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0
BB-kb+ner-1016123
[ { "id": "BB-kb+ner-1016123__text", "type": "abstract", "text": [ "An evaluation of selective broths based on the bi-selenite ion and on hypertonic strontium chloride in Salmonellae detection in egg products. Of the 104 isolations of Salmonella sp. from egg pulp, 97 were obtained from strontium chloride M broth, 42 from strontium selenite broth and 57 from strontium selenite A broth. The results suggest that the first medium may be used more successfully than bi-selenite based media for enrichment and subsequent detection of salmonellae in egg products; however, the growth of S. pullorum was not satisfactory in strontium chloride M broth. " ], "offsets": [ [ 0, 581 ] ] } ]
[ { "id": "BB-kb+ner-1016123_T3", "type": "Habitat", "text": [ "selective broths based", "on hypertonic strontium chloride" ], "offsets": [ [ 17, 39 ], [ 67, 99 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-1016123_T4", "type": "Habitat", "text": [ "selective broths based on the bi-selenite ion" ], "offsets": [ [ 17, 62 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-1016123_T5", "type": "Microorganism", "text": [ "Salmonellae" ], "offsets": [ [ 103, 114 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "590" } ] }, { "id": "BB-kb+ner-1016123_T6", "type": "Habitat", "text": [ "egg products" ], "offsets": [ [ 128, 140 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001086" } ] }, { "id": "BB-kb+ner-1016123_T7", "type": "Habitat", "text": [ "egg" ], "offsets": [ [ 128, 131 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001847" } ] }, { "id": "BB-kb+ner-1016123_T8", "type": "Microorganism", "text": [ "Salmonella" ], "offsets": [ [ 167, 177 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "599" } ] }, { "id": "BB-kb+ner-1016123_T9", "type": "Habitat", "text": [ "egg" ], "offsets": [ [ 187, 190 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001847" } ] }, { "id": "BB-kb+ner-1016123_T10", "type": "Habitat", "text": [ "egg pulp" ], "offsets": [ [ 187, 195 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001086" } ] }, { "id": "BB-kb+ner-1016123_T11", "type": "Habitat", "text": [ "strontium chloride M broth" ], "offsets": [ [ 219, 245 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-1016123_T12", "type": "Habitat", "text": [ "strontium selenite broth" ], "offsets": [ [ 255, 279 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-1016123_T13", "type": "Habitat", "text": [ "strontium selenite A broth" ], "offsets": [ [ 292, 318 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-1016123_T14", "type": "Habitat", "text": [ "bi-selenite based media" ], "offsets": [ [ 397, 420 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-1016123_T15", "type": "Microorganism", "text": [ "salmonellae" ], "offsets": [ [ 464, 475 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "590" } ] }, { "id": "BB-kb+ner-1016123_T16", "type": "Habitat", "text": [ "egg products" ], "offsets": [ [ 479, 491 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001086" } ] }, { "id": "BB-kb+ner-1016123_T17", "type": "Habitat", "text": [ "egg" ], "offsets": [ [ 479, 482 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001847" } ] }, { "id": "BB-kb+ner-1016123_T18", "type": "Microorganism", "text": [ "S. pullorum" ], "offsets": [ [ 516, 527 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "605" } ] }, { "id": "BB-kb+ner-1016123_T19", "type": "Habitat", "text": [ "strontium chloride M broth" ], "offsets": [ [ 552, 578 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] } ]
[]
[]
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1
BB-kb+ner-10492485
[ { "id": "BB-kb+ner-10492485__text", "type": "abstract", "text": [ "Application of ozone for enhancing the microbiological safety and quality of foods: a review. Ozone (O3) is a strong antimicrobial agent with numerous potential applications in the food industry. High reactivity, penetrability, and spontaneous decomposition to a nontoxic product (i.e., O2) make ozone a viable disinfectant for ensuring the microbiological safety of food products. Ozone has been used for decades in many countries and recently, the generally recognized as safe (GRAS) status of this gas has been reaffirmed in the United States. Ozone, in the gaseous or aqueous phases, is effective against the majority of microorganisms tested by numerous research groups. Relatively low concentrations of ozone and short contact time are sufficient to inactivate bacteria, molds, yeasts, parasites, and viruses. However, rates of inactivation are greater in ozone demand-free systems than when the medium contains oxidizable organic substances. Susceptibility of microorganisms to ozone also varies with the physiological state of the culture, pH of the medium, temperature, humidity, and presence of additives (e.g., acids, surfactants, and sugars). Ozone applications in the food industry are mostly related to decontamination of product surface and water treatment. Ozone has been used with mixed success to inactivate contaminant microflora on meat, poultry, eggs, fish, fruits, vegetables, and dry foods. The gas also is useful in detoxification and elimination of mycotoxins and pesticide residues from some agricultural products. Excessive use of ozone, however, may cause oxidation of some ingredients on food surface. This usually results in discoloration and deterioration of food flavor. Additional research is needed to elucidate the kinetics and mechanisms of microbial inactivation by ozone and to optimize its use in food applications. " ], "offsets": [ [ 0, 1856 ] ] } ]
[ { "id": "BB-kb+ner-10492485_T3", "type": "Habitat", "text": [ "ozone" ], "offsets": [ [ 15, 20 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T4", "type": "Habitat", "text": [ "foods" ], "offsets": [ [ 77, 82 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000094" } ] }, { "id": "BB-kb+ner-10492485_T5", "type": "Habitat", "text": [ "Ozone" ], "offsets": [ [ 94, 99 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T6", "type": "Habitat", "text": [ "O3" ], "offsets": [ [ 101, 103 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T7", "type": "Habitat", "text": [ "food" ], "offsets": [ [ 181, 185 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000094" } ] }, { "id": "BB-kb+ner-10492485_T8", "type": "Habitat", "text": [ "food industry" ], "offsets": [ [ 181, 194 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001557" } ] }, { "id": "BB-kb+ner-10492485_T9", "type": "Habitat", "text": [ "ozone" ], "offsets": [ [ 296, 301 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T10", "type": "Habitat", "text": [ "food products" ], "offsets": [ [ 367, 380 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000094" } ] }, { "id": "BB-kb+ner-10492485_T11", "type": "Habitat", "text": [ "Ozone" ], "offsets": [ [ 382, 387 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T12", "type": "Habitat", "text": [ "Ozone" ], "offsets": [ [ 547, 552 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T13", "type": "Habitat", "text": [ "ozone" ], "offsets": [ [ 709, 714 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T14", "type": "Phenotype", "text": [ "parasites" ], "offsets": [ [ 792, 801 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000372" } ] }, { "id": "BB-kb+ner-10492485_T15", "type": "Habitat", "text": [ "ozone" ], "offsets": [ [ 862, 867 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T16", "type": "Habitat", "text": [ "ozone" ], "offsets": [ [ 985, 990 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T17", "type": "Habitat", "text": [ "additives" ], "offsets": [ [ 1105, 1114 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T18", "type": "Habitat", "text": [ "acids" ], "offsets": [ [ 1122, 1127 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T19", "type": "Habitat", "text": [ "surfactants" ], "offsets": [ [ 1129, 1140 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T20", "type": "Habitat", "text": [ "sugars" ], "offsets": [ [ 1146, 1152 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001340" } ] }, { "id": "BB-kb+ner-10492485_T21", "type": "Habitat", "text": [ "sugars" ], "offsets": [ [ 1146, 1152 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001340" } ] }, { "id": "BB-kb+ner-10492485_T22", "type": "Habitat", "text": [ "Ozone" ], "offsets": [ [ 1155, 1160 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T23", "type": "Habitat", "text": [ "food industry" ], "offsets": [ [ 1181, 1194 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001557" } ] }, { "id": "BB-kb+ner-10492485_T24", "type": "Habitat", "text": [ "food industry" ], "offsets": [ [ 1181, 1194 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001557" } ] }, { "id": "BB-kb+ner-10492485_T25", "type": "Habitat", "text": [ "food" ], "offsets": [ [ 1181, 1185 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000094" } ] }, { "id": "BB-kb+ner-10492485_T26", "type": "Habitat", "text": [ "product surface" ], "offsets": [ [ 1236, 1251 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000902" } ] }, { "id": "BB-kb+ner-10492485_T27", "type": "Habitat", "text": [ "water" ], "offsets": [ [ 1256, 1261 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000468" } ] }, { "id": "BB-kb+ner-10492485_T28", "type": "Habitat", "text": [ "Ozone" ], "offsets": [ [ 1273, 1278 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T29", "type": "Habitat", "text": [ "contaminant microflora" ], "offsets": [ [ 1326, 1348 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000113" } ] }, { "id": "BB-kb+ner-10492485_T30", "type": "Habitat", "text": [ "meat" ], "offsets": [ [ 1352, 1356 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001200" } ] }, { "id": "BB-kb+ner-10492485_T31", "type": "Habitat", "text": [ "poultry" ], "offsets": [ [ 1358, 1365 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002199" } ] }, { "id": "BB-kb+ner-10492485_T32", "type": "Habitat", "text": [ "eggs" ], "offsets": [ [ 1367, 1371 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001847" } ] }, { "id": "BB-kb+ner-10492485_T33", "type": "Habitat", "text": [ "fish" ], "offsets": [ [ 1373, 1377 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001549" } ] }, { "id": "BB-kb+ner-10492485_T34", "type": "Habitat", "text": [ "fruits" ], "offsets": [ [ 1379, 1385 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001122" } ] }, { "id": "BB-kb+ner-10492485_T35", "type": "Habitat", "text": [ "vegetables" ], "offsets": [ [ 1387, 1397 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001126" } ] }, { "id": "BB-kb+ner-10492485_T36", "type": "Habitat", "text": [ "dry foods" ], "offsets": [ [ 1403, 1412 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001526" } ] }, { "id": "BB-kb+ner-10492485_T37", "type": "Habitat", "text": [ "agricultural products" ], "offsets": [ [ 1518, 1539 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000034" } ] }, { "id": "BB-kb+ner-10492485_T38", "type": "Habitat", "text": [ "ozone" ], "offsets": [ [ 1558, 1563 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T39", "type": "Habitat", "text": [ "food surface" ], "offsets": [ [ 1617, 1629 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000902" } ] }, { "id": "BB-kb+ner-10492485_T40", "type": "Habitat", "text": [ "food" ], "offsets": [ [ 1690, 1694 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000094" } ] }, { "id": "BB-kb+ner-10492485_T41", "type": "Habitat", "text": [ "ozone" ], "offsets": [ [ 1803, 1808 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000477" } ] }, { "id": "BB-kb+ner-10492485_T42", "type": "Habitat", "text": [ "food" ], "offsets": [ [ 1836, 1840 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000094" } ] } ]
[]
[]
[]
2
BB-kb+ner-10658649
[ { "id": "BB-kb+ner-10658649__text", "type": "abstract", "text": [ "Identification of a novel glycoprotein-binding activity in Streptococcus pyogenes regulated by the mga gene. The interaction between Streptococcus pyogenes and the host cell surface is not completely understood. Characterization of the adhesion mechanisms of the bacterium to the host cell surface is needed in order to develop new vaccines and anti-adhesion drugs. The presence of glycoprotein-binding activities among streptococcal strains was investigated. An activity binding to thyroglobulin, fetuin, asialofetuin and mucin but not non-glycosylated proteins was found to be present in the majority of the S. pyogenes strains studied. Cross-inhibition experiments suggested that the glycoproteins share a common structure recognized by the bacteria. The glycoprotein-binding activity was found to be proteinaceous, tightly attached to the bacterial surface and it also mediated the adherence of bacteria to solid surfaces coated with glycoproteins. The activity was found by transposon mutagenesis and complementation to be regulated by the multiple-gene regulator Mga, which has been implicated as a regulator of S. pyogenes virulence factors. " ], "offsets": [ [ 0, 1150 ] ] } ]
[ { "id": "BB-kb+ner-10658649_T3", "type": "Phenotype", "text": [ "glycoprotein-binding activity" ], "offsets": [ [ 26, 55 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-10658649_T4", "type": "Microorganism", "text": [ "Streptococcus pyogenes" ], "offsets": [ [ 59, 81 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1314" } ] }, { "id": "BB-kb+ner-10658649_T5", "type": "Microorganism", "text": [ "Streptococcus pyogenes" ], "offsets": [ [ 133, 155 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1314" } ] }, { "id": "BB-kb+ner-10658649_T6", "type": "Habitat", "text": [ "host cell" ], "offsets": [ [ 164, 173 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-10658649_T7", "type": "Phenotype", "text": [ "adhesion mechanisms" ], "offsets": [ [ 236, 255 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-10658649_T8", "type": "Habitat", "text": [ "host cell" ], "offsets": [ [ 280, 289 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-10658649_T9", "type": "Habitat", "text": [ "vaccines" ], "offsets": [ [ 332, 340 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000464" } ] }, { "id": "BB-kb+ner-10658649_T10", "type": "Phenotype", "text": [ "glycoprotein-binding activities" ], "offsets": [ [ 382, 413 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-10658649_T11", "type": "Microorganism", "text": [ "streptococcal" ], "offsets": [ [ 420, 433 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1314" } ] }, { "id": "BB-kb+ner-10658649_T12", "type": "Phenotype", "text": [ "activity binding to", "fetuin" ], "offsets": [ [ 463, 482 ], [ 498, 504 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-10658649_T13", "type": "Phenotype", "text": [ "activity binding to", "asialofetuin" ], "offsets": [ [ 463, 482 ], [ 506, 518 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-10658649_T14", "type": "Phenotype", "text": [ "activity binding to thyroglobulin" ], "offsets": [ [ 463, 496 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-10658649_T15", "type": "Phenotype", "text": [ "activity binding to", "mucin" ], "offsets": [ [ 463, 482 ], [ 523, 528 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-10658649_T16", "type": "Microorganism", "text": [ "S. pyogenes" ], "offsets": [ [ 610, 621 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1314" } ] }, { "id": "BB-kb+ner-10658649_T17", "type": "Phenotype", "text": [ "glycoprotein-binding activity" ], "offsets": [ [ 758, 787 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-10658649_T18", "type": "Phenotype", "text": [ "adherence" ], "offsets": [ [ 886, 895 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-10658649_T19", "type": "Microorganism", "text": [ "S. pyogenes" ], "offsets": [ [ 1118, 1129 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1314" } ] }, { "id": "BB-kb+ner-10658649_T20", "type": "Phenotype", "text": [ "virulence" ], "offsets": [ [ 1130, 1139 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] } ]
[]
[]
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3
BB-kb+ner-10738994
[ { "id": "BB-kb+ner-10738994__text", "type": "abstract", "text": [ "Genotyping by restriction endonuclease analysis compared to phenotyping by antibiogram for typing methicillin-resistant Staphylococcus aureus strains colonizing patients in a nursing home. To assist in defining patterns of methicillin-resistant Staphylococcus aureus (MRSA) colonization in a skilled nursing facility (SNF), we compared genotyping by field-inversion gel electrophoresis (FIGE) restriction endonuclease digestion analysis (REA) with phenotyping by antibiogram for defining strain relatedness among MRSA isolates from SNF patients. Prospective screening culture surveillance for MRSA among patients in a community SNF. Nares and stool swab cultures were obtained from newly admitted patients and from all patients quarterly. MRSA were isolated by oxacillin screening agar. Antibiograms were determined by the disk-diffusion method, and genotyping was by FIGE REA. It was shown that, among isolates with the same genotypes, many had different antibiograms; among isolates with the same antibiograms, many had different genotypes; and the discriminatory indices for isolates of MRSA by FIGE REA and by antibiogram were 0.56 and 0.78, respectively. Our study demonstrated that, in patients from one SNF, genotyping by FIGE REA identified two prevalent REA DNA types, but with variability of antibiogram patterns within each DNA type; the antibiogram also identified prevalent patterns with variability of REA DNA type within each antibiogram pattern. The discriminatory index of antibiograms alone, or of genotypes alone as determined by FIGE REA, was poor for strains of MRSA isolated from the SNF patients in our study. " ], "offsets": [ [ 0, 1634 ] ] } ]
[ { "id": "BB-kb+ner-10738994_T7", "type": "Phenotype", "text": [ "methicillin-resistant" ], "offsets": [ [ 98, 119 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-10738994_T8", "type": "Microorganism", "text": [ "Staphylococcus aureus" ], "offsets": [ [ 120, 141 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-10738994_T9", "type": "Habitat", "text": [ "patients" ], "offsets": [ [ 161, 169 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003285" } ] }, { "id": "BB-kb+ner-10738994_T10", "type": "Habitat", "text": [ "nursing home" ], "offsets": [ [ 175, 187 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001231" } ] }, { "id": "BB-kb+ner-10738994_T11", "type": "Phenotype", "text": [ "methicillin-resistant" ], "offsets": [ [ 223, 244 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-10738994_T12", "type": "Microorganism", "text": [ "Staphylococcus aureus" ], "offsets": [ [ 245, 266 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-10738994_T13", "type": "Microorganism", "text": [ "MRSA" ], "offsets": [ [ 268, 272 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-10738994_T14", "type": "Phenotype", "text": [ "MRSA" ], "offsets": [ [ 268, 272 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-10738994_T15", "type": "Habitat", "text": [ "skilled nursing facility" ], "offsets": [ [ 292, 316 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001231" }, { "db_name": "OntoBiotope", "db_id": "OBT002518" } ] }, { "id": "BB-kb+ner-10738994_T16", "type": "Habitat", "text": [ "SNF" ], "offsets": [ [ 318, 321 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002518" }, { "db_name": "OntoBiotope", "db_id": "OBT001231" } ] }, { "id": "BB-kb+ner-10738994_T17", "type": "Microorganism", "text": [ "MRSA" ], "offsets": [ [ 513, 517 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-10738994_T18", "type": "Phenotype", "text": [ "MRSA" ], "offsets": [ [ 513, 517 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-10738994_T19", "type": "Habitat", "text": [ "SNF patients" ], "offsets": [ [ 532, 544 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-10738994_T20", "type": "Habitat", "text": [ "SNF" ], "offsets": [ [ 532, 535 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002518" }, { "db_name": "OntoBiotope", "db_id": "OBT001231" } ] }, { "id": "BB-kb+ner-10738994_T21", "type": "Microorganism", "text": [ "MRSA" ], "offsets": [ [ 593, 597 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-10738994_T22", "type": "Phenotype", "text": [ "MRSA" ], "offsets": [ [ 593, 597 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-10738994_T23", "type": "Habitat", "text": [ "patients" ], "offsets": [ [ 604, 612 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-10738994_T24", "type": "Habitat", "text": [ "community SNF" ], "offsets": [ [ 618, 631 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001231" }, { "db_name": "OntoBiotope", "db_id": "OBT002518" } ] }, { "id": "BB-kb+ner-10738994_T25", "type": "Habitat", "text": [ "Nares", "swab cultures" ], "offsets": [ [ 633, 638 ], [ 649, 662 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001228" }, { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-10738994_T26", "type": "Habitat", "text": [ "Nares" ], "offsets": [ [ 633, 638 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000754" } ] }, { "id": "BB-kb+ner-10738994_T27", "type": "Habitat", "text": [ "stool swab cultures" ], "offsets": [ [ 643, 662 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001737" }, { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-10738994_T28", "type": "Habitat", "text": [ "stool" ], "offsets": [ [ 643, 648 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001102" } ] }, { "id": "BB-kb+ner-10738994_T29", "type": "Habitat", "text": [ "patients" ], "offsets": [ [ 697, 705 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-10738994_T30", "type": "Habitat", "text": [ "patients" ], "offsets": [ [ 719, 727 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-10738994_T31", "type": "Microorganism", "text": [ "MRSA" ], "offsets": [ [ 739, 743 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-10738994_T32", "type": "Phenotype", "text": [ "MRSA" ], "offsets": [ [ 739, 743 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-10738994_T33", "type": "Habitat", "text": [ "oxacillin screening agar" ], "offsets": [ [ 761, 785 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000031" } ] }, { "id": "BB-kb+ner-10738994_T34", "type": "Microorganism", "text": [ "MRSA" ], "offsets": [ [ 1090, 1094 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-10738994_T35", "type": "Phenotype", "text": [ "MRSA" ], "offsets": [ [ 1090, 1094 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-10738994_T36", "type": "Habitat", "text": [ "patients from one SNF" ], "offsets": [ [ 1192, 1213 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-10738994_T37", "type": "Habitat", "text": [ "SNF" ], "offsets": [ [ 1210, 1213 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002518" }, { "db_name": "OntoBiotope", "db_id": "OBT001231" } ] }, { "id": "BB-kb+ner-10738994_T38", "type": "Microorganism", "text": [ "MRSA" ], "offsets": [ [ 1583, 1587 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-10738994_T39", "type": "Phenotype", "text": [ "MRSA" ], "offsets": [ [ 1583, 1587 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-10738994_T40", "type": "Habitat", "text": [ "SNF" ], "offsets": [ [ 1606, 1609 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001231" }, { "db_name": "OntoBiotope", "db_id": "OBT002518" } ] }, { "id": "BB-kb+ner-10738994_T41", "type": "Habitat", "text": [ "SNF patients" ], "offsets": [ [ 1606, 1618 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] } ]
