ROTGRID/APA/Irregular and other pain in the a** Tables
Opened this issue · 12 comments
We need to create a way to make such tables machine readable.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5237462/
activity_result | table_no | tabletype | notes
3. Results and Discussion >> 3.1 Antioxidant Activity | Table 2 | ROTGRID(OAP5+X) |
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- Results and Discussion >> 3.4 Larvacidal Activity | Table 3 | ROTGRID(OAS*P7+X) | ROTGRID
- Results and Discussion >> 3,3 Antimicrobial Activity | Table 4 | ROTGRID(OAS*P4) |
- Results and Discussion >> 3,3 Antimicrobial Activity | Table 5 | GRID(OAS*P4) |
- Results and Discussion >> 3.4 Larvacidal Activity | Table 6 | ROTGRID(OAS*P6) | Abnormal table.
ID | activity (antimicrobial = antibacterial + antifungal) | activity_method | activity_result | table_no | tabletype | notes | table_title | Table_footnote |
---|---|---|---|---|---|---|---|---|
PMC5324201 | Antioxidant | Methods >> Antioxidant activity | Results >> Antioxidant activity on DPPH radical | Table 11 | IRREG(OC2A*P8) ?? | CHECK P VALUE because the Standard antioxidants seem to share values in their Dose and Log columns, but have individual columns for each of their Average percent values | Antioxidant activity of Anethum sowa L. root essential oil and standards | ASA Ascorbic acid, BHT Tert-butyl-1-hydroxytoluene, Mean ± SD |
PMC5324201 | Cytotoxicity | Methods >> Cytotoxic activity of brine shrimp lethality bioassay | Results >> Brine shrimp cytotoxicity assay | Table 12 | APA(OCA*P8) | Effect of vincristine sulphate and essential oil of Anethum sowa L root on brine shrimp cytotoxicity assay | ASA Ascorbic acid, BHT Tert-butyl-1-hydroxytoluene, Mean ± SD | |
PMC5324201 | Antimicrobial | Methods >> Antimicrobial activity test | Results >> Antimicrobial activity of Anethum sowa L. root essential oil | Table 13 | APA(OC2AS10P5) | Anti-bacterial activity (Zone of Inhibition) of Anethum sowa L. root essential oil by diffusion method | CP Standard Ciprofloxacin (5 μg/disc), TE Standard Tetracycline (30 μg/disc) | |
PMC5324201 | Antimicrobial | Methods >> Antimicrobial activity test | Results >> Antimicrobial activity of Anethum sowa L. root essential oil | Table 14 | APA(OCA*P2) | I'm treating MIC and MBC as two parameters tested against one oil and one Control. I hope that’s correct. | Minimum inhibitory concentration (MIC) and Minimum bactericidal concentration (MBC) of Anethum sowa L. root essential oil and standard ciprofloxacin | Std. CP Standard Ciprofloxacin |
These tables are Bananas.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397855/
ID | activity (antimicrobial = antibacterial + antifungal) | activity_method | activity_result | table_no | tabletype_draft (Manny) | notes | tabletype_final (Peter) | table_title | Table_footnote | Col1 | Col2 | Col3 | Col4 | Col5 |
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PMC5397855 | Insecticidal (EO Test) | MATERIALS AND METHODS >> Repellency test | METHODS >> Mortality test | Table 1 | GRID(OC2AS3P4??? | In this case S = Instect stage (Larva, Pupa, Adult). Also note the footnote says 2LC50 and 99 but the table results is 90, not 99). I don’t konw how to account for the two concentrations. Perhaps as two controls?? | Lethal concentrations of the garlic essential oil against different developmental stages of Tenebrio molitor after 48 hours exposure. | 1IS, insect stage; 2LC50 and 99, lethal concentration causing 50, 90 and 99% mortality; 3EV, estimated value; 4CI, confidential interval; 5X2, chi-squared value for the lethal concentrations and fiducial limits based on a log scale with significance level at P < 0.001. | 1IS | 2LC | 3VE | 4IC | 5 X 2 | |
-- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
PMC5397855 | Insecticidal (EO Constituents: diallyl sulfide and diallyl disulfide) | MATERIALS AND METHODS >> Repellency test | METHODS >> Mortality test | Table 3 | GRID(O2AS3*??? | Notes: O = EO constituents in this case, not a whole EO. S = Different life stages of the same species, | Lethal concentrations of the diallyl sulfide and diallyl disulfide on different developmental stages of Tenebrio molitor after 48 hours exposure. | 1IS, insect stage; 2LC50 and 99, lethal concentration causing 50, 90 and 99% mortality; 3EV, estimated value; 4CI, confidential interval; 5X2, chi-squared value for the lethal concentrations and fiducial limits based on a log scale with significance level at P < 0.001. | Compounds | 1IS | 2LC | 3VE mg mL −1 | 4IC mg mL −1 |
APA
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5412227/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5423258/
ID | activity (antimicrobial = antibacterial + antifungal) | activity_method | activity_result | table_no | tabletype_draft (Manny) |
---|---|---|---|---|---|
5412227 | Antimicrobial | Material and methods >> Minimum inhibition concentration (MIC) and minimal bactericidal concentration (MBC) | Results and Discussion >> Antimicrobial activity | Table 3 | APA(OC2AS12P3) |
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5423258 | antimicrobial | Experimental >> Testing for antimicrobial activities | Results and Discussion >> | Table 4 | APA(O3CA2S8*P2) |
APA
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454990/
ID | activity (antimicrobial = antibacterial + antifungal) | activity_method | activity_result | table_no | tabletype_draft (Manny) | notes | tabletype_final (Peter) | table_title | Table_footnote | Col1 | Col2 | Col3 | Col4 | Col5 | Col6 | Col7 |
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PMC5454990 | Antibacterial and Cytotoxicity | Materials and Methods >> Antibacterial Assay | Results and Discussion >> Antimicrobial and Cytotoxic Activities | Table 3 | APA( | Antimicrobial and cytotoxic activities of Ocotea essential oils and some major essential oil components. MIC, minimum inhibitory concentration; IC50, median inhibitory concentration. | P. aer (Pseudomonas aeruginosa), E. coli (Escherichia coli), S. epi (Staphylococcus epidermidis), S. aur (Staphylococcus aureus), B. cer (Bacillus cereus). | Material {oils and components} | P. aer | E. coli | S. epi | S. aur | B. cer | -MCF7.00 | ||
-- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
APA
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5485486/
ID | activity (antimicrobial = antibacterial + antifungal) | activity_method | activity_result | table_no | tabletype_draft (Manny) | notes | tabletype_final (Peter) | table_title | Table_footnote | Col1 | Col2 | Col3 | Col4 | Col5 | Col6 | Col7 | Col8 |
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5485486 | Antibacterial | Material and Methods >> Bacterial Culturing Conditions >> MICs and MBCs Determination | Results >> Antibacterial Assays >> Determination of MIC and MBC | Table 3 | APA(OC2AS3*P7) | Inhibition zone diameters (mm) of A. citriodora essential oils on bacterial strains. | ∗AG: Agadir. BM: Beni Mellal. BE: Berkane. DE: Demnate. MA: Marrakech. | Bacterial strains | AG∗ | BM∗ | BE∗ | DE∗ | MA∗ | Ceftriaxone | Ofloxacin | ||
-- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
APA
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5485486/
NOVELTY: This one has EO Origin as first (unnamed) column!
