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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T61","span":{"begin":198,"end":202},"obj":"Body_part"},{"id":"T62","span":{"begin":357,"end":368},"obj":"Body_part"},{"id":"T63","span":{"begin":663,"end":674},"obj":"Body_part"},{"id":"T64","span":{"begin":1329,"end":1337},"obj":"Body_part"},{"id":"T65","span":{"begin":1356,"end":1361},"obj":"Body_part"},{"id":"T66","span":{"begin":1557,"end":1563},"obj":"Body_part"},{"id":"T67","span":{"begin":1679,"end":1690},"obj":"Body_part"},{"id":"T68","span":{"begin":1735,"end":1741},"obj":"Body_part"}],"attributes":[{"id":"A61","pred":"fma_id","subj":"T61","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A62","pred":"fma_id","subj":"T62","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A63","pred":"fma_id","subj":"T63","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A64","pred":"fma_id","subj":"T64","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A65","pred":"fma_id","subj":"T65","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A66","pred":"fma_id","subj":"T66","obj":"http://purl.org/sig/ont/fma/fma84116"},{"id":"A67","pred":"fma_id","subj":"T67","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A68","pred":"fma_id","subj":"T68","obj":"http://purl.org/sig/ont/fma/fma84116"}],"text":"In order to achieve a balance between the number of peptides needed to cover the whole SARS-CoV-2 proteome, the costs for peptide synthesis and the design of peptide sets that allow for detecting T cell responses with high sensitivity, three OLP sets were designed (Table 2). Shorter peptides (15 mers) with longer sequence overlap between adjacent OLP (11 amino acids) offer high resolution detection of responses, thus lowering the risk of missing longer epitopes located in the OLP overlap. The consequence, however, will be a higher number of peptides to synthesize and screen, in this case a set of 2821 OLP. When the overlap between OLP was reduced from 11 amino acids to 10, the sensitivity of OLP testing is maintained, but some longer epitopes located in the overlap of two OLP may be missed. With this caveat in mind, an OLP set of 15-mers overlapping by 10 residues helped reduce the number of peptides needed by 560 OLP (total number OLP required 2262). Similarly, longer peptides (18 mers) significantly reduce the number of OLP to be synthesized, but tend to reduce in vitro sensitivity [55]. This approach, with an 11 mer overlap, reduced the number of needed OLP to 1561. The final decision for a specific design may also be driven by the assay system used for screening, an a-priori focus on fewer or more viral proteins and the available cells and funding to test immunogenicity. The three full OLP sets with their entropies are included in Table S1. Of note, the 15–11 OLP sequences were subjected to a search for homologies in the human genome to predict molecular mimicry events related to the autoimmune process. A blastp search (\u003e8aa consecutive identical amino acids per OLP) of the whole set against the human genome yielded no hits."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T41","span":{"begin":87,"end":95},"obj":"Disease"}],"attributes":[{"id":"A41","pred":"mondo_id","subj":"T41","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"In order to achieve a balance between the number of peptides needed to cover the whole SARS-CoV-2 proteome, the costs for peptide synthesis and the design of peptide sets that allow for detecting T cell responses with high sensitivity, three OLP sets were designed (Table 2). Shorter peptides (15 mers) with longer sequence overlap between adjacent OLP (11 amino acids) offer high resolution detection of responses, thus lowering the risk of missing longer epitopes located in the OLP overlap. The consequence, however, will be a higher number of peptides to synthesize and screen, in this case a set of 2821 OLP. When the overlap between OLP was reduced from 11 amino acids to 10, the sensitivity of OLP testing is maintained, but some longer epitopes located in the overlap of two OLP may be missed. With this caveat in mind, an OLP set of 15-mers overlapping by 10 residues helped reduce the number of peptides needed by 560 OLP (total number OLP required 2262). Similarly, longer peptides (18 mers) significantly reduce the number of OLP to be synthesized, but tend to reduce in vitro sensitivity [55]. This approach, with an 11 mer overlap, reduced the number of needed OLP to 1561. The final decision for a specific design may also be driven by the assay system used for screening, an a-priori focus on fewer or more viral proteins and the available cells and funding to test immunogenicity. The three full OLP sets with their entropies are included in Table S1. Of note, the 15–11 OLP sequences were subjected to a search for homologies in the human genome to predict molecular mimicry events related to the autoimmune process. A blastp search (\u003e8aa consecutive identical amino acids per OLP) of the whole set against the human genome yielded no hits."}