[]
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4
BB-kb+ner-11162736
[ { "id": "BB-kb+ner-11162736__text", "type": "abstract", "text": [ "A new purification method for overproduced proteins sensitive to endogenous proteases. Proteolysisis a major problem in purification of overproduced proteins for structural studies. We developed a new method to avoid proteolysis of the products even in cases where popular protease inhibitors do not work effectively. When we cloned FlgF, a flagellar rod protein, from Salmonella typhimurium and overproduced it in Escherichia coli, FlgF was highly susceptible to cleavage by endogenous proteases after cell disruption even in the presence of various protease inhibitors. However, FlgF was not digested when the cells were disrupted in the presence of urea, which allowed us to develop the following new purification procedure. After cell disruption in the presence of urea and removal of the cell debris, the supernatant was passed through tandem-connected cation- and anion-exchange columns. Proteases were trapped in the cation-exchange column, and protease-free FlgF was eluted from the disconnected anion-exchange column. This gave a stable full-length product suitable for crystallization trials. The key procedures are cell disruption in the presence of urea and linked ion-exchange chromatography to quickly remove proteases as well as urea. This fast and simple method can be applied to purification of other overproduced proteins that are very sensitive to proteolysis. " ], "offsets": [ [ 0, 1381 ] ] } ]
[ { "id": "BB-kb+ner-11162736_T3", "type": "Microorganism", "text": [ "Salmonella typhimurium" ], "offsets": [ [ 369, 391 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "90371" } ] }, { "id": "BB-kb+ner-11162736_T4", "type": "Microorganism", "text": [ "Escherichia coli" ], "offsets": [ [ 415, 431 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-11162736_T5", "type": "Microorganism", "text": [ "Escherichia coli" ], "offsets": [ [ 415, 431 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-11162736_T6", "type": "Microorganism", "text": [ "Escherichia coli" ], "offsets": [ [ 415, 431 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] } ]
[]
[]
[]
5
BB-kb+ner-11410343
[ { "id": "BB-kb+ner-11410343__text", "type": "abstract", "text": [ "Effects of 2,2',5,5'-tetrachlorobiphenyl and biphenyl on cell membranes of Ralstonia eutropha H850. The effects of 2,2',5,5'-tetrachlorobiphenyl (TeCB), a PCB congener, and biphenyl on the cytoplasmic membranes of Ralstonia eutropha H850 were investigated by measuring fluorescence polarization using 1,6-diphenyl-1,3,5-hexatriene (DPH) as the probe, and determining the cellular fatty acid compositions. TeCB significantly affected the membrane of R. eutropha H850 cells grown on fructose by decreasing DPH fluorescence polarization. In contrast, the membrane of cells grown on biphenyl showed a considerably less significant effect of TeCB on membrane polarization than in fructose-grown cells. An increase in the ratio of total saturated to unsaturated fatty acids in cells grown on biphenyl suggested less of a fluidizing effect of TeCB on membranes in those cells. When biphenyl-grown cells were transferred back to a fructose medium, they required 25 generations for the membrane polarization and fatty acid compositions of these cells to revert back to those of the initial fructose-grown cells. The re-adaptation to a change in temperature required only five generations to return to normal. These results show that biphenyl affects cells in more ways than simply fluidizing the cytoplasmic membrane. " ], "offsets": [ [ 0, 1310 ] ] } ]
[ { "id": "BB-kb+ner-11410343_T3", "type": "Microorganism", "text": [ "Ralstonia eutropha H850" ], "offsets": [ [ 75, 98 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "53482" } ] }, { "id": "BB-kb+ner-11410343_T4", "type": "Microorganism", "text": [ "Ralstonia eutropha H850" ], "offsets": [ [ 214, 237 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "53482" } ] }, { "id": "BB-kb+ner-11410343_T5", "type": "Microorganism", "text": [ "R. eutropha H850" ], "offsets": [ [ 449, 465 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "53482" } ] }, { "id": "BB-kb+ner-11410343_T6", "type": "Habitat", "text": [ "fructose" ], "offsets": [ [ 481, 489 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-11410343_T7", "type": "Habitat", "text": [ "biphenyl" ], "offsets": [ [ 579, 587 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-11410343_T8", "type": "Habitat", "text": [ "fructose" ], "offsets": [ [ 675, 683 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-11410343_T9", "type": "Habitat", "text": [ "biphenyl" ], "offsets": [ [ 786, 794 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-11410343_T10", "type": "Habitat", "text": [ "biphenyl" ], "offsets": [ [ 875, 883 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-11410343_T11", "type": "Habitat", "text": [ "fructose medium" ], "offsets": [ [ 923, 938 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-11410343_T12", "type": "Habitat", "text": [ "fructose" ], "offsets": [ [ 1081, 1089 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] } ]
[]
[]
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6
BB-kb+ner-11437594
[ { "id": "BB-kb+ner-11437594__text", "type": "abstract", "text": [ "Optimization of the production of Chondrus crispus hexose oxidase in Pichia pastoris. Hexose oxidase (D-hexose:O(2)-oxidoreductase, EC 1.1.3.5, HOX) normally found in the red alga Chondrus crispus was produced heterologously in different host systems. Full-length HOX polypeptide was produced in Escherichia coli, but no HOX activity could be detected. In contrast, active HOX could be produced in the methylotrophic yeast Pichia pastoris. Several growth physiological and genetic approaches for optimization of hexose oxidase production in P. pastoris were investigated. Our results indicate that specific growth conditions are essential in order to produce active HOX with the correct conformation. Furthermore, HOX seems to be activated by proteolytic cleavage of the full-length polypeptide chain into two fragments, which remain physically associated. Attempts to direct HOX to the extracellular compartment using the widely used secretion signals from Saccharomyces cerevisiae invertase or alpha-mating factor failed. However, we show in this study that HOX is transported out of P. pastoris via a hitherto unknown mechanism and that it is possible to enhance this secretion by mutagenesis from below the detection limit to at least 250 mg extracellular enzyme per liter. " ], "offsets": [ [ 0, 1279 ] ] } ]
[ { "id": "BB-kb+ner-11437594_T3", "type": "Habitat", "text": [ "Chondrus crispus" ], "offsets": [ [ 34, 50 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002758" } ] }, { "id": "BB-kb+ner-11437594_T4", "type": "Microorganism", "text": [ "Pichia pastoris" ], "offsets": [ [ 69, 84 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "4922" } ] }, { "id": "BB-kb+ner-11437594_T5", "type": "Habitat", "text": [ "red alga Chondrus crispus" ], "offsets": [ [ 171, 196 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002758" } ] }, { "id": "BB-kb+ner-11437594_T6", "type": "Microorganism", "text": [ "Escherichia coli" ], "offsets": [ [ 296, 312 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-11437594_T7", "type": "Phenotype", "text": [ "HOX activity" ], "offsets": [ [ 321, 333 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000371" } ] }, { "id": "BB-kb+ner-11437594_T8", "type": "Phenotype", "text": [ "methylotrophic" ], "offsets": [ [ 402, 416 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000734" } ] }, { "id": "BB-kb+ner-11437594_T9", "type": "Microorganism", "text": [ "Pichia pastoris" ], "offsets": [ [ 423, 438 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "4922" } ] }, { "id": "BB-kb+ner-11437594_T10", "type": "Phenotype", "text": [ "hexose oxidase production" ], "offsets": [ [ 512, 537 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000371" } ] }, { "id": "BB-kb+ner-11437594_T11", "type": "Microorganism", "text": [ "P. pastoris" ], "offsets": [ [ 541, 552 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "4922" } ] }, { "id": "BB-kb+ner-11437594_T12", "type": "Microorganism", "text": [ "Saccharomyces cerevisiae" ], "offsets": [ [ 958, 982 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "4932" } ] }, { "id": "BB-kb+ner-11437594_T13", "type": "Phenotype", "text": [ "alpha-mating" ], "offsets": [ [ 996, 1008 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000173" } ] }, { "id": "BB-kb+ner-11437594_T14", "type": "Microorganism", "text": [ "P. pastoris" ], "offsets": [ [ 1086, 1097 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "4922" } ] } ]
[]
[]
[ { "id": "BB-kb+ner-11437594_R1", "type": "Exhibits", "arg1_id": "BB-kb+ner-11437594_T9", "arg2_id": "BB-kb+ner-11437594_T8", "normalized": [] } ]
7
BB-kb+ner-12728302
[ { "id": "BB-kb+ner-12728302__text", "type": "abstract", "text": [ "Heat-shock response and its contribution to thermotolerance of the nitrogen-fixing cyanobacterium Anabaena sp. strain L-31. Compared to Escherichia coli, the nitrogen-fixing soil cyanobacterium Anabaena sp. strain L-31 exhibited significantly superior abilities to survive prolonged and continuous heat stress and recover therefrom. Temperature upshift induced the synthesis of heat-shock proteins of similar molecular mass in the two microbes. However, in Anabaena sp. strain L-31 the heat-shock proteins (particularly the GroEL proteins) were synthesised throughout the stress period, were much more stable and accumulated during heat stress. In contrast, in E. coli the heat-shock proteins were transiently synthesised, quickly turned over and did not accumulate. Nitrogenase activity of Anabaena cells of sp. strain L-31 continuously exposed to heat stress for 7 days rapidly recovered from thermal injury, although growth recovery was delayed. Exposure of E. coli cells to >4.5 h of heat stress resulted in a complete loss of viability and the ability to recover. Marked differences in the synthesis, stability and accumulation of heat-shock proteins appear to distinguish these bacteria in their thermotolerance and recovery from heat stress. " ], "offsets": [ [ 0, 1250 ] ] } ]
[ { "id": "BB-kb+ner-12728302_T3", "type": "Phenotype", "text": [ "thermotolerance" ], "offsets": [ [ 44, 59 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002290" } ] }, { "id": "BB-kb+ner-12728302_T4", "type": "Phenotype", "text": [ "nitrogen-fixing" ], "offsets": [ [ 67, 82 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-12728302_T5", "type": "Microorganism", "text": [ "cyanobacterium" ], "offsets": [ [ 83, 97 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1117" } ] }, { "id": "BB-kb+ner-12728302_T6", "type": "Microorganism", "text": [ "Anabaena sp. strain L-31" ], "offsets": [ [ 98, 122 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "29412" } ] }, { "id": "BB-kb+ner-12728302_T7", "type": "Microorganism", "text": [ "Escherichia coli" ], "offsets": [ [ 136, 152 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-12728302_T8", "type": "Phenotype", "text": [ "nitrogen-fixing" ], "offsets": [ [ 158, 173 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-12728302_T9", "type": "Habitat", "text": [ "soil" ], "offsets": [ [ 174, 178 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000427" } ] }, { "id": "BB-kb+ner-12728302_T10", "type": "Microorganism", "text": [ "cyanobacterium" ], "offsets": [ [ 179, 193 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1117" } ] }, { "id": "BB-kb+ner-12728302_T11", "type": "Microorganism", "text": [ "Anabaena sp. strain L-31" ], "offsets": [ [ 194, 218 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "29412" } ] }, { "id": "BB-kb+ner-12728302_T12", "type": "Phenotype", "text": [ "abilities to survive prolonged and continuous heat stress" ], "offsets": [ [ 252, 309 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002480" } ] }, { "id": "BB-kb+ner-12728302_T13", "type": "Microorganism", "text": [ "Anabaena sp. strain L-31" ], "offsets": [ [ 457, 481 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "29412" } ] }, { "id": "BB-kb+ner-12728302_T14", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 661, 668 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-12728302_T15", "type": "Phenotype", "text": [ "Nitrogenase activity" ], "offsets": [ [ 767, 787 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-12728302_T16", "type": "Microorganism", "text": [ "Anabaena" ], "offsets": [ [ 791, 799 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "29412" } ] }, { "id": "BB-kb+ner-12728302_T17", "type": "Microorganism", "text": [ "L-31" ], "offsets": [ [ 820, 824 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "29412" } ] }, { "id": "BB-kb+ner-12728302_T18", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 961, 968 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-12728302_T19", "type": "Phenotype", "text": [ "thermotolerance" ], "offsets": [ [ 1202, 1217 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002290" } ] } ]
[]
[]
[ { "id": "BB-kb+ner-12728302_R1", "type": "Exhibits", "arg1_id": "BB-kb+ner-12728302_T6", "arg2_id": "BB-kb+ner-12728302_T4", "normalized": [] }, { "id": "BB-kb+ner-12728302_R2", "type": "Exhibits", "arg1_id": "BB-kb+ner-12728302_T6", "arg2_id": "BB-kb+ner-12728302_T3", "normalized": [] }, { "id": "BB-kb+ner-12728302_R3", "type": "Lives_In", "arg1_id": "BB-kb+ner-12728302_T11", "arg2_id": "BB-kb+ner-12728302_T9", "normalized": [] }, { "id": "BB-kb+ner-12728302_R4", "type": "Exhibits", "arg1_id": "BB-kb+ner-12728302_T11", "arg2_id": "BB-kb+ner-12728302_T12", "normalized": [] }, { "id": "BB-kb+ner-12728302_R5", "type": "Exhibits", "arg1_id": "BB-kb+ner-12728302_T11", "arg2_id": "BB-kb+ner-12728302_T8", "normalized": [] }, { "id": "BB-kb+ner-12728302_R6", "type": "Exhibits", "arg1_id": "BB-kb+ner-12728302_T17", "arg2_id": "BB-kb+ner-12728302_T15", "normalized": [] }, { "id": "BB-kb+ner-12728302_R7", "type": "Exhibits", "arg1_id": "BB-kb+ner-12728302_T17", "arg2_id": "BB-kb+ner-12728302_T19", "normalized": [] } ]
8
BB-kb+ner-12781527
[ { "id": "BB-kb+ner-12781527__text", "type": "abstract", "text": [ "Campylobacter--a tale of two protein glycosylation systems. Post-translational glycosylation is a universal modification of proteins in eukarya, archaea and bacteria. Two recent publications describe the first confirmed report of a bacterial N-linked glycosylation pathway in the human gastrointestinal pathogen Campylobacter jejuni. In addition, an O-linked glycosylation pathway has been identified and characterized in C. jejuni and the related species Campylobacter coli. Both pathways have similarity to the respective N- and O-linked glycosylation processes in eukaryotes. In bacteria, homologues of the genes in both pathways are found in other organisms, the complex glycans linked to the glycoproteins share common biosynthetic precursors and these modifications could play similar biological roles. Thus, Campylobacter provides a unique model system for the elucidation and exploitation of glycoprotein biosynthesis. " ], "offsets": [ [ 0, 928 ] ] } ]
[ { "id": "BB-kb+ner-12781527_T3", "type": "Microorganism", "text": [ "Campylobacter" ], "offsets": [ [ 0, 13 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "194" } ] }, { "id": "BB-kb+ner-12781527_T4", "type": "Phenotype", "text": [ "human gastrointestinal pathogen" ], "offsets": [ [ 280, 311 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002806" } ] }, { "id": "BB-kb+ner-12781527_T5", "type": "Habitat", "text": [ "human" ], "offsets": [ [ 280, 285 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002488" } ] }, { "id": "BB-kb+ner-12781527_T6", "type": "Habitat", "text": [ "human gastrointestinal" ], "offsets": [ [ 280, 302 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000641" } ] }, { "id": "BB-kb+ner-12781527_T7", "type": "Microorganism", "text": [ "Campylobacter jejuni" ], "offsets": [ [ 312, 332 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "197" } ] }, { "id": "BB-kb+ner-12781527_T8", "type": "Microorganism", "text": [ "C. jejuni" ], "offsets": [ [ 422, 431 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "197" } ] }, { "id": "BB-kb+ner-12781527_T9", "type": "Microorganism", "text": [ "Campylobacter coli" ], "offsets": [ [ 456, 474 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "195" } ] }, { "id": "BB-kb+ner-12781527_T10", "type": "Microorganism", "text": [ "Campylobacter" ], "offsets": [ [ 815, 828 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "194" } ] } ]
[]
[]
[ { "id": "BB-kb+ner-12781527_R1", "type": "Lives_In", "arg1_id": "BB-kb+ner-12781527_T7", "arg2_id": "BB-kb+ner-12781527_T5", "normalized": [] }, { "id": "BB-kb+ner-12781527_R2", "type": "Lives_In", "arg1_id": "BB-kb+ner-12781527_T7", "arg2_id": "BB-kb+ner-12781527_T6", "normalized": [] }, { "id": "BB-kb+ner-12781527_R3", "type": "Exhibits", "arg1_id": "BB-kb+ner-12781527_T7", "arg2_id": "BB-kb+ner-12781527_T4", "normalized": [] } ]
9
BB-kb+ner-12970344
[ { "id": "BB-kb+ner-12970344__text", "type": "abstract", "text": [ "The three-dimensional structures of two beta-agarases. Agars are important gelifying agents for biochemical use and the food industry. To cleave the beta-1,4-linkages between beta-d-galactose and alpha-l-3,6-anhydro-galactose residues in the red algal galactans known as agars, marine bacteria produce polysaccharide hydrolases called beta-agarases. Beta-agarases A and B from Zobellia galactanivorans Dsij have recently been biochemically characterized. Here we report the first crystal structure of these two beta-agarases. The two proteins were overproduced in Escherichia coli and crystallized, and the crystal structures were determined at 1.48 and 2.3 A for beta-agarases A and B, respectively. The structure of beta-agarase A was solved by the multiple anomalous diffraction method, whereas beta-agarase B was solved with molecular replacement using beta-agarase A as model. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic machinery, namely the nucleophilic residues Glu-147 and Glu-184 and the acid/base residues Glu-152 and Glu-189 for beta-agarases A and B, respectively. The structures of the agarases were compared with those of two lichenases and of a kappa-carrageenase, which all belong to family 16 of the glycoside hydrolases in order to pinpoint the residues responsible for their widely differing substrate specificity. The relationship between structure and enzymatic activity of the two beta-agarases from Z. galactanivorans Dsij was studied by analysis of the degradation products starting with different oligosaccharides. The combination of the structural and biochemical results allowed the determination of the number of subsites present in the catalytic cleft of the beta-agarases. " ], "offsets": [ [ 0, 1758 ] ] } ]
