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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T83","span":{"begin":15,"end":22},"obj":"Body_part"},{"id":"T84","span":{"begin":191,"end":198},"obj":"Body_part"},{"id":"T85","span":{"begin":373,"end":384},"obj":"Body_part"},{"id":"T86","span":{"begin":716,"end":720},"obj":"Body_part"},{"id":"T87","span":{"begin":795,"end":799},"obj":"Body_part"},{"id":"T88","span":{"begin":1405,"end":1409},"obj":"Body_part"}],"attributes":[{"id":"A83","pred":"fma_id","subj":"T83","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A84","pred":"fma_id","subj":"T84","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A85","pred":"fma_id","subj":"T85","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A86","pred":"fma_id","subj":"T86","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A87","pred":"fma_id","subj":"T87","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A88","pred":"fma_id","subj":"T88","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"3.5. Conserved Protein Sequences Matching Other Coronavirus Family Member and Identification of Pan-Coronavirus Sequences\nIn addition to variable positions, we also evaluated the presence of protein regions conserved among coronavirus species, as these may support the design of immunogen sequences for pan-coronavirus vaccines. A total of 26 regions, ranging from 8 to 23 amino acids, were identified as being conserved in at least one of the three different sequence alignments (Table 3). Fifteen fragments were identified in the pan-coronavirus alignment, 17 in the beta-coronavirus alignment and 12 in the human coronavirus alignment. Seven of them were detected in all three alignments. To identify potential T cell epitopes in these conserved regions, we searched the IEDB for described T-cell epitopes similar (\u003e90% sequence identity) to the conserved peptides present in the CoV-2 consensus sequence. Interestingly, the majority of the conserved regions contained several matches, most of which were described epitopes derived from SARS-CoV. In total, 125 similar epitopes were identified, from all but two of the conserved regions (Table 3). The similar epitopes were found to be derived from the following organisms; SARS-CoV: 71, Human coronavirus 229E: 1, Alphacoronavirus 1: 1, Unknown origin: 3, and Homo sapiens: 47. Interestingly, 24 out of 26 fragments contained the described SARS-CoV T cell epitopes, indicating that these regions are immunogenic in humans and reinforcing the idea that some degree of cross-reactivity among coronavirus can be expected [11,58]. Also, the majority, i.e., 40 of the 47 human epitopes, clustered around one single region conserved in the beta-coronavirus alignment (QGPPGTGKSH). Several conserved peptides have thus been identified, which could potentially contain epitopes cross-reactive among different Coronavirus species. These conserved peptides can thus provide valuable information to understand if the immune response to SARS-CoV-2 is affected by previous infection with other coronaviruses and for pan-coronavirus vaccine design (Figure S2)."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T45","span":{"begin":1040,"end":1048},"obj":"Disease"},{"id":"T46","span":{"begin":1227,"end":1235},"obj":"Disease"},{"id":"T47","span":{"begin":1394,"end":1402},"obj":"Disease"},{"id":"T48","span":{"begin":1979,"end":1987},"obj":"Disease"},{"id":"T49","span":{"begin":2014,"end":2023},"obj":"Disease"}],"attributes":[{"id":"A45","pred":"mondo_id","subj":"T45","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A46","pred":"mondo_id","subj":"T46","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A47","pred":"mondo_id","subj":"T47","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A48","pred":"mondo_id","subj":"T48","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A49","pred":"mondo_id","subj":"T49","obj":"http://purl.obolibrary.org/obo/MONDO_0005550"}],"text":"3.5. Conserved Protein Sequences Matching Other Coronavirus Family Member and Identification of Pan-Coronavirus Sequences\nIn addition to variable positions, we also evaluated the presence of protein regions conserved among coronavirus species, as these may support the design of immunogen sequences for pan-coronavirus vaccines. A total of 26 regions, ranging from 8 to 23 amino acids, were identified as being conserved in at least one of the three different sequence alignments (Table 3). Fifteen fragments were identified in the pan-coronavirus alignment, 17 in the beta-coronavirus alignment and 12 in the human coronavirus alignment. Seven of them were detected in all three alignments. To identify potential T cell epitopes in these conserved regions, we searched the IEDB for described T-cell epitopes similar (\u003e90% sequence identity) to the conserved peptides present in the CoV-2 consensus sequence. Interestingly, the majority of the conserved regions contained several matches, most of which were described epitopes derived from SARS-CoV. In total, 125 similar epitopes were identified, from all but two of the conserved regions (Table 3). The similar epitopes were found to be derived from the following organisms; SARS-CoV: 71, Human coronavirus 229E: 1, Alphacoronavirus 1: 1, Unknown origin: 3, and Homo sapiens: 47. Interestingly, 24 out of 26 fragments contained the described SARS-CoV T cell epitopes, indicating that these regions are immunogenic in humans and reinforcing the idea that some degree of cross-reactivity among coronavirus can be expected [11,58]. Also, the majority, i.e., 40 of the 47 human epitopes, clustered around one single region conserved in the beta-coronavirus alignment (QGPPGTGKSH). Several conserved peptides have thus been identified, which could potentially contain epitopes cross-reactive among different Coronavirus species. These conserved peptides can thus provide valuable information to understand if the immune response to SARS-CoV-2 is affected by previous infection with other coronaviruses and for pan-coronavirus vaccine design (Figure S2)."}