LitCovid-PD-CLO

LitCovid-PubTator

{"project":"LitCovid-PubTator","denotations":[{"id":"159","span":{"begin":87,"end":97},"obj":"Species"},{"id":"160","span":{"begin":1551,"end":1556},"obj":"Species"},{"id":"161","span":{"begin":1729,"end":1734},"obj":"Species"}],"attributes":[{"id":"A159","pred":"tao:has_database_id","subj":"159","obj":"Tax:2697049"},{"id":"A160","pred":"tao:has_database_id","subj":"160","obj":"Tax:9606"},{"id":"A161","pred":"tao:has_database_id","subj":"161","obj":"Tax:9606"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}],"text":"In order to achieve a balance between the number of peptides needed to cover the whole SARS-CoV-2 proteome, the costs for peptide synthesis and the design of peptide sets that allow for detecting T cell responses with high sensitivity, three OLP sets were designed (Table 2). Shorter peptides (15 mers) with longer sequence overlap between adjacent OLP (11 amino acids) offer high resolution detection of responses, thus lowering the risk of missing longer epitopes located in the OLP overlap. The consequence, however, will be a higher number of peptides to synthesize and screen, in this case a set of 2821 OLP. When the overlap between OLP was reduced from 11 amino acids to 10, the sensitivity of OLP testing is maintained, but some longer epitopes located in the overlap of two OLP may be missed. With this caveat in mind, an OLP set of 15-mers overlapping by 10 residues helped reduce the number of peptides needed by 560 OLP (total number OLP required 2262). Similarly, longer peptides (18 mers) significantly reduce the number of OLP to be synthesized, but tend to reduce in vitro sensitivity [55]. This approach, with an 11 mer overlap, reduced the number of needed OLP to 1561. The final decision for a specific design may also be driven by the assay system used for screening, an a-priori focus on fewer or more viral proteins and the available cells and funding to test immunogenicity. The three full OLP sets with their entropies are included in Table S1. Of note, the 15–11 OLP sequences were subjected to a search for homologies in the human genome to predict molecular mimicry events related to the autoimmune process. A blastp search (\u003e8aa consecutive identical amino acids per OLP) of the whole set against the human genome yielded no hits."}

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T13","span":{"begin":122,"end":139},"obj":"http://purl.obolibrary.org/obo/GO_0043043"},{"id":"T14","span":{"begin":130,"end":139},"obj":"http://purl.obolibrary.org/obo/GO_0009058"}],"text":"In order to achieve a balance between the number of peptides needed to cover the whole SARS-CoV-2 proteome, the costs for peptide synthesis and the design of peptide sets that allow for detecting T cell responses with high sensitivity, three OLP sets were designed (Table 2). Shorter peptides (15 mers) with longer sequence overlap between adjacent OLP (11 amino acids) offer high resolution detection of responses, thus lowering the risk of missing longer epitopes located in the OLP overlap. The consequence, however, will be a higher number of peptides to synthesize and screen, in this case a set of 2821 OLP. When the overlap between OLP was reduced from 11 amino acids to 10, the sensitivity of OLP testing is maintained, but some longer epitopes located in the overlap of two OLP may be missed. With this caveat in mind, an OLP set of 15-mers overlapping by 10 residues helped reduce the number of peptides needed by 560 OLP (total number OLP required 2262). Similarly, longer peptides (18 mers) significantly reduce the number of OLP to be synthesized, but tend to reduce in vitro sensitivity [55]. This approach, with an 11 mer overlap, reduced the number of needed OLP to 1561. The final decision for a specific design may also be driven by the assay system used for screening, an a-priori focus on fewer or more viral proteins and the available cells and funding to test immunogenicity. The three full OLP sets with their entropies are included in Table S1. Of note, the 15–11 OLP sequences were subjected to a search for homologies in the human genome to predict molecular mimicry events related to the autoimmune process. A blastp search (\u003e8aa consecutive identical amino acids per OLP) of the whole set against the human genome yielded no hits."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T84","span":{"begin":0,"end":275},"obj":"Sentence"},{"id":"T85","span":{"begin":276,"end":493},"obj":"Sentence"},{"id":"T86","span":{"begin":494,"end":613},"obj":"Sentence"},{"id":"T87","span":{"begin":614,"end":801},"obj":"Sentence"},{"id":"T88","span":{"begin":802,"end":965},"obj":"Sentence"},{"id":"T89","span":{"begin":966,"end":1106},"obj":"Sentence"},{"id":"T90","span":{"begin":1107,"end":1187},"obj":"Sentence"},{"id":"T91","span":{"begin":1188,"end":1397},"obj":"Sentence"},{"id":"T92","span":{"begin":1398,"end":1468},"obj":"Sentence"},{"id":"T93","span":{"begin":1469,"end":1634},"obj":"Sentence"},{"id":"T94","span":{"begin":1635,"end":1758},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"In order to achieve a balance between the number of peptides needed to cover the whole SARS-CoV-2 proteome, the costs for peptide synthesis and the design of peptide sets that allow for detecting T cell responses with high sensitivity, three OLP sets were designed (Table 2). Shorter peptides (15 mers) with longer sequence overlap between adjacent OLP (11 amino acids) offer high resolution detection of responses, thus lowering the risk of missing longer epitopes located in the OLP overlap. The consequence, however, will be a higher number of peptides to synthesize and screen, in this case a set of 2821 OLP. When the overlap between OLP was reduced from 11 amino acids to 10, the sensitivity of OLP testing is maintained, but some longer epitopes located in the overlap of two OLP may be missed. With this caveat in mind, an OLP set of 15-mers overlapping by 10 residues helped reduce the number of peptides needed by 560 OLP (total number OLP required 2262). Similarly, longer peptides (18 mers) significantly reduce the number of OLP to be synthesized, but tend to reduce in vitro sensitivity [55]. This approach, with an 11 mer overlap, reduced the number of needed OLP to 1561. The final decision for a specific design may also be driven by the assay system used for screening, an a-priori focus on fewer or more viral proteins and the available cells and funding to test immunogenicity. The three full OLP sets with their entropies are included in Table S1. Of note, the 15–11 OLP sequences were subjected to a search for homologies in the human genome to predict molecular mimicry events related to the autoimmune process. A blastp search (\u003e8aa consecutive identical amino acids per OLP) of the whole set against the human genome yielded no hits."}