id stringlengths 1 3 | document_id stringlengths 18 45 | passages list | entities list | events list | coreferences list | relations list |
|---|---|---|---|---|---|---|
0 | PMC2565068-02-Results-07 | [
{
"id": "PMC2565068-02-Results-07__text",
"type": "abstract",
"text": [
"scpC and slo are insufficient singly for the pathogenesis of invasive infections \nFinally, we assessed the influence of enhanced expression of the scpC or the slo gene on the virulence in a mouse model. As shown in Table 1, ... | [
{
"id": "PMC2565068-02-Results-07_T1",
"type": "Protein",
"text": [
"scpC"
],
"offsets": [
[
0,
4
]
],
"normalized": []
},
{
"id": "PMC2565068-02-Results-07_T2",
"type": "Protein",
"text": [
"slo"
],
"offsets": [
[
... | [
{
"id": "PMC2565068-02-Results-07_E1",
"type": "Process",
"trigger": {
"text": [
"infections"
],
"offsets": [
[
70,
80
]
]
},
"arguments": []
},
{
"id": "PMC2565068-02-Results-07_E2",
"type": "Regulation",
"trigg... | [] | [] |
1 | PMC2816692-03-Discussion-02 | [
{
"id": "PMC2816692-03-Discussion-02__text",
"type": "abstract",
"text": [
"Implications for type III secretion function \nThe interaction between SrcA and SsaN supports an emerging paradigm whereby secretion chaperones bring effector cargo to the T3SS through physical interaction with the hexamer... | [
{
"id": "PMC2816692-03-Discussion-02_T1",
"type": "Protein",
"text": [
"SrcA"
],
"offsets": [
[
70,
74
]
],
"normalized": []
},
{
"id": "PMC2816692-03-Discussion-02_T2",
"type": "Protein",
"text": [
"SsaN"
],
"offsets": [
... | [
{
"id": "PMC2816692-03-Discussion-02_E1",
"type": "Binding",
"trigger": {
"text": [
"interaction"
],
"offsets": [
[
50,
61
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMC2816692-03-Discussion-02_T1"... | [] | [] |
2 | PMC2858072-02-Results_and_Discussion-02 | [
{
"id": "PMC2858072-02-Results_and_Discussion-02__text",
"type": "abstract",
"text": [
"Regulation of carbon and nitrogen metabolism \nOne of the remarkable findings observed in our microarray analysis was that several genes related with metabolism were also differentially expressed. These include... | [
{
"id": "PMC2858072-02-Results_and_Discussion-02_T1",
"type": "Chemical",
"text": [
"carbon"
],
"offsets": [
[
14,
20
]
],
"normalized": []
},
{
"id": "PMC2858072-02-Results_and_Discussion-02_T2",
"type": "Chemical",
"text": [
"nitr... | [
{
"id": "PMC2858072-02-Results_and_Discussion-02_E1",
"type": "Gene_expression",
"trigger": {
"text": [
"expressed"
],
"offsets": [
[
185,
194
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMC2858072-... | [
{
"id": "PMC2858072-02-Results_and_Discussion-02_1",
"entity_ids": [
"PMC2858072-02-Results_and_Discussion-02_T3",
"PMC2858072-02-Results_and_Discussion-02_T4"
]
},
{
"id": "PMC2858072-02-Results_and_Discussion-02_2",
"entity_ids": [
"PMC2858072-02-Results_and_Discussion-02... | [] |
3 | PMC2639726-02-Results-04 | [
{
"id": "PMC2639726-02-Results-04__text",
"type": "abstract",
"text": [
"Validation of SPI-2 regulation \nSPI-2 encodes a type III secretion system and secreted effectors required for systemic mouse infection [8],[9]. To assess the effects of growth conditions on expression of the SPI-2 secretion ... | [
{
"id": "PMC2639726-02-Results-04_T1",
"type": "Organism",
"text": [
"mouse"
],
"offsets": [
[
119,
124
]
],
"normalized": []
},
{
"id": "PMC2639726-02-Results-04_T2",
"type": "Protein",
"text": [
"lacZ"
],
"offsets": [
... | [
{
"id": "PMC2639726-02-Results-04_E1",
"type": "Gene_expression",
"trigger": {
"text": [
"expression"
],
"offsets": [
[
339,
349
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMC2639726-02-Results-04_... | [
