PMC:7642385 / 22711-23639 JSONTXT

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T176","span":{"begin":124,"end":132},"obj":"Body_part"},{"id":"T177","span":{"begin":159,"end":172},"obj":"Body_part"},{"id":"T178","span":{"begin":694,"end":698},"obj":"Body_part"},{"id":"T179","span":{"begin":868,"end":872},"obj":"Body_part"}],"attributes":[{"id":"A176","pred":"fma_id","subj":"T176","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A177","pred":"fma_id","subj":"T177","obj":"http://purl.org/sig/ont/fma/fma9825"},{"id":"A178","pred":"fma_id","subj":"T178","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A179","pred":"fma_id","subj":"T179","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"One limitation to the study is that we do not consider the frequency of pathogens nor the potential expression level of the proteins and accessibility for the immune system. Both arguably have an effect on the likelihood that an epitope can raise a robust immune response. However, both variables can only be assessed with great uncertainty. Additionally, our analysis hone in on pathogens with the largest number of k-mers matching SARS-CoV-2 epitopes, which may exclude relevant pathogens producing few but highly immunogenic SARS-CoV-2 similar epitopes. Another limitation to the study is the reliance on sequence similarity; although related epitopes are likely to interact with the same T cell receptor, this is not guaranteed51. This is also observed in the report by Mateus et al.24 where a peptide with 80% similarity to a SARS-CoV-2 epitope did not raise a T cell response, while a peptide with only 33% similarity did."}

{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T7","span":{"begin":159,"end":172},"obj":"Body_part"}],"attributes":[{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0002405"}],"text":"One limitation to the study is that we do not consider the frequency of pathogens nor the potential expression level of the proteins and accessibility for the immune system. Both arguably have an effect on the likelihood that an epitope can raise a robust immune response. However, both variables can only be assessed with great uncertainty. Additionally, our analysis hone in on pathogens with the largest number of k-mers matching SARS-CoV-2 epitopes, which may exclude relevant pathogens producing few but highly immunogenic SARS-CoV-2 similar epitopes. Another limitation to the study is the reliance on sequence similarity; although related epitopes are likely to interact with the same T cell receptor, this is not guaranteed51. This is also observed in the report by Mateus et al.24 where a peptide with 80% similarity to a SARS-CoV-2 epitope did not raise a T cell response, while a peptide with only 33% similarity did."}

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T95","span":{"begin":433,"end":441},"obj":"Disease"},{"id":"T96","span":{"begin":528,"end":536},"obj":"Disease"},{"id":"T97","span":{"begin":831,"end":839},"obj":"Disease"}],"attributes":[{"id":"A95","pred":"mondo_id","subj":"T95","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A96","pred":"mondo_id","subj":"T96","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A97","pred":"mondo_id","subj":"T97","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"}],"text":"One limitation to the study is that we do not consider the frequency of pathogens nor the potential expression level of the proteins and accessibility for the immune system. Both arguably have an effect on the likelihood that an epitope can raise a robust immune response. However, both variables can only be assessed with great uncertainty. Additionally, our analysis hone in on pathogens with the largest number of k-mers matching SARS-CoV-2 epitopes, which may exclude relevant pathogens producing few but highly immunogenic SARS-CoV-2 similar epitopes. Another limitation to the study is the reliance on sequence similarity; although related epitopes are likely to interact with the same T cell receptor, this is not guaranteed51. This is also observed in the report by Mateus et al.24 where a peptide with 80% similarity to a SARS-CoV-2 epitope did not raise a T cell response, while a peptide with only 33% similarity did."}

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T172","span":{"begin":159,"end":172},"obj":"http://purl.obolibrary.org/obo/UBERON_0002405"},{"id":"T173","span":{"begin":247,"end":248},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T174","span":{"begin":692,"end":698},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T175","span":{"begin":796,"end":797},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T176","span":{"begin":798,"end":805},"obj":"http://purl.obolibrary.org/obo/PR_000018263"},{"id":"T177","span":{"begin":829,"end":830},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T178","span":{"begin":864,"end":865},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T179","span":{"begin":866,"end":872},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T180","span":{"begin":889,"end":890},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T181","span":{"begin":891,"end":898},"obj":"http://purl.obolibrary.org/obo/PR_000018263"}],"text":"One limitation to the study is that we do not consider the frequency of pathogens nor the potential expression level of the proteins and accessibility for the immune system. Both arguably have an effect on the likelihood that an epitope can raise a robust immune response. However, both variables can only be assessed with great uncertainty. Additionally, our analysis hone in on pathogens with the largest number of k-mers matching SARS-CoV-2 epitopes, which may exclude relevant pathogens producing few but highly immunogenic SARS-CoV-2 similar epitopes. Another limitation to the study is the reliance on sequence similarity; although related epitopes are likely to interact with the same T cell receptor, this is not guaranteed51. This is also observed in the report by Mateus et al.24 where a peptide with 80% similarity to a SARS-CoV-2 epitope did not raise a T cell response, while a peptide with only 33% similarity did."}