[ { "id": "BB-kb+ner-12970344_T3", "type": "Habitat", "text": [ "food" ], "offsets": [ [ 120, 124 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000094" } ] }, { "id": "BB-kb+ner-12970344_T4", "type": "Habitat", "text": [ "red algal" ], "offsets": [ [ 242, 251 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002758" } ] }, { "id": "BB-kb+ner-12970344_T5", "type": "Habitat", "text": [ "marine" ], "offsets": [ [ 278, 284 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000338" } ] }, { "id": "BB-kb+ner-12970344_T6", "type": "Microorganism", "text": [ "Zobellia galactanivorans Dsij" ], "offsets": [ [ 377, 406 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "63186" } ] }, { "id": "BB-kb+ner-12970344_T7", "type": "Microorganism", "text": [ "Escherichia coli" ], "offsets": [ [ 564, 580 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-12970344_T8", "type": "Microorganism", "text": [ "Z. galactanivorans Dsij" ], "offsets": [ [ 1476, 1499 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "63186" } ] } ]
[]
[]
[ { "id": "BB-kb+ner-12970344_R1", "type": "Lives_In", "arg1_id": "BB-kb+ner-12970344_T6", "arg2_id": "BB-kb+ner-12970344_T5", "normalized": [] } ]
10
BB-kb+ner-14645268
[ { "id": "BB-kb+ner-14645268__text", "type": "abstract", "text": [ "XopC and XopJ, two novel type III effector proteins from Xanthomonas campestris pv. vesicatoria. Pathogenicity of the gram-negative plant pathogen Xanthomonas campestris pv. vesicatoria depends on a type III secretion (TTS) system which translocates bacterial effector proteins into the plant cell. Previous transcriptome analysis identified a genome-wide regulon of putative virulence genes that are coexpressed with the TTS system. In this study, we characterized two of these genes, xopC and xopJ. Both genes encode Xanthomonas outer proteins (Xops) that were shown to be secreted by the TTS system. In addition, type III-dependent translocation of both proteins into the plant cell was demonstrated using the AvrBs3 effector domain as a reporter. XopJ belongs to the AvrRxv/YopJ family of effector proteins from plant and animal pathogenic bacteria. By contrast, XopC does not share significant homology to proteins in the database. Sequence analysis revealed that the xopC locus contains several features that are reminiscent of pathogenicity islands. Interestingly, the xopC region is flanked by 62-bp inverted repeats that are also associated with members of the Xanthomonas avrBs3 effector family. Besides xopC, a second gene of the locus, designated hpaJ, was shown to be coexpressed with the TTS system. hpaJ encodes a protein with similarity to transglycosylases and to the Pseudomonas syringae pv. maculicola protein HopPmaG. HpaJ secretion and translocation by the X. campestris pv. vesicatoria TTS system was not detectable, which is consistent with its predicted Sec signal and a putative function as transglycosylase in the bacterial periplasm. " ], "offsets": [ [ 0, 1662 ] ] } ]
[ { "id": "BB-kb+ner-14645268_T3", "type": "Microorganism", "text": [ "Xanthomonas campestris pv. vesicatoria" ], "offsets": [ [ 57, 95 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "456327" } ] }, { "id": "BB-kb+ner-14645268_T4", "type": "Phenotype", "text": [ "Pathogenicity" ], "offsets": [ [ 97, 110 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] }, { "id": "BB-kb+ner-14645268_T5", "type": "Phenotype", "text": [ "gram-negative" ], "offsets": [ [ 118, 131 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000648" } ] }, { "id": "BB-kb+ner-14645268_T6", "type": "Habitat", "text": [ "plant" ], "offsets": [ [ 132, 137 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000393" } ] }, { "id": "BB-kb+ner-14645268_T7", "type": "Phenotype", "text": [ "plant pathogen" ], "offsets": [ [ 132, 146 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002732" } ] }, { "id": "BB-kb+ner-14645268_T8", "type": "Microorganism", "text": [ "Xanthomonas campestris pv. vesicatoria" ], "offsets": [ [ 147, 185 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "456327" } ] }, { "id": "BB-kb+ner-14645268_T9", "type": "Phenotype", "text": [ "type III secretion" ], "offsets": [ [ 199, 217 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-14645268_T10", "type": "Habitat", "text": [ "plant cell" ], "offsets": [ [ 287, 297 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" }, { "db_name": "OntoBiotope", "db_id": "OBT000395" } ] }, { "id": "BB-kb+ner-14645268_T11", "type": "Habitat", "text": [ "plant" ], "offsets": [ [ 287, 292 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000393" } ] }, { "id": "BB-kb+ner-14645268_T12", "type": "Phenotype", "text": [ "virulence" ], "offsets": [ [ 376, 385 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] }, { "id": "BB-kb+ner-14645268_T13", "type": "Microorganism", "text": [ "Xanthomonas" ], "offsets": [ [ 519, 530 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "456327" } ] }, { "id": "BB-kb+ner-14645268_T14", "type": "Habitat", "text": [ "plant cell" ], "offsets": [ [ 675, 685 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000395" }, { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-14645268_T15", "type": "Habitat", "text": [ "plant" ], "offsets": [ [ 675, 680 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000393" } ] }, { "id": "BB-kb+ner-14645268_T16", "type": "Habitat", "text": [ "plant" ], "offsets": [ [ 816, 821 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000393" } ] }, { "id": "BB-kb+ner-14645268_T17", "type": "Phenotype", "text": [ "plant", "pathogenic" ], "offsets": [ [ 816, 821 ], [ 833, 843 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002732" } ] }, { "id": "BB-kb+ner-14645268_T18", "type": "Habitat", "text": [ "animal" ], "offsets": [ [ 826, 832 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000193" } ] }, { "id": "BB-kb+ner-14645268_T19", "type": "Phenotype", "text": [ "animal pathogenic" ], "offsets": [ [ 826, 843 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002669" } ] }, { "id": "BB-kb+ner-14645268_T20", "type": "Phenotype", "text": [ "pathogenicity" ], "offsets": [ [ 1034, 1047 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] }, { "id": "BB-kb+ner-14645268_T21", "type": "Microorganism", "text": [ "Xanthomonas" ], "offsets": [ [ 1170, 1181 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "338" } ] }, { "id": "BB-kb+ner-14645268_T22", "type": "Microorganism", "text": [ "Pseudomonas syringae pv. maculicola" ], "offsets": [ [ 1385, 1420 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "59511" } ] }, { "id": "BB-kb+ner-14645268_T23", "type": "Microorganism", "text": [ "X. campestris pv. vesicatoria" ], "offsets": [ [ 1478, 1507 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "456327" } ] }, { "id": "BB-kb+ner-14645268_T24", "type": "Phenotype", "text": [ "function as transglycosylase" ], "offsets": [ [ 1604, 1632 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] } ]
[]
[]
[ { "id": "BB-kb+ner-14645268_R4", "type": "Lives_In", "arg1_id": "BB-kb+ner-14645268_T8", "arg2_id": "BB-kb+ner-14645268_T11", "normalized": [] }, { "id": "BB-kb+ner-14645268_R5", "type": "Lives_In", "arg1_id": "BB-kb+ner-14645268_T8", "arg2_id": "BB-kb+ner-14645268_T6", "normalized": [] }, { "id": "BB-kb+ner-14645268_R1", "type": "Exhibits", "arg1_id": "BB-kb+ner-14645268_T8", "arg2_id": "BB-kb+ner-14645268_T5", "normalized": [] }, { "id": "BB-kb+ner-14645268_R2", "type": "Exhibits", "arg1_id": "BB-kb+ner-14645268_T8", "arg2_id": "BB-kb+ner-14645268_T7", "normalized": [] }, { "id": "BB-kb+ner-14645268_R3", "type": "Exhibits", "arg1_id": "BB-kb+ner-14645268_T8", "arg2_id": "BB-kb+ner-14645268_T4", "normalized": [] } ]
11
BB-kb+ner-15358511
[ { "id": "BB-kb+ner-15358511__text", "type": "abstract", "text": [ "Attachment of Escherichia coli O157:H7 grown in tryptic soy broth and nutrient broth to apple and lettuce surfaces as related to cell hydrophobicity, surface charge, and capsule production. This study investigated the effect of growth in tryptic soy broth (TSB) and nutrient broth (NB) on the ability Escherichia coli O157:H7 to attach to lettuce and apple surfaces. In addition, cell surface hydrophobicity, charge and capsule production were determined on cells grown in these media. Cells grown in NB attached less to lettuce and apple surfaces than did those grown in TSB. TSB, but not NB, supported capsule production by E. coli O157:H7. Cells grown in TSB were more hydrophilic than those grown in NB. No difference was found in the electrokinetic properties of cells grown in these media. Electrostatic and hydrophobic interactions and surface proteins did not appear to play an important role in the attachment of E. coli O157:H7 to these surfaces. Of the factors studied, only capsule production was associated with attachment ability. " ], "offsets": [ [ 0, 1046 ] ] } ]
[ { "id": "BB-kb+ner-15358511_T3", "type": "Phenotype", "text": [ "Attachment" ], "offsets": [ [ 0, 10 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-15358511_T4", "type": "Microorganism", "text": [ "Escherichia coli O157:H7" ], "offsets": [ [ 14, 38 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "83334" } ] }, { "id": "BB-kb+ner-15358511_T5", "type": "Habitat", "text": [ "tryptic soy broth" ], "offsets": [ [ 48, 65 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-15358511_T6", "type": "Habitat", "text": [ "soy" ], "offsets": [ [ 56, 59 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003304" } ] }, { "id": "BB-kb+ner-15358511_T7", "type": "Habitat", "text": [ "nutrient broth" ], "offsets": [ [ 70, 84 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-15358511_T8", "type": "Habitat", "text": [ "apple", "surfaces" ], "offsets": [ [ 88, 93 ], [ 106, 114 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000902" } ] }, { "id": "BB-kb+ner-15358511_T9", "type": "Habitat", "text": [ "apple" ], "offsets": [ [ 88, 93 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002341" } ] }, { "id": "BB-kb+ner-15358511_T10", "type": "Habitat", "text": [ "lettuce surfaces" ], "offsets": [ [ 98, 114 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000902" } ] }, { "id": "BB-kb+ner-15358511_T11", "type": "Habitat", "text": [ "lettuce" ], "offsets": [ [ 98, 105 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002506" } ] }, { "id": "BB-kb+ner-15358511_T12", "type": "Habitat", "text": [ "cell" ], "offsets": [ [ 129, 133 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-15358511_T13", "type": "Phenotype", "text": [ "capsule production" ], "offsets": [ [ 170, 188 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000614" } ] }, { "id": "BB-kb+ner-15358511_T14", "type": "Habitat", "text": [ "tryptic soy broth" ], "offsets": [ [ 238, 255 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-15358511_T15", "type": "Habitat", "text": [ "soy" ], "offsets": [ [ 246, 249 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003304" } ] }, { "id": "BB-kb+ner-15358511_T16", "type": "Habitat", "text": [ "TSB" ], "offsets": [ [ 257, 260 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-15358511_T17", "type": "Habitat", "text": [ "nutrient broth" ], "offsets": [ [ 266, 280 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-15358511_T18", "type": "Habitat", "text": [ "NB" ], "offsets": [ [ 282, 284 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-15358511_T19", "type": "Phenotype", "text": [ "ability", "to attach" ], "offsets": [ [ 293, 300 ], [ 326, 335 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-15358511_T20", "type": "Microorganism", "text": [ "Escherichia coli O157:H7" ], "offsets": [ [ 301, 325 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "83334" } ] }, { "id": "BB-kb+ner-15358511_T21", "type": "Habitat", "text": [ "lettuce" ], "offsets": [ [ 339, 346 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002506" } ] }, { "id": "BB-kb+ner-15358511_T22", "type": "Habitat", "text": [ "lettuce", "surfaces" ], "offsets": [ [ 339, 346 ], [ 357, 365 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000902" } ] }, { "id": "BB-kb+ner-15358511_T23", "type": "Habitat", "text": [ "apple" ], "offsets": [ [ 351, 356 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002341" } ] }, { "id": "BB-kb+ner-15358511_T24", "type": "Habitat", "text": [ "apple surfaces" ], "offsets": [ [ 351, 365 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000902" } ] }, { "id": "BB-kb+ner-15358511_T25", "type": "Habitat", "text": [ "cell" ], "offsets": [ [ 380, 384 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-15358511_T26", "type": "Phenotype", "text": [ "capsule production" ], "offsets": [ [ 420, 438 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000614" } ] }, { "id": "BB-kb+ner-15358511_T27", "type": "Habitat", "text": [ "NB" ], "offsets": [ [ 501, 503 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-15358511_T28", "type": "Habitat", "text": [ "lettuce" ], "offsets": [ [ 521, 528 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002506" } ] }, { "id": "BB-kb+ner-15358511_T29", "type": "Habitat", "text": [ "lettuce", "surfaces" ], "offsets": [ [ 521, 528 ], [ 539, 547 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000902" } ] }, { "id": "BB-kb+ner-15358511_T30", "type": "Habitat", "text": [ "apple" ], "offsets": [ [ 533, 538 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002341" } ] }, { "id": "BB-kb+ner-15358511_T31", "type": "Habitat", "text": [ "apple surfaces" ], "offsets": [ [ 533, 547 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000902" } ] }, { "id": "BB-kb+ner-15358511_T32", "type": "Habitat", "text": [ "TSB" ], "offsets": [ [ 572, 575 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-15358511_T33", "type": "Habitat", "text": [ "TSB" ], "offsets": [ [ 577, 580 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-15358511_T34", "type": "Habitat", "text": [ "NB" ], "offsets": [ [ 590, 592 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-15358511_T35", "type": "Phenotype", "text": [ "capsule production" ], "offsets": [ [ 604, 622 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000614" } ] }, { "id": "BB-kb+ner-15358511_T36", "type": "Microorganism", "text": [ "E. coli O157:H7" ], "offsets": [ [ 626, 641 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "83334" } ] }, { "id": "BB-kb+ner-15358511_T37", "type": "Habitat", "text": [ "TSB" ], "offsets": [ [ 658, 661 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-15358511_T38", "type": "Habitat", "text": [ "NB" ], "offsets": [ [ 704, 706 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000360" } ] }, { "id": "BB-kb+ner-15358511_T39", "type": "Phenotype", "text": [ "attachment" ], "offsets": [ [ 908, 918 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-15358511_T40", "type": "Microorganism", "text": [ "E. coli O157:H7" ], "offsets": [ [ 922, 937 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "83334" } ] }, { "id": "BB-kb+ner-15358511_T41", "type": "Phenotype", "text": [ "capsule production" ], "offsets": [ [ 986, 1004 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000614" } ] }, { "id": "BB-kb+ner-15358511_T42", "type": "Phenotype", "text": [ "attachment ability" ], "offsets": [ [ 1025, 1043 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] } ]
[]
[ { "id": "BB-kb+ner-15358511_1", "entity_ids": [ "BB-kb+ner-15358511_T18", "BB-kb+ner-15358511_T17" ] }, { "id": "BB-kb+ner-15358511_2", "entity_ids": [ "BB-kb+ner-15358511_T14", "BB-kb+ner-15358511_T16" ] } ]
[ { "id": "BB-kb+ner-15358511_R1", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T4", "arg2_id": "BB-kb+ner-15358511_T8", "normalized": [] }, { "id": "BB-kb+ner-15358511_R2", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T4", "arg2_id": "BB-kb+ner-15358511_T11", "normalized": [] }, { "id": "BB-kb+ner-15358511_R3", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T4", "arg2_id": "BB-kb+ner-15358511_T9", "normalized": [] }, { "id": "BB-kb+ner-15358511_R4", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T4", "arg2_id": "BB-kb+ner-15358511_T10", "normalized": [] }, { "id": "BB-kb+ner-15358511_R5", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T4", "arg2_id": "BB-kb+ner-15358511_T7", "normalized": [] }, { "id": "BB-kb+ner-15358511_R6", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T4", "arg2_id": "BB-kb+ner-15358511_T5", "normalized": [] }, { "id": "BB-kb+ner-15358511_R7", "type": "Exhibits", "arg1_id": "BB-kb+ner-15358511_T4", "arg2_id": "BB-kb+ner-15358511_T3", "normalized": [] }, { "id": "BB-kb+ner-15358511_R8", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T24", "normalized": [] }, { "id": "BB-kb+ner-15358511_R9", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T16", "normalized": [] }, { "id": "BB-kb+ner-15358511_R10", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T22", "normalized": [] }, { "id": "BB-kb+ner-15358511_R11", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T29", "normalized": [] }, { "id": "BB-kb+ner-15358511_R12", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T18", "normalized": [] }, { "id": "BB-kb+ner-15358511_R13", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T17", "normalized": [] }, { "id": "BB-kb+ner-15358511_R14", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T28", "normalized": [] }, { "id": "BB-kb+ner-15358511_R15", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T31", "normalized": [] }, { "id": "BB-kb+ner-15358511_R16", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T21", "normalized": [] }, { "id": "BB-kb+ner-15358511_R17", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T30", "normalized": [] }, { "id": "BB-kb+ner-15358511_R18", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T27", "normalized": [] }, { "id": "BB-kb+ner-15358511_R19", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T32", "normalized": [] }, { "id": "BB-kb+ner-15358511_R20", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T23", "normalized": [] }, { "id": "BB-kb+ner-15358511_R21", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T20", "arg2_id": "BB-kb+ner-15358511_T14", "normalized": [] }, { "id": "BB-kb+ner-15358511_R22", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T36", "arg2_id": "BB-kb+ner-15358511_T38", "normalized": [] }, { "id": "BB-kb+ner-15358511_R23", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T36", "arg2_id": "BB-kb+ner-15358511_T34", "normalized": [] }, { "id": "BB-kb+ner-15358511_R24", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T36", "arg2_id": "BB-kb+ner-15358511_T33", "normalized": [] }, { "id": "BB-kb+ner-15358511_R25", "type": "Lives_In", "arg1_id": "BB-kb+ner-15358511_T36", "arg2_id": "BB-kb+ner-15358511_T37", "normalized": [] }, { "id": "BB-kb+ner-15358511_R26", "type": "Exhibits", "arg1_id": "BB-kb+ner-15358511_T36", "arg2_id": "BB-kb+ner-15358511_T35", "normalized": [] }, { "id": "BB-kb+ner-15358511_R27", "type": "Exhibits", "arg1_id": "BB-kb+ner-15358511_T40", "arg2_id": "BB-kb+ner-15358511_T42", "normalized": [] }, { "id": "BB-kb+ner-15358511_R28", "type": "Exhibits", "arg1_id": "BB-kb+ner-15358511_T40", "arg2_id": "BB-kb+ner-15358511_T39", "normalized": [] }, { "id": "BB-kb+ner-15358511_R29", "type": "Exhibits", "arg1_id": "BB-kb+ner-15358511_T40", "arg2_id": "BB-kb+ner-15358511_T41", "normalized": [] } ]
12
BB-kb+ner-16263187
[ { "id": "BB-kb+ner-16263187__text", "type": "abstract", "text": [ "Ability of Lactobacillus gasseri K 7 to inhibit Escherichia coli adhesion in vitro on Caco-2 cells and ex vivo on pigs' jejunal tissue. The ability of Lactobacillus (Lb.) gasseri K 7 to inhibit adhesion of Escherichia coli O8:K88 to intestinal mucosa was studied on cultured Caco-2 cells and ex vivo on pigs' small intestinal tissue. Lactobacilli were added simultaneously with E. coli, before E. coli and after E. coli for competition, exclusion and displacement assays. The concentration of lactobacilli on fully differentiated Caco-2 cells was 4.5+/-0.3 x 10(8) cfu/well, while the concentration of E. coli varied from 1.5 x 10(6) to 4.3 x 10(8) cfu/well. The number of E. coli adhered to Caco-2 monolayer (cfu/well) was lineary correlated (R(2)=0.97) to the concentration of added cells. In the assay simulating exclusion, E. coli adhesion was reduced by Lb. gasseri K 7 strain by 0.1 to 0.6 log cfu/well. The binding of E. coli was inhibited even more when incubated simultaneously with lactobacilli, particularly at the lowest concentration of E. coli (ratio E. coli/lactobacilli 1:248), where five-times reduction (or 0.7 log) was observed. When adhesion to tissue derived from pigs' jejunum was tested, concentration of E. coli was constant (6.9+/-0.14 x 10(7) cfu/ml), while the concentration of Lb. gasseri K 7 was 5.9 x 10(7) and 1.3 x 10(7) cfu/ml in two independent experiments, respectively. The adhesion of E. coli and Lb. gasseri K 7 cells to jejunal mucosa was similar (1.0+/-0.17 x 10(6) and 1.54+/-0.10 x 10(6) cfu/cm(2)) when the concentrations of single strains in suspensions were approximately the same. No significant competition, exclusion or displacement of E. coli by lactobacilli was observed on jejunal tissue. In conclusion, Lb. gasseri K 7 was found to be effective in reducing E. coli adhesion to Caco-2 enterocytes, but it was not able to do so in ex vivo conditions tested for pig jejunal tissue. " ], "offsets": [ [ 0, 1932 ] ] } ]
