nikolamilosevic86 / TableDbSearch

Search for Tables in PMC

TableDbSearch

Search for Tables in PMC. This project is dependent on database that is produced by TableAnnotator project. It provides functionality for indexing and searching both tables as a whole and individual cells.

Running instructions

###Indexing You need to set up database connection information in settings.cfg file. Then for indexing tables run: java -cp TableDbSearch.jar TableDbSearchMain -index indexPath indexPath - path where index file is saved

For indexing cells run: java -cp TableDbSearch.jar CellDbSearch -index indexPath

###Searching Once database is indexed, tables can be searched in the following manner for tables containing "baseline characteristics" java -cp TableDbSearch.jar TableDbsearchMain -s -query "baseline characteristic"

Output will look like:

Searching for: (pmc_id:baseline pmc_id:characteristics) (pm_id:baseline pm_id:characteristics) (table_order:baseline table_order:characteristics) (table_caption:baseline table_caption:characteristics) (table_footer:baseline table_footer:characteristics) (table_footer:baseline table_footer:characteristics) (article_title:baseline article_title:characteristics) (spec_pragmatic:baseline spec_pragmatic:characteristics) (table_header:baseline table_header:characteristics) (table_stub:baseline table_stub:characteristics) (table_superRow:baseline table_superRow:characteristics) (table_data:baseline table_data:characteristics)
Time: 41ms
4408 total matching documents
1. 3393621
	Table:Table 1
   table_caption: Patient characteristics
2. 2361244
	Table:Table 2
   table_caption: Prognostic factors for overall survival, event-free survival and disease relapse (distant or local): univariate analysis
3. 1894974
	Table:Table 1
   table_caption: 
4. 3195264
	Table:Table 1
   table_caption: Demographic and baseline characteristics, indications for multidetector computer tomography (MDCT) and patient condition. BMI Body mass index
5. 3551874
	Table:Table without label
   table_caption: Table 1. Baseline characteristics and antibody response
6. 3277821
	Table:Table 1
   table_caption: Baseline demographics and clinical characteristics of study patients
7. 3162912
	Table:Table 4
   table_caption: Univariate analysis of time to progression (TTP) and overall survival (OS) using the Cox proportional hazard model
8. 526774
	Table:Table 1
   table_caption: Baseline characteristics for each group given at the individual and cluster levels.
9. 2699710
	Table:Table 1
   table_caption: Baseline demographics, disease characteristics, and changes after the 8-week treatment
10. 2927614
	Table:Table 2
   table_caption: Baseline characteristics of the cohort
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First number is order of the result, the second is PMC id.

Cells can be search with the following command: java -cp TableDbSearch.jar CellDbSearch -s -query "Age" or with query generation:

java -cp TableDbSearch.jar CellQuestionAnswering

Output will look like this:

Searching for: pmc_id:age pm_id:age table_order:age table_caption:age table_footer:age article_title:age spec_pragmatic:age cell_header:age cell_stub:age cell_superRow:age cell_data:age
3420 total matching documents
1. PMC:2686318
	Table:Table 1
   table_caption: Baseline demographics and patient history of SERF study participants
   cell_data: ?Age < 65
   cell_header: Baseline demographics/history ; Risk factor ;  ; 
   cell_stub: ?Age < 65
   cell_superRow:  Age
2. PMC:2686318
	Table:Table 3
   table_caption: Univariate and multivariate predictors of death in the SERF study
   cell_data: ?80 ? age vs. age < 65
   cell_header: Risk factor ;  ; 
   cell_stub: ?80 ? age vs. age < 65
   cell_superRow:  Age
3. PMC:3326700
	Table:Table 1
   table_caption: General demographic and clinics characteristics
   cell_data: Age
   cell_header: Variables ; 
   cell_stub: Age
   cell_superRow: 
4. PMC:3405223
	Table:Table 1
   table_caption: Patient baseline characteristics
   cell_data: ?Median age (range), years
   cell_header: Characteristic, n (% unless otherwise stated) ; 
   cell_stub: ?Median age (range), years
   cell_superRow:  Age
5. PMC:3164103
	Table:Table 5
   table_caption: Sociodemographic and clinical characteristics associated with control of treated hypertension, dyslipidaemia, type 2 diabetes, and obesity
   cell_data: Age
   cell_header: Control of hypertension (BP <140/90 mmHg)a odds ratio (95% CI) ; 
   cell_stub: Age
   cell_superRow: 
6. PMC:2693527
	Table:Table 1
   table_caption: Patient characteristics at time of accrual.
   cell_data: Age
   cell_header: Parameter ; 
   cell_stub: Age
   cell_superRow: 
7. PMC:1570351
	Table:Table 1
   table_caption: Clinical characteristics, pattern of care and outcome of HIV-seronegative patients (n = 81). MMC = mitomycin-C, RT = radiotherapy, OS = overall survival, CSS = cancer-specific survival, m = months.
   cell_data: age
   cell_header: Variable ; 
   cell_stub: age
   cell_superRow: 
8. PMC:3388560
	Table:Table 1
   table_caption: ?Patient characteristics
   cell_data: Age
   cell_header: Variable ; 
   cell_stub: Age
   cell_superRow: 
9. PMC:2853514
	Table:Table 5
   table_caption: Patient satisfaction 6-months after surgery correlated with selected preoperative variables and other measures of surgical outcome at 6 months.
   cell_data: Age
   cell_header:  ; 
   cell_stub: Age
   cell_superRow: 
10. PMC:3103451
	Table:Table 3
   table_caption: Factors influencing treatment response
   cell_data: Age
   cell_header: Factor ; 
   cell_stub: Age
   cell_superRow: 
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