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  1. Article ; Online: DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update).

    Sherman, Brad T / Hao, Ming / Qiu, Ju / Jiao, Xiaoli / Baseler, Michael W / Lane, H Clifford / Imamichi, Tomozumi / Chang, Weizhong

    Nucleic acids research

    2022  Volume 50, Issue W1, Page(s) W216–W221

    Abstract: DAVID is a popular bioinformatics resource system including a web server and web service ... a set of functional analysis tools. Here, we report all updates made in 2021. The DAVID Gene system was ... All existing annotation types have been updated, if available, based on the new DAVID Gene system. Compared ...

    Abstract DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene lists. It consists of a comprehensive knowledgebase and a set of functional analysis tools. Here, we report all updates made in 2021. The DAVID Gene system was rebuilt to gain coverage of more organisms, which increased the taxonomy coverage from 17 399 to 55 464. All existing annotation types have been updated, if available, based on the new DAVID Gene system. Compared with the last version, the number of gene-term records for most annotation types within the updated Knowledgebase have significantly increased. Moreover, we have incorporated new annotations in the Knowledgebase including small molecule-gene interactions from PubChem, drug-gene interactions from DrugBank, tissue expression information from the Human Protein Atlas, disease information from DisGeNET, and pathways from WikiPathways and PathBank. Eight of ten subgroups split from Uniprot Keyword annotation were assigned to specific types. Finally, we added a species parameter for uploading a list of gene symbols to minimize the ambiguity between species, which increases the efficiency of the list upload and eliminates confusion for users. These current updates have significantly expanded the Knowledgebase and enhanced the discovery power of DAVID.
    MeSH term(s) Humans ; Software ; Databases, Genetic ; Computational Biology ; Computers ; Knowledge Bases ; Molecular Sequence Annotation ; Internet
    Language English
    Publishing date 2022-03-24
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkac194
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

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  2. Article ; Online: DAVID Knowledgebase

    Baseler Michael W / Stephens Robert / Liu David / Bour Stephan / Guo Yongjian / Tan Qina / Huang Da / Sherman Brad T / Lane H Clifford / Lempicki Richard A

    BMC Bioinformatics, Vol 8, Iss 1, p

    a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

    2007  Volume 426

    Abstract: ... knowledgebase is in demand for high throughput gene functional analysis. Description The DAVID Knowledgebase is ... built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene ... protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping ...

    Abstract Abstract Background Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis. Description The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner. Conclusion The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/ .
    Keywords Computer applications to medicine. Medical informatics ; R858-859.7 ; Biology (General) ; QH301-705.5
    Subject code 004
    Language English
    Publishing date 2007-11-01T00:00:00Z
    Publisher BMC
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  3. Article ; Online: David Himmelstein and Steffie Woolhandler: advocates for an equitable US health system.

    Lane, Richard

    Lancet (London, England)

    2017  Volume 389, Issue 10077, Page(s) 1389

    Language English
    Publishing date 2017-04-08
    Publishing country England
    Document type Journal Article
    ZDB-ID 3306-6
    ISSN 1474-547X ; 0023-7507 ; 0140-6736
    ISSN (online) 1474-547X
    ISSN 0023-7507 ; 0140-6736
    DOI 10.1016/S0140-6736(17)30900-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.MG 94: Show issues

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  4. Book ; Online: Chapter 16 Regulated Market Socialism

    Lane, David

    2023  

    Keywords Globalization ; Socialism & left-of-centre democratic ideologies ; Political economy ; Economic systems & structures ; International business ; Democratic government; Economic crisis; Environmental sustainability; Ideology; Inequality; Institutions; Neoliberalism; Post-industrial society; Social disruption; Socialism; World system
    Language English
    Size 1 electronic resource (41 pages)
    Publisher Bristol University Press
    Publishing place Bristol
    Document type Book ; Online
    Note English
    HBZ-ID HT030381534
    ISBN 9781529220902 ; 1529220904
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  5. Book ; Online: Chapter 3 Neoliberalism

