. All these resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.


Assuntos
Biologia Computacional/métodos , Bases de Dados Genéticas , Bases de Dados de Ácidos Nucleicos , Algoritmos , Animais , Biologia Computacional/tendências , Bases de Dados de Proteínas , Genoma Bacteriano , Genoma Viral , Humanos , Armazenamento e Recuperação da Informação/métodos , Internet , National Institutes of Health (U.S.) , National Library of Medicine (U.S.) , Software , Estados Unidos
10.
Nucleic Acids Res ; 37(Database issue): D5-15, 2009 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-18940862

RESUMO

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through the NCBI web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the web applications is custom implementation of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.


Assuntos
Bases de Dados Genéticas , Expressão Gênica , Genes , Genômica , Genótipo , National Library of Medicine (U.S.) , Fenótipo , Estrutura Terciária de Proteína , Proteômica , PubMed , Homologia de Sequência , Integração de Sistemas , Estados Unidos
11.
Nucleic Acids Res ; 36(Database issue): D13-21, 2008 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-18045790

RESUMO

In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link, Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace, Assembly, and Short Read Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus, Entrez Probe, GENSAT, Database of Genotype and Phenotype, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting the web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.


Assuntos
Bases de Dados Genéticas , National Library of Medicine (U.S.) , Animais , Bases de Dados de Ácidos Nucleicos , Expressão Gênica , Genômica , Genótipo , Humanos , Internet , Modelos Moleculares , Fenótipo , Proteômica , Alinhamento de Sequência , Estados Unidos
12.
Nucleic Acids Res ; 35(Database issue): D5-12, 2007 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-17170002

RESUMO

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, My NCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link(BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genome, Genome Project and related tools, the Trace and Assembly Archives, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Viral Genotyping Tools, Influenza Viral Resources, HIV-1/Human Protein Interaction Database, Gene Expression Omnibus (GEO), Entrez Probe, GENSAT, Online Mendelian Inheritance in Man (OMIM), Online Mendelian Inheritance in Animals (OMIA), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), the Conserved Domain Architecture Retrieval Tool (CDART) and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. These resources can be accessed through the NCBI home page at www.ncbi.nlm.nih.gov.


Assuntos
Bases de Dados Genéticas , National Library of Medicine (U.S.) , Animais , Bases de Dados de Ácidos Nucleicos , Bases de Dados de Proteínas , Expressão Gênica , Genômica , Humanos , Internet , Fenótipo , Proteômica , PubMed , Alinhamento de Sequência , Software , Estados Unidos
13.
Nucleic Acids Res ; 34(Database issue): D173-80, 2006 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-16381840

RESUMO

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utilities, MyNCBI, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, Splign, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups, Retroviral Genotyping Tools, HIV-1, Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus, Entrez Probe, GENSAT, Online Mendelian Inheritance in Man, Online Mendelian Inheritance in Animals, the Molecular Modeling Database, the Conserved Domain Database, the Conserved Domain Architecture Retrieval Tool and the PubChem suite of small molecule databases. Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.


Assuntos
Bases de Dados Genéticas , National Library of Medicine (U.S.) , Bases de Dados de Ácidos Nucleicos , Bases de Dados de Proteínas , Regulação da Expressão Gênica , Genes , Genômica , Humanos , Internet , PubMed , Alinhamento de Sequência , Análise de Sequência de DNA , Software , Estados Unidos
14.
Database (Oxford) ; 20182018 01 01.
Artigo em Inglês | MEDLINE | ID: mdl-30239682

RESUMO

PubMed is a freely accessible system for searching the biomedical literature, with ~ 2.5 million users worldwide on an average workday. In order to better meet our users' needs in an era of information overload, we have recently developed PubMed Labs (www.pubmed.gov/labs), an experimental system for users to test new search features/tools (e.g. Best Match) and provide feedback, which enables us to make more informed decisions about potential changes to improve the search quality and overall usability of PubMed. In addition, PubMed Labs features a mobile-first and responsive layout that offers better support for accessing PubMed from increasingly popular mobiles and small-screen devices. In this paper, we detail PubMed Labs, its purpose, new features and best practices. We also encourage users to share their experience with us; based on which we are continuously improving PubMed Labs with more advanced features and better user experience.


Assuntos
PubMed , Publicações , Ferramenta de Busca , Estatística como Assunto
15.
Nucleic Acids Res ; 33(Database issue): D39-45, 2005 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-15608222

RESUMO

In addition to maintaining the GenBank nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data retrieval systems and computational resources for the analysis of data in GenBank and other biological data made available through NCBI's website. NCBI resources include Entrez, Entrez Programming Utilities, PubMed, PubMed Central, Entrez Gene, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR, OrfFinder, Spidey, RefSeq, UniGene, HomoloGene, ProtEST, dbMHC, dbSNP, Cancer Chromosomes, Entrez Genomes and related tools, the Map Viewer, Model Maker, Evidence Viewer, Clusters of Orthologous Groups (COGs), Retroviral Genotyping Tools, HIV-1/Human Protein Interaction Database, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD) and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized datasets. All of the resources can be accessed through the NCBI home page at http://www.ncbi.nlm.nih.gov.


Assuntos
Bases de Dados Genéticas , National Library of Medicine (U.S.) , Sequência de Aminoácidos , Animais , Biologia Computacional , Sequência Conservada , Bases de Dados Factuais , Perfilação da Expressão Gênica , Genes , Genômica , Humanos , Modelos Moleculares , Fenótipo , Mapeamento de Interação de Proteínas , Estrutura Terciária de Proteína , Alinhamento de Sequência , Software , Estados Unidos
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