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LitCovid-PubTator

LitCovid-PMC-OGER-BB

LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T1","span":{"begin":441,"end":444},"obj":"Body_part"},{"id":"T2","span":{"begin":880,"end":884},"obj":"Body_part"},{"id":"T3","span":{"begin":1131,"end":1134},"obj":"Body_part"},{"id":"T4","span":{"begin":1193,"end":1197},"obj":"Body_part"}],"attributes":[{"id":"A1","pred":"fma_id","subj":"T1","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A2","pred":"fma_id","subj":"T2","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A3","pred":"fma_id","subj":"T3","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A4","pred":"fma_id","subj":"T4","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"Background: The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China.\nMethods: The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0.\nResults: We report in silico identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a de novo search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential.\nConclusions: Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T1","span":{"begin":758,"end":791},"obj":"Disease"},{"id":"T2","span":{"begin":813,"end":817},"obj":"Disease"}],"attributes":[{"id":"A1","pred":"mondo_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A2","pred":"mondo_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"Background: The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China.\nMethods: The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0.\nResults: We report in silico identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a de novo search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential.\nConclusions: Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T3","span":{"begin":64,"end":67},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T4","span":{"begin":74,"end":75},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T5","span":{"begin":138,"end":140},"obj":"http://purl.obolibrary.org/obo/CLO_0050510"},{"id":"T6","span":{"begin":160,"end":163},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T7","span":{"begin":320,"end":321},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T8","span":{"begin":360,"end":368},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T9","span":{"begin":401,"end":409},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T10","span":{"begin":569,"end":570},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T11","span":{"begin":605,"end":613},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T12","span":{"begin":736,"end":744},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T13","span":{"begin":878,"end":884},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T14","span":{"begin":915,"end":917},"obj":"http://purl.obolibrary.org/obo/CLO_0001382"},{"id":"T15","span":{"begin":923,"end":931},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T16","span":{"begin":939,"end":940},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T17","span":{"begin":984,"end":992},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T18","span":{"begin":1063,"end":1064},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T19","span":{"begin":1099,"end":1107},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T20","span":{"begin":1191,"end":1197},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T21","span":{"begin":1269,"end":1270},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T22","span":{"begin":1350,"end":1358},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T23","span":{"begin":1364,"end":1365},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T24","span":{"begin":1514,"end":1515},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"text":"Background: The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China.\nMethods: The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0.\nResults: We report in silico identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a de novo search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential.\nConclusions: Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline."}

LitCovid-PD-CHEBI

{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T1","span":{"begin":360,"end":368},"obj":"Chemical"},{"id":"T2","span":{"begin":401,"end":409},"obj":"Chemical"},{"id":"T3","span":{"begin":605,"end":613},"obj":"Chemical"},{"id":"T4","span":{"begin":736,"end":744},"obj":"Chemical"},{"id":"T5","span":{"begin":923,"end":931},"obj":"Chemical"},{"id":"T6","span":{"begin":984,"end":992},"obj":"Chemical"},{"id":"T7","span":{"begin":1099,"end":1107},"obj":"Chemical"},{"id":"T8","span":{"begin":1350,"end":1358},"obj":"Chemical"}],"attributes":[{"id":"A1","pred":"chebi_id","subj":"T1","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A2","pred":"chebi_id","subj":"T2","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A3","pred":"chebi_id","subj":"T3","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A4","pred":"chebi_id","subj":"T4","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A5","pred":"chebi_id","subj":"T5","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A6","pred":"chebi_id","subj":"T6","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A7","pred":"chebi_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"},{"id":"A8","pred":"chebi_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/CHEBI_16670"}],"text":"Background: The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China.\nMethods: The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0.\nResults: We report in silico identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a de novo search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential.\nConclusions: Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T5","span":{"begin":0,"end":11},"obj":"Sentence"},{"id":"T6","span":{"begin":12,"end":105},"obj":"Sentence"},{"id":"T7","span":{"begin":106,"end":259},"obj":"Sentence"},{"id":"T8","span":{"begin":260,"end":268},"obj":"Sentence"},{"id":"T9","span":{"begin":269,"end":369},"obj":"Sentence"},{"id":"T10","span":{"begin":370,"end":521},"obj":"Sentence"},{"id":"T11","span":{"begin":522,"end":530},"obj":"Sentence"},{"id":"T12","span":{"begin":531,"end":711},"obj":"Sentence"},{"id":"T13","span":{"begin":712,"end":892},"obj":"Sentence"},{"id":"T14","span":{"begin":893,"end":1041},"obj":"Sentence"},{"id":"T15","span":{"begin":1042,"end":1396},"obj":"Sentence"},{"id":"T16","span":{"begin":1397,"end":1409},"obj":"Sentence"},{"id":"T17","span":{"begin":1410,"end":1613},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Background: The newly identified coronavirus known as 2019-nCoV has posed a serious global health threat. According to the latest report (18-February-2020), it has infected more than 72,000 people globally and led to deaths of more than 1,016 people in China.\nMethods: The 2019 novel coronavirus proteome was aligned to a curated database of viral immunogenic peptides. The immunogenicity of detected peptides and their binding potential to HLA alleles was predicted by immunogenicity predictive models and NetMHCpan 4.0.\nResults: We report in silico identification of a comprehensive list of immunogenic peptides that can be used as potential targets for 2019 novel coronavirus (2019-nCoV) vaccine development. First, we found 28 nCoV peptides identical to Severe acute respiratory syndrome-related coronavirus (SARS CoV) that have previously been characterized immunogenic by T cell assays. Second, we identified 48 nCoV peptides having a high degree of similarity with immunogenic peptides deposited in The Immune Epitope Database (IEDB). Lastly, we conducted a de novo search of 2019-nCoV 9-mer peptides that i) bind to common HLA alleles in Chinese and European population and ii) have T Cell Receptor (TCR) recognition potential by positional weight matrices and a recently developed immunogenicity algorithm, iPred, and identified in total 63 peptides with a high immunogenicity potential.\nConclusions: Given the limited time and resources to develop vaccine and treatments for 2019-nCoV, our work provides a shortlist of candidates for experimental validation and thus can accelerate development pipeline."}