    Lane, David

    A Critique

    2023  

    Keywords Globalization ; Socialism & left-of-centre democratic ideologies ; Political economy ; Economic systems & structures ; International business ; Democratic government; Economic crisis; Environmental sustainability; Ideology; Inequality; Institutions; Neoliberalism; Post-industrial society; Social disruption; Socialism; World system
    Language English
    Size 1 electronic resource (34 pages)
    Publisher Bristol University Press
    Publishing place Bristol
    Document type Book ; Online
    Note English
    HBZ-ID HT030374636
    ISBN 9781529220902 ; 1529220904
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  6. Book ; Online: Global Neoliberal Capitalism and the Alternatives

    Lane, David

    From Social Democracy to State Capitalisms

    2023  

    Keywords Globalization ; Socialism & left-of-centre democratic ideologies ; Political economy ; Economic systems & structures ; International business ; Democratic government; Economic crisis; Environmental sustainability; Ideology; Inequality; Institutions; Neoliberalism; Post-industrial society; Social disruption; Socialism; World system
    Language English
    Size 1 electronic resource (334 pages)
    Publisher Bristol University Press
    Publishing place Bristol
    Document type Book ; Online
    Note English
    HBZ-ID HT030374727
    ISBN 9781529220926 ; 1529220920
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  7. Article ; Online: DAVID gene ID conversion tool.

    Huang, Da Wei / Sherman, Brad T / Stephens, Robert / Baseler, Michael W / Lane, H Clifford / Lempicki, Richard A

    Bioinformation

    2008  Volume 2, Issue 10, Page(s) 428–430

    Abstract: ... from microarray and proteomic experiments. The DAVID Gene ID Conversion Tool (DICT), a web-based application, is ... david.abcc.ncifcrf.gov/conversion.jsp. ...

    Abstract Unlabelled: Our current biological knowledge is spread over many independent bioinformatics databases where many different types of gene and protein identifiers are used. The heterogeneous and redundant nature of these identifiers limits data analysis across different bioinformatics resources. It is an even more serious bottleneck of data analysis for larger datasets, such as gene lists derived from microarray and proteomic experiments. The DAVID Gene ID Conversion Tool (DICT), a web-based application, is able to convert user's input gene or gene product identifiers from one type to another in a more comprehensive and high-throughput manner with a uniquely enhanced ID-ID mapping database.
    Availability: http://david.abcc.ncifcrf.gov/conversion.jsp.
    Language English
    Publishing date 2008-07-30
    Publishing country Singapore
    Document type Journal Article
    ZDB-ID 2203786-X
    ISSN 0973-2063 ; 0973-2063
    ISSN (online) 0973-2063
    ISSN 0973-2063
    DOI 10.6026/97320630002428
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: DAVID-WS: a stateful web service to facilitate gene/protein list analysis.

    Jiao, Xiaoli / Sherman, Brad T / Huang, Da Wei / Stephens, Robert / Baseler, Michael W / Lane, H Clifford / Lempicki, Richard A

    Bioinformatics (Oxford, England)

    2012  Volume 28, Issue 13, Page(s) 1805–1806

    Abstract: Summary: The database for annotation, visualization and integrated discovery (DAVID), which can be ... freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource ... However, the current web interface does not support programmatic access to DAVID, and the uniform resource locator (URL ...

    Abstract Summary: The database for annotation, visualization and integrated discovery (DAVID), which can be freely accessed at http://david.abcc.ncifcrf.gov/, is a web-based online bioinformatics resource that aims to provide tools for the functional interpretation of large lists of genes/proteins. It has been used by researchers from more than 5000 institutes worldwide, with a daily submission rate of ∼1200 gene lists from ∼400 unique researchers, and has been cited by more than 6000 scientific publications. However, the current web interface does not support programmatic access to DAVID, and the uniform resource locator (URL)-based application programming interface (API) has a limit on URL size and is stateless in nature as it uses URL request and response messages to communicate with the server, without keeping any state-related details. DAVID-WS (web service) has been developed to automate user tasks by providing stateful web services to access DAVID programmatically without the need for human interactions.
    Availability: The web service and sample clients (written in Java, Perl, Python and Matlab) are made freely available under the DAVID License at http://david.abcc.ncifcrf.gov/content.jsp?file=WS.html.
    MeSH term(s) Computational Biology ; Databases, Genetic ; Genes ; Internet ; Molecular Sequence Annotation ; Proteins ; Software
    Chemical Substances Proteins
    Language English
    Publishing date 2012-04-27
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/bts251
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 2374: Show issues Location:
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  9. Article ; Online: DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists.

