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LitCovid-PD-FMA-UBERON

{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T10","span":{"begin":76,"end":80},"obj":"Body_part"},{"id":"T11","span":{"begin":478,"end":489},"obj":"Body_part"},{"id":"T12","span":{"begin":523,"end":527},"obj":"Body_part"},{"id":"T13","span":{"begin":783,"end":791},"obj":"Body_part"},{"id":"T14","span":{"begin":1035,"end":1044},"obj":"Body_part"},{"id":"T15","span":{"begin":1054,"end":1057},"obj":"Body_part"},{"id":"T16","span":{"begin":1289,"end":1297},"obj":"Body_part"},{"id":"T17","span":{"begin":1441,"end":1445},"obj":"Body_part"},{"id":"T18","span":{"begin":1504,"end":1508},"obj":"Body_part"},{"id":"T19","span":{"begin":1557,"end":1565},"obj":"Body_part"},{"id":"T20","span":{"begin":1672,"end":1676},"obj":"Body_part"}],"attributes":[{"id":"A10","pred":"fma_id","subj":"T10","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A11","pred":"fma_id","subj":"T11","obj":"http://purl.org/sig/ont/fma/fma82739"},{"id":"A12","pred":"fma_id","subj":"T12","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A13","pred":"fma_id","subj":"T13","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A14","pred":"fma_id","subj":"T14","obj":"http://purl.org/sig/ont/fma/fma62852"},{"id":"A15","pred":"fma_id","subj":"T15","obj":"http://purl.org/sig/ont/fma/fma84795"},{"id":"A16","pred":"fma_id","subj":"T16","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A17","pred":"fma_id","subj":"T17","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A18","pred":"fma_id","subj":"T18","obj":"http://purl.org/sig/ont/fma/fma68646"},{"id":"A19","pred":"fma_id","subj":"T19","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A20","pred":"fma_id","subj":"T20","obj":"http://purl.org/sig/ont/fma/fma68646"}],"text":"Ex-vivo immune analyses of samples from infected individuals can identify T cell responses to specific pathogens like viruses. Such analyses can help to better understand the role of host immunity in virus control and to guide successful vaccine development. However, they rely on the use of the correct recall antigens that can elicit specific responses in vitro. The urgency of the current SARS-CoV-2 pandemic has led researchers to tackle the problem of screening the 10,000 amino acids of the SARS-CoV-2 proteome for T cell responses by selecting viral sequences based on different criteria: (i) bioinformatically predicted epitopes, (ii) homology of SARS-CoV-2 sequences with epitopes defined in other coronaviruses (mainly SARS-CoV) or (iii) selecting some specific SARS-CoV-2 proteins over others [5,7,9,11,14,15,16,17,18,19]. However, all these approaches have intrinsic limitations. Bioinformatic prediction tools are trained on sets of previously described epitopes, but since the available epitope repertoire for many human leukocyte antigen (HLA) alleles is limited, its prediction capacity is also limited [20,21]. Inferences based on epitope sequence homology with other coronaviruses are hampered because past studies on SARS-CoV-1 and MERS only included few selected viral proteins. This is of concern, since screening only a part of the SARS-CoV-2 proteome will potentially miss an important portion of the virus-specific T cell response. Indeed, recent data indicate the existence of T cell responses against structural and non-structural proteins [5,9] for SARS-CoV-2 and other viral infections [22]. Finally, no study has considered the existence of T cell responses to epitopes encoded by open-reading frames (ORF) in alternative frames, as reported for other viral infections [23,24,25,26]."}

