
PubMed:1718025
Annnotations
jnlpba-st-training
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T1 | 0-26 | protein | denotes | T-helper-cell determinants |
T2 | 30-46 | protein | denotes | protein antigens |
T3 | 77-107 | protein | denotes | cysteine-rich antigen segments |
T4 | 145-166 | protein | denotes | cathepsin B, L, and D |
T5 | 240-262 | protein | denotes | T-helper-cell epitopes |
T6 | 266-281 | protein | denotes | protein antigen |
T7 | 283-285 | protein | denotes | Ag |
T8 | 304-306 | protein | denotes | Ag |
T9 | 307-326 | protein | denotes | amino acid sequence |
T10 | 398-400 | protein | denotes | Ag |
T11 | 463-484 | protein | denotes | cathepsin B, L, and D |
T12 | 506-513 | protein | denotes | enzymes |
T13 | 553-571 | protein | denotes | soluble protein Ag |
T14 | 578-581 | protein | denotes | APC |
T15 | 587-605 | protein | denotes | resistant segments |
T16 | 609-611 | protein | denotes | Ag |
T17 | 656-675 | protein | denotes | T-cell determinants |
T18 | 681-701 | protein | denotes | susceptible segments |
T19 | 790-797 | protein | denotes | enzymes |
T20 | 857-886 | protein | denotes | S2, S1, S1', and S2' subsites |
T21 | 890-907 | protein | denotes | cathepsin B and L |
T22 | 924-926 | protein | denotes | S1 |
T23 | 931-934 | protein | denotes | S1' |
T24 | 947-958 | protein | denotes | cathepsin D |
T25 | 991-1030 | protein | denotes | cysteine-containing T-cell determinants |
T26 | 1046-1056 | protein | denotes | protein Ag |
T27 | 1185-1187 | protein | denotes | Ag |
T28 | 1324-1343 | protein | denotes | T-cell determinants |
T29 | 1351-1353 | protein | denotes | Ag |
T30 | 1470-1472 | protein | denotes | Ag |
T31 | 1487-1528 | protein | denotes | amphipatic alpha-helical protein segments |
T32 | 1579-1598 | protein | denotes | T-cell determinants |
pubmed-sentences-benchmark
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
S1 | 0-167 | Sentence | denotes | T-helper-cell determinants in protein antigens are preferentially located in cysteine-rich antigen segments resistant to proteolytic cleavage by cathepsin B, L, and D. |
S2 | 168-327 | Sentence | denotes | We report on a computer algorithm capable of predicting the location of T-helper-cell epitopes in protein antigen (Ag) by analysing the Ag amino acid sequence. |
S3 | 328-485 | Sentence | denotes | The algorithm was constructed with the aim of identifying segments in Ag which are resistant to proteolytic degradation by the enzymes cathepsin B, L, and D. |
S4 | 486-702 | Sentence | denotes | These are prominent enzymes in the endocytic pathway through which soluble protein Ag enter APC, and resistant segments in Ag may, therefore, be expected to contain more T-cell determinants than susceptible segments. |
S5 | 703-959 | Sentence | denotes | From information available in the literature on the substrate specificity of the three enzymes, it is clear that a cysteine is not accepted in any of the S2, S1, S1', and S2' subsites of cathepsin B and L, and not in the S1 and S1' subsites of cathepsin D. |
S6 | 960-1163 | Sentence | denotes | Moreover, we have noticed that cysteine-containing T-cell determinants in a number of protein Ag are particularly rich in the amino acids alanine, glycine, lysine, leucine, serine, threonine, and valine. |
S7 | 1164-1415 | Sentence | denotes | By searching protein Ag for clusters of amino acids containing cysteine and two of the other amino acids we were able to predict 17 out of 23 empirically known T-cell determinants in the Ag with a relatively low number of false (positive) predictions. |
S8 | 1416-1529 | Sentence | denotes | Furthermore, we present a new principle for searching Ag for potential amphipatic alpha-helical protein segments. |
