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LitCovid-PubTator

LitCovid-PD-HP

{"project":"LitCovid-PD-HP","denotations":[{"id":"T21","span":{"begin":439,"end":448},"obj":"Phenotype"},{"id":"T22","span":{"begin":643,"end":652},"obj":"Phenotype"},{"id":"T23","span":{"begin":993,"end":1002},"obj":"Phenotype"},{"id":"T24","span":{"begin":1173,"end":1182},"obj":"Phenotype"},{"id":"T25","span":{"begin":1912,"end":1921},"obj":"Phenotype"},{"id":"T26","span":{"begin":2000,"end":2009},"obj":"Phenotype"},{"id":"T27","span":{"begin":2081,"end":2090},"obj":"Phenotype"},{"id":"T28","span":{"begin":2272,"end":2281},"obj":"Phenotype"},{"id":"T29","span":{"begin":2814,"end":2823},"obj":"Phenotype"}],"attributes":[{"id":"A21","pred":"hp_id","subj":"T21","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A22","pred":"hp_id","subj":"T22","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A23","pred":"hp_id","subj":"T23","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A24","pred":"hp_id","subj":"T24","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A25","pred":"hp_id","subj":"T25","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A26","pred":"hp_id","subj":"T26","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A27","pred":"hp_id","subj":"T27","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A28","pred":"hp_id","subj":"T28","obj":"http://purl.obolibrary.org/obo/HP_0002090"},{"id":"A29","pred":"hp_id","subj":"T29","obj":"http://purl.obolibrary.org/obo/HP_0002090"}],"text":"We used the multi-modal data sets from four public data sets and one hospital (Youan hospital) in our research and split the hybrid data set in the following manner.For X-data: The CXR images of COVID-19 cases collected from the public CCD52 contained 212 patients diagnosed with COVID-19 and were resized to 512 × 512. Each image contained 1–2 suspected areas with inflammatory lesions (SAs). We also collected 5100 normal cases and 3100 pneumonia cases from another public data set (RSNA)53. In addition, The CXR images collected from the Youan hospital contained 45 cases diagnosed with COVID-19, 503 normal cases, 435 cases diagnosed with pneumonia (not COVID-19 patients), and 145 cases diagnosed as influenza. The CXR images collected from the Youan hospital were obtained using the Carestream DRX-Revolution system. All the CXR images of COVID-19 cases were analyzed by the two experienced radiologists to determine the lesion areas. The X-data of the normal cases (XNPDS), that of the pneumonia cases (XPPDS), and that of the COVID-19 cases (XCPDS) from public data sets constituted the X public data set (XPDS). The X-data of the normal cases (XNHDS), that of the pneumonia cases (XPHDS), and that of the COVID-19 cases (XCHDS) from the Youan hospital constituted the X hospital data set (XHDS).\nFor CT-data: We collected CT-data of 120 normal cases from a public lung CT-data set (LUNA16, a large data set for automatic nodule detection in the lungs54), which was a subset of LIDC-IDRI (The LIDC-IDRI contains a total of 1018 helical thoracic CT scans collected using manufacturers from eight medical imaging companies including AGFA Healthcare, Carestream Health, Inc., Fuji Photo Film Co., GE Healthcare, iCAD, Inc., Philips Healthcare, Riverain Medical, and Siemens Medical Solutions)55. It was confirmed by the two experienced radiologists from the Youan Hospital that no lesion areas of COVID-19, pneumonia, or influenza were present in the 120 cases. We also collected the CT-data of pneumonia cases from a public data set (images of COVID-19 positive and negative pneumonia patients: ICNP)56. The CT-data collected from the Youan hospital contained 95 patients diagnosed with COVID-19, 50 patients diagnosed with influenza and 215 patients diagnosed with pneumonia. The images of the CT scans collected from the Youan hospital were obtained using the PHILIPS Brilliance iCT 256 system (Which was also used for the LIDC-IDRI data set). The slice thickness of the CT scans was 5 mm, and the CT-data images were grayscale images with 512 × 512 pixels. Areas with 2–5 SAs were annotated by the two experienced radiologists using a rapid keystroke-entry format in the images for each case, and these areas ranged from 16 × 16 to 64 × 64 pixels. The CT-data of the normal cases (CTNPDS) and that of the pneumonia cases (CTPPDS) from the public data sets constituted the CT public data set (CTPDS). The CT-data of the COVID-19 cases from the Youan hospital (CTCHDS), the influenza cases from the Youan hospital (CTIHDS), and the normal cases from the Youan hospital (CTNHDS) constituted the CT hospital (clinically-diagnosed) data set (CTHDS).\nFor clinical indicator data: Five clinical indicators (white blood cell count, neutrophil percentage, lymphocyte percentage, procalcitonin, C-reactive protein) of 95 COVID-19 cases were obtained from the Youan hospital, as shown in Supplementary Table 20. A total of 95 data pairs from the 95 COVID-19 cases (369 images of the lesion area and the 95 × 5 clinical indicators) were collected from the Youan hospital for the correlation analysis of the lesion areas of the COVID-19 and the five clinical indicators. The images of the SAs and the clinical indicator data constituted the correlation analysis data set (CADS)."}