LitCovid-PD-MONDO

{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T20","span":{"begin":392,"end":400},"obj":"Disease"},{"id":"T21","span":{"begin":497,"end":505},"obj":"Disease"},{"id":"T22","span":{"begin":655,"end":663},"obj":"Disease"},{"id":"T23","span":{"begin":729,"end":737},"obj":"Disease"},{"id":"T24","span":{"begin":772,"end":780},"obj":"Disease"},{"id":"T25","span":{"begin":1236,"end":1244},"obj":"Disease"},{"id":"T26","span":{"begin":1354,"end":1362},"obj":"Disease"},{"id":"T27","span":{"begin":1576,"end":1584},"obj":"Disease"},{"id":"T28","span":{"begin":1597,"end":1613},"obj":"Disease"},{"id":"T29","span":{"begin":1781,"end":1797},"obj":"Disease"}],"attributes":[{"id":"A20","pred":"mondo_id","subj":"T20","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A21","pred":"mondo_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A22","pred":"mondo_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A23","pred":"mondo_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A24","pred":"mondo_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A25","pred":"mondo_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A26","pred":"mondo_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A27","pred":"mondo_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/MONDO_0005091"},{"id":"A28","pred":"mondo_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/MONDO_0005108"},{"id":"A29","pred":"mondo_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/MONDO_0005108"}],"text":"Ex-vivo immune analyses of samples from infected individuals can identify T cell responses to specific pathogens like viruses. Such analyses can help to better understand the role of host immunity in virus control and to guide successful vaccine development. However, they rely on the use of the correct recall antigens that can elicit specific responses in vitro. The urgency of the current SARS-CoV-2 pandemic has led researchers to tackle the problem of screening the 10,000 amino acids of the SARS-CoV-2 proteome for T cell responses by selecting viral sequences based on different criteria: (i) bioinformatically predicted epitopes, (ii) homology of SARS-CoV-2 sequences with epitopes defined in other coronaviruses (mainly SARS-CoV) or (iii) selecting some specific SARS-CoV-2 proteins over others [5,7,9,11,14,15,16,17,18,19]. However, all these approaches have intrinsic limitations. Bioinformatic prediction tools are trained on sets of previously described epitopes, but since the available epitope repertoire for many human leukocyte antigen (HLA) alleles is limited, its prediction capacity is also limited [20,21]. Inferences based on epitope sequence homology with other coronaviruses are hampered because past studies on SARS-CoV-1 and MERS only included few selected viral proteins. This is of concern, since screening only a part of the SARS-CoV-2 proteome will potentially miss an important portion of the virus-specific T cell response. Indeed, recent data indicate the existence of T cell responses against structural and non-structural proteins [5,9] for SARS-CoV-2 and other viral infections [22]. Finally, no study has considered the existence of T cell responses to epitopes encoded by open-reading frames (ORF) in alternative frames, as reported for other viral infections [23,24,25,26]."}

LitCovid-PD-CLO

{"project":"LitCovid-PD-CLO","denotations":[{"id":"T20","span":{"begin":74,"end":80},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T21","span":{"begin":118,"end":125},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T22","span":{"begin":200,"end":205},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T23","span":{"begin":412,"end":415},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T24","span":{"begin":521,"end":527},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T25","span":{"begin":1029,"end":1034},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_9606"},{"id":"T26","span":{"begin":1340,"end":1341},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T27","span":{"begin":1424,"end":1429},"obj":"http://purl.obolibrary.org/obo/NCBITaxon_10239"},{"id":"T28","span":{"begin":1439,"end":1445},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T29","span":{"begin":1502,"end":1508},"obj":"http://purl.obolibrary.org/obo/CL_0000084"},{"id":"T30","span":{"begin":1615,"end":1617},"obj":"http://purl.obolibrary.org/obo/CLO_0050507"},{"id":"T31","span":{"begin":1638,"end":1641},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T32","span":{"begin":1670,"end":1676},"obj":"http://purl.obolibrary.org/obo/CL_0000084"}],"text":"Ex-vivo immune analyses of samples from infected individuals can identify T cell responses to specific pathogens like viruses. Such analyses can help to better understand the role of host immunity in virus control and to guide successful vaccine development. However, they rely on the use of the correct recall antigens that can elicit specific responses in vitro. The urgency of the current SARS-CoV-2 pandemic has led researchers to tackle the problem of screening the 10,000 amino acids of the SARS-CoV-2 proteome for T cell responses by selecting viral sequences based on different criteria: (i) bioinformatically predicted epitopes, (ii) homology of SARS-CoV-2 sequences with epitopes defined in other coronaviruses (mainly SARS-CoV) or (iii) selecting some specific SARS-CoV-2 proteins over others [5,7,9,11,14,15,16,17,18,19]. However, all these approaches have intrinsic limitations. Bioinformatic prediction tools are trained on sets of previously described epitopes, but since the available epitope repertoire for many human leukocyte antigen (HLA) alleles is limited, its prediction capacity is also limited [20,21]. Inferences based on epitope sequence homology with other coronaviruses are hampered because past studies on SARS-CoV-1 and MERS only included few selected viral proteins. This is of concern, since screening only a part of the SARS-CoV-2 proteome will potentially miss an important portion of the virus-specific T cell response. Indeed, recent data indicate the existence of T cell responses against structural and non-structural proteins [5,9] for SARS-CoV-2 and other viral infections [22]. Finally, no study has considered the existence of T cell responses to epitopes encoded by open-reading frames (ORF) in alternative frames, as reported for other viral infections [23,24,25,26]."}