S9 | 1530-1753 | Sentence | denotes | Such segments accord well with empirically known T-cell determinants and our algorithm produces a lower number of false positive predictions than the principle based on discrete Fourier transformations previously described. |
genia-medco-coref
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
C2 | 38-46 | NP | denotes | antigens |
C1 | 30-46 | NP | denotes | protein antigens |
C4 | 145-159 | NP | denotes | cathepsin B, L |
C5 | 165-166 | NP | denotes | D |
C3 | 145-166 | NP | denotes | cathepsin B, L, and D |
C6 | 181-201 | NP | denotes | a computer algorithm |
C8 | 274-286 | NP | denotes | antigen (Ag) |
C7 | 266-286 | NP | denotes | protein antigen (Ag) |
C9 | 328-341 | NP | denotes | The algorithm |
C10 | 398-400 | NP | denotes | Ag |
C11 | 401-406 | NP | denotes | which |
C13 | 463-477 | NP | denotes | cathepsin B, L |
C12 | 451-484 | NP | denotes | the enzymes cathepsin B, L, and D |
C14 | 486-491 | NP | denotes | These |
C15 | 496-513 | NP | denotes | prominent enzymes |
C17 | 569-571 | NP | denotes | Ag |
C16 | 553-571 | NP | denotes | soluble protein Ag |
C18 | 609-611 | NP | denotes | Ag |
C19 | 780-797 | NP | denotes | the three enzymes |
C20 | 816-826 | NP | denotes | a cysteine |
C21 | 865-886 | NP | denotes | S1', and S2' subsites |
C22 | 890-907 | NP | denotes | cathepsin B and L |
C23 | 920-943 | NP | denotes | the S1 and S1' subsites |
C24 | 947-958 | NP | denotes | cathepsin D |
C26 | 1054-1056 | NP | denotes | Ag |
C25 | 1046-1056 | NP | denotes | protein Ag |
C28 | 1086-1097 | NP | denotes | amino acids |
C27 | 1082-1162 | NP | denotes | the amino acids alanine, glycine, lysine, leucine, serine, threonine, and valine |
C30 | 1185-1187 | NP | denotes | Ag |
C29 | 1177-1187 | NP | denotes | protein Ag |
C31 | 1204-1215 | NP | denotes | amino acids |
C32 | 1227-1235 | NP | denotes | cysteine |
C34 | 1257-1268 | NP | denotes | amino acids |
C33 | 1240-1268 | NP | denotes | two of the other amino acids |
C35 | 1347-1353 | NP | denotes | the Ag |
C36 | 1386-1414 | NP | denotes | false (positive) predictions |
C37 | 1470-1472 | NP | denotes | Ag |
C38 | 1477-1528 | NP | denotes | potential amphipatic alpha-helical protein segments |
C39 | 1530-1543 | NP | denotes | Such segments |
C40 | 1603-1616 | NP | denotes | our algorithm |
C41 | 1644-1670 | NP | denotes | false positive predictions |
R1 | C8 | C2 | coref-ident | antigen (Ag),antigens |
R2 | C7 | C1 | coref-ident | protein antigen (Ag),protein antigens |
R3 | C9 | C6 | coref-ident | The algorithm,a computer algorithm |
R4 | C10 | C8 | coref-ident | Ag,antigen (Ag) |
R5 | C11 | C10 | coref-relat | which,Ag |
R6 | C13 | C4 | coref-ident | "cathepsin B, L","cathepsin B, L" |
R7 | C12 | C3 | coref-ident | "the enzymes cathepsin B, L, and D","cathepsin B, L, and D" |
R8 | C14 | C12 | coref-pron | These,"the enzymes cathepsin B, L, and D" |
R9 | C15 | C12 | coref-ident | prominent enzymes,"the enzymes cathepsin B, L, and D" |
R10 | C17 | C10 | coref-ident | Ag,Ag |
R11 | C16 | C7 | coref-ident | soluble protein Ag,protein antigen (Ag) |
R12 | C18 | C17 | coref-ident | Ag,Ag |
R13 | C19 | C12 | coref-ident | the three enzymes,"the enzymes cathepsin B, L, and D" |
R14 | C22 | C13 | coref-ident | cathepsin B and L,"cathepsin B, L" |
R15 | C23 | C21 | coref-ident | the S1 and S1' subsites,"S1', and S2' subsites" |
R16 | C24 | C5 | coref-ident | cathepsin D,D |
R17 | C26 | C18 | coref-ident | Ag,Ag |
R18 | C25 | C16 | coref-ident | protein Ag,soluble protein Ag |
R19 | C30 | C26 | coref-ident | Ag,Ag |
R20 | C29 | C25 | coref-ident | protein Ag,protein Ag |
R21 | C31 | C28 | coref-ident | amino acids,amino acids |
R22 | C32 | C20 | coref-ident | cysteine,a cysteine |
R23 | C34 | C31 | coref-ident | amino acids,amino acids |
