| Literature DB >> 24965054 |
Arnd Gross1, Sibylle Schirm, Markus Scholz.
Abstract
BACKGROUND: Mathematical modelling of biological processes often requires a large variety of different data sets for parameter estimation and validation. It is common practice that clinical data are not available in raw formats but are provided as graphical representations. Hence, in order to include these data into environments used for model simulations and statistical analyses, it is necessary to extract them from their presentations in the literature. For this purpose, we developed the freely available open source tool ycasd. After establishing a coordinate system by simple axes definitions, it supports convenient retrieval of data points from arbitrary figures.Entities:
Mesh:
Year: 2014 PMID: 24965054 PMCID: PMC4085079 DOI: 10.1186/1471-2105-15-219
Source DB: PubMed Journal: BMC Bioinformatics ISSN: 1471-2105 Impact factor: 3.169
Figure 1Vector representation. Pixels p1 to p4 define the coordinate system and correspond to axis intercepts y2, y1, x1, and x2, respectively. For each new pixel p5, coordinates x3, y3 will be calculated by ycasd.
Figure 2interface window. Representation of ycasd interface window. Settings apart from default as well as outputs are shown in black. White letters on grey background are labels for: “Define axes” area (a), Pixels p1 to p4 corresponding to axis intercepts (b), Values corresponding to axis intercepts (c), “Reset p*” button (d), Logarithmic y-Axis selector (e), Estimated clicking error (f), “Start/Stop capturing” button (g), “New data set” button (h), “Define output” area (i), Output matrix type selector (j), Output accuracy (k), Output text box (m).
Figure 3Sample figure.
Tool survey
| License | GPLv2 | GPLv2 | GPLv2 | GPLv2 | GPLv2, LGPLv2 | GPLv3 | GPLv3 |
| Platform | Java | R | Linux, Windows | Linux, Windows | Java | HTML5 | Windows |
| Version | 0.5a | 0.0.2 | 5.1 | 1.5.4 | 2.6.4 | 2.6 | 1.5 |
| Documentation | Sufficient | Sparse | Extensive | Sparse | Sufficient | Extensive | Sufficient |
| Single window | Yes | No | No | Yes | No | No | Yes |
| Figure import | Graphic | Graphic | Graphic, clipboard | Graphic | Graphic | Graphic, clipboard (Chrome) | not necessary |
| Diagram type | Cartesian | Cartesian | Raw pixel, Cartesian, polar, map | Cartesian | Raw pixel, Cartesian | Raw pixel, Cartesian, polar, ternary, map | Raw pixel, Cartesian |
| Calibration points | 4 | 4 | 3 | 4 | 4 (optional 3) | 4 | 4 |
| Log Axis | Both | n.a. | Both | Both | Both | Both | y-axis |
| Magnifier | Yes | No | No | Yes | No | Yes | No |
| Data point correction | Delete | Not available | Insert, delete, shift | Delete last point | Insert, delete, shift (only XML) | Delete | Insert, delete, overwrite |
| Axis correction | Shift | Re-capture | Shift | Re-capture | n.a. | Re-capture | Re-capture |
| Distortion correction level | Rotated, skewed | None | Rotated, skewed | Rotated, skewed | Rotated | Rotated, skewed | Rotated, skewed |
| Output format | Delimiter | R | Delimiter | Delimiter | Delimiter, xml | Delimiter, plotly | Matlab, R |
Comparison of tools regarding different categories. Not supported functions are denoted as “n.a.” (not available).