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T15","span":{"begin":256,"end":271},"obj":"http://purl.obolibrary.org/obo/GO_0006955"}],"text":"One limitation to the study is that we do not consider the frequency of pathogens nor the potential expression level of the proteins and accessibility for the immune system. Both arguably have an effect on the likelihood that an epitope can raise a robust immune response. However, both variables can only be assessed with great uncertainty. Additionally, our analysis hone in on pathogens with the largest number of k-mers matching SARS-CoV-2 epitopes, which may exclude relevant pathogens producing few but highly immunogenic SARS-CoV-2 similar epitopes. Another limitation to the study is the reliance on sequence similarity; although related epitopes are likely to interact with the same T cell receptor, this is not guaranteed51. This is also observed in the report by Mateus et al.24 where a peptide with 80% similarity to a SARS-CoV-2 epitope did not raise a T cell response, while a peptide with only 33% similarity did."}

{"project":"LitCovid-sentences","denotations":[{"id":"T167","span":{"begin":0,"end":173},"obj":"Sentence"},{"id":"T168","span":{"begin":174,"end":272},"obj":"Sentence"},{"id":"T169","span":{"begin":273,"end":341},"obj":"Sentence"},{"id":"T170","span":{"begin":342,"end":556},"obj":"Sentence"},{"id":"T171","span":{"begin":557,"end":734},"obj":"Sentence"},{"id":"T172","span":{"begin":735,"end":928},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"One limitation to the study is that we do not consider the frequency of pathogens nor the potential expression level of the proteins and accessibility for the immune system. Both arguably have an effect on the likelihood that an epitope can raise a robust immune response. However, both variables can only be assessed with great uncertainty. Additionally, our analysis hone in on pathogens with the largest number of k-mers matching SARS-CoV-2 epitopes, which may exclude relevant pathogens producing few but highly immunogenic SARS-CoV-2 similar epitopes. Another limitation to the study is the reliance on sequence similarity; although related epitopes are likely to interact with the same T cell receptor, this is not guaranteed51. This is also observed in the report by Mateus et al.24 where a peptide with 80% similarity to a SARS-CoV-2 epitope did not raise a T cell response, while a peptide with only 33% similarity did."}

{"project":"LitCovid-PubTator","denotations":[{"id":"475","span":{"begin":433,"end":443},"obj":"Species"},{"id":"476","span":{"begin":528,"end":538},"obj":"Species"},{"id":"477","span":{"begin":831,"end":841},"obj":"Species"}],"attributes":[{"id":"A475","pred":"tao:has_database_id","subj":"475","obj":"Tax:2697049"},{"id":"A476","pred":"tao:has_database_id","subj":"476","obj":"Tax:2697049"},{"id":"A477","pred":"tao:has_database_id","subj":"477","obj":"Tax:2697049"}],"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":"One limitation to the study is that we do not consider the frequency of pathogens nor the potential expression level of the proteins and accessibility for the immune system. Both arguably have an effect on the likelihood that an epitope can raise a robust immune response. However, both variables can only be assessed with great uncertainty. Additionally, our analysis hone in on pathogens with the largest number of k-mers matching SARS-CoV-2 epitopes, which may exclude relevant pathogens producing few but highly immunogenic SARS-CoV-2 similar epitopes. Another limitation to the study is the reliance on sequence similarity; although related epitopes are likely to interact with the same T cell receptor, this is not guaranteed51. This is also observed in the report by Mateus et al.24 where a peptide with 80% similarity to a SARS-CoV-2 epitope did not raise a T cell response, while a peptide with only 33% similarity did."}