LitCovid-sentences

{"project":"LitCovid-sentences","denotations":[{"id":"T314","span":{"begin":0,"end":176},"obj":"Sentence"},{"id":"T315","span":{"begin":177,"end":319},"obj":"Sentence"},{"id":"T316","span":{"begin":320,"end":393},"obj":"Sentence"},{"id":"T317","span":{"begin":394,"end":493},"obj":"Sentence"},{"id":"T318","span":{"begin":494,"end":715},"obj":"Sentence"},{"id":"T319","span":{"begin":716,"end":822},"obj":"Sentence"},{"id":"T320","span":{"begin":823,"end":940},"obj":"Sentence"},{"id":"T321","span":{"begin":941,"end":1120},"obj":"Sentence"},{"id":"T322","span":{"begin":1121,"end":1304},"obj":"Sentence"},{"id":"T323","span":{"begin":1305,"end":1317},"obj":"Sentence"},{"id":"T324","span":{"begin":1318,"end":1800},"obj":"Sentence"},{"id":"T325","span":{"begin":1801,"end":1966},"obj":"Sentence"},{"id":"T326","span":{"begin":1967,"end":2109},"obj":"Sentence"},{"id":"T327","span":{"begin":2110,"end":2282},"obj":"Sentence"},{"id":"T328","span":{"begin":2283,"end":2451},"obj":"Sentence"},{"id":"T329","span":{"begin":2452,"end":2565},"obj":"Sentence"},{"id":"T330","span":{"begin":2566,"end":2756},"obj":"Sentence"},{"id":"T331","span":{"begin":2757,"end":2908},"obj":"Sentence"},{"id":"T332","span":{"begin":2909,"end":3153},"obj":"Sentence"},{"id":"T333","span":{"begin":3154,"end":3182},"obj":"Sentence"},{"id":"T334","span":{"begin":3183,"end":3409},"obj":"Sentence"},{"id":"T335","span":{"begin":3410,"end":3666},"obj":"Sentence"},{"id":"T336","span":{"begin":3667,"end":3774},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"text":"We used the multi-modal data sets from four public data sets and one hospital (Youan hospital) in our research and split the hybrid data set in the following manner.For X-data: The CXR images of COVID-19 cases collected from the public CCD52 contained 212 patients diagnosed with COVID-19 and were resized to 512 × 512. Each image contained 1–2 suspected areas with inflammatory lesions (SAs). We also collected 5100 normal cases and 3100 pneumonia cases from another public data set (RSNA)53. In addition, The CXR images collected from the Youan hospital contained 45 cases diagnosed with COVID-19, 503 normal cases, 435 cases diagnosed with pneumonia (not COVID-19 patients), and 145 cases diagnosed as influenza. The CXR images collected from the Youan hospital were obtained using the Carestream DRX-Revolution system. All the CXR images of COVID-19 cases were analyzed by the two experienced radiologists to determine the lesion areas. The X-data of the normal cases (XNPDS), that of the pneumonia cases (XPPDS), and that of the COVID-19 cases (XCPDS) from public data sets constituted the X public data set (XPDS). The X-data of the normal cases (XNHDS), that of the pneumonia cases (XPHDS), and that of the COVID-19 cases (XCHDS) from the Youan hospital constituted the X hospital data set (XHDS).\nFor CT-data: We collected CT-data of 120 normal cases from a public lung CT-data set (LUNA16, a large data set for automatic nodule detection in the lungs54), which was a subset of LIDC-IDRI (The LIDC-IDRI contains a total of 1018 helical thoracic CT scans collected using manufacturers from eight medical imaging companies including AGFA Healthcare, Carestream Health, Inc., Fuji Photo Film Co., GE Healthcare, iCAD, Inc., Philips Healthcare, Riverain Medical, and Siemens Medical Solutions)55. It was confirmed by the two experienced radiologists from the Youan Hospital that no lesion areas of COVID-19, pneumonia, or influenza were present in the 120 cases. We also collected the CT-data of pneumonia cases from a public data set (images of COVID-19 positive and negative pneumonia patients: ICNP)56. The CT-data collected from the Youan hospital contained 95 patients diagnosed with COVID-19, 50 patients diagnosed with influenza and 215 patients diagnosed with pneumonia. The images of the CT scans collected from the Youan hospital were obtained using the PHILIPS Brilliance iCT 256 system (Which was also used for the LIDC-IDRI data set). The slice thickness of the CT scans was 5 mm, and the CT-data images were grayscale images with 512 × 512 pixels. Areas with 2–5 SAs were annotated by the two experienced radiologists using a rapid keystroke-entry format in the images for each case, and these areas ranged from 16 × 16 to 64 × 64 pixels. The CT-data of the normal cases (CTNPDS) and that of the pneumonia cases (CTPPDS) from the public data sets constituted the CT public data set (CTPDS). The CT-data of the COVID-19 cases from the Youan hospital (CTCHDS), the influenza cases from the Youan hospital (CTIHDS), and the normal cases from the Youan hospital (CTNHDS) constituted the CT hospital (clinically-diagnosed) data set (CTHDS).\nFor clinical indicator data: Five clinical indicators (white blood cell count, neutrophil percentage, lymphocyte percentage, procalcitonin, C-reactive protein) of 95 COVID-19 cases were obtained from the Youan hospital, as shown in Supplementary Table 20. A total of 95 data pairs from the 95 COVID-19 cases (369 images of the lesion area and the 95 × 5 clinical indicators) were collected from the Youan hospital for the correlation analysis of the lesion areas of the COVID-19 and the five clinical indicators. The images of the SAs and the clinical indicator data constituted the correlation analysis data set (CADS)."}

PMC:7782580 / 42136-45910 JSONTXT

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LitCovid-PubTator

LitCovid-PD-HP

LitCovid-sentences

PMC:7782580 / 42136-45910 JSON TXT