[ { "id": "BB-kb+ner-16263187_T3", "type": "Microorganism", "text": [ "Lactobacillus gasseri K 7" ], "offsets": [ [ 11, 36 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1334627" } ] }, { "id": "BB-kb+ner-16263187_T4", "type": "Microorganism", "text": [ "Escherichia coli" ], "offsets": [ [ 48, 64 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-16263187_T5", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 65, 73 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-16263187_T6", "type": "Habitat", "text": [ "Caco-2 cells" ], "offsets": [ [ 86, 98 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000062" }, { "db_name": "OntoBiotope", "db_id": "OBT000268" } ] }, { "id": "BB-kb+ner-16263187_T7", "type": "Habitat", "text": [ "pigs' jejunal tissue" ], "offsets": [ [ 114, 134 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002993" } ] }, { "id": "BB-kb+ner-16263187_T8", "type": "Habitat", "text": [ "pigs" ], "offsets": [ [ 114, 118 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003337" } ] }, { "id": "BB-kb+ner-16263187_T9", "type": "Habitat", "text": [ "jejunal" ], "offsets": [ [ 120, 127 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001605" } ] }, { "id": "BB-kb+ner-16263187_T10", "type": "Microorganism", "text": [ "Lactobacillus (Lb.) gasseri K 7" ], "offsets": [ [ 151, 182 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1334627" } ] }, { "id": "BB-kb+ner-16263187_T11", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 194, 202 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-16263187_T12", "type": "Microorganism", "text": [ "Escherichia coli O8:K88" ], "offsets": [ [ 206, 229 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T13", "type": "Habitat", "text": [ "intestinal mucosa" ], "offsets": [ [ 233, 250 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002993" } ] }, { "id": "BB-kb+ner-16263187_T14", "type": "Habitat", "text": [ "intestinal" ], "offsets": [ [ 233, 243 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002810" } ] }, { "id": "BB-kb+ner-16263187_T15", "type": "Habitat", "text": [ "cultured Caco-2 cells" ], "offsets": [ [ 266, 287 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000062" }, { "db_name": "OntoBiotope", "db_id": "OBT000268" } ] }, { "id": "BB-kb+ner-16263187_T16", "type": "Habitat", "text": [ "pigs' small intestinal tissue" ], "offsets": [ [ 303, 332 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002993" } ] }, { "id": "BB-kb+ner-16263187_T17", "type": "Habitat", "text": [ "pigs" ], "offsets": [ [ 303, 307 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003337" } ] }, { "id": "BB-kb+ner-16263187_T18", "type": "Habitat", "text": [ "small intestinal" ], "offsets": [ [ 309, 325 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003303" } ] }, { "id": "BB-kb+ner-16263187_T19", "type": "Microorganism", "text": [ "Lactobacilli" ], "offsets": [ [ 334, 346 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1334627" } ] }, { "id": "BB-kb+ner-16263187_T20", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 378, 385 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T21", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 394, 401 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T22", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 412, 419 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T23", "type": "Microorganism", "text": [ "lactobacilli" ], "offsets": [ [ 493, 505 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1334627" } ] }, { "id": "BB-kb+ner-16263187_T24", "type": "Habitat", "text": [ "fully differentiated Caco-2 cells" ], "offsets": [ [ 509, 542 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-16263187_T25", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 602, 609 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T26", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 673, 680 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T27", "type": "Habitat", "text": [ "Caco-2" ], "offsets": [ [ 692, 698 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-16263187_T28", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 827, 834 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T29", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 835, 843 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-16263187_T30", "type": "Microorganism", "text": [ "Lb. gasseri K 7" ], "offsets": [ [ 859, 874 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1334627" } ] }, { "id": "BB-kb+ner-16263187_T31", "type": "Phenotype", "text": [ "binding" ], "offsets": [ [ 914, 921 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-16263187_T32", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 925, 932 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T33", "type": "Microorganism", "text": [ "lactobacilli" ], "offsets": [ [ 992, 1004 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1334627" } ] }, { "id": "BB-kb+ner-16263187_T34", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 1050, 1057 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T35", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 1065, 1072 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T36", "type": "Microorganism", "text": [ "lactobacilli" ], "offsets": [ [ 1073, 1085 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1334627" } ] }, { "id": "BB-kb+ner-16263187_T37", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 1153, 1161 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-16263187_T38", "type": "Habitat", "text": [ "tissue derived from pigs' jejunum" ], "offsets": [ [ 1165, 1198 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002993" } ] }, { "id": "BB-kb+ner-16263187_T39", "type": "Habitat", "text": [ "pigs' jejunum" ], "offsets": [ [ 1185, 1198 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001605" } ] }, { "id": "BB-kb+ner-16263187_T40", "type": "Habitat", "text": [ "pigs" ], "offsets": [ [ 1185, 1189 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003337" } ] }, { "id": "BB-kb+ner-16263187_T41", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 1228, 1235 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T42", "type": "Microorganism", "text": [ "Lb. gasseri K 7" ], "offsets": [ [ 1305, 1320 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1334627" } ] }, { "id": "BB-kb+ner-16263187_T43", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 1410, 1418 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-16263187_T44", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 1422, 1429 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T45", "type": "Microorganism", "text": [ "Lb. gasseri K 7" ], "offsets": [ [ 1434, 1449 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1334627" } ] }, { "id": "BB-kb+ner-16263187_T46", "type": "Habitat", "text": [ "jejunal" ], "offsets": [ [ 1459, 1466 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001605" } ] }, { "id": "BB-kb+ner-16263187_T47", "type": "Habitat", "text": [ "jejunal mucosa" ], "offsets": [ [ 1459, 1473 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002993" } ] }, { "id": "BB-kb+ner-16263187_T48", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 1684, 1691 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T49", "type": "Microorganism", "text": [ "lactobacilli" ], "offsets": [ [ 1695, 1707 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1334627" } ] }, { "id": "BB-kb+ner-16263187_T50", "type": "Habitat", "text": [ "jejunal" ], "offsets": [ [ 1724, 1731 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001605" } ] }, { "id": "BB-kb+ner-16263187_T51", "type": "Habitat", "text": [ "jejunal tissue" ], "offsets": [ [ 1724, 1738 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002993" } ] }, { "id": "BB-kb+ner-16263187_T52", "type": "Microorganism", "text": [ "Lb. gasseri K 7" ], "offsets": [ [ 1755, 1770 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1334627" } ] }, { "id": "BB-kb+ner-16263187_T53", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 1809, 1816 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1010796" } ] }, { "id": "BB-kb+ner-16263187_T54", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 1817, 1825 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-16263187_T55", "type": "Habitat", "text": [ "Caco-2 enterocytes" ], "offsets": [ [ 1829, 1847 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000268" } ] }, { "id": "BB-kb+ner-16263187_T56", "type": "Habitat", "text": [ "pig jejunal tissue" ], "offsets": [ [ 1911, 1929 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000196" }, { "db_name": "OntoBiotope", "db_id": "OBT002993" } ] }, { "id": "BB-kb+ner-16263187_T57", "type": "Habitat", "text": [ "pig" ], "offsets": [ [ 1911, 1914 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003337" } ] }, { "id": "BB-kb+ner-16263187_T58", "type": "Habitat", "text": [ "jejunal" ], "offsets": [ [ 1915, 1922 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001605" } ] } ]
[]
[]
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13
BB-kb+ner-16432479
[ { "id": "BB-kb+ner-16432479__text", "type": "abstract", "text": [ "Challenges in the control of gonorrhea in South America and the Caribbean: monitoring the development of resistance to antibiotics. : The objective of this study was to ascertain the antimicrobial susceptibility of Neisseria gonorrhoeae isolates from 6 South American and 13 Caribbean countries participating in the Gonococcal Antimicrobial Surveillance Program (GASP) from 1990 to 1999. : A GASP network of laboratories was launched in the Americas and the Caribbean during the 1990s. Standardized methods and interpretative criteria were established for the isolation of N. gonorrhoeae, strain identification, and determination, and quality control of antimicrobial susceptibility. : Two countries (Argentina and Uruguay) maintained continuous surveillance during the study period. Some countries gathered data periodically and several others were unable to initiate antimicrobial surveillance as a result of lack of resources. The percentage of penicillin-resistant N. gonorrhoeae isolated in the region over the decade varied considerably (1.0-11.9% carried chromosomal resistance and 17.9-38.8% produced beta-lactamase) with an overall trend to declining numbers of penicillin-resistant isolates. For tetracycline, 7.4% to 36.3% carried chromosomal resistance, whereas 12.0% to 27.4% carried plasmid-mediated resistance. There were no reports of ciprofloxacin-resistant isolates, although N. gonorrhoeae with decreased susceptibility to ciprofloxacin and azithromycin as well as spectinomycin-resistant isolates were identified in some countries. " ], "offsets": [ [ 0, 1553 ] ] } ]
[ { "id": "BB-kb+ner-16432479_T5", "type": "Phenotype", "text": [ "resistance to antibiotics" ], "offsets": [ [ 105, 130 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002674" } ] }, { "id": "BB-kb+ner-16432479_T6", "type": "Phenotype", "text": [ "antimicrobial susceptibility" ], "offsets": [ [ 183, 211 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002338" } ] }, { "id": "BB-kb+ner-16432479_T7", "type": "Microorganism", "text": [ "Neisseria gonorrhoeae" ], "offsets": [ [ 215, 236 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "485" } ] }, { "id": "BB-kb+ner-16432479_T8", "type": "Habitat", "text": [ "laboratories" ], "offsets": [ [ 408, 420 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001169" } ] }, { "id": "BB-kb+ner-16432479_T9", "type": "Microorganism", "text": [ "N. gonorrhoeae" ], "offsets": [ [ 573, 587 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "485" } ] }, { "id": "BB-kb+ner-16432479_T10", "type": "Phenotype", "text": [ "antimicrobial susceptibility" ], "offsets": [ [ 654, 682 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002338" } ] }, { "id": "BB-kb+ner-16432479_T11", "type": "Phenotype", "text": [ "penicillin-resistant" ], "offsets": [ [ 948, 968 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002829" } ] }, { "id": "BB-kb+ner-16432479_T12", "type": "Microorganism", "text": [ "N. gonorrhoeae" ], "offsets": [ [ 969, 983 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "485" } ] }, { "id": "BB-kb+ner-16432479_T13", "type": "Phenotype", "text": [ "resistance" ], "offsets": [ [ 1074, 1084 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002829" } ] }, { "id": "BB-kb+ner-16432479_T14", "type": "Phenotype", "text": [ "penicillin-resistant" ], "offsets": [ [ 1171, 1191 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002829" } ] }, { "id": "BB-kb+ner-16432479_T15", "type": "Phenotype", "text": [ "resistance" ], "offsets": [ [ 1254, 1264 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002869" } ] }, { "id": "BB-kb+ner-16432479_T16", "type": "Phenotype", "text": [ "resistance" ], "offsets": [ [ 1314, 1324 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002869" } ] }, { "id": "BB-kb+ner-16432479_T17", "type": "Phenotype", "text": [ "ciprofloxacin-resistant" ], "offsets": [ [ 1351, 1374 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002773" } ] }, { "id": "BB-kb+ner-16432479_T18", "type": "Microorganism", "text": [ "N. gonorrhoeae" ], "offsets": [ [ 1394, 1408 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "485" } ] }, { "id": "BB-kb+ner-16432479_T19", "type": "Phenotype", "text": [ "decreased susceptibility to", "azithromycin" ], "offsets": [ [ 1414, 1441 ], [ 1460, 1472 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002864" } ] }, { "id": "BB-kb+ner-16432479_T20", "type": "Phenotype", "text": [ "decreased susceptibility to ciprofloxacin" ], "offsets": [ [ 1414, 1455 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002774" } ] }, { "id": "BB-kb+ner-16432479_T21", "type": "Phenotype", "text": [ "spectinomycin-resistant" ], "offsets": [ [ 1484, 1507 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002857" } ] } ]
[]
[]
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14
BB-kb+ner-16436701
[ { "id": "BB-kb+ner-16436701__text", "type": "abstract", "text": [ "Antibacterial properties of dermaseptin S4 derivatives under extreme incubation conditions. Antibacterial properties of the frog-derived peptide dermaseptin S4 and a series of synthetic derivatives against the food pathogen Escherichia coli O157:H7 were investigated under extreme incubation conditions. The 28-mer analog K4K20S4 (P28) displayed an MIC of 8 microM and rapid bactericidal kinetics under standard culture conditions. Potent bactericidal properties were maintained at high salt concentrations, under acidic or basic conditions, and at extreme temperatures. The N-terminal 14-mer sequence (P14) displayed higher potency (MIC, 4 microM) but only within a narrow range of incubation conditions, pointing to the importance of the C-terminal domain of P28. The potency range was reextended upon conjugation of aminododecanoic acid to P14. The resulting lipopeptide was even more potent (MIC, 2 microM) and affected bacterial viability under most of the conditions tested, including in commercial apple juice. The mechanistic implications of peptides' hydrophobicity, charge, structure, and binding to an idealized membrane were probed and are discussed here. Collectively, the data indicate interest in simple peptide-based compounds for design of antimicrobials that affect pathogens under a variable range of incubation conditions. " ], "offsets": [ [ 0, 1344 ] ] } ]
[ { "id": "BB-kb+ner-16436701_T3", "type": "Habitat", "text": [ "frog" ], "offsets": [ [ 124, 128 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003052" } ] }, { "id": "BB-kb+ner-16436701_T4", "type": "Habitat", "text": [ "food" ], "offsets": [ [ 210, 214 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000094" } ] }, { "id": "BB-kb+ner-16436701_T5", "type": "Phenotype", "text": [ "pathogen" ], "offsets": [ [ 215, 223 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] }, { "id": "BB-kb+ner-16436701_T6", "type": "Microorganism", "text": [ "Escherichia coli O157:H7" ], "offsets": [ [ 224, 248 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "83334" } ] }, { "id": "BB-kb+ner-16436701_T7", "type": "Habitat", "text": [ "commercial apple juice" ], "offsets": [ [ 994, 1016 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003575" } ] }, { "id": "BB-kb+ner-16436701_T8", "type": "Phenotype", "text": [ "pathogens" ], "offsets": [ [ 1284, 1293 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] } ]
[]
[]
[ { "id": "BB-kb+ner-16436701_R2", "type": "Lives_In", "arg1_id": "BB-kb+ner-16436701_T6", "arg2_id": "BB-kb+ner-16436701_T4", "normalized": [] }, { "id": "BB-kb+ner-16436701_R1", "type": "Exhibits", "arg1_id": "BB-kb+ner-16436701_T6", "arg2_id": "BB-kb+ner-16436701_T5", "normalized": [] } ]
15
BB-kb+ner-16990433
[ { "id": "BB-kb+ner-16990433__text", "type": "abstract", "text": [ "An extensive repertoire of type III secretion effectors in Escherichia coli O157 and the role of lambdoid phages in their dissemination. Several pathogenic strains of Escherichia coli exploit type III secretion to inject \"effector proteins\" into human cells, which then subvert eukaryotic cell biology to the bacterium's advantage. We have exploited bioinformatics and experimental approaches to establish that the effector repertoire in the Sakai strain of enterohemorrhagic E. coli (EHEC) O157:H7 is much larger than previously thought. Homology searches led to the identification of >60 putative effector genes. Thirteen of these were judged to be likely pseudogenes, whereas 49 were judged to be potentially functional. In total, 39 proteins were confirmed experimentally as effectors: 31 through proteomics and 28 through translocation assays. At the protein level, the EHEC effector sequences fall into >20 families. The largest family, the NleG family, contains 14 members in the Sakai strain alone. EHEC also harbors functional homologs of effectors from plant pathogens (HopPtoH, HopW, AvrA) and from Shigella (OspD, OspE, OspG), and two additional members of the Map/IpgB family. Genes encoding proven or predicted effectors occur in >20 exchangeable effector loci scattered throughout the chromosome. Crucially, the majority of functional effector genes are encoded by nine exchangeable effector loci that lie within lambdoid prophages. Thus, type III secretion in E. coli is linked to a vast phage \"metagenome,\" acting as a crucible for the evolution of pathogenicity. " ], "offsets": [ [ 0, 1582 ] ] } ]
[ { "id": "BB-kb+ner-16990433_T3", "type": "Phenotype", "text": [ "type III secretion" ], "offsets": [ [ 27, 45 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-16990433_T4", "type": "Microorganism", "text": [ "Escherichia coli O157" ], "offsets": [ [ 59, 80 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1045010" } ] }, { "id": "BB-kb+ner-16990433_T5", "type": "Microorganism", "text": [ "lambdoid phages" ], "offsets": [ [ 97, 112 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "186765" } ] }, { "id": "BB-kb+ner-16990433_T6", "type": "Phenotype", "text": [ "pathogenic" ], "offsets": [ [ 145, 155 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002806" } ] }, { "id": "BB-kb+ner-16990433_T7", "type": "Microorganism", "text": [ "Escherichia coli" ], "offsets": [ [ 167, 183 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-16990433_T8", "type": "Phenotype", "text": [ "type III secretion" ], "offsets": [ [ 192, 210 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-16990433_T9", "type": "Habitat", "text": [ "human cells" ], "offsets": [ [ 246, 257 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-16990433_T10", "type": "Habitat", "text": [ "human" ], "offsets": [ [ 246, 251 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002488" } ] }, { "id": "BB-kb+ner-16990433_T11", "type": "Habitat", "text": [ "eukaryotic cell" ], "offsets": [ [ 278, 293 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-16990433_T12", "type": "Microorganism", "text": [ "Sakai" ], "offsets": [ [ 442, 447 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "386585" } ] }, { "id": "BB-kb+ner-16990433_T13", "type": "Phenotype", "text": [ "enterohemorrhagic" ], "offsets": [ [ 458, 475 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002806" } ] }, { "id": "BB-kb+ner-16990433_T14", "type": "Microorganism", "text": [ "E. coli (EHEC) O157:H7" ], "offsets": [ [ 476, 498 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "83334" } ] }, { "id": "BB-kb+ner-16990433_T15", "type": "Phenotype", "text": [ "EHEC" ], "offsets": [ [ 485, 489 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002806" } ] }, { "id": "BB-kb+ner-16990433_T16", "type": "Phenotype", "text": [ "EHEC" ], "offsets": [ [ 875, 879 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002806" } ] }, { "id": "BB-kb+ner-16990433_T17", "type": "Microorganism", "text": [ "EHEC" ], "offsets": [ [ 875, 879 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "386585" } ] }, { "id": "BB-kb+ner-16990433_T18", "type": "Microorganism", "text": [ "Sakai" ], "offsets": [ [ 987, 992 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "386585" } ] }, { "id": "BB-kb+ner-16990433_T19", "type": "Phenotype", "text": [ "EHEC" ], "offsets": [ [ 1007, 1011 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002806" } ] }, { "id": "BB-kb+ner-16990433_T20", "type": "Microorganism", "text": [ "EHEC" ], "offsets": [ [ 1007, 1011 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-16990433_T21", "type": "Phenotype", "text": [ "plant pathogens" ], "offsets": [ [ 1063, 1078 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002732" } ] }, { "id": "BB-kb+ner-16990433_T22", "type": "Habitat", "text": [ "plant" ], "offsets": [ [ 1063, 1068 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000393" } ] }, { "id": "BB-kb+ner-16990433_T23", "type": "Microorganism", "text": [ "Shigella" ], "offsets": [ [ 1110, 1118 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "620" } ] }, { "id": "BB-kb+ner-16990433_T24", "type": "Microorganism", "text": [ "lambdoid prophages" ], "offsets": [ [ 1428, 1446 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "186765" } ] }, { "id": "BB-kb+ner-16990433_T25", "type": "Phenotype", "text": [ "type III secretion" ], "offsets": [ [ 1454, 1472 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-16990433_T26", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 1476, 1483 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-16990433_T27", "type": "Phenotype", "text": [ "pathogenicity" ], "offsets": [ [ 1566, 1579 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002806" } ] } ]