{
"id": "PMC2639726-02-Results-04_1",
"entity_ids": [
"PMC2639726-02-Results-04_T23",
"PMC2639726-02-Results-04_T24"
]
}
] | [] |
4 | PMC2816692-02-Results-05 | [
{
"id": "PMC2816692-02-Results-05__text",
"type": "abstract",
"text": [
"SrcA binds effector cargo destined for the SPI-2 T3SS \nSince structural and biochemical data unambiguously defined SrcA as a T3SS-associated chaperone, we used two experimental approaches to identify SrcA cargo(s). First, we... | [
{
"id": "PMC2816692-02-Results-05_T1",
"type": "Protein",
"text": [
"SrcA"
],
"offsets": [
[
0,
4
]
],
"normalized": []
},
{
"id": "PMC2816692-02-Results-05_T2",
"type": "Protein",
"text": [
"SrcA"
],
"offsets": [
[
... | [
{
"id": "PMC2816692-02-Results-05_E1",
"type": "Binding",
"trigger": {
"text": [
"binds"
],
"offsets": [
[
5,
10
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMC2816692-02-Results-05_T1"
}
... | [] | [] |
5 | PMC1913099-02-Results-Discussion-06 | [
{
"id": "PMC1913099-02-Results-Discussion-06__text",
"type": "abstract",
"text": [
"Differential Expression of Genes from Diverse Functional Categories \nWe identified a number of genes encoding proteins involved in housekeeping processes (such as carbohydrate and coenzyme metabolism) that were di... | [
{
"id": "PMC1913099-02-Results-Discussion-06_T1",
"type": "Chemical",
"text": [
"folate"
],
"offsets": [
[
373,
379
]
],
"normalized": []
},
{
"id": "PMC1913099-02-Results-Discussion-06_T2",
"type": "Chemical",
"text": [
"ATP"
]... | [
{
"id": "PMC1913099-02-Results-Discussion-06_E1",
"type": "Process",
"trigger": {
"text": [
"virulence"
],
"offsets": [
[
1201,
1210
]
]
},
"arguments": []
},
{
"id": "PMC1913099-02-Results-Discussion-06_E2",
"type":... | [
{
"id": "PMC1913099-02-Results-Discussion-06_1",
"entity_ids": [
"PMC1913099-02-Results-Discussion-06_T4",
"PMC1913099-02-Results-Discussion-06_T3"
]
}
] | [] |
6 | PMC2682197-02-Results-04 | [
{
"id": "PMC2682197-02-Results-04__text",
"type": "abstract",
"text": [
"M. tuberculosis Rv2623 is a nucleotide-binding protein \nWe began a biochemical characterization of Rv2623 in order to gain insight into the relationship between the molecular structure/function of this USP and it's growth-re... | [
{
"id": "PMC2682197-02-Results-04_T1",
"type": "Organism",
"text": [
"M. tuberculosis"
],
"offsets": [
[
0,
15
]
],
"normalized": []
},
{
"id": "PMC2682197-02-Results-04_T2",
"type": "Protein",
"text": [
"Rv2623"
],
"offsets... | [
{
"id": "PMC2682197-02-Results-04_E1",
"type": "Gene_expression",
"trigger": {
"text": [
"expressed"
],
"offsets": [
[
272,
281
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMC2682197-02-Results-04_T... | [] | [] |
7 | PMC2639726-03-Discussion-01 | [
{
"id": "PMC2639726-03-Discussion-01__text",
"type": "abstract",
"text": [
"Discussion \nDuring systemic mouse infection, Salmonella processes multiple environmental cues via more than 14 regulators We performed virulence assays on 83 regulators previously identified as required for Salmonella ent... | [
{
"id": "PMC2639726-03-Discussion-01_T1",
"type": "Organism",
"text": [
"mouse"
],
"offsets": [
[
28,
33
]
],
"normalized": []
},
{
"id": "PMC2639726-03-Discussion-01_T2",
"type": "Organism",
"text": [
"Salmonella"
],
"offse... | [
{
"id": "PMC2639726-03-Discussion-01_E1",
"type": "Process",
"trigger": {
"text": [
"infection"
],
"offsets": [
[
34,
43
]
]
},
"arguments": [
{
"role": "Participant",
"ref_id": "PMC2639726-03-Discussion-01... | [] | [] |
8 | PMC2593050-00-TIAB | [
{
"id": "PMC2593050-00-TIAB__text",
"type": "abstract",