ID | activity (antimicrobial = antibacterial + antifungal) | activity_method | activity_result | table_no | tabletype_draft (Manny) | notes | tabletype_final (Peter) | table_title | Table_footnote | Col1 | Col2 | Col3 | Col4 | Col5 |
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PMC5485486 | Cytotoxicity | Material and Methods >> Cytotoxicity Assay | Results >> Essential Oils Mediated Cell Cytotoxicity | Table 4 | APA | This one has EO Origin as first (unnamed) column! | Minimal inhibitory concentrations (MIC) and minimal bactericidal concentrations (MBC) of A. citriodora essential oils. | ∗AG: Agadir. BM: Beni Mellal. BE: Berkane. DE: Demnate. MA: Marrakech. | EO Origin | MIC | MBC | MIC | MBC | |
-- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
APA
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5497343/
Tricky one. Although there are only 7k column headings, below he header, the first 5 are split into two columns each representing Oil and Control
ID | activity (antimicrobial = antibacterial + antifungal) | activity_method | activity_result | table_no | tabletype_draft (Manny) | notes | tabletype_final (Peter) | table_title | Table_footnote | Col1 | Col2 | Col3 | Col4 | Col5 | Col6 | Col7 |
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5497343 | antibacterial | Antibacterial test >> Determination of antibacterial properties | Result >> MBC of the essential oil | Table 3 | APA | Tricky one. Although there are only 7k column headings, below he header, the first 5 are split into two columns each representing Oil and Control | [table_titl Minimum inhibitory concentrations (MIC) of essential oil of T. minuta flower e] | Key: A = Essential oil, B = ciprofloxacin, + = Growth, − = no growth | Bacteria | 0.5 | 0.25 | 0.125 | 0.06 | 0.03 | MIC(mg/mL) | |
-- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
5497343 | Antibacterial (Bactericidal) | Antibacterial test >> Determination of antibacterial properties | Result >> MBC of the essential oil | Table 4 | APA | Tricky one. Although there are only 7k column headings, below he header, the first 5 are split into two columns each representing Oil and Control | Minimum bactericidal concentrations (MBC) of essential oil of T. minuta flower | Key: A = oil, B = ciprofloxacin, + = Growth, − = no growth | Bacteria | 0.5 | 0.25 | 0.125 | 0.06 | 0.03 | MIC(mg/mL) | |
-- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
APA
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5543433/
ID | activity (antimicrobial = antibacterial + antifungal) | activity_method | activity_result | table_no | tabletype_draft (Manny) | notes | tabletype_final (Peter) | table_title | Table_footnote | Col1 | Col2 | Col3 | Col4 |
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PM5543433 | Antimicrobial | Antimicrobial activity >> Determination of MIC and MFC | Results and discussion >> Antimicrobial activities | Table 2 | APA(OCAS9*P2) | Note: Includes Gram pos/neg separation rows I don’t know why there is only one MIC … unless the one for the control is a known quantity. | Antifungal activity of ClEO and determination of the Minimum Fungicidal Concentrations (MFCs) expressed in mg/ml | Values are given as mean ± S.D. of triplicate experiments aDiameter of inhibition zones of including diameter of disc 6 mm b EO Lemon citrus essential oil (50 μl/well) cThe used concentration of Gentamicin was 10 μg/well | Strains | EOb | Gentamicinc | MIC (mg/ml) | |
-- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- |
IRREG
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5543433/
See notes
ID | activity (antimicrobial = antibacterial + antifungal) | activity_method | activity_result | table_no | tabletype_draft (Manny) | notes | tabletype_final (Peter) | table_title | Table_footnote | Col1 | Col2 | Col3 | Col4 | Col5 | Col6 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
5543433 | pH value changes?? | Methods >> Antioxidant testing assays >> DPPH radical scavenging activity | Results and discussion >> Antioxidant activities | Table 4 | IRREG | ??? Instead of a column heading, there are two below-the-header sections (similar to gram-pro/neg), to distinguish rows measuring pH and TBARS | Effect of ClEO and their combination with BHT on pH and TBARS (mg of malonaldehyde equivalents per kg of sample (mg/kg) of raw minced meat beef during storage at 4 °C | ±: Standard Error a-dAverages with different letters in the same column, for each parameter, are different (P < 0.05); C (Control), T1 (EO: 0.06%), T2 (EO: 0.312%), T3 (BHT: 0.01%), T4 (EO 0.312% and BHT 0.01%) | ??? Instead of a column heading, there are two below-the-header sections (similar to gram-pro/neg), to distinguish rows measuring pH and TBARS | 0 | 2 | 4 | 8 | 10 | |
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... ok, now they're just screwing with us. SOO irregular
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5551175/
ID | activity (antimicrobial = antibacterial + antifungal) | activity_method | activity_result | table_no | tabletype_draft (Manny) | notes | tabletype_final (Peter) | table_title | Table_footnote | Col1 | Col2 | Col3 | Col4 |
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5551175 | antitrypanosomal | ?? | Results and Discussion >> Inhibition of Trypanosoma brucei Proliferation : antitrypanosomal | Table 2 | IRREG | Inhibitory effects of essential oils from Cameroonian plants against Trypanosoma brucei brucei TC221 and Balb/3T3 cells. | IC50: half maximal inhibitory concentration. | Treatment | T. b. brucei (TC221) | Balb/3T3 | Selectivity Index (SI) | ||
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Thanks for committing the images of tables; these will be useful and we can discuss