The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data
Publication Date
December 04, 2014
Journal
PLOS Computational Biology
Authors
Norman E. Davey, Venkata P. Satagopam, Salvador Santiago Mozos, Carlos Villacorta Martin, et al
Volume
10
Issue
12
Pages
e1003951
DOI
http://doi.org/10.1371/journal.pcbi.1003951
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1003951
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/25474213
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256008
Europe PMC
http://europepmc.org/abstract/MED/25474213
Web of Science
000346656700015
Scopus
84919681014
Mendeley
http://www.mendeley.com/research/hiv-mutation-browser-resource-human-immunodeficiency-virus-mutagenesis-polymorphism-data
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Mendeley | Further Information

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Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1822730"], "description"=>"<p>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.</p>", "links"=>[], "tags"=>["health burden advocates", "HIV mutation browser", "HIV research community", "research effort", "HIV mutation literature", "Human Immunodeficiency Virus Mutagenesis"], "article_id"=>1260961, "categories"=>["Uncategorised"], "users"=>["Norman E. Davey", "Venkata P. Satagopam", "Salvador Santiago-Mozos", "Carlos Villacorta-Martin", "Tanmay A. M. Bharat", "Reinhard Schneider", "John A. G. Briggs"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003951.g001", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schema_describing_article_acquisition_mutation_curation_and_data_presentation_for_the_HIV_mutation_browser_/1260961", "title"=>"Schema describing article acquisition, mutation curation and data presentation for the HIV mutation browser.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:31:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1822749"], "description"=>"<p>(1) Options bar for the residue view section of the interface. (2) Mutation information. (3) User feedback buttons. (4) Mutation information download links. (5) Ancillary residue information panel.</p>", "links"=>[], "tags"=>["health burden advocates", "HIV mutation browser", "HIV research community", "research effort", "HIV mutation literature", "Human Immunodeficiency Virus Mutagenesis"], "article_id"=>1260970, "categories"=>["Uncategorised"], "users"=>["Norman E. Davey", "Venkata P. Satagopam", "Salvador Santiago-Mozos", "Carlos Villacorta-Martin", "Tanmay A. M. Bharat", "Reinhard Schneider", "John A. G. Briggs"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003951.g003", "stats"=>{"downloads"=>2, "page_views"=>22, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_HIV_Mutation_Browser_interface_for_Vpu_residue_51_showing_the_navigation_protein_and_residue_panels_/1260970", "title"=>"HIV Mutation Browser interface for Vpu residue 51 showing the navigation, protein and residue panels.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:31:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1822769", "https://ndownloader.figshare.com/files/1822770", "https://ndownloader.figshare.com/files/1822771"], "description"=>"<div><p>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: <a href=\"http://hivmut.org\" target=\"_blank\">http://hivmut.org</a>.</p></div>", "links"=>[], "tags"=>["health burden advocates", "HIV mutation browser", "HIV research community", "research effort", "HIV mutation literature", "Human Immunodeficiency Virus Mutagenesis"], "article_id"=>1260980, "categories"=>["Uncategorised"], "users"=>["Norman E. Davey", "Venkata P. Satagopam", "Salvador Santiago-Mozos", "Carlos Villacorta-Martin", "Tanmay A. M. Bharat", "Reinhard Schneider", "John A. G. Briggs"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1003951.s001", "https://dx.doi.org/10.1371/journal.pcbi.1003951.s002", "https://dx.doi.org/10.1371/journal.pcbi.1003951.s003"], "stats"=>{"downloads"=>28, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_HIV_Mutation_Browser_A_Resource_for_Human_Immunodeficiency_Virus_Mutagenesis_and_Polymorphism_Data_/1260980", "title"=>"The HIV Mutation Browser: A Resource for Human Immunodeficiency Virus Mutagenesis and Polymorphism Data", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-12-04 03:31:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1822742"], "description"=>"<p>(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.</p>", "links"=>[], "tags"=>["health burden advocates", "HIV mutation browser", "HIV research community", "research effort", "HIV mutation literature", "Human Immunodeficiency Virus Mutagenesis"], "article_id"=>1260965, "categories"=>["Uncategorised"], "users"=>["Norman E. Davey", "Venkata P. Satagopam", "Salvador Santiago-Mozos", "Carlos Villacorta-Martin", "Tanmay A. M. Bharat", "Reinhard Schneider", "John A. G. Briggs"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003951.g002", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Overview_of_the_distribution_of_mutation_data_across_the_HIV_proteome_/1260965", "title"=>"Overview of the distribution of mutation data across the HIV proteome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:31:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/1822762"], "description"=>"<p>(A) Representative simple and complex examples of sentences recognised by the templates used to perform the mutation text-mining of articles (see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003951#pcbi.1003951.s001\" target=\"_blank\">Table S1</a> for complete list). Information of interest representing the wildtype residue (blue) and mutated residue (green) are coloured and position of the mutations are underlined. (B) Illustration of the distinct numbering schemes for different chains of the same protein. The shown peptide sequence is a short region (497–527) of the HIV Envelope glycoprotein gp160 (Env) overlapping the site cleaved by the host furin to produce the Surface protein gp120 and Transmembrane protein gp41 chains. The cleavage site is denoted by a grey triangle. The numbering above the sequence defines the position relative to the start of the gp160 protein and the numbering below the sequence defines the position relative to the start of the gp41 chain. (C) Examples of three sentences from the HIV literature where each article uses a different nomenclature or numbering scheme (blue) to describe the same mutation at the same site, Valine at residue 513 in the gp160 protein. Each article also refers to the protein by the chain name, gp41, rather than the name of the unprocessed protein, Envelope glycoprotein gp160 (Env), used for mapping in the HIV mutation resource. One example sentence refers to the gp41 chain while utilising the numbering for the unprocessed protein.</p>", "links"=>[], "tags"=>["health burden advocates", "HIV mutation browser", "HIV research community", "research effort", "HIV mutation literature", "Human Immunodeficiency Virus Mutagenesis"], "article_id"=>1260973, "categories"=>["Uncategorised"], "users"=>["Norman E. Davey", "Venkata P. Satagopam", "Salvador Santiago-Mozos", "Carlos Villacorta-Martin", "Tanmay A. M. Bharat", "Reinhard Schneider", "John A. G. Briggs"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003951.g004", "stats"=>{"downloads"=>1, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_illustrations_of_issues_associated_with_parsing_and_mapping_mutation_data_/1260973", "title"=>"Example illustrations of issues associated with parsing and mapping mutation data.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-12-04 03:31:12"}

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Relative Metric

{"start_date"=>"2014-01-01T00:00:00Z", "end_date"=>"2014-12-31T00:00:00Z", "subject_areas"=>[]}
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