"text": [
"The Two-Component Regulatory System VicRK is Important to Virulence of Streptococcus equi Subspecies equi \nThis study aims at evaluating the importance of the two-component regulatory system VicRK to virulence of the horse pathoge... | [
{
"id": "PMC2593050-00-TIAB_T1",
"type": "Two-component-system",
"text": [
"VicRK"
],
"offsets": [
[
36,
41
]
],
"normalized": []
},
{
"id": "PMC2593050-00-TIAB_T2",
"type": "Protein",
"text": [
"VicR"
],
"offsets": [
... | [
{
"id": "PMC2593050-00-TIAB_E1",
"type": "Regulation",
"trigger": {
"text": [
"Important"
],
"offsets": [
[
45,
54
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMC2593050-00-TIAB_E2"
},
{... | [] | [] |
9 | PMC2774163-02-Results-01 | [
{
"id": "PMC2774163-02-Results-01__text",
"type": "abstract",
"text": [
"Results \nThe formation of biofilms has been proposed to be controlled in response to environmental signals [39]. Given that protein phosphorylation is a common modification system used in signal transduction that changes the... | [
{
"id": "PMC2774163-02-Results-01_T1",
"type": "Organism",
"text": [
"P. aeruginosa"
],
"offsets": [
[
1668,
1681
]
],
"normalized": []
},
{
"id": "PMC2774163-02-Results-01_T2",
"type": "Organism",
"text": [
"P. aeruginosa"
],
... | [] | [] | [] |
10 | PMC2242835-02-Results-05 | [
{
"id": "PMC2242835-02-Results-05__text",
"type": "abstract",
"text": [
"Link between Mutation in phoP and Secretion of ESAT-6 \nAs PhoP fulfills important regulatory functions in M. tuberculosis [21,22], it was of primary interest to identify and study potential effector molecules whose involveme... | [
{
"id": "PMC2242835-02-Results-05_T1",
"type": "Protein",
"text": [
"phoP"
],
"offsets": [
[
25,
29
]
],
"normalized": []
},
{
"id": "PMC2242835-02-Results-05_T2",
"type": "Protein",
"text": [
"ESAT-6"
],
"offsets": [
... | [
{
"id": "PMC2242835-02-Results-05_E1",
"type": "Localization",
"trigger": {
"text": [
"Secretion"
],
"offsets": [
[
34,
43
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMC2242835-02-Results-05_T2"
... | [
{
"id": "PMC2242835-02-Results-05_1",
"entity_ids": [
"PMC2242835-02-Results-05_T17",
"PMC2242835-02-Results-05_T18"
]
}
] | [] |
11 | PMC2593050-04-DISCUSSION | [
{
"id": "PMC2593050-04-DISCUSSION__text",
"type": "abstract",
"text": [
"DISCUSSION \nVicK is essential in B. subtilis [2] and S. aureus [3] but not in S. pneumoniae [7], S. mutans [8], and S. pyogenes [6]. We successfully deleted the vicK gene of S. equi. Thus, VicK is not essential in S. equi. H... | [
{
"id": "PMC2593050-04-DISCUSSION_T1",
"type": "Protein",
"text": [
"VicK"
],
"offsets": [
[
12,
16
]
],
"normalized": []
},
{
"id": "PMC2593050-04-DISCUSSION_T2",
"type": "Organism",
"text": [
"B. subtilis"
],
"offsets": [
... | [
{
"id": "PMC2593050-04-DISCUSSION_E1",
"type": "Negative_regulation",
"trigger": {
"text": [
"attenuated"
],
"offsets": [
[
256,
266
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMC2593050-04-DISCUSS... | [] | [] |
12 | PMC2581603-03-Discussion | [
{
"id": "PMC2581603-03-Discussion__text",
"type": "abstract",
"text": [
"Discussion \nInfections caused by P. aeruginosa continue to be a leading cause of mortality among immunocompromised patients. The ability of P. aeruginosa to form biofilms promotes survival of the bacteria in the presence of ... | [
{
"id": "PMC2581603-03-Discussion_T1",
"type": "Organism",
"text": [
"P. aeruginosa"
],
"offsets": [
[
33,
46
]
],
"normalized": []
},
{
"id": "PMC2581603-03-Discussion_T2",
"type": "Organism",
"text": [
"patients"
],
"offse... | [
{
"id": "PMC2581603-03-Discussion_E1",
