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The main functions of HIVDB are:
- To store, analyze and make available the diverse forms of data underlying drug resistance knowledge to the broad community of researchers and clinicians studying HIV drug resistance and using HIV drug resistance tests;
- To provide a publicly available online resource to help those performing HIV drug resistance surveillance, interpreting HIV drug resistance tests, and developing new antiretroviral drugs;
- To identify gaps in drug resistance knowledge that could be filled by retrospective or prospective studies.
What is the purpose of the HIV Drug Resistance Database (HIVDB)?
HIV drug resistance data are critical for HIV drug resistance surveillance, ARV drug design, and the management of persons infected with drug-resistant HIV. These data are best represented in a database that not only catalogs mutations associated with drug resistance but also links complete genetic sequences to other forms of data.
What types of data are in HIVDB?
HIVDB collects the three fundamental types of correlations that form the basis of drug resistance knowledge: (1) Correlations between genotypic data with the treatments of persons from whom sequenced HIV-1 isolates have been obtained (genotype-treatment); (2) Correlations between genotype and in vitro drug susceptibility (genotype-phenotype); and (3) Correlations between genotype and the clinical response to a new treatment regimen (genotype-outcome). The particular advantages of each type of data are outlined in previous publications (Shafer 2006). The three HIV targets currently in HIVDB are Protease (PR), Reverse Transcriptase (RT), and Integrase (IN).
How much data is in HIVDB?
HIVDB contains more than 90,000 PR, RT, or IN sequences from more than 80,000 distinct virus isolations obtained from nearly 40,000 individuals. 98%-99% of the viruses are human HIV-1 isolates; 1%-2% of viruses are human HIV-2 isolates or other non-human primate lentiviruses (NHPL).
Where is the HIVDB data from?
The data have been obtained from more than 900 literature and GenBank references. About 15% of the data have been obtained from published research performed at Stanford University whereas the remainder is from published papers and/or GenBank. In some cases, a published paper or a GenBank submission contains sufficient data for entry into HIVDB. In other cases, data within a paper must be linked on a sequence by sequence basis to establish the correlations between a sequence and the ARV treatment of the person from whom the sequenced virus were obtained. In a large proportion of cases, contributors to the database have provided essential information directly to the HIVDB staff to make it possible to add their data to the database.
How is HIVDB funded?
HIVDB has been funded primarily by the NIH including the NIAID and the NIGMS. Each of the pharmaceutical companies that have manufactured ARV drug has also provided one or more unrestricted educational grant. Additional funders have included the California University-wide AIDS Research Program (2004-2005), the Stanford University Bio-X Interdisciplinary Initiative (2000-2001), and several diagnostic and biotech companies, particularly Celera. A complete list of the funds received by the database can be found at http://hivdb.stanford.edu/pages/acknowledgements.html
How should HIVDB be cited?
HIVDB and its programs have been described in several publications (Betts and Shafer 2003; Kantor et al. 2001; Kuiken et al. 2003; Liu and Shafer 2006; Rhee et al. 2003; Rhee et al. 2006a; Shafer 2006; Shafer et al. 2000a; Shafer et al. 2000b; Shafer et al. 1999). However, recommended that the most recent general review by Rhee et al in 2003 be cited: Rhee, S. Y., M. J. Gonzales, R. Kantor, B. J. Betts, J. Ravela, and R. W. Shafer. 2003. Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res 31:298-303. Although the database publications have been cited about 400 times, most papers that refer to the database do not cite a publication. Instead, the authors refer to the “Stanford database” or provide its URL.
Why is HIVDB publicly available?
Data is the most important commodity in science and its management is of critical importance to the discovery of new knowledge. An HIV drug resistance database that provides unfettered access to the types of data described in the preceding paragraphs must be publicly available to the broadest number of users to promote discovery in the most efficient manner. Proprietary databases that deny access to the majority of researchers are not only inefficient but also counterproductive because the company or small group of researchers with a stake in such a database will often act to thwart the nonproprietary dissemination of data in order to maintain the perceived commercial or research value of their monopoly. Conclusions drawn from a proprietary database may also be unduly influenced by the interests of those who submit and retrieve the data.
How does one contribute to HIVDB?
The criteria for publication in the database include: (1) Sequence data – nucleic acid sequences are preferred but in rare instances we have accepted amino acid sequence data and (2) Correlated data consisting of either treatment histories, phenotypic test results, and/or virologic outcome data following the change to a new treatment regimen. In addition, we strongly prefer data that has been published in a peer-review journal and that has been submitted to GenBank for two main reasons. First data that have been published are generally of higher quality than unpublished data. Second, our database operates on the principle that once data have been published, it belongs in the public domain so that others can verify and build on the results. Indeed, we have been inspired by the quotation “If I have seen further it is by standing on the shoulders of giants” (Isaac Newton 1676). The long-term success of HIVDB and other biomedical databases depends on how many medical researchers are willing to be giants.