Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences
The antibody repertoires of individuals and groups have been used to explore disease states, understand vaccine responses, and drive therapeutic development. The arrival of B‐cell receptor repertoire sequencing has enabled researchers to get a snapshot of these antibody repertoires, and as more data...
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| Veröffentlicht in: | Protein science 2022-01, Vol.31 (1), p.141-146 |
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| description | The antibody repertoires of individuals and groups have been used to explore disease states, understand vaccine responses, and drive therapeutic development. The arrival of B‐cell receptor repertoire sequencing has enabled researchers to get a snapshot of these antibody repertoires, and as more data are generated, increasingly in‐depth studies are possible. However, most publicly available data only exist as raw FASTQ files, making the data hard to access, process, and compare. The Observed Antibody Space (OAS) database was created in 2018 to offer clean, annotated, and translated repertoire data. In this paper, we describe an update to OAS that has been driven by the increasing volume of data and the appearance of paired (VH/VL) sequence data. OAS is now accessible via a new web server, with standardized search parameters and a new sequence‐based search option. The new database provides both nucleotides and amino acids for every sequence, with additional sequence annotations to make the data Minimal Information about Adaptive Immune Receptor Repertoire compliant, and comments on potential problems with the sequence. OAS now contains 25 new studies, including severe acute respiratory syndrome coronavirus 2 data and paired sequencing data. The new database is accessible at http://opig.stats.ox.ac.uk/webapps/oas/, and all data are freely available for download. |
| doi_str_mv | 10.1002/pro.4205 |
| format | Article |
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Boyles, Fergus ; Deane, Charlotte M.</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c4775-3989321ab9a819b37ae2e96e134249772b2ea2b75b058babfa1af768582d5c9b3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Accessibility</topic><topic>Amino Acid Sequence</topic><topic>Amino acids</topic><topic>Animals</topic><topic>annotated antibody sequences</topic><topic>Annotations</topic><topic>Antibodies</topic><topic>Antibodies - chemistry</topic><topic>Antibodies - immunology</topic><topic>antibody database</topic><topic>antibody repertoire</topic><topic>antibody sequence</topic><topic>BCR‐seq</topic><topic>Coronaviruses</topic><topic>COVID-19 - immunology</topic><topic>Databases, Protein</topic><topic>Downloading</topic><topic>Humans</topic><topic>Immunoglobulin Heavy Chains - chemistry</topic><topic>Immunoglobulin Heavy Chains - immunology</topic><topic>Immunoglobulin Light Chains - chemistry</topic><topic>Immunoglobulin Light Chains - immunology</topic><topic>Immunoglobulin Variable Region - chemistry</topic><topic>Immunoglobulin Variable Region - immunology</topic><topic>Nucleotide sequence</topic><topic>Nucleotides</topic><topic>Observed Antibody Space (OAS)</topic><topic>Receptors</topic><topic>SARS-CoV-2 - immunology</topic><topic>Severe acute respiratory syndrome</topic><topic>Severe acute respiratory syndrome coronavirus 2</topic><topic>Tools for Protein Science</topic><topic>Viral diseases</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Olsen, Tobias H.</creatorcontrib><creatorcontrib>Boyles, Fergus</creatorcontrib><creatorcontrib>Deane, Charlotte M.</creatorcontrib><collection>Wiley Online Library Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Biotechnology Research Abstracts</collection><collection>Immunology Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Virology and AIDS Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>AIDS and Cancer Research Abstracts</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Protein science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Olsen, Tobias H.</au><au>Boyles, Fergus</au><au>Deane, Charlotte M.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences</atitle><jtitle>Protein science</jtitle><addtitle>Protein Sci</addtitle><date>2022-01</date><risdate>2022</risdate><volume>31</volume><issue>1</issue><spage>141</spage><epage>146</epage><pages>141-146</pages><issn>0961-8368</issn><eissn>1469-896X</eissn><abstract>The antibody repertoires of individuals and groups have been used to explore disease states, understand vaccine responses, and drive therapeutic development. The arrival of B‐cell receptor repertoire sequencing has enabled researchers to get a snapshot of these antibody repertoires, and as more data are generated, increasingly in‐depth studies are possible. However, most publicly available data only exist as raw FASTQ files, making the data hard to access, process, and compare. The Observed Antibody Space (OAS) database was created in 2018 to offer clean, annotated, and translated repertoire data. In this paper, we describe an update to OAS that has been driven by the increasing volume of data and the appearance of paired (VH/VL) sequence data. OAS is now accessible via a new web server, with standardized search parameters and a new sequence‐based search option. The new database provides both nucleotides and amino acids for every sequence, with additional sequence annotations to make the data Minimal Information about Adaptive Immune Receptor Repertoire compliant, and comments on potential problems with the sequence. 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| source | Wiley Free Content; MEDLINE; Wiley Online Library Journals Frontfile Complete; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Accessibility Amino Acid Sequence Amino acids Animals annotated antibody sequences Annotations Antibodies Antibodies - chemistry Antibodies - immunology antibody database antibody repertoire antibody sequence BCR‐seq Coronaviruses COVID-19 - immunology Databases, Protein Downloading Humans Immunoglobulin Heavy Chains - chemistry Immunoglobulin Heavy Chains - immunology Immunoglobulin Light Chains - chemistry Immunoglobulin Light Chains - immunology Immunoglobulin Variable Region - chemistry Immunoglobulin Variable Region - immunology Nucleotide sequence Nucleotides Observed Antibody Space (OAS) Receptors SARS-CoV-2 - immunology Severe acute respiratory syndrome Severe acute respiratory syndrome coronavirus 2 Tools for Protein Science Viral diseases |
| title | Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences |
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