    Huang, Da Wei / Sherman, Brad T / Tan, Qina / Kir, Joseph / Liu, David / Bryant, David / Guo, Yongjian / Stephens, Robert / Baseler, Michael W / Lane, H Clifford / Lempicki, Richard A

    Nucleic acids research

    2007  Volume 35, Issue Web Server issue, Page(s) W169–75

    Abstract: All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large ... lists of genes derived from genomic studies. The newly updated DAVID Bioinformatics Resources consists ... of the DAVID Knowledgebase and five integrated, web-based functional annotation tool suites: the DAVID Gene ...

    Abstract All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies. The newly updated DAVID Bioinformatics Resources consists of the DAVID Knowledgebase and five integrated, web-based functional annotation tool suites: the DAVID Gene Functional Classification Tool, the DAVID Functional Annotation Tool, the DAVID Gene ID Conversion Tool, the DAVID Gene Name Viewer and the DAVID NIAID Pathogen Genome Browser. The expanded DAVID Knowledgebase now integrates almost all major and well-known public bioinformatics resources centralized by the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of diverse gene/protein identifiers and annotation terms from a variety of public bioinformatics databases. For any uploaded gene list, the DAVID Resources now provides not only the typical gene-term enrichment analysis, but also new tools and functions that allow users to condense large gene lists into gene functional groups, convert between gene/protein identifiers, visualize many-genes-to-many-terms relationships, cluster redundant and heterogeneous terms into groups, search for interesting and related genes or terms, dynamically view genes from their lists on bio-pathways and more. With DAVID (http://david.niaid.nih.gov), investigators gain more power to interpret the biological mechanisms associated with large gene lists.
    MeSH term(s) Algorithms ; Computational Biology/methods ; Data Interpretation, Statistical ; Databases, Genetic ; Databases, Nucleic Acid ; Gene Expression Profiling/statistics & numerical data ; Genomics ; Humans ; Information Storage and Retrieval/methods ; Internet ; Oligonucleotide Array Sequence Analysis/methods ; Pattern Recognition, Automated ; Software
    Language English
    Publishing date 2007-07
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2205588-5
    ISSN 1362-4962 ; 1746-8272 ; 0305-1048 ; 0261-3166
    ISSN (online) 1362-4962 ; 1746-8272
    ISSN 0305-1048 ; 0261-3166
    DOI 10.1093/nar/gkm415
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis.

    Sherman, Brad T / Huang, Da Wei / Tan, Qina / Guo, Yongjian / Bour, Stephan / Liu, David / Stephens, Robert / Baseler, Michael W / Lane, H Clifford / Lempicki, Richard A

    BMC bioinformatics

    2007  Volume 8, Page(s) 426

    Abstract: ... knowledgebase is in demand for high throughput gene functional analysis.: Description: The DAVID ... Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions ... of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters ...

    Abstract Background: Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis.
    Description: The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner.
    Conclusion: The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/.
    MeSH term(s) Algorithms ; Animals ; Computational Biology/instrumentation ; Computational Biology/methods ; Database Management Systems ; Databases, Genetic ; Databases, Protein ; Genomics/methods ; Humans ; Information Storage and Retrieval ; Information Systems ; Internet ; Knowledge Bases ; Models, Genetic ; Multigene Family ; Oligonucleotide Array Sequence Analysis ; User-Computer Interface
    Language English
    Publishing date 2007-11-02
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2041484-5
    ISSN 1471-2105 ; 1471-2105
    ISSN (online) 1471-2105
    ISSN 1471-2105
    DOI 10.1186/1471-2105-8-426
    Database MEDical Literature Analysis and Retrieval System OnLINE

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