"type": "Process",
"trigger": {
"text": [
"Infections"
],
"offsets": [
[
12,
22
]
]
},
"arguments": [
{
"role": "Participant",
"ref_id": "PMC2581603-03-Discussion_T1"
... | [] | [] |
13 | PMC2266911-02-Results_and_Discussion-02-01-02 | [
{
"id": "PMC2266911-02-Results_and_Discussion-02-01-02__text",
"type": "abstract",
"text": [
"Hemolysins or hemagglutinin-related proteins \nThese extracellular toxins target red blood cells to provide access to iron, but often show activity against immune cells, thus contributing to the bacterial... | [
{
"id": "PMC2266911-02-Results_and_Discussion-02-01-02_T1",
"type": "Chemical",
"text": [
"iron"
],
"offsets": [
[
117,
121
]
],
"normalized": []
},
{
"id": "PMC2266911-02-Results_and_Discussion-02-01-02_T2",
"type": "Organism",
"text": [... | [
{
"id": "PMC2266911-02-Results_and_Discussion-02-01-02_E1",
"type": "Localization",
"trigger": {
"text": [
"transported"
],
"offsets": [
[
721,
732
]
]
},
"arguments": [
{
"role": "Theme",
"ref_id": "PMC226... | [] | [] |
14 | PMC2565068-00-TIAB | [
{
"id": "PMC2565068-00-TIAB__text",
"type": "abstract",
"text": [
"Incompetence of Neutrophils to Invasive Group A streptococcus Is Attributed to Induction of Plural Virulence Factors by Dysfunction of a Regulator \nGroup A streptococcus (GAS) causes variety of diseases ranging from common pharyng... | [
{
"id": "PMC2565068-00-TIAB_T1",
"type": "Organism",
"text": [
"Invasive Group A streptococcus"
],
"offsets": [
[
31,
61
]
],
"normalized": []
},
{
"id": "PMC2565068-00-TIAB_T2",
"type": "Organism",
"text": [
"Group A streptococcus"... | [
{
"id": "PMC2565068-00-TIAB_E1",
"type": "Process",
"trigger": {
"text": [
"Virulence"
],
"offsets": [
[
99,
108
]
]
},
"arguments": []
},
{
"id": "PMC2565068-00-TIAB_E2",
"type": "Process",
"trigger": {
"t... | [
{
"id": "PMC2565068-00-TIAB_1",
"entity_ids": [
"PMC2565068-00-TIAB_T2",
"PMC2565068-00-TIAB_T3"
]
},
{
"id": "PMC2565068-00-TIAB_2",
"entity_ids": [
"PMC2565068-00-TIAB_T9",
"PMC2565068-00-TIAB_T10"
]
}
] | [] |
15 | PMC1913099-00-TIAB | [
{
"id": "PMC1913099-00-TIAB__text",
"type": "abstract",
"text": [
"Novel Algorithms Reveal Streptococcal Transcriptomes and Clues about Undefined Genes \nBacteria-host interactions are dynamic processes, and understanding transcriptional responses that directly or indirectly regulate the expressio... | [
{
"id": "PMC1913099-00-TIAB_T1",
"type": "Organism",
"text": [
"group A streptococci"
],
"offsets": [
[
440,
460
]
],
"normalized": []
},
{
"id": "PMC1913099-00-TIAB_T2",
"type": "Organism",
"text": [
"streptococci"
],
"offs... | [
{
"id": "PMC1913099-00-TIAB_E1",
"type": "Process",
"trigger": {
"text": [
"infection"
],
"offsets": [
[
261,
270
]
]
},
"arguments": []
},
{
"id": "PMC1913099-00-TIAB_E2",
"type": "Process",
"trigger": {
"... | [] | [] |
End of preview. Expand in Data Studio
Dataset Card for BioNLP 2011 ID
The dataset of the Infectious Diseases (ID) task of BioNLP Shared Task 2011.
Citation Information
@inproceedings{pyysalo-etal-2011-overview,
title = "Overview of the Infectious Diseases ({ID}) task of {B}io{NLP} Shared Task 2011",
author = "Pyysalo, Sampo and
Ohta, Tomoko and
Rak, Rafal and
Sullivan, Dan and
Mao, Chunhong and
Wang, Chunxia and
Sobral, Bruno and
Tsujii, Jun{'}ichi and
Ananiadou, Sophia",
booktitle = "Proceedings of {B}io{NLP} Shared Task 2011 Workshop",
month = jun,
year = "2011",
address = "Portland, Oregon, USA",
publisher = "Association for Computational Linguistics",
url = "https://aclanthology.org/W11-1804",
pages = "26--35",
}
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