LitCovid-PD-CLO

LitCovid-PubTator

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T16","span":{"begin":1960,"end":1975},"obj":"http://purl.obolibrary.org/obo/GO_0006955"}],"text":"3.5. Conserved Protein Sequences Matching Other Coronavirus Family Member and Identification of Pan-Coronavirus Sequences\nIn addition to variable positions, we also evaluated the presence of protein regions conserved among coronavirus species, as these may support the design of immunogen sequences for pan-coronavirus vaccines. A total of 26 regions, ranging from 8 to 23 amino acids, were identified as being conserved in at least one of the three different sequence alignments (Table 3). Fifteen fragments were identified in the pan-coronavirus alignment, 17 in the beta-coronavirus alignment and 12 in the human coronavirus alignment. Seven of them were detected in all three alignments. To identify potential T cell epitopes in these conserved regions, we searched the IEDB for described T-cell epitopes similar (\u003e90% sequence identity) to the conserved peptides present in the CoV-2 consensus sequence. Interestingly, the majority of the conserved regions contained several matches, most of which were described epitopes derived from SARS-CoV. In total, 125 similar epitopes were identified, from all but two of the conserved regions (Table 3). The similar epitopes were found to be derived from the following organisms; SARS-CoV: 71, Human coronavirus 229E: 1, Alphacoronavirus 1: 1, Unknown origin: 3, and Homo sapiens: 47. Interestingly, 24 out of 26 fragments contained the described SARS-CoV T cell epitopes, indicating that these regions are immunogenic in humans and reinforcing the idea that some degree of cross-reactivity among coronavirus can be expected [11,58]. Also, the majority, i.e., 40 of the 47 human epitopes, clustered around one single region conserved in the beta-coronavirus alignment (QGPPGTGKSH). Several conserved peptides have thus been identified, which could potentially contain epitopes cross-reactive among different Coronavirus species. These conserved peptides can thus provide valuable information to understand if the immune response to SARS-CoV-2 is affected by previous infection with other coronaviruses and for pan-coronavirus vaccine design (Figure S2)."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T113","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T114","span":{"begin":5,"end":121},"obj":"Sentence"},{"id":"T115","span":{"begin":122,"end":328},"obj":"Sentence"},{"id":"T116","span":{"begin":329,"end":490},"obj":"Sentence"},{"id":"T117","span":{"begin":491,"end":638},"obj":"Sentence"},{"id":"T118","span":{"begin":639,"end":691},"obj":"Sentence"},{"id":"T119","span":{"begin":692,"end":908},"obj":"Sentence"},{"id":"T120","span":{"begin":909,"end":1049},"obj":"Sentence"},{"id":"T121","span":{"begin":1050,"end":1150},"obj":"Sentence"},{"id":"T122","span":{"begin":1151,"end":1236},"obj":"Sentence"},{"id":"T123","span":{"begin":1237,"end":1264},"obj":"Sentence"},{"id":"T124","span":{"begin":1265,"end":1287},"obj":"Sentence"},{"id":"T125","span":{"begin":1288,"end":1306},"obj":"Sentence"},{"id":"T126","span":{"begin":1307,"end":1327},"obj":"Sentence"},{"id":"T127","span":{"begin":1328,"end":1331},"obj":"Sentence"},{"id":"T128","span":{"begin":1332,"end":1580},"obj":"Sentence"},{"id":"T129","span":{"begin":1581,"end":1728},"obj":"Sentence"},{"id":"T130","span":{"begin":1729,"end":1875},"obj":"Sentence"},{"id":"T131","span":{"begin":1876,"end":2100},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"3.5. Conserved Protein Sequences Matching Other Coronavirus Family Member and Identification of Pan-Coronavirus Sequences\nIn addition to variable positions, we also evaluated the presence of protein regions conserved among coronavirus species, as these may support the design of immunogen sequences for pan-coronavirus vaccines. A total of 26 regions, ranging from 8 to 23 amino acids, were identified as being conserved in at least one of the three different sequence alignments (Table 3). Fifteen fragments were identified in the pan-coronavirus alignment, 17 in the beta-coronavirus alignment and 12 in the human coronavirus alignment. Seven of them were detected in all three alignments. To identify potential T cell epitopes in these conserved regions, we searched the IEDB for described T-cell epitopes similar (\u003e90% sequence identity) to the conserved peptides present in the CoV-2 consensus sequence. Interestingly, the majority of the conserved regions contained several matches, most of which were described epitopes derived from SARS-CoV. In total, 125 similar epitopes were identified, from all but two of the conserved regions (Table 3). The similar epitopes were found to be derived from the following organisms; SARS-CoV: 71, Human coronavirus 229E: 1, Alphacoronavirus 1: 1, Unknown origin: 3, and Homo sapiens: 47. Interestingly, 24 out of 26 fragments contained the described SARS-CoV T cell epitopes, indicating that these regions are immunogenic in humans and reinforcing the idea that some degree of cross-reactivity among coronavirus can be expected [11,58]. Also, the majority, i.e., 40 of the 47 human epitopes, clustered around one single region conserved in the beta-coronavirus alignment (QGPPGTGKSH). Several conserved peptides have thus been identified, which could potentially contain epitopes cross-reactive among different Coronavirus species. These conserved peptides can thus provide valuable information to understand if the immune response to SARS-CoV-2 is affected by previous infection with other coronaviruses and for pan-coronavirus vaccine design (Figure S2)."}