[]
[]
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16
BB-kb+ner-17237163
[ { "id": "BB-kb+ner-17237163__text", "type": "abstract", "text": [ "Quorum-sensing regulation of adhesion in Serratia marcescens MG1 is surface dependent. Serratia marcescens is an opportunistic pathogen and a major cause of ocular infections. In previous studies of S. marcescens MG1, we showed that biofilm maturation and sloughing were regulated by N-acyl homoserine lactone (AHL)-based quorum sensing (QS). Because of the importance of adhesion in initiating biofilm formation and infection, the primary goal of this study was to determine whether QS is important in adhesion to both abiotic and biotic surfaces, as assessed by determining the degree of attachment to hydrophilic tissue culture plates and human corneal epithelial (HCE) cells. Our results demonstrate that while adhesion to the abiotic surface was AHL regulated, adhesion to the HCE cell biotic surface was not. Type I fimbriae were identified as the critical adhesin for non-QS-mediated attachment to the biotic HCE cell surface but played no role in adhesion to the abiotic surface. While we were not able to identify a single QS-regulated adhesin essential for attachment to the abiotic surface, four AHL-regulated genes involved in adhesion to the abiotic surface were identified. Interestingly, two of these genes, bsmA and bsmB, were also shown to be involved in adhesion to the biotic surface in a non-QS-controlled fashion. Therefore, the expression of these two genes appears to be cocontrolled by regulators other than the QS system for mediation of attachment to HCE cells. We also found that QS in S. marcescens regulates other potential cell surface adhesins, including exopolysaccharide and the outer membrane protein OmpX. We concluded that S. marcescens MG1 utilizes different regulatory systems and adhesins in attachment to biotic and abiotic surfaces and that QS is a main regulatory pathway in adhesion to an abiotic surface but not in adhesion to a biotic surface. " ], "offsets": [ [ 0, 1890 ] ] } ]
[ { "id": "BB-kb+ner-17237163_T3", "type": "Phenotype", "text": [ "Quorum-sensing" ], "offsets": [ [ 0, 14 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000143" } ] }, { "id": "BB-kb+ner-17237163_T4", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 29, 37 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T5", "type": "Microorganism", "text": [ "Serratia marcescens MG1" ], "offsets": [ [ 41, 64 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "615" } ] }, { "id": "BB-kb+ner-17237163_T6", "type": "Microorganism", "text": [ "Serratia marcescens" ], "offsets": [ [ 87, 106 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "615" } ] }, { "id": "BB-kb+ner-17237163_T7", "type": "Phenotype", "text": [ "opportunistic pathogen" ], "offsets": [ [ 113, 135 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000776" } ] }, { "id": "BB-kb+ner-17237163_T8", "type": "Habitat", "text": [ "ocular" ], "offsets": [ [ 157, 163 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000627" } ] }, { "id": "BB-kb+ner-17237163_T9", "type": "Microorganism", "text": [ "S. marcescens MG1" ], "offsets": [ [ 199, 216 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "615" } ] }, { "id": "BB-kb+ner-17237163_T10", "type": "Habitat", "text": [ "biofilm" ], "offsets": [ [ 233, 240 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000054" } ] }, { "id": "BB-kb+ner-17237163_T11", "type": "Phenotype", "text": [ "biofilm maturation" ], "offsets": [ [ 233, 251 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001444" } ] }, { "id": "BB-kb+ner-17237163_T12", "type": "Phenotype", "text": [ "N-acyl homoserine lactone (AHL)-based quorum sensing" ], "offsets": [ [ 284, 336 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000143" } ] }, { "id": "BB-kb+ner-17237163_T13", "type": "Phenotype", "text": [ "QS" ], "offsets": [ [ 338, 340 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000143" } ] }, { "id": "BB-kb+ner-17237163_T14", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 372, 380 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T15", "type": "Habitat", "text": [ "biofilm" ], "offsets": [ [ 395, 402 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000054" } ] }, { "id": "BB-kb+ner-17237163_T16", "type": "Phenotype", "text": [ "biofilm formation" ], "offsets": [ [ 395, 412 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001444" } ] }, { "id": "BB-kb+ner-17237163_T17", "type": "Phenotype", "text": [ "QS" ], "offsets": [ [ 484, 486 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000143" } ] }, { "id": "BB-kb+ner-17237163_T18", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 503, 511 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T19", "type": "Habitat", "text": [ "abiotic", "surfaces" ], "offsets": [ [ 520, 527 ], [ 539, 547 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-17237163_T20", "type": "Habitat", "text": [ "biotic surfaces" ], "offsets": [ [ 532, 547 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-17237163_T21", "type": "Phenotype", "text": [ "attachment" ], "offsets": [ [ 590, 600 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T22", "type": "Habitat", "text": [ "hydrophilic tissue culture plates" ], "offsets": [ [ 604, 637 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000103" } ] }, { "id": "BB-kb+ner-17237163_T23", "type": "Habitat", "text": [ "hydrophilic tissue culture" ], "offsets": [ [ 604, 630 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000062" } ] }, { "id": "BB-kb+ner-17237163_T24", "type": "Habitat", "text": [ "human corneal epithelial (HCE) cells" ], "offsets": [ [ 642, 678 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-17237163_T25", "type": "Habitat", "text": [ "human" ], "offsets": [ [ 642, 647 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002488" } ] }, { "id": "BB-kb+ner-17237163_T26", "type": "Habitat", "text": [ "corneal" ], "offsets": [ [ 648, 655 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000573" } ] }, { "id": "BB-kb+ner-17237163_T27", "type": "Habitat", "text": [ "epithelial" ], "offsets": [ [ 656, 666 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001091" } ] }, { "id": "BB-kb+ner-17237163_T28", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 715, 723 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T29", "type": "Habitat", "text": [ "abiotic surface" ], "offsets": [ [ 731, 746 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-17237163_T30", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 766, 774 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T31", "type": "Habitat", "text": [ "HCE cell" ], "offsets": [ [ 782, 790 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-17237163_T32", "type": "Habitat", "text": [ "HCE cell biotic surface" ], "offsets": [ [ 782, 805 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000062" } ] }, { "id": "BB-kb+ner-17237163_T33", "type": "Phenotype", "text": [ "QS" ], "offsets": [ [ 879, 881 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000143" } ] }, { "id": "BB-kb+ner-17237163_T34", "type": "Phenotype", "text": [ "attachment" ], "offsets": [ [ 891, 901 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T35", "type": "Habitat", "text": [ "biotic HCE cell surface" ], "offsets": [ [ 909, 932 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000062" } ] }, { "id": "BB-kb+ner-17237163_T36", "type": "Habitat", "text": [ "HCE cell" ], "offsets": [ [ 916, 924 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-17237163_T37", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 955, 963 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T38", "type": "Habitat", "text": [ "abiotic surface" ], "offsets": [ [ 971, 986 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-17237163_T39", "type": "Phenotype", "text": [ "QS" ], "offsets": [ [ 1032, 1034 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000143" } ] }, { "id": "BB-kb+ner-17237163_T40", "type": "Phenotype", "text": [ "attachment" ], "offsets": [ [ 1067, 1077 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T41", "type": "Habitat", "text": [ "abiotic surface" ], "offsets": [ [ 1085, 1100 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-17237163_T42", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 1139, 1147 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T43", "type": "Habitat", "text": [ "abiotic surface" ], "offsets": [ [ 1155, 1170 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-17237163_T44", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 1272, 1280 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T45", "type": "Habitat", "text": [ "biotic surface" ], "offsets": [ [ 1288, 1302 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000062" } ] }, { "id": "BB-kb+ner-17237163_T46", "type": "Phenotype", "text": [ "QS" ], "offsets": [ [ 1312, 1314 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000143" } ] }, { "id": "BB-kb+ner-17237163_T47", "type": "Phenotype", "text": [ "QS" ], "offsets": [ [ 1436, 1438 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000143" } ] }, { "id": "BB-kb+ner-17237163_T48", "type": "Phenotype", "text": [ "attachment" ], "offsets": [ [ 1463, 1473 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T49", "type": "Habitat", "text": [ "HCE cells" ], "offsets": [ [ 1477, 1486 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-17237163_T50", "type": "Phenotype", "text": [ "QS" ], "offsets": [ [ 1507, 1509 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000143" } ] }, { "id": "BB-kb+ner-17237163_T51", "type": "Microorganism", "text": [ "S. marcescens" ], "offsets": [ [ 1513, 1526 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "615" } ] }, { "id": "BB-kb+ner-17237163_T52", "type": "Microorganism", "text": [ "S. marcescens MG1" ], "offsets": [ [ 1659, 1676 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "615" } ] }, { "id": "BB-kb+ner-17237163_T53", "type": "Phenotype", "text": [ "attachment" ], "offsets": [ [ 1731, 1741 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T54", "type": "Habitat", "text": [ "biotic", "surfaces" ], "offsets": [ [ 1745, 1751 ], [ 1764, 1772 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000062" } ] }, { "id": "BB-kb+ner-17237163_T55", "type": "Habitat", "text": [ "abiotic surfaces" ], "offsets": [ [ 1756, 1772 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-17237163_T56", "type": "Phenotype", "text": [ "QS" ], "offsets": [ [ 1782, 1784 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000143" } ] }, { "id": "BB-kb+ner-17237163_T57", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 1817, 1825 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T58", "type": "Habitat", "text": [ "abiotic surface" ], "offsets": [ [ 1832, 1847 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-17237163_T59", "type": "Phenotype", "text": [ "adhesion" ], "offsets": [ [ 1859, 1867 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000029" } ] }, { "id": "BB-kb+ner-17237163_T60", "type": "Habitat", "text": [ "biotic surface" ], "offsets": [ [ 1873, 1887 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000062" } ] } ]
[]
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17
BB-kb+ner-17687514
[ { "id": "BB-kb+ner-17687514__text", "type": "abstract", "text": [ "Unveiling molecular mechanisms of bacterial surface proteins: Streptococcus pneumoniae as a model organism for structural studies. Bacteria present a variety of molecules either on their surface or in a cell-free form. These molecules take part in numerous processes in the interactions with their host, with its tissues and other molecules. These molecules are essential to bacterial pathogenesis either during colonization or the spread/invasion stages, and most are virulence factors. This review is focused on such molecules using Streptococcus pneumoniae, a Gram-positive bacterium, as an example. Selected surface proteins are introduced, their structure described, and, whenever available, their mechanisms of function on an atomic level are explained. Such mechanisms for hyaluronate lyase, pneumococcal surface protein A, pneumolysin, histidine-triad and fibronectin-binding proteins are discussed. Elucidation of molecular mechanisms of virulence factors is essential for the understanding of bacteria and their functional properties. Structural biology appears pivotal for these studies, as structural and mechanistic insights facilitate rational approach to the development of new treatments. " ], "offsets": [ [ 0, 1206 ] ] } ]
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[]
[]
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18
BB-kb+ner-18687046
[ { "id": "BB-kb+ner-18687046__text", "type": "abstract", "text": [ "Impact of intracranial pressure monitor prophylaxis on central nervous system infections and bacterial multi-drug resistance. Routine intracranial pressure monitor (ICP) prophylaxis is not practiced at our institution. Nevertheless, some patients receive de facto prophylaxis as a result of the use of antibiotics for injuries such as open or facial fractures. We tested the hypothesis that prophylactic antibiotics do not reduce the incidence of central nervous system (CNS) infections but instead are associated with the acquisition of multi-drug resistant (MDR) bacterial infections. Patients admitted to the trauma intensive care unit (TICU) from January, 2001 through December, 2004 with blunt, non-operative traumatic brain injury who were managed solely with an ICP monitor were identified from our trauma registry and divided into two groups: (1) Those receiving no antibiotics prior to or during ICP monitoring (NONE; n = 71); and (2) those already receiving antibiotics at the time of ICP monitor insertion (PRO; n = 84). Groups were stratified on the basis of age, Injury Severity Score (ISS), Glasgow Coma Scale (GCS) Score, base excess (BE), ICP days, transfusions in 24 h, ICU days, ventilator days, head Abbreviated Injury Score (AIS), and chest AIS. The study groups did not differ with respect to age, ISS, GCS, BE, ICP days, 24-h transfusions, ICU days, ventilator days, head AIS, or length of stay. In all, 183 patients were identified, of whom 28 died within seven days and were excluded from the analysis. All patients were followed until discharge for both CNS infections and subsequent infectious complications. Only two patients, both in the PRO group, developed CNS infection. Both infectious complications (0.7 vs 1.4 per patient; p < 0.05) and infections secondary to MDR pathogens (0.03 vs. 0.33 per patient; p < 0.01) were significantly more common in the PRO group. Twenty-nine percent of the ventilator-associated pneumonias and 33% of the blood stream infections in the PRO group were MDR, whereas only two blood stream infections in the NONE group (4% of the total infections) were MDR. The routine use of prophylactic antibiotics for ICP monitor insertion is not warranted. This practice does not reduce the CNS infection rate and is associated with more MDR pathogens in any subsequent infectious complications. " ], "offsets": [ [ 0, 2348 ] ] } ]
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"facial fractures" ], "offsets": [ [ 343, 359 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000526" } ] }, { "id": "BB-kb+ner-18687046_T12", "type": "Habitat", "text": [ "facial" ], "offsets": [ [ 343, 349 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001142" } ] }, { "id": "BB-kb+ner-18687046_T13", "type": "Habitat", "text": [ "central nervous system" ], "offsets": [ [ 447, 469 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001028" } ] }, { "id": "BB-kb+ner-18687046_T14", "type": "Habitat", "text": [ "CNS" ], "offsets": [ [ 471, 474 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001028" } ] }, { "id": "BB-kb+ner-18687046_T15", "type": "Phenotype", "text": [ "multi-drug resistant" ], "offsets": [ [ 538, 558 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000598" } ] }, { "id": "BB-kb+ner-18687046_T16", "type": "Phenotype", "text": [ "MDR" ], "offsets": [ [ 560, 563 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000598" } ] }, { "id": "BB-kb+ner-18687046_T17", "type": "Habitat", "text": [ "Patients" ], "offsets": [ [ 587, 595 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-18687046_T18", "type": "Habitat", "text": [ "trauma intensive care unit" ], "offsets": [ [ 612, 638 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000328" } ] }, { "id": "BB-kb+ner-18687046_T19", "type": "Habitat", "text": [ "TICU" ], "offsets": [ [ 640, 644 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000328" } ] }, { "id": "BB-kb+ner-18687046_T20", "type": "Habitat", "text": [ "brain" ], "offsets": [ [ 724, 729 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002689" } ] }, { "id": "BB-kb+ner-18687046_T21", "type": "Habitat", "text": [ "brain injury" ], "offsets": [ [ 724, 736 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000970" } ] }, { "id": "BB-kb+ner-18687046_T22", "type": "Habitat", "text": [ "ICU" ], "offsets": [ [ 1187, 1190 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000328" } ] }, { "id": "BB-kb+ner-18687046_T23", "type": "Habitat", "text": [ "ICU" ], "offsets": [ [ 1362, 1365 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000328" } ] }, { "id": "BB-kb+ner-18687046_T24", "type": "Habitat", "text": [ "patients" ], "offsets": [ [ 1430, 1438 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-18687046_T25", "type": "Habitat", "text": [ "patients" ], "offsets": [ [ 1531, 1539 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-18687046_T26", "type": "Habitat", "text": [ "CNS" ], "offsets": [ [ 1579, 1582 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001028" } ] }, { "id": "BB-kb+ner-18687046_T27", "type": "Habitat", "text": [ "patients" ], "offsets": [ [ 1644, 1652 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-18687046_T28", "type": "Habitat", "text": [ "CNS" ], "offsets": [ [ 1687, 1690 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001028" } ] }, { "id": "BB-kb+ner-18687046_T29", "type": "Habitat", "text": [ "patient" ], "offsets": [ [ 1748, 1755 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-18687046_T30", "type": "Phenotype", "text": [ "MDR" ], "offsets": [ [ 1795, 1798 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000598" } ] }, { "id": "BB-kb+ner-18687046_T31", "type": "Phenotype", "text": [ "pathogens" ], "offsets": [ [ 1799, 1808 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] }, { "id": "BB-kb+ner-18687046_T32", "type": "Habitat", "text": [ "patient" ], "offsets": [ [ 1828, 1835 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-18687046_T33", "type": "Habitat", "text": [ "blood stream" ], "offsets": [ [ 1971, 1983 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000521" } ] }, { "id": "BB-kb+ner-18687046_T34", "type": "Phenotype", "text": [ "MDR" ], "offsets": [ [ 2017, 2020 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000598" } ] }, { "id": "BB-kb+ner-18687046_T35", "type": "Habitat", "text": [ "blood stream" ], "offsets": [ [ 2039, 2051 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000521" } ] }, { "id": "BB-kb+ner-18687046_T36", "type": "Phenotype", "text": [ "MDR" ], "offsets": [ [ 2115, 2118 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000598" } ] }, { "id": "BB-kb+ner-18687046_T37", "type": "Habitat", "text": [ "CNS" ], "offsets": [ [ 2242, 2245 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001028" } ] }, { "id": "BB-kb+ner-18687046_T38", "type": "Phenotype", "text": [ "MDR" ], "offsets": [ [ 2289, 2292 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000598" } ] }, { "id": "BB-kb+ner-18687046_T39", "type": "Phenotype", "text": [ "pathogens" ], "offsets": [ [ 2293, 2302 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] } ]