LitCovid-PubTator

LitCovid-PD-GO-BP

{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T5","span":{"begin":1597,"end":1613},"obj":"http://purl.obolibrary.org/obo/GO_0016032"},{"id":"T6","span":{"begin":1781,"end":1797},"obj":"http://purl.obolibrary.org/obo/GO_0016032"}],"text":"Ex-vivo immune analyses of samples from infected individuals can identify T cell responses to specific pathogens like viruses. Such analyses can help to better understand the role of host immunity in virus control and to guide successful vaccine development. However, they rely on the use of the correct recall antigens that can elicit specific responses in vitro. The urgency of the current SARS-CoV-2 pandemic has led researchers to tackle the problem of screening the 10,000 amino acids of the SARS-CoV-2 proteome for T cell responses by selecting viral sequences based on different criteria: (i) bioinformatically predicted epitopes, (ii) homology of SARS-CoV-2 sequences with epitopes defined in other coronaviruses (mainly SARS-CoV) or (iii) selecting some specific SARS-CoV-2 proteins over others [5,7,9,11,14,15,16,17,18,19]. However, all these approaches have intrinsic limitations. Bioinformatic prediction tools are trained on sets of previously described epitopes, but since the available epitope repertoire for many human leukocyte antigen (HLA) alleles is limited, its prediction capacity is also limited [20,21]. Inferences based on epitope sequence homology with other coronaviruses are hampered because past studies on SARS-CoV-1 and MERS only included few selected viral proteins. This is of concern, since screening only a part of the SARS-CoV-2 proteome will potentially miss an important portion of the virus-specific T cell response. Indeed, recent data indicate the existence of T cell responses against structural and non-structural proteins [5,9] for SARS-CoV-2 and other viral infections [22]. Finally, no study has considered the existence of T cell responses to epitopes encoded by open-reading frames (ORF) in alternative frames, as reported for other viral infections [23,24,25,26]."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T18","span":{"begin":0,"end":126},"obj":"Sentence"},{"id":"T19","span":{"begin":127,"end":258},"obj":"Sentence"},{"id":"T20","span":{"begin":259,"end":364},"obj":"Sentence"},{"id":"T21","span":{"begin":365,"end":833},"obj":"Sentence"},{"id":"T22","span":{"begin":834,"end":891},"obj":"Sentence"},{"id":"T23","span":{"begin":892,"end":1127},"obj":"Sentence"},{"id":"T24","span":{"begin":1128,"end":1298},"obj":"Sentence"},{"id":"T25","span":{"begin":1299,"end":1455},"obj":"Sentence"},{"id":"T26","span":{"begin":1456,"end":1619},"obj":"Sentence"},{"id":"T27","span":{"begin":1620,"end":1812},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"Ex-vivo immune analyses of samples from infected individuals can identify T cell responses to specific pathogens like viruses. Such analyses can help to better understand the role of host immunity in virus control and to guide successful vaccine development. However, they rely on the use of the correct recall antigens that can elicit specific responses in vitro. The urgency of the current SARS-CoV-2 pandemic has led researchers to tackle the problem of screening the 10,000 amino acids of the SARS-CoV-2 proteome for T cell responses by selecting viral sequences based on different criteria: (i) bioinformatically predicted epitopes, (ii) homology of SARS-CoV-2 sequences with epitopes defined in other coronaviruses (mainly SARS-CoV) or (iii) selecting some specific SARS-CoV-2 proteins over others [5,7,9,11,14,15,16,17,18,19]. However, all these approaches have intrinsic limitations. Bioinformatic prediction tools are trained on sets of previously described epitopes, but since the available epitope repertoire for many human leukocyte antigen (HLA) alleles is limited, its prediction capacity is also limited [20,21]. Inferences based on epitope sequence homology with other coronaviruses are hampered because past studies on SARS-CoV-1 and MERS only included few selected viral proteins. This is of concern, since screening only a part of the SARS-CoV-2 proteome will potentially miss an important portion of the virus-specific T cell response. Indeed, recent data indicate the existence of T cell responses against structural and non-structural proteins [5,9] for SARS-CoV-2 and other viral infections [22]. Finally, no study has considered the existence of T cell responses to epitopes encoded by open-reading frames (ORF) in alternative frames, as reported for other viral infections [23,24,25,26]."}