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The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data.

Davey NE, Satagopam VP, Santiago-Mozos S, Villacorta-Martin C, Bharat TA, Schneider R, Briggs JA - PLoS Comput. Biol. (2014)

Bottom Line: The results of this research effort are recorded in the scientific literature, but it is difficult for virologists to rapidly find it.Accordingly, the HIV research community would benefit from a resource cataloguing the available HIV mutation literature.The current release of the HIV mutation browser describes the phenotypes of 7,608 unique mutations at 2,520 sites in the HIV proteome, resulting from the analysis of 120,899 papers.

View Article: PubMed Central - PubMed

Affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; Department of Physiology and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America.

ABSTRACT
Huge research effort has been invested over many years to determine the phenotypes of natural or artificial mutations in HIV proteins--interpretation of mutation phenotypes is an invaluable source of new knowledge. The results of this research effort are recorded in the scientific literature, but it is difficult for virologists to rapidly find it. Manually locating data on phenotypic variation within the approximately 270,000 available HIV-related research articles, or the further 1,500 articles that are published each month is a daunting task. Accordingly, the HIV research community would benefit from a resource cataloguing the available HIV mutation literature. We have applied computational text-mining techniques to parse and map mutagenesis and polymorphism information from the HIV literature, have enriched the data with ancillary information and have developed a public, web-based interface through which it can be intuitively explored: the HIV mutation browser. The current release of the HIV mutation browser describes the phenotypes of 7,608 unique mutations at 2,520 sites in the HIV proteome, resulting from the analysis of 120,899 papers. The mutation information for each protein is organised in a residue-centric manner and each residue is linked to the relevant experimental literature. The importance of HIV as a global health burden advocates extensive effort to maximise the efficiency of HIV research. The HIV mutation browser provides a valuable new resource for the research community. The HIV mutation browser is available at: http://hivmut.org.

Show MeSH
Schema describing article acquisition, mutation curation and data presentation for the HIV mutation browser.A list of HIV-related PubMed article identifiers (PMIDs) are retrieved from PubMed. The publishing journal of each article is compared against a list of participating publishers (i.e. publishers that have given permission for bulk PDF downloading, computational parsing of PDF and display of articles details). Permitted articles are retrieved from the publishers website as PDF files. Retrieved articles are computationally text-mined to parse patterns commonly used in the literature to denote mutations. Each mutation is then mapped onto the HIV proteome. Mutations are stored in a relational database and accessed through a web interface, the HIV mutation browser. The HIV mutation browser organises the data by protein and residue and integrates ancillary information relevant to the users. See methods section for more details.
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pcbi-1003951-g001: Schema describing article acquisition, mutation curation and data presentation for the HIV mutation browser.A list of HIV-related PubMed article identifiers (PMIDs) are retrieved from PubMed. The publishing journal of each article is compared against a list of participating publishers (i.e. publishers that have given permission for bulk PDF downloading, computational parsing of PDF and display of articles details). Permitted articles are retrieved from the publishers website as PDF files. Retrieved articles are computationally text-mined to parse patterns commonly used in the literature to denote mutations. Each mutation is then mapped onto the HIV proteome. Mutations are stored in a relational database and accessed through a web interface, the HIV mutation browser. The HIV mutation browser organises the data by protein and residue and integrates ancillary information relevant to the users. See methods section for more details.

Mentions: Creation of the HIV mutation browser required a number of steps (Figure 1). First, we obtained permission from publishers, identified, and accessed the relevant literature. Second, we established and applied text-mining techniques to retrieve data on mutagenesis and polymorphism from the HIV literature. Third, we associated the mutation data to the appropriate residues within the HIV proteome. Finally, we developed a browser through which the data can be accessed in an intuitive and informative way.


The HIV mutation browser: a resource for human immunodeficiency virus mutagenesis and polymorphism data.

Davey NE, Satagopam VP, Santiago-Mozos S, Villacorta-Martin C, Bharat TA, Schneider R, Briggs JA - PLoS Comput. Biol. (2014)

Schema describing article acquisition, mutation curation and data presentation for the HIV mutation browser.A list of HIV-related PubMed article identifiers (PMIDs) are retrieved from PubMed. The publishing journal of each article is compared against a list of participating publishers (i.e. publishers that have given permission for bulk PDF downloading, computational parsing of PDF and display of articles details). Permitted articles are retrieved from the publishers website as PDF files. Retrieved articles are computationally text-mined to parse patterns commonly used in the literature to denote mutations. Each mutation is then mapped onto the HIV proteome. Mutations are stored in a relational database and accessed through a web interface, the HIV mutation browser. The HIV mutation browser organises the data by protein and residue and integrates ancillary information relevant to the users. See methods section for more details.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4256008&req=5

pcbi-1003951-g001: Schema describing article acquisition, mutation curation and data presentation for the HIV mutation browser.A list of HIV-related PubMed article identifiers (PMIDs) are retrieved from PubMed. The publishing journal of each article is compared against a list of participating publishers (i.e. publishers that have given permission for bulk PDF downloading, computational parsing of PDF and display of articles details). Permitted articles are retrieved from the publishers website as PDF files. Retrieved articles are computationally text-mined to parse patterns commonly used in the literature to denote mutations. Each mutation is then mapped onto the HIV proteome. Mutations are stored in a relational database and accessed through a web interface, the HIV mutation browser. The HIV mutation browser organises the data by protein and residue and integrates ancillary information relevant to the users. See methods section for more details.
Mentions: Creation of the HIV mutation browser required a number of steps (Figure 1). First, we obtained permission from publishers, identified, and accessed the relevant literature. Second, we established and applied text-mining techniques to retrieve data on mutagenesis and polymorphism from the HIV literature. Third, we associated the mutation data to the appropriate residues within the HIV proteome. Finally, we developed a browser through which the data can be accessed in an intuitive and informative way.

Bottom Line: The results of this research effort are recorded in the scientific literature, but it is difficult for virologists to rapidly find it.Accordingly, the HIV research community would benefit from a resource cataloguing the available HIV mutation literature.The current release of the HIV mutation browser describes the phenotypes of 7,608 unique mutations at 2,520 sites in the HIV proteome, resulting from the analysis of 120,899 papers.

View Article: PubMed Central - PubMed

Affiliation: Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany; Department of Physiology and Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America.

ABSTRACT
Huge research effort has been invested over many years to determine the phenotypes of natural or artificial mutations in HIV proteins--interpretation of mutation phenotypes is an invaluable source of new knowledge. The results of this research effort are recorded in the scientific literature, but it is difficult for virologists to rapidly find it. Manually locating data on phenotypic variation within the approximately 270,000 available HIV-related research articles, or the further 1,500 articles that are published each month is a daunting task. Accordingly, the HIV research community would benefit from a resource cataloguing the available HIV mutation literature. We have applied computational text-mining techniques to parse and map mutagenesis and polymorphism information from the HIV literature, have enriched the data with ancillary information and have developed a public, web-based interface through which it can be intuitively explored: the HIV mutation browser. The current release of the HIV mutation browser describes the phenotypes of 7,608 unique mutations at 2,520 sites in the HIV proteome, resulting from the analysis of 120,899 papers. The mutation information for each protein is organised in a residue-centric manner and each residue is linked to the relevant experimental literature. The importance of HIV as a global health burden advocates extensive effort to maximise the efficiency of HIV research. The HIV mutation browser provides a valuable new resource for the research community. The HIV mutation browser is available at: http://hivmut.org.

Show MeSH