[]
[]
[]
19
BB-kb+ner-18845825
[ { "id": "BB-kb+ner-18845825__text", "type": "abstract", "text": [ "High genetic diversity of nontypeable Haemophilus influenzae isolates from two children attending a day care center. Twenty-one nontypeable Haemophilus influenzae (NTHi) isolates from the throats of two healthy children were genotyped by multilocus sequence typing. Nine unique sequence types (STs) were identified. These STs were scattered throughout the phylogenetic tree of reported NTHi STs, demonstrating the high level of NTHi diversity found in colonized children. " ], "offsets": [ [ 0, 473 ] ] } ]
[ { "id": "BB-kb+ner-18845825_T3", "type": "Microorganism", "text": [ "Haemophilus influenzae" ], "offsets": [ [ 38, 60 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "727" } ] }, { "id": "BB-kb+ner-18845825_T4", "type": "Habitat", "text": [ "children attending a day care center" ], "offsets": [ [ 79, 115 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003188" } ] }, { "id": "BB-kb+ner-18845825_T5", "type": "Habitat", "text": [ "day care center" ], "offsets": [ [ 100, 115 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000403" } ] }, { "id": "BB-kb+ner-18845825_T6", "type": "Microorganism", "text": [ "Haemophilus influenzae" ], "offsets": [ [ 140, 162 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "727" } ] }, { "id": "BB-kb+ner-18845825_T7", "type": "Microorganism", "text": [ "NTHi" ], "offsets": [ [ 164, 168 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "727" } ] }, { "id": "BB-kb+ner-18845825_T8", "type": "Habitat", "text": [ "throats of two healthy children" ], "offsets": [ [ 188, 219 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000918" } ] }, { "id": "BB-kb+ner-18845825_T9", "type": "Habitat", "text": [ "healthy children" ], "offsets": [ [ 203, 219 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003188" }, { "db_name": "OntoBiotope", "db_id": "OBT002712" } ] }, { "id": "BB-kb+ner-18845825_T10", "type": "Microorganism", "text": [ "NTHi" ], "offsets": [ [ 386, 390 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "727" } ] }, { "id": "BB-kb+ner-18845825_T11", "type": "Microorganism", "text": [ "NTHi" ], "offsets": [ [ 428, 432 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "727" } ] }, { "id": "BB-kb+ner-18845825_T12", "type": "Habitat", "text": [ "colonized children" ], "offsets": [ [ 452, 470 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003188" }, { "db_name": "OntoBiotope", "db_id": "OBT002712" } ] } ]
[]
[ { "id": "BB-kb+ner-18845825_1", "entity_ids": [ "BB-kb+ner-18845825_T6", "BB-kb+ner-18845825_T7" ] } ]
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20
BB-kb+ner-19049879
[ { "id": "BB-kb+ner-19049879__text", "type": "abstract", "text": [ "Molecular cloning and expression of MyD88 in large yellow croaker, Pseudosciaena crocea. Myeloid differentiation factor 88 (MyD88) is an adaptor protein involved in the interleukin-1 receptor and Toll-like receptor-induced activation of nuclear factor-kappaB (NF-kappaB). In this report, the full-length cDNA of MyD88 was cloned from the large yellow croaker, Pseudosciaena crocea. It was of 1574 bp, including a 5'-terminal untranslated region (UTR) of 89 bp, a 3'-terminal UTR of 621bp and an open reading frame (ORF) of 864 bp encoding a polypeptide of 287 amino acids. It contained a typical death domain at the N-terminal and a conservative Toll/IL-1R (TIR) domain structure at the C-terminal. The quantitative real-time reverse transcription PCR analysis revealed a broad expression of MyD88 with the highest expression in the spleen and the weakest expression in the muscle. The expression of MyD88 after challenge with formalin-inactivated Gram-negative bacterium Vibrio parahaemolyticus was tested in blood, spleen and liver. It suggested that the highest expression was in the spleen (p<0.05) with 1.9 times (at 48 h) as much as that in the control and the lowest expression of MyD88 was in the liver (p<0.05) with 0.29 times (at 3h) of that in the control. These results indicated that as a universal key adaptor in the Toll-like receptor pathway in mammals, MyD88 might play an important role in large yellow croaker defense against pathogenic infection. " ], "offsets": [ [ 0, 1468 ] ] } ]
[ { "id": "BB-kb+ner-19049879_T3", "type": "Habitat", "text": [ "large yellow croaker" ], "offsets": [ [ 45, 65 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003264" } ] }, { "id": "BB-kb+ner-19049879_T4", "type": "Habitat", "text": [ "Pseudosciaena crocea" ], "offsets": [ [ 67, 87 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003264" } ] }, { "id": "BB-kb+ner-19049879_T5", "type": "Habitat", "text": [ "large yellow croaker" ], "offsets": [ [ 338, 358 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003264" } ] }, { "id": "BB-kb+ner-19049879_T6", "type": "Habitat", "text": [ "Pseudosciaena crocea" ], "offsets": [ [ 360, 380 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003264" } ] }, { "id": "BB-kb+ner-19049879_T7", "type": "Habitat", "text": [ "spleen" ], "offsets": [ [ 833, 839 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000890" } ] }, { "id": "BB-kb+ner-19049879_T8", "type": "Habitat", "text": [ "muscle" ], "offsets": [ [ 874, 880 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001226" } ] }, { "id": "BB-kb+ner-19049879_T9", "type": "Phenotype", "text": [ "Gram-negative" ], "offsets": [ [ 948, 961 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000648" } ] }, { "id": "BB-kb+ner-19049879_T10", "type": "Microorganism", "text": [ "Vibrio parahaemolyticus" ], "offsets": [ [ 972, 995 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "670" } ] }, { "id": "BB-kb+ner-19049879_T11", "type": "Habitat", "text": [ "blood" ], "offsets": [ [ 1010, 1015 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000521" } ] }, { "id": "BB-kb+ner-19049879_T12", "type": "Habitat", "text": [ "spleen" ], "offsets": [ [ 1017, 1023 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000890" } ] }, { "id": "BB-kb+ner-19049879_T13", "type": "Habitat", "text": [ "liver" ], "offsets": [ [ 1028, 1033 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002725" } ] }, { "id": "BB-kb+ner-19049879_T14", "type": "Habitat", "text": [ "spleen" ], "offsets": [ [ 1087, 1093 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000890" } ] }, { "id": "BB-kb+ner-19049879_T15", "type": "Habitat", "text": [ "liver" ], "offsets": [ [ 1205, 1210 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002725" } ] }, { "id": "BB-kb+ner-19049879_T16", "type": "Habitat", "text": [ "mammals" ], "offsets": [ [ 1361, 1368 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001625" } ] }, { "id": "BB-kb+ner-19049879_T17", "type": "Habitat", "text": [ "large yellow croaker" ], "offsets": [ [ 1408, 1428 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003264" } ] }, { "id": "BB-kb+ner-19049879_T18", "type": "Phenotype", "text": [ "pathogenic" ], "offsets": [ [ 1445, 1455 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002669" } ] } ]
[]
[]
[ { "id": "BB-kb+ner-19049879_R1", "type": "Exhibits", "arg1_id": "BB-kb+ner-19049879_T10", "arg2_id": "BB-kb+ner-19049879_T9", "normalized": [] } ]
21
BB-kb+ner-19075662
[ { "id": "BB-kb+ner-19075662__text", "type": "abstract", "text": [ "Prevention and treatment of Staphylococcus biofilms. Staphylococcus growth on medical devices represents a common occurrence that can lead to serious illness and death. Biomaterial-associated infection, mostly caused by Staphylococcus epidermidis and Staphylococcus aureus, is fairly complicated by the organism' development of a biofilm, which provides a microenvironment that protects from attack by the host immune system and antibiotics. In this review we present recent insights regarding S. aureus and S. epidermidis structural and functional factors that are effective in biofilm development and describe the regulation of their expression. On the basis of the knowledge gained, we also present the potential and limits of current biochemical and biophysical strategies aimed at preventing biofilm formation or at the treatment of established mature biofilms. " ], "offsets": [ [ 0, 868 ] ] } ]
[ { "id": "BB-kb+ner-19075662_T3", "type": "Microorganism", "text": [ "Staphylococcus" ], "offsets": [ [ 28, 42 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1279" } ] }, { "id": "BB-kb+ner-19075662_T4", "type": "Habitat", "text": [ "biofilms" ], "offsets": [ [ 43, 51 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000054" } ] }, { "id": "BB-kb+ner-19075662_T5", "type": "Microorganism", "text": [ "Staphylococcus" ], "offsets": [ [ 53, 67 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1279" } ] }, { "id": "BB-kb+ner-19075662_T6", "type": "Habitat", "text": [ "medical devices" ], "offsets": [ [ 78, 93 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000108" } ] }, { "id": "BB-kb+ner-19075662_T7", "type": "Habitat", "text": [ "Biomaterial" ], "offsets": [ [ 169, 180 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000108" } ] }, { "id": "BB-kb+ner-19075662_T8", "type": "Microorganism", "text": [ "Staphylococcus epidermidis" ], "offsets": [ [ 220, 246 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1282" } ] }, { "id": "BB-kb+ner-19075662_T9", "type": "Microorganism", "text": [ "Staphylococcus aureus" ], "offsets": [ [ 251, 272 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-19075662_T10", "type": "Phenotype", "text": [ "development of a biofilm" ], "offsets": [ [ 313, 337 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001444" } ] }, { "id": "BB-kb+ner-19075662_T11", "type": "Habitat", "text": [ "biofilm" ], "offsets": [ [ 330, 337 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000054" } ] }, { "id": "BB-kb+ner-19075662_T12", "type": "Habitat", "text": [ "host immune system" ], "offsets": [ [ 406, 424 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000321" } ] }, { "id": "BB-kb+ner-19075662_T13", "type": "Microorganism", "text": [ "S. aureus" ], "offsets": [ [ 494, 503 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-19075662_T14", "type": "Microorganism", "text": [ "S. epidermidis" ], "offsets": [ [ 508, 522 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1282" } ] }, { "id": "BB-kb+ner-19075662_T15", "type": "Habitat", "text": [ "biofilm" ], "offsets": [ [ 579, 586 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000054" } ] }, { "id": "BB-kb+ner-19075662_T16", "type": "Phenotype", "text": [ "biofilm development" ], "offsets": [ [ 579, 598 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001444" } ] }, { "id": "BB-kb+ner-19075662_T17", "type": "Habitat", "text": [ "biofilm" ], "offsets": [ [ 797, 804 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000054" } ] }, { "id": "BB-kb+ner-19075662_T18", "type": "Phenotype", "text": [ "biofilm formation" ], "offsets": [ [ 797, 814 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001444" } ] }, { "id": "BB-kb+ner-19075662_T19", "type": "Habitat", "text": [ "established mature biofilms" ], "offsets": [ [ 838, 865 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000054" } ] } ]
[]
[]
[ { "id": "BB-kb+ner-19075662_R1", "type": "Lives_In", "arg1_id": "BB-kb+ner-19075662_T3", "arg2_id": "BB-kb+ner-19075662_T4", "normalized": [] }, { "id": "BB-kb+ner-19075662_R2", "type": "Lives_In", "arg1_id": "BB-kb+ner-19075662_T5", "arg2_id": "BB-kb+ner-19075662_T6", "normalized": [] }, { "id": "BB-kb+ner-19075662_R3", "type": "Lives_In", "arg1_id": "BB-kb+ner-19075662_T8", "arg2_id": "BB-kb+ner-19075662_T7", "normalized": [] }, { "id": "BB-kb+ner-19075662_R4", "type": "Lives_In", "arg1_id": "BB-kb+ner-19075662_T8", "arg2_id": "BB-kb+ner-19075662_T11", "normalized": [] }, { "id": "BB-kb+ner-19075662_R5", "type": "Exhibits", "arg1_id": "BB-kb+ner-19075662_T8", "arg2_id": "BB-kb+ner-19075662_T10", "normalized": [] }, { "id": "BB-kb+ner-19075662_R6", "type": "Lives_In", "arg1_id": "BB-kb+ner-19075662_T9", "arg2_id": "BB-kb+ner-19075662_T7", "normalized": [] }, { "id": "BB-kb+ner-19075662_R7", "type": "Lives_In", "arg1_id": "BB-kb+ner-19075662_T9", "arg2_id": "BB-kb+ner-19075662_T11", "normalized": [] }, { "id": "BB-kb+ner-19075662_R8", "type": "Exhibits", "arg1_id": "BB-kb+ner-19075662_T9", "arg2_id": "BB-kb+ner-19075662_T10", "normalized": [] }, { "id": "BB-kb+ner-19075662_R9", "type": "Lives_In", "arg1_id": "BB-kb+ner-19075662_T13", "arg2_id": "BB-kb+ner-19075662_T15", "normalized": [] }, { "id": "BB-kb+ner-19075662_R10", "type": "Exhibits", "arg1_id": "BB-kb+ner-19075662_T13", "arg2_id": "BB-kb+ner-19075662_T16", "normalized": [] }, { "id": "BB-kb+ner-19075662_R11", "type": "Lives_In", "arg1_id": "BB-kb+ner-19075662_T14", "arg2_id": "BB-kb+ner-19075662_T15", "normalized": [] }, { "id": "BB-kb+ner-19075662_R12", "type": "Exhibits", "arg1_id": "BB-kb+ner-19075662_T14", "arg2_id": "BB-kb+ner-19075662_T16", "normalized": [] } ]
22
BB-kb+ner-19099664
[ { "id": "BB-kb+ner-19099664__text", "type": "abstract", "text": [ "[Changes of pathogens and susceptibility to antibiotics in hematology ward from years 2001 to 2005]. The purpose of this study was to determine the changes of pathogens in hematological ward and susceptibility of patients received chemotherapy to antibiotics. The pathogens were taken from blood, urine and sputum of patients who accepted chemotherapy from years 2001 to 2005, then were isolated and identified. The susceptibility test was performed by disk diffusion method. The results showed that the total of 418 strains were detected. Gram-negative bacteria were the most common of nosocomial infection. Pseudomonas aeruginosa, Enterobacter cloacae, E. coli account for the most of Gram negative- bacteria infection and most resistant to broad-spectrum penicillin, Acinetobacter baumannii showed a trend of increase. The ratios of gram positive bacteria and fungi were increased slowly, mainly as Enterococcus and Candida. Enterococcus is the most common cause of Gram-positive bacterial infection. Vancomycin resistance did not occur. It is concluded that Gram-negative bacteria are main cause of nosocomial infection in patients with hematological malignancies. Gram positive bacteria and fungi had been more frequent. Strains resistant to antimicrobial agents increase. " ], "offsets": [ [ 0, 1279 ] ] } ]
[ { "id": "BB-kb+ner-19099664_T3", "type": "Phenotype", "text": [ "pathogens" ], "offsets": [ [ 12, 21 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] }, { "id": "BB-kb+ner-19099664_T4", "type": "Phenotype", "text": [ "susceptibility to antibiotics" ], "offsets": [ [ 26, 55 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002675" } ] }, { "id": "BB-kb+ner-19099664_T5", "type": "Habitat", "text": [ "hematology ward" ], "offsets": [ [ 59, 74 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000097" } ] }, { "id": "BB-kb+ner-19099664_T6", "type": "Phenotype", "text": [ "pathogens" ], "offsets": [ [ 159, 168 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] }, { "id": "BB-kb+ner-19099664_T7", "type": "Habitat", "text": [ "hematological ward" ], "offsets": [ [ 172, 190 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000097" } ] }, { "id": "BB-kb+ner-19099664_T8", "type": "Habitat", "text": [ "patients received chemotherapy" ], "offsets": [ [ 213, 243 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-19099664_T9", "type": "Phenotype", "text": [ "pathogens" ], "offsets": [ [ 264, 273 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] }, { "id": "BB-kb+ner-19099664_T10", "type": "Habitat", "text": [ "blood", "of patients who accepted chemotherapy" ], "offsets": [ [ 290, 295 ], [ 314, 351 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000521" } ] }, { "id": "BB-kb+ner-19099664_T11", "type": "Habitat", "text": [ "urine", "of patients who accepted chemotherapy" ], "offsets": [ [ 297, 302 ], [ 314, 351 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001367" } ] }, { "id": "BB-kb+ner-19099664_T12", "type": "Habitat", "text": [ "sputum of patients who accepted chemotherapy" ], "offsets": [ [ 307, 351 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001335" } ] }, { "id": "BB-kb+ner-19099664_T13", "type": "Habitat", "text": [ "patients who accepted chemotherapy" ], "offsets": [ [ 317, 351 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-19099664_T14", "type": "Phenotype", "text": [ "Gram-negative" ], "offsets": [ [ 540, 553 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000648" } ] }, { "id": "BB-kb+ner-19099664_T15", "type": "Habitat", "text": [ "nosocomial" ], "offsets": [ [ 587, 597 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000011" } ] }, { "id": "BB-kb+ner-19099664_T16", "type": "Microorganism", "text": [ "Pseudomonas aeruginosa" ], "offsets": [ [ 609, 631 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "287" } ] }, { "id": "BB-kb+ner-19099664_T17", "type": "Microorganism", "text": [ "Enterobacter cloacae" ], "offsets": [ [ 633, 653 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "550" } ] }, { "id": "BB-kb+ner-19099664_T18", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 655, 662 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "110766" } ] }, { "id": "BB-kb+ner-19099664_T19", "type": "Phenotype", "text": [ "Gram negative" ], "offsets": [ [ 687, 700 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000648" } ] }, { "id": "BB-kb+ner-19099664_T20", "type": "Phenotype", "text": [ "resistant to broad-spectrum penicillin" ], "offsets": [ [ 730, 768 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002829" } ] }, { "id": "BB-kb+ner-19099664_T21", "type": "Microorganism", "text": [ "Acinetobacter baumannii" ], "offsets": [ [ 770, 793 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "470" } ] }, { "id": "BB-kb+ner-19099664_T22", "type": "Phenotype", "text": [ "gram positive" ], "offsets": [ [ 836, 849 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000649" } ] }, { "id": "BB-kb+ner-19099664_T23", "type": "Microorganism", "text": [ "Enterococcus" ], "offsets": [ [ 902, 914 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1350" } ] }, { "id": "BB-kb+ner-19099664_T24", "type": "Microorganism", "text": [ "Candida" ], "offsets": [ [ 919, 926 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1535326" } ] }, { "id": "BB-kb+ner-19099664_T25", "type": "Microorganism", "text": [ "Enterococcus" ], "offsets": [ [ 928, 940 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1350" } ] }, { "id": "BB-kb+ner-19099664_T26", "type": "Phenotype", "text": [ "Gram-positive" ], "offsets": [ [ 969, 982 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000649" } ] }, { "id": "BB-kb+ner-19099664_T27", "type": "Phenotype", "text": [ "Vancomycin resistance" ], "offsets": [ [ 1004, 1025 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002874" } ] }, { "id": "BB-kb+ner-19099664_T28", "type": "Phenotype", "text": [ "Gram-negative" ], "offsets": [ [ 1062, 1075 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000648" } ] }, { "id": "BB-kb+ner-19099664_T29", "type": "Habitat", "text": [ "nosocomial" ], "offsets": [ [ 1103, 1113 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000011" } ] }, { "id": "BB-kb+ner-19099664_T30", "type": "Habitat", "text": [ "patients with hematological malignancies" ], "offsets": [ [ 1127, 1167 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-19099664_T31", "type": "Phenotype", "text": [ "Gram positive" ], "offsets": [ [ 1169, 1182 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000649" } ] }, { "id": "BB-kb+ner-19099664_T32", "type": "Phenotype", "text": [ "resistant to antimicrobial agents" ], "offsets": [ [ 1234, 1267 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002337" } ] } ]
[]
[]
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23
BB-kb+ner-19175621
