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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.

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Overview of the distribution of mutation data across the HIV proteome.(A) Barplot of the counts of (i) the number of articles describing mutations, (ii) the number of distinct mutations and (iii) the number of residues with mutation data in the database for each protein in the HIV proteome. (B) Barplot of the counts of the number of curated articles in the database describing mutagenesis experiments or polymorphisms for each residue mapped onto the HIV proteome/genome. (C) Reverse transcriptase p66 subunit with residues coloured by number of articles referring to them. Most highly cited residues are in contact with the nucleotides or are known drug resistance mutations. White denotes no papers, full red denotes 50 or more papers, colouring is linearly scaled between 0 and 50.
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pcbi-1003951-g002: Overview of the distribution of mutation data across the HIV proteome.(A) Barplot of the counts of (i) the number of articles describing mutations, (ii) the number of distinct mutations and (iii) the number of residues with mutation data in the database for each protein in the HIV proteome. (B) Barplot of the counts of the number of curated articles in the database describing mutagenesis experiments or polymorphisms for each residue mapped onto the HIV proteome/genome. (C) Reverse transcriptase p66 subunit with residues coloured by number of articles referring to them. Most highly cited residues are in contact with the nucleotides or are known drug resistance mutations. White denotes no papers, full red denotes 50 or more papers, colouring is linearly scaled between 0 and 50.

Mentions: The identified mutations shed light on the nature of the HIV research effort of the last decades. On the one hand it has been broad in scope: 2,520 of the 3,118 residues in the HIV proteome have one or more associated references to a mutation in the repository. On the other hand it has been narrow in focus: the coverage is far from uniform and certain regions such as the catalytic sites of the protease and reverse transcriptase, as well as host interaction interfaces, are much more highly studied (Figure 2).


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)

Overview of the distribution of mutation data across the HIV proteome.(A) Barplot of the counts of (i) the number of articles describing mutations, (ii) the number of distinct mutations and (iii) the number of residues with mutation data in the database for each protein in the HIV proteome. (B) Barplot of the counts of the number of curated articles in the database describing mutagenesis experiments or polymorphisms for each residue mapped onto the HIV proteome/genome. (C) Reverse transcriptase p66 subunit with residues coloured by number of articles referring to them. Most highly cited residues are in contact with the nucleotides or are known drug resistance mutations. White denotes no papers, full red denotes 50 or more papers, colouring is linearly scaled between 0 and 50.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1003951-g002: Overview of the distribution of mutation data across the HIV proteome.(A) Barplot of the counts of (i) the number of articles describing mutations, (ii) the number of distinct mutations and (iii) the number of residues with mutation data in the database for each protein in the HIV proteome. (B) Barplot of the counts of the number of curated articles in the database describing mutagenesis experiments or polymorphisms for each residue mapped onto the HIV proteome/genome. (C) Reverse transcriptase p66 subunit with residues coloured by number of articles referring to them. Most highly cited residues are in contact with the nucleotides or are known drug resistance mutations. White denotes no papers, full red denotes 50 or more papers, colouring is linearly scaled between 0 and 50.
Mentions: The identified mutations shed light on the nature of the HIV research effort of the last decades. On the one hand it has been broad in scope: 2,520 of the 3,118 residues in the HIV proteome have one or more associated references to a mutation in the repository. On the other hand it has been narrow in focus: the coverage is far from uniform and certain regions such as the catalytic sites of the protease and reverse transcriptase, as well as host interaction interfaces, are much more highly studied (Figure 2).

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