R24 | C33 | C27 | coref-other | two of the other amino acids,"the amino acids alanine, glycine, lysine, leucine, serine, threonine, and valine" |
R25 | C35 | C30 | coref-ident | the Ag,Ag |
R26 | C37 | C35 | coref-ident | Ag,the Ag |
R27 | C39 | C38 | coref-ident | Such segments,potential amphipatic alpha-helical protein segments |
R28 | C40 | C9 | coref-ident | our algorithm,The algorithm |
R29 | C41 | C36 | coref-ident | false positive predictions,false (positive) predictions |
GENIAcorpus
Id | Subject | Object | Predicate | Lexical cue |
---|---|---|---|---|
T1 | 0-26 | protein_domain_or_region | denotes | T-helper-cell determinants |
T2 | 30-46 | protein_family_or_group | denotes | protein antigens |
T3 | 77-107 | protein_domain_or_region | denotes | cysteine-rich antigen segments |
T4 | 121-141 | other_name | denotes | proteolytic cleavage |
T5 | 183-201 | other_name | denotes | computer algorithm |
T6 | 240-262 | protein_domain_or_region | denotes | T-helper-cell epitopes |
T7 | 266-281 | protein_family_or_group | denotes | protein antigen |
T8 | 283-285 | protein_family_or_group | denotes | Ag |
T9 | 304-306 | protein_family_or_group | denotes | Ag |
T10 | 307-326 | protein_domain_or_region | denotes | amino acid sequence |
T11 | 398-400 | protein_family_or_group | denotes | Ag |
T12 | 424-447 | other_name | denotes | proteolytic degradation |
T13 | 506-513 | protein_family_or_group | denotes | enzymes |
T14 | 553-568 | protein_family_or_group | denotes | soluble protein |
T15 | 569-571 | protein_family_or_group | denotes | Ag |
T16 | 578-581 | protein_complex | denotes | APC |
T17 | 587-605 | protein_domain_or_region | denotes | resistant segments |
T18 | 609-611 | protein_family_or_group | denotes | Ag |
T19 | 656-675 | protein_domain_or_region | denotes | T-cell determinants |
T20 | 681-701 | protein_domain_or_region | denotes | susceptible segments |
T21 | 755-776 | other_name | denotes | substrate specificity |
T22 | 790-797 | protein_family_or_group | denotes | enzymes |
T23 | 818-826 | amino_acid_monomer | denotes | cysteine |
T24 | 924-926 | protein_domain_or_region | denotes | S1 |
T25 | 931-934 | protein_domain_or_region | denotes | S1' |
T26 | 947-958 | protein_domain_or_region | denotes | cathepsin D |
T27 | 991-999 | amino_acid_monomer | denotes | cysteine |
T28 | 1046-1053 | protein_family_or_group | denotes | protein |
T29 | 1054-1056 | protein_family_or_group | denotes | Ag |
T30 | 1086-1097 | amino_acid_monomer | denotes | amino acids |
T31 | 1098-1105 | amino_acid_monomer | denotes | alanine |
T32 | 1107-1114 | amino_acid_monomer | denotes | glycine |
T33 | 1116-1122 | amino_acid_monomer | denotes | lysine |
T34 | 1124-1131 | amino_acid_monomer | denotes | leucine |
T35 | 1133-1139 | amino_acid_monomer | denotes | serine |
T36 | 1141-1150 | amino_acid_monomer | denotes | threonine |
T37 | 1156-1162 | amino_acid_monomer | denotes | valine |
T38 | 1185-1187 | protein_family_or_group | denotes | Ag |
T39 | 1204-1215 | amino_acid_monomer | denotes | amino acids |
T40 | 1227-1235 | amino_acid_monomer | denotes | cysteine |
T41 | 1257-1268 | amino_acid_monomer | denotes | amino acids |
T42 | 1324-1343 | protein_domain_or_region | denotes | T-cell determinants |
T43 | 1351-1353 | protein_family_or_group | denotes | Ag |
T44 | 1470-1472 | protein_family_or_group | denotes | Ag |
T45 | 1487-1528 | protein_domain_or_region | denotes | amphipatic alpha-helical protein segments |
T46 | 1579-1598 | protein_domain_or_region | denotes | T-cell determinants |
T47 | 1607-1616 | other_name | denotes | algorithm |
T48 | 1650-1670 | other_name | denotes | positive predictions |
T49 | 1699-1731 | other_name | denotes | discrete Fourier transformations |