[ { "id": "BB-kb+ner-19175621__text", "type": "abstract", "text": [ "Occurrence of extended-spectrum beta-lactamase-producing Salmonella enterica in northern Spain with evidence of CTX-M-9 clonal spread among animals and humans. Among the 1233 Salmonella enterica isolates obtained in two Spanish hospitals, five isolates (0.4%) (serovars: Virchow, four; Livingstone, one) had the phenotype of an extended-spectrum beta-lactamase (ESBL) producer. The genetic characterization of the ESBL of S. enterica Livingstone revealed a bla(SHV-2) gene. The bla(CTX-M-10) gene in a phage-related genetic environment was found in one S. enterica Virchow isolate, and the bla(CTX-M-9) gene within the In60 integron was found in the three remaining Virchow isolates. These three isolates presented indistinguishable or closely related pulsed-field gel electrophoresis patterns among themselves and also as compared with the two other bla(CTX-M-9)-containing isolates previously obtained from animals. ESBL production is an emerging mechanism of resistance in S. enterica in the two studied hospitals. " ], "offsets": [ [ 0, 1019 ] ] } ]
[ { "id": "BB-kb+ner-19175621_T3", "type": "Phenotype", "text": [ "beta-lactamase-producing" ], "offsets": [ [ 32, 56 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-19175621_T4", "type": "Microorganism", "text": [ "Salmonella enterica" ], "offsets": [ [ 57, 76 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "28901" } ] }, { "id": "BB-kb+ner-19175621_T5", "type": "Habitat", "text": [ "animals" ], "offsets": [ [ 140, 147 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000193" } ] }, { "id": "BB-kb+ner-19175621_T6", "type": "Habitat", "text": [ "humans" ], "offsets": [ [ 152, 158 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002488" } ] }, { "id": "BB-kb+ner-19175621_T7", "type": "Microorganism", "text": [ "Salmonella enterica" ], "offsets": [ [ 175, 194 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "28901" } ] }, { "id": "BB-kb+ner-19175621_T8", "type": "Habitat", "text": [ "Spanish hospitals" ], "offsets": [ [ 220, 237 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002714" } ] }, { "id": "BB-kb+ner-19175621_T9", "type": "Microorganism", "text": [ "Virchow" ], "offsets": [ [ 271, 278 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "48409" } ] }, { "id": "BB-kb+ner-19175621_T10", "type": "Microorganism", "text": [ "Livingstone" ], "offsets": [ [ 286, 297 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "260680" } ] }, { "id": "BB-kb+ner-19175621_T11", "type": "Phenotype", "text": [ "extended-spectrum beta-lactamase (ESBL) producer" ], "offsets": [ [ 328, 376 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-19175621_T12", "type": "Microorganism", "text": [ "S. enterica Livingstone" ], "offsets": [ [ 422, 445 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "260680" } ] }, { "id": "BB-kb+ner-19175621_T13", "type": "Microorganism", "text": [ "S. enterica Virchow" ], "offsets": [ [ 553, 572 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "48409" } ] }, { "id": "BB-kb+ner-19175621_T14", "type": "Microorganism", "text": [ "Virchow" ], "offsets": [ [ 666, 673 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "48409" } ] }, { "id": "BB-kb+ner-19175621_T15", "type": "Habitat", "text": [ "animals" ], "offsets": [ [ 909, 916 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000193" } ] }, { "id": "BB-kb+ner-19175621_T16", "type": "Phenotype", "text": [ "ESBL production" ], "offsets": [ [ 918, 933 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000019" } ] }, { "id": "BB-kb+ner-19175621_T17", "type": "Phenotype", "text": [ "resistance" ], "offsets": [ [ 962, 972 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000598" } ] }, { "id": "BB-kb+ner-19175621_T18", "type": "Microorganism", "text": [ "S. enterica" ], "offsets": [ [ 976, 987 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "28901" } ] }, { "id": "BB-kb+ner-19175621_T19", "type": "Habitat", "text": [ "hospitals" ], "offsets": [ [ 1007, 1016 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002714" } ] } ]
[]
[]
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24
BB-kb+ner-19396518
[ { "id": "BB-kb+ner-19396518__text", "type": "abstract", "text": [ "Rapid detection of eight causative pathogens for the diagnosis of bacterial meningitis by real-time PCR. We aimed to detect causative pathogens in cerebrospinal fluid (CSF) collected from patients diagnosed with bacterial meningitis by real-time polymerase chain reaction (PCR). In addition to Streptococcus pneumoniae, Haemophilus influenzae, and Mycoplasma pneumoniae described previously, five other pathogens, Neisseria meningitidis, Escherichia coli, Streptococcus agalactiae, Staphylococcus aureus, and Listeria monocytogenes, were targeted, based on a large-scale surveillance in Japan. Results in CSF from neonates and children (n=150), and from adults (n=18) analyzed by real-time PCR with molecular beacon probes were compared with those of conventional culturing. The total time from DNA extraction from CSF to PCR analysis was 1.5 h. The limit of detection for these pathogens ranged from 5 copies to 28 copies per tube. Nonspecific positive reactions were not recognized for 37 microorganisms in clinical isolates as a negative control. The pathogens were detected in 72.0% of the samples by real-time PCR, but in only 48.2% by culture, although the microorganisms were completely concordant. With the real-time PCR, the detection rate of H. influenzae from CSF was high, at 45.2%, followed by S. pneumoniae (21.4%), S. agalactiae (2.4%), E. coli (1.8%), L. monocytogenes (0.6%), and M. pneumoniae (0.6%). The detection rate with PCR was significantly better than that with cultures in patients with antibiotic administration (chi2=18.3182; P=0.0000). In conclusion, detection with real-time PCR is useful for rapidly identifying the causative pathogens of meningitis and for examining the clinical course of chemotherapy. " ], "offsets": [ [ 0, 1737 ] ] } ]
[ { "id": "BB-kb+ner-19396518_T3", "type": "Phenotype", "text": [ "pathogens" ], "offsets": [ [ 35, 44 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] }, { "id": "BB-kb+ner-19396518_T4", "type": "Phenotype", "text": [ "pathogens" ], "offsets": [ [ 134, 143 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002806" } ] }, { "id": "BB-kb+ner-19396518_T5", "type": "Habitat", "text": [ "cerebrospinal fluid" ], "offsets": [ [ 147, 166 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000550" } ] }, { "id": "BB-kb+ner-19396518_T6", "type": "Habitat", "text": [ "CSF" ], "offsets": [ [ 168, 171 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000550" } ] }, { "id": "BB-kb+ner-19396518_T7", "type": "Habitat", "text": [ "patients diagnosed with bacterial meningitis" ], "offsets": [ [ 188, 232 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003269" } ] }, { "id": "BB-kb+ner-19396518_T8", "type": "Microorganism", "text": [ "Streptococcus pneumoniae" ], "offsets": [ [ 294, 318 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1313" } ] }, { "id": "BB-kb+ner-19396518_T9", "type": "Microorganism", "text": [ "Haemophilus influenzae" ], "offsets": [ [ 320, 342 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "727" } ] }, { "id": "BB-kb+ner-19396518_T10", "type": "Microorganism", "text": [ "Mycoplasma pneumoniae" ], "offsets": [ [ 348, 369 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "2104" } ] }, { "id": "BB-kb+ner-19396518_T11", "type": "Phenotype", "text": [ "pathogens" ], "offsets": [ [ 403, 412 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002806" } ] }, { "id": "BB-kb+ner-19396518_T12", "type": "Microorganism", "text": [ "Neisseria meningitidis" ], "offsets": [ [ 414, 436 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "487" } ] }, { "id": "BB-kb+ner-19396518_T13", "type": "Microorganism", "text": [ "Escherichia coli" ], "offsets": [ [ 438, 454 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-19396518_T14", "type": "Microorganism", "text": [ "Streptococcus agalactiae" ], "offsets": [ [ 456, 480 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1311" } ] }, { "id": "BB-kb+ner-19396518_T15", "type": "Microorganism", "text": [ "Staphylococcus aureus" ], "offsets": [ [ 482, 503 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-19396518_T16", "type": "Microorganism", "text": [ "Listeria monocytogenes" ], "offsets": [ [ 509, 531 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1639" } ] }, { "id": "BB-kb+ner-19396518_T17", "type": "Habitat", "text": [ "CSF from neonates and children" ], "offsets": [ [ 605, 635 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000550" } ] }, { "id": "BB-kb+ner-19396518_T18", "type": "Habitat", "text": [ "CSF", "from adults" ], "offsets": [ [ 605, 608 ], [ 649, 660 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000550" } ] }, { "id": "BB-kb+ner-19396518_T19", "type": "Habitat", "text": [ "neonates" ], "offsets": [ [ 614, 622 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003453" }, { "db_name": "OntoBiotope", "db_id": "OBT003269" } ] }, { "id": "BB-kb+ner-19396518_T20", "type": "Habitat", "text": [ "children" ], "offsets": [ [ 627, 635 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003188" }, { "db_name": "OntoBiotope", "db_id": "OBT003269" } ] }, { "id": "BB-kb+ner-19396518_T21", "type": "Habitat", "text": [ "adults" ], "offsets": [ [ 654, 660 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003245" }, { "db_name": "OntoBiotope", "db_id": "OBT003269" } ] }, { "id": "BB-kb+ner-19396518_T22", "type": "Habitat", "text": [ "CSF" ], "offsets": [ [ 815, 818 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000550" } ] }, { "id": "BB-kb+ner-19396518_T23", "type": "Phenotype", "text": [ "pathogens" ], "offsets": [ [ 879, 888 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002806" } ] }, { "id": "BB-kb+ner-19396518_T24", "type": "Habitat", "text": [ "clinical" ], "offsets": [ [ 1009, 1017 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003220" } ] }, { "id": "BB-kb+ner-19396518_T25", "type": "Phenotype", "text": [ "pathogens" ], "offsets": [ [ 1054, 1063 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002806" } ] }, { "id": "BB-kb+ner-19396518_T26", "type": "Microorganism", "text": [ "H. influenzae" ], "offsets": [ [ 1252, 1265 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "727" } ] }, { "id": "BB-kb+ner-19396518_T27", "type": "Habitat", "text": [ "CSF" ], "offsets": [ [ 1271, 1274 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000550" } ] }, { "id": "BB-kb+ner-19396518_T28", "type": "Microorganism", "text": [ "S. pneumoniae" ], "offsets": [ [ 1307, 1320 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1313" } ] }, { "id": "BB-kb+ner-19396518_T29", "type": "Microorganism", "text": [ "S. agalactiae" ], "offsets": [ [ 1330, 1343 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1311" } ] }, { "id": "BB-kb+ner-19396518_T30", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 1352, 1359 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-19396518_T31", "type": "Microorganism", "text": [ "L. monocytogenes" ], "offsets": [ [ 1368, 1384 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1639" } ] }, { "id": "BB-kb+ner-19396518_T32", "type": "Microorganism", "text": [ "M. pneumoniae" ], "offsets": [ [ 1397, 1410 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1313" } ] }, { "id": "BB-kb+ner-19396518_T33", "type": "Habitat", "text": [ "patients with antibiotic administration" ], "offsets": [ [ 1499, 1538 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003269" } ] }, { "id": "BB-kb+ner-19396518_T34", "type": "Phenotype", "text": [ "pathogens" ], "offsets": [ [ 1657, 1666 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002806" } ] } ]
[]
[]
[ { "id": "BB-kb+ner-19396518_R2", "type": "Exhibits", "arg1_id": "BB-kb+ner-19396518_T8", "arg2_id": "BB-kb+ner-19396518_T11", "normalized": [] }, { "id": "BB-kb+ner-19396518_R4", "type": "Exhibits", "arg1_id": "BB-kb+ner-19396518_T9", "arg2_id": "BB-kb+ner-19396518_T11", "normalized": [] }, { "id": "BB-kb+ner-19396518_R6", "type": "Exhibits", "arg1_id": "BB-kb+ner-19396518_T10", "arg2_id": "BB-kb+ner-19396518_T11", "normalized": [] }, { "id": "BB-kb+ner-19396518_R8", "type": "Exhibits", "arg1_id": "BB-kb+ner-19396518_T12", "arg2_id": "BB-kb+ner-19396518_T11", "normalized": [] }, { "id": "BB-kb+ner-19396518_R10", "type": "Exhibits", "arg1_id": "BB-kb+ner-19396518_T13", "arg2_id": "BB-kb+ner-19396518_T11", "normalized": [] }, { "id": "BB-kb+ner-19396518_R12", "type": "Exhibits", "arg1_id": "BB-kb+ner-19396518_T14", "arg2_id": "BB-kb+ner-19396518_T11", "normalized": [] }, { "id": "BB-kb+ner-19396518_R14", "type": "Exhibits", "arg1_id": "BB-kb+ner-19396518_T15", "arg2_id": "BB-kb+ner-19396518_T11", "normalized": [] }, { "id": "BB-kb+ner-19396518_R16", "type": "Exhibits", "arg1_id": "BB-kb+ner-19396518_T16", "arg2_id": "BB-kb+ner-19396518_T11", "normalized": [] }, { "id": "BB-kb+ner-19396518_R17", "type": "Lives_In", "arg1_id": "BB-kb+ner-19396518_T26", "arg2_id": "BB-kb+ner-19396518_T27", "normalized": [] }, { "id": "BB-kb+ner-19396518_R18", "type": "Lives_In", "arg1_id": "BB-kb+ner-19396518_T26", "arg2_id": "BB-kb+ner-19396518_T33", "normalized": [] }, { "id": "BB-kb+ner-19396518_R19", "type": "Lives_In", "arg1_id": "BB-kb+ner-19396518_T28", "arg2_id": "BB-kb+ner-19396518_T27", "normalized": [] }, { "id": "BB-kb+ner-19396518_R20", "type": "Lives_In", "arg1_id": "BB-kb+ner-19396518_T28", "arg2_id": "BB-kb+ner-19396518_T33", "normalized": [] }, { "id": "BB-kb+ner-19396518_R21", "type": "Lives_In", "arg1_id": "BB-kb+ner-19396518_T29", "arg2_id": "BB-kb+ner-19396518_T33", "normalized": [] }, { "id": "BB-kb+ner-19396518_R22", "type": "Lives_In", "arg1_id": "BB-kb+ner-19396518_T29", "arg2_id": "BB-kb+ner-19396518_T27", "normalized": [] }, { "id": "BB-kb+ner-19396518_R23", "type": "Lives_In", "arg1_id": "BB-kb+ner-19396518_T30", "arg2_id": "BB-kb+ner-19396518_T27", "normalized": [] }, { "id": "BB-kb+ner-19396518_R24", "type": "Lives_In", "arg1_id": "BB-kb+ner-19396518_T30", "arg2_id": "BB-kb+ner-19396518_T33", "normalized": [] }, { "id": "BB-kb+ner-19396518_R25", "type": "Lives_In", "arg1_id": "BB-kb+ner-19396518_T31", "arg2_id": "BB-kb+ner-19396518_T27", "normalized": [] }, { "id": "BB-kb+ner-19396518_R26", "type": "Lives_In", "arg1_id": "BB-kb+ner-19396518_T31", "arg2_id": "BB-kb+ner-19396518_T33", "normalized": [] }, { "id": "BB-kb+ner-19396518_R27", "type": "Lives_In", "arg1_id": "BB-kb+ner-19396518_T32", "arg2_id": "BB-kb+ner-19396518_T27", "normalized": [] }, { "id": "BB-kb+ner-19396518_R28", "type": "Lives_In", "arg1_id": "BB-kb+ner-19396518_T32", "arg2_id": "BB-kb+ner-19396518_T33", "normalized": [] } ]
25
BB-kb+ner-19501788
[ { "id": "BB-kb+ner-19501788__text", "type": "abstract", "text": [ "Construction of an attenuated Pseudomonas fluorescens strain and evaluation of its potential as a cross-protective vaccine. Ferric uptake regulator (Fur) is a global transcription regulator that is ubiquitous to Gram-negative bacteria and regulates diverse biological processes, including iron uptake, cellular metabolism, stress response, and production of virulence determinants. As a result, for many pathogenic bacteria, Fur plays a crucial role in the course of infection and disease development. In this study, the fur gene was cloned from a pathogenic Pseudomonas fluorescens strain, TSS, isolated from diseased Japanese flounder cultured in a local farm. TSS Fur can partially complement the defective phenotype of an Escherichia coli fur mutant. A TSS fur null mutant, TFM, was constructed. Compared to TSS, TFM exhibits reduced growth ability, aberrant production of outer membrane proteins, decreased resistance against host serum bactericidal activity, impaired ability to disseminate in host blood and tissues, and drastic attenuation in overall bacterial virulence in a Japanese flounder infection model. When used as a live vaccine administered via the injection, immersion, and oral routes, TFM affords high levels of protection upon Japanese flounder against not only P. fluorescens infection but also Aeromonas hydrophila infection. Furthermore, a plasmid, pJAQ, was constructed, which expresses the coding element of the Vibrio harveyi antigen AgaV-DegQ. TFM harboring pJAQ can secret AgaV-DegQ into the extracellular milieu. Vaccination of Japanese flounder with live TFM/pJAQ elicited strong immunoprotection against both V. harveyi and A. hydrophila infections. " ], "offsets": [ [ 0, 1685 ] ] } ]
[ { "id": "BB-kb+ner-19501788_T3", "type": "Microorganism", "text": [ "Pseudomonas fluorescens" ], "offsets": [ [ 30, 53 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "294" } ] }, { "id": "BB-kb+ner-19501788_T4", "type": "Habitat", "text": [ "cross-protective vaccine" ], "offsets": [ [ 98, 122 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000464" } ] }, { "id": "BB-kb+ner-19501788_T5", "type": "Phenotype", "text": [ "Gram-negative" ], "offsets": [ [ 212, 225 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000648" } ] }, { "id": "BB-kb+ner-19501788_T6", "type": "Phenotype", "text": [ "virulence" ], "offsets": [ [ 358, 367 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] }, { "id": "BB-kb+ner-19501788_T7", "type": "Phenotype", "text": [ "pathogenic" ], "offsets": [ [ 404, 414 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000375" } ] }, { "id": "BB-kb+ner-19501788_T8", "type": "Phenotype", "text": [ "pathogenic" ], "offsets": [ [ 548, 558 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002669" } ] }, { "id": "BB-kb+ner-19501788_T9", "type": "Microorganism", "text": [ "Pseudomonas fluorescens strain, TSS" ], "offsets": [ [ 559, 594 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "294" } ] }, { "id": "BB-kb+ner-19501788_T10", "type": "Habitat", "text": [ "diseased Japanese flounder cultured in a local farm" ], "offsets": [ [ 610, 661 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000491" }, { "db_name": "OntoBiotope", "db_id": "OBT003553" } ] }, { "id": "BB-kb+ner-19501788_T11", "type": "Habitat", "text": [ "local farm" ], "offsets": [ [ 651, 661 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000630" } ] }, { "id": "BB-kb+ner-19501788_T12", "type": "Microorganism", "text": [ "TSS" ], "offsets": [ [ 663, 666 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "294" } ] }, { "id": "BB-kb+ner-19501788_T13", "type": "Microorganism", "text": [ "Escherichia coli" ], "offsets": [ [ 726, 742 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-19501788_T14", "type": "Phenotype", "text": [ "fur mutant" ], "offsets": [ [ 743, 753 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000118" } ] }, { "id": "BB-kb+ner-19501788_T15", "type": "Microorganism", "text": [ "TSS" ], "offsets": [ [ 757, 760 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "294" } ] }, { "id": "BB-kb+ner-19501788_T16", "type": "Phenotype", "text": [ "fur null mutant" ], "offsets": [ [ 761, 776 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000118" } ] }, { "id": "BB-kb+ner-19501788_T17", "type": "Microorganism", "text": [ "TFM" ], "offsets": [ [ 778, 781 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-19501788_T18", "type": "Microorganism", "text": [ "TSS" ], "offsets": [ [ 812, 815 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "294" } ] }, { "id": "BB-kb+ner-19501788_T19", "type": "Microorganism", "text": [ "TFM" ], "offsets": [ [ 817, 820 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-19501788_T20", "type": "Phenotype", "text": [ "decreased resistance against host serum bactericidal activity" ], "offsets": [ [ 902, 963 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000152" } ] }, { "id": "BB-kb+ner-19501788_T21", "type": "Habitat", "text": [ "host serum" ], "offsets": [ [ 931, 941 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000524" } ] }, { "id": "BB-kb+ner-19501788_T22", "type": "Habitat", "text": [ "host", "tissues" ], "offsets": [ [ 1000, 1004 ], [ 1015, 1022 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000196" } ] }, { "id": "BB-kb+ner-19501788_T23", "type": "Habitat", "text": [ "host blood" ], "offsets": [ [ 1000, 1010 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000521" } ] }, { "id": "BB-kb+ner-19501788_T24", "type": "Phenotype", "text": [ "bacterial virulence" ], "offsets": [ [ 1059, 1078 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002669" } ] }, { "id": "BB-kb+ner-19501788_T25", "type": "Habitat", "text": [ "Japanese flounder" ], "offsets": [ [ 1084, 1101 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003553" }, { "db_name": "OntoBiotope", "db_id": "OBT000700" } ] }, { "id": "BB-kb+ner-19501788_T26", "type": "Habitat", "text": [ "live vaccine" ], "offsets": [ [ 1134, 1146 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000464" } ] }, { "id": "BB-kb+ner-19501788_T27", "type": "Habitat", "text": [ "oral" ], "offsets": [ [ 1194, 1198 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001653" } ] }, { "id": "BB-kb+ner-19501788_T28", "type": "Microorganism", "text": [ "TFM" ], "offsets": [ [ 1207, 1210 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-19501788_T29", "type": "Habitat", "text": [ "Japanese flounder" ], "offsets": [ [ 1250, 1267 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000700" }, { "db_name": "OntoBiotope", "db_id": "OBT003553" } ] }, { "id": "BB-kb+ner-19501788_T30", "type": "Microorganism", "text": [ "P. fluorescens" ], "offsets": [ [ 1285, 1299 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "294" } ] }, { "id": "BB-kb+ner-19501788_T31", "type": "Microorganism", "text": [ "Aeromonas hydrophila" ], "offsets": [ [ 1319, 1339 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "644" } ] }, { "id": "BB-kb+ner-19501788_T32", "type": "Microorganism", "text": [ "Vibrio harveyi" ], "offsets": [ [ 1440, 1454 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "669" } ] }, { "id": "BB-kb+ner-19501788_T33", "type": "Microorganism", "text": [ "TFM" ], "offsets": [ [ 1474, 1477 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-19501788_T34", "type": "Habitat", "text": [ "Japanese flounder" ], "offsets": [ [ 1560, 1577 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003553" }, { "db_name": "OntoBiotope", "db_id": "OBT000700" } ] }, { "id": "BB-kb+ner-19501788_T35", "type": "Microorganism", "text": [ "TFM" ], "offsets": [ [ 1588, 1591 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "562" } ] }, { "id": "BB-kb+ner-19501788_T36", "type": "Microorganism", "text": [ "V. harveyi" ], "offsets": [ [ 1643, 1653 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "669" } ] }, { "id": "BB-kb+ner-19501788_T37", "type": "Microorganism", "text": [ "A. hydrophila" ], "offsets": [ [ 1658, 1671 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "644" } ] } ]
[]
[]
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26
BB-kb+ner-19622846
[ { "id": "BB-kb+ner-19622846__text", "type": "abstract", "text": [ "Detection of Staphylococcus aureus including MRSA on environmental surfaces in a jail setting. We examined jail environmental surfaces to explore whether they might serve as reservoirs of viable methicillin-resistant Staphylococcus aureus (MRSA). We swabbed 132 surfaces, inoculated primary and secondary mannitol salts and oxacillin-resistant screening agar, and used API tests to identify S. aureus and E-tests to determine methicillin/oxacillin resistance. We recovered S. aureus from 10 (7.6%) surfaces; eight (6.1%) isolates were MRSA. We ran pulsed-field gel electrophoresis on six resistant isolates and observed three patterns, one of which was identical to that identified in a previous study of inmates' nasal specimens. Finding MRSA-contaminated surfaces on a variety of environmental surfaces in the absence of an overt outbreak emphasizes that correctional facilities should have protocols for environmental cleaning as a component of MRSA prevention. " ], "offsets": [ [ 0, 966 ] ] } ]
[ { "id": "BB-kb+ner-19622846_T3", "type": "Microorganism", "text": [ "Staphylococcus aureus" ], "offsets": [ [ 13, 34 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-19622846_T4", "type": "Microorganism", "text": [ "MRSA" ], "offsets": [ [ 45, 49 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-19622846_T5", "type": "Phenotype", "text": [ "MRSA" ], "offsets": [ [ 45, 49 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-19622846_T6", "type": "Habitat", "text": [ "environmental surfaces in a jail setting" ], "offsets": [ [ 53, 93 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000006" } ] }, { "id": "BB-kb+ner-19622846_T7", "type": "Habitat", "text": [ "jail" ], "offsets": [ [ 81, 85 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000695" } ] }, { "id": "BB-kb+ner-19622846_T8", "type": "Habitat", "text": [ "jail" ], "offsets": [ [ 107, 111 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000695" } ] }, { "id": "BB-kb+ner-19622846_T9", "type": "Habitat", "text": [ "jail environmental surfaces" ], "offsets": [ [ 107, 134 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000006" } ] }, { "id": "BB-kb+ner-19622846_T10", "type": "Phenotype", "text": [ "methicillin-resistant" ], "offsets": [ [ 195, 216 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-19622846_T11", "type": "Microorganism", "text": [ "Staphylococcus aureus" ], "offsets": [ [ 217, 238 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-19622846_T12", "type": "Microorganism", "text": [ "MRSA" ], "offsets": [ [ 240, 244 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-19622846_T13", "type": "Phenotype", "text": [ "MRSA" ], "offsets": [ [ 240, 244 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-19622846_T14", "type": "Habitat", "text": [ "primary and secondary mannitol salts" ], "offsets": [ [ 283, 319 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000007" } ] }, { "id": "BB-kb+ner-19622846_T15", "type": "Habitat", "text": [ "oxacillin-resistant screening agar" ], "offsets": [ [ 324, 358 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000041" }, { "db_name": "OntoBiotope", "db_id": "OBT000031" } ] }, { "id": "BB-kb+ner-19622846_T16", "type": "Phenotype", "text": [ "oxacillin-resistant" ], "offsets": [ [ 324, 343 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002920" } ] }, { "id": "BB-kb+ner-19622846_T17", "type": "Microorganism", "text": [ "S. aureus" ], "offsets": [ [ 391, 400 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-19622846_T18", "type": "Phenotype", "text": [ "methicillin", "resistance" ], "offsets": [ [ 426, 437 ], [ 448, 458 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-19622846_T19", "type": "Phenotype", "text": [ "oxacillin resistance" ], "offsets": [ [ 438, 458 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002920" } ] }, { "id": "BB-kb+ner-19622846_T20", "type": "Microorganism", "text": [ "S. aureus" ], "offsets": [ [ 473, 482 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-19622846_T21", "type": "Microorganism", "text": [ "MRSA" ], "offsets": [ [ 535, 539 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-19622846_T22", "type": "Phenotype", "text": [ "MRSA" ], "offsets": [ [ 535, 539 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-19622846_T23", "type": "Phenotype", "text": [ "resistant" ], "offsets": [ [ 588, 597 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" }, { "db_name": "OntoBiotope", "db_id": "OBT002920" } ] }, { "id": "BB-kb+ner-19622846_T24", "type": "Habitat", "text": [ "inmates' nasal" ], "offsets": [ [ 705, 719 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000767" } ] }, { "id": "BB-kb+ner-19622846_T25", "type": "Habitat", "text": [ "inmates" ], "offsets": [ [ 705, 712 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003291" } ] }, { "id": "BB-kb+ner-19622846_T26", "type": "Microorganism", "text": [ "MRSA" ], "offsets": [ [ 739, 743 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-19622846_T27", "type": "Phenotype", "text": [ "MRSA" ], "offsets": [ [ 739, 743 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] }, { "id": "BB-kb+ner-19622846_T28", "type": "Habitat", "text": [ "correctional facilities" ], "offsets": [ [ 857, 880 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000695" } ] }, { "id": "BB-kb+ner-19622846_T29", "type": "Microorganism", "text": [ "MRSA" ], "offsets": [ [ 948, 952 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1280" } ] }, { "id": "BB-kb+ner-19622846_T30", "type": "Phenotype", "text": [ "MRSA" ], "offsets": [ [ 948, 952 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002817" } ] } ]
[]
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27
BB-kb+ner-20005916
[ { "id": "BB-kb+ner-20005916__text", "type": "abstract", "text": [ "Usage of signaling in neurodegeneration and regeneration of peripheral nerves by leprosy bacteria. Multiple signaling pathways play key regulatory roles during the development of peripheral nervous system (PNS) and also in neuroregeneration process following nerve degeneration. Schwann cells, the glial cells of the PNS, by interacting with neuronal (axonal) ligands, mainly neuregulins via receptor tyrosine kinase (RTK) complex, ErbB2/ErbB3, initiate intracellular signaling pathways to drive proliferation and differentiation of Schwann cells, both during development and the process of regeneration and re-myelination after nerve injury. One of the major signaling kinases, extracellular signal-regulated kinase-1/2 (ERK1/2), that is also a downstream signaling pathway of neuregulin-ErbB2/ErbB3 activation, has been identified as a key regulator of Schwann cell proliferation, differentiation, demyelination and nerve regeneration. Recent studies have provided evidence that the bacterium that causes human leprosy, Mycobacterium leprae that has a unique capacity to invade Schwann cells of the adult PNS, utilizes the neuregulin-ErbB2/ErbB3 associated signaling network to the bacterial advantage. M. leprae directly bind to ErbB2 on myelinated Schwann cells and activate the RTK by a novel route that bypasses the classical neuregulin/growth factor-induced ErbB2-ErbB3 heterodimerization, and subsequently induce downstream the canonical Erk1/2 signaling, leading to myelin breakdown and subsequent axonal damage. This initial injury provides a survival advantage for M. leprae as it induces de-differentiation and generates myelin-free cells, which are highly susceptible to M. leprae invasion and promote bacterial survival. Once invaded M. leprae activate Erk1/2 via a non-canonical pathway and subsequently increase the cell proliferation and maintain the infected cells in de-differentiated state, thereby preventing remyelination. Therefore, by subverting major RTKs and signaling pathways in adult Schwann cells M. leprae appear to propagate the bacterial niche and maintain survival within the PNS. These studies may also provide new insights into our understanding of signaling mechanisms involve in both neurodegeneration and neuroregeneration. " ], "offsets": [ [ 0, 2264 ] ] } ]
[ { "id": "BB-kb+ner-20005916_T3", "type": "Habitat", "text": [ "peripheral nerves" ], "offsets": [ [ 60, 77 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000765" } ] }, { "id": "BB-kb+ner-20005916_T4", "type": "Habitat", "text": [ "peripheral nervous system" ], "offsets": [ [ 179, 204 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001251" } ] }, { "id": "BB-kb+ner-20005916_T5", "type": "Habitat", "text": [ "PNS" ], "offsets": [ [ 206, 209 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001251" } ] }, { "id": "BB-kb+ner-20005916_T6", "type": "Habitat", "text": [ "nerve" ], "offsets": [ [ 259, 264 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000765" } ] }, { "id": "BB-kb+ner-20005916_T7", "type": "Habitat", "text": [ "Schwann cells" ], "offsets": [ [ 279, 292 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000647" } ] }, { "id": "BB-kb+ner-20005916_T8", "type": "Habitat", "text": [ "glial cells of the PNS" ], "offsets": [ [ 298, 320 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000647" } ] }, { "id": "BB-kb+ner-20005916_T9", "type": "Habitat", "text": [ "PNS" ], "offsets": [ [ 317, 320 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001251" } ] }, { "id": "BB-kb+ner-20005916_T10", "type": "Habitat", "text": [ "Schwann cells" ], "offsets": [ [ 533, 546 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000647" } ] }, { "id": "BB-kb+ner-20005916_T11", "type": "Habitat", "text": [ "nerve" ], "offsets": [ [ 629, 634 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000765" } ] }, { "id": "BB-kb+ner-20005916_T12", "type": "Habitat", "text": [ "nerve injury" ], "offsets": [ [ 629, 641 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000970" } ] }, { "id": "BB-kb+ner-20005916_T13", "type": "Habitat", "text": [ "Schwann cell" ], "offsets": [ [ 855, 867 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000647" } ] }, { "id": "BB-kb+ner-20005916_T14", "type": "Habitat", "text": [ "nerve" ], "offsets": [ [ 918, 923 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000765" } ] }, { "id": "BB-kb+ner-20005916_T15", "type": "Habitat", "text": [ "human" ], "offsets": [ [ 1007, 1012 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002488" } ] }, { "id": "BB-kb+ner-20005916_T16", "type": "Microorganism", "text": [ "Mycobacterium leprae" ], "offsets": [ [ 1022, 1042 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1769" } ] }, { "id": "BB-kb+ner-20005916_T17", "type": "Habitat", "text": [ "Schwann cells of the adult PNS" ], "offsets": [ [ 1080, 1110 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000647" } ] }, { "id": "BB-kb+ner-20005916_T18", "type": "Habitat", "text": [ "adult" ], "offsets": [ [ 1101, 1106 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003245" } ] }, { "id": "BB-kb+ner-20005916_T19", "type": "Habitat", "text": [ "adult PNS" ], "offsets": [ [ 1101, 1110 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001251" } ] }, { "id": "BB-kb+ner-20005916_T20", "type": "Microorganism", "text": [ "M. leprae" ], "offsets": [ [ 1205, 1214 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1769" } ] }, { "id": "BB-kb+ner-20005916_T21", "type": "Habitat", "text": [ "myelinated Schwann cells" ], "offsets": [ [ 1241, 1265 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000647" } ] }, { "id": "BB-kb+ner-20005916_T22", "type": "Habitat", "text": [ "injury" ], "offsets": [ [ 1535, 1541 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000970" } ] }, { "id": "BB-kb+ner-20005916_T23", "type": "Microorganism", "text": [ "M. leprae" ], "offsets": [ [ 1576, 1585 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1769" } ] }, { "id": "BB-kb+ner-20005916_T24", "type": "Habitat", "text": [ "myelin-free cells" ], "offsets": [ [ 1633, 1650 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000647" } ] }, { "id": "BB-kb+ner-20005916_T25", "type": "Microorganism", "text": [ "M. leprae" ], "offsets": [ [ 1684, 1693 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1769" } ] }, { "id": "BB-kb+ner-20005916_T26", "type": "Microorganism", "text": [ "M. leprae" ], "offsets": [ [ 1748, 1757 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1769" } ] }, { "id": "BB-kb+ner-20005916_T27", "type": "Habitat", "text": [ "cell" ], "offsets": [ [ 1832, 1836 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000647" } ] }, { "id": "BB-kb+ner-20005916_T28", "type": "Habitat", "text": [ "infected cells" ], "offsets": [ [ 1868, 1882 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000647" } ] }, { "id": "BB-kb+ner-20005916_T29", "type": "Habitat", "text": [ "adult" ], "offsets": [ [ 2007, 2012 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT003245" } ] }, { "id": "BB-kb+ner-20005916_T30", "type": "Habitat", "text": [ "adult Schwann cells" ], "offsets": [ [ 2007, 2026 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000647" } ] }, { "id": "BB-kb+ner-20005916_T31", "type": "Microorganism", "text": [ "M. leprae" ], "offsets": [ [ 2027, 2036 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "1769" } ] }, { "id": "BB-kb+ner-20005916_T32", "type": "Habitat", "text": [ "PNS" ], "offsets": [ [ 2110, 2113 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT001251" } ] } ]
[]
[]
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BB-kb+ner-20073421
[ { "id": "BB-kb+ner-20073421__text", "type": "abstract", "text": [ "The effect of interferon-gamma and lipopolysaccharide on the growth of Francisella tularensis LVS in murine macrophage-like cell line J774. Francisella tularensis, a causative agent of human tularemia, displaying the ability to proliferate inside the human cells. To evaluate the growth potential of F. tularensis LVS strain in macrophage-like cell line J774 modulated by recombinant interferon gamma and E. coli derived lipopolysaccharide. Stimulation of J774 cells either by interferon-gamma or lipopolysaccharide alone, or especially in combination before infection F. tularensis, revealed protective effects. Higher concentrations of stimulating agents were needed to inhibit ongoing F. tularensis infection. Stimulation of J774 cell line by combination of interferon-gamma with lipopolysaccharide inhibits the intracellular growth of F. tularensis. " ], "offsets": [ [ 0, 855 ] ] } ]
[ { "id": "BB-kb+ner-20073421_T6", "type": "Microorganism", "text": [ "Francisella tularensis LVS" ], "offsets": [ [ 71, 97 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "263" } ] }, { "id": "BB-kb+ner-20073421_T7", "type": "Habitat", "text": [ "murine macrophage" ], "offsets": [ [ 101, 118 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002995" } ] }, { "id": "BB-kb+ner-20073421_T8", "type": "Habitat", "text": [ "murine" ], "offsets": [ [ 101, 107 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002530" } ] }, { "id": "BB-kb+ner-20073421_T9", "type": "Habitat", "text": [ "murine macrophage-like cell line J774" ], "offsets": [ [ 101, 138 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000062" } ] }, { "id": "BB-kb+ner-20073421_T10", "type": "Microorganism", "text": [ "Francisella tularensis" ], "offsets": [ [ 140, 162 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "263" } ] }, { "id": "BB-kb+ner-20073421_T11", "type": "Phenotype", "text": [ "causative agent of human tularemia" ], "offsets": [ [ 166, 200 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002806" } ] }, { "id": "BB-kb+ner-20073421_T12", "type": "Habitat", "text": [ "human" ], "offsets": [ [ 185, 190 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002488" } ] }, { "id": "BB-kb+ner-20073421_T13", "type": "Phenotype", "text": [ "ability to proliferate inside the human cells" ], "offsets": [ [ 217, 262 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000195" } ] }, { "id": "BB-kb+ner-20073421_T14", "type": "Habitat", "text": [ "human" ], "offsets": [ [ 251, 256 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002488" } ] }, { "id": "BB-kb+ner-20073421_T15", "type": "Habitat", "text": [ "human cells" ], "offsets": [ [ 251, 262 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000061" } ] }, { "id": "BB-kb+ner-20073421_T16", "type": "Microorganism", "text": [ "F. tularensis LVS" ], "offsets": [ [ 300, 317 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "263" } ] }, { "id": "BB-kb+ner-20073421_T17", "type": "Habitat", "text": [ "macrophage-like cell line J774" ], "offsets": [ [ 328, 358 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT000062" } ] }, { "id": "BB-kb+ner-20073421_T18", "type": "Habitat", "text": [ "macrophage" ], "offsets": [ [ 328, 338 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002995" } ] }, { "id": "BB-kb+ner-20073421_T19", "type": "Microorganism", "text": [ "E. coli" ], "offsets": [ [ 405, 412 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "110766" } ] }, { "id": "BB-kb+ner-20073421_T20", "type": "Habitat", "text": [ "J774 cells" ], "offsets": [ [ 456, 466 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002995" }, { "db_name": "OntoBiotope", "db_id": "OBT000062" } ] }, { "id": "BB-kb+ner-20073421_T21", "type": "Microorganism", "text": [ "F. tularensis" ], "offsets": [ [ 569, 582 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "263" } ] }, { "id": "BB-kb+ner-20073421_T22", "type": "Microorganism", "text": [ "F. tularensis" ], "offsets": [ [ 688, 701 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "263" } ] }, { "id": "BB-kb+ner-20073421_T23", "type": "Habitat", "text": [ "J774 cell line" ], "offsets": [ [ 728, 742 ] ], "normalized": [ { "db_name": "OntoBiotope", "db_id": "OBT002995" }, { "db_name": "OntoBiotope", "db_id": "OBT000062" } ] }, { "id": "BB-kb+ner-20073421_T24", "type": "Microorganism", "text": [ "F. tularensis" ], "offsets": [ [ 839, 852 ] ], "normalized": [ { "db_name": "NCBI_Taxonomy", "db_id": "263" } ] } ]
[]
[]
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Dataset Card for BioNLP 2019 BB

The task focuses on the extraction of the locations and phenotypes of microorganisms from PubMed abstracts and full-text excerpts, and the characterization of these entities with respect to reference knowledge sources (NCBI taxonomy, OntoBiotope ontology). The task is motivated by the importance of the knowledge on biodiversity for fundamental research and applications in microbiology.

Citation Information

@inproceedings{bossy-etal-2019-bacteria,
    title = "Bacteria Biotope at {B}io{NLP} Open Shared Tasks 2019",
    author = "Bossy, Robert  and
      Del{'e}ger, Louise  and
      Chaix, Estelle  and
      Ba, Mouhamadou  and
      N{'e}dellec, Claire",
    booktitle = "Proceedings of The 5th Workshop on BioNLP Open Shared Tasks",
    month = nov,
    year = "2019",
    address = "Hong Kong, China",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/D19-5719",
    doi = "10.18653/v1/D19-5719",
    pages = "121--131",
    abstract = "This paper presents the fourth edition of the Bacteria
    Biotope task at BioNLP Open Shared Tasks 2019. The task focuses on
    the extraction of the locations and phenotypes of microorganisms
    from PubMed abstracts and full-text excerpts, and the characterization
    of these entities with respect to reference knowledge sources (NCBI
    taxonomy, OntoBiotope ontology). The task is motivated by the importance
    of the knowledge on biodiversity for fundamental research and applications
    in microbiology. The paper describes the different proposed subtasks, the
    corpus characteristics, and the challenge organization. We also provide an
    analysis of the results obtained by participants, and inspect the evolution
    of the results since the last edition in 2016.",
}
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