Search

Free text searches can be performed by entering key words like 'ATP liver' in the text field. This will retrieve all entries containing the search terms (also if only appearing in the publication title).
More sophisticated searches can be performed using the 'Advanced Search' tab. learn more


      
Advanced Search

  • enter search term(s) as free text (like Google)
  • press 'magnification glass' to start search
  • search results will be displayed below (scroll down ↓)
  • select entries (mark checkboxes)
  • if you want to export data, click the checkbox for each entry and finally click on the symbol in the upper right corner to proceed
<< back to single entry list

Bioschemas JSON definition for Entry ID 4064

          {
            "@context": "http://schema.org",
            "@type": "Dataset",
            "url": "http://sabiork.h-its.org/newSearch/index?q=entryID:4064",
            "mainEntity": {
                "@context": "http://schema.org",
                "@type": "Record",
                "@id": "http://identifiers.org/sabiork.kineticrecord:4064",
                "additionalType": "http://semanticscience.org/resource/SIO_000998",
                "identifier": "4064",
                "mainEntityOfPage": "http://sabiork.h-its.org/newSearch/index?q=entryID:4064"
             },
             "isPartOf": {
                "@type": "Dataset",
                "@id": "http://sabiork.h-its.org"
             },
             "citation": {
                    "@id": "http://www.identifiers.org/pubmed/15723541",
                    "@type": "ScholarlyArticle",
                    "additionalType": "http://semanticscience.org/resource/SIO_000087",
                    "name": {
                            "@language": "en",
                            "@value": "Kinetic and crystallographic analysis of active site mutants of Escherichia coli gamma-aminobutyrate aminotransferase"
                            }
             },
             "dateCreated": "2008-10-15 00:00:00.0",
             "additionalProperty": [
                {
                "@type": "PropertyValue",
                "additionalType": "http://semanticscience.org/resource/SIO_010000", 
                "name": "organism",
                "description": "Escherichia coli",
                "value": "http://identifiers.org/taxonomy:null"
                },
                {
                "@type": "PropertyValue",
                "additionalType": "http://semanticscience.org/resource/SIO_010043",
                "name": "protein",
                "value": "http://www.uniprot.org/uniprot/P22256 P50457",            
                "description": "P22256 P50457"
                },
                {
                "@type": "PropertyValue",
                "additionalType": "http://semanticscience.org/resource/SIO_010343", 
                "name": "enzyme",
                "value": "https://www.genome.jp/dbget-bin/www_bget?ec:2.6.1.19",
                "description": "4-aminobutyrate transaminase"
                },
                {
                "@type": "PropertyValue",
                "additionalType": "http://semanticscience.org/resource/SIO_010345",
                "name": "catalyzedReaction",
                "description": "4-Aminobutanoate + 2-Oxoglutarate = L-Glutamate + Succinate semialdehyde",
                "value": "https://www.genome.jp/dbget-bin/www_bget?rn:R01648" 
                },
                {
                "@type": "PropertyValue",
                "additionalType": "http://semanticscience.org/resource/SIO_000797",
                "name": "substrate",
                "description": "4-Aminobutanoate"
                },
                {
                "@type": "PropertyValue",
                "additionalType": "http://semanticscience.org/resource/SIO_000797",
                "name": "substrate",
                "description": "2-Oxoglutarate"
                },
                {
                "@type": "PropertyValue",
                "additionalType": "http://semanticscience.org/resource/SIO_000798",
                "name": "product",
                "description": "Succinate semialdehyde"
                },
                {
                "@type": "PropertyValue",
                "additionalType": "http://semanticscience.org/resource/SIO_000798",
                "name": "product",
                "description": "L-Glutamate"
                },
                {
                "@type": "PropertyValue",
                "additionalType": "http://semanticscience.org/resource/SIO_000803",
                "name": "inhibitor",
                "description": "Succinate"
                }
            ]
           }

Overview of the Entry Data   (go to Help / Information)
 One line in Overview represents one entry in the database.
 Click on the key/axis name to sort by that key. Hover over the heatmap to see the data values.
 Select values by clicking on the heatmap area. Multiple categories or ranges are selected by brushing.
 Overview visible axis/keys can be set in 'Visible Overview Axes' (click to open/close)
 Selection on all graphs can be reset by using 'Reset Highlighting'.
 Selected color scheme (set in 'Color Scheme (PC, SPM, KPPC, KPSP)'): Plasma (Warm, Dark)
  

    * Keys/axis take the appropriate selection from the whole color scheme (color legend can be seen when sorting by that key) e.g.
    two valued keys (e.g. Rate Equation) use the end colors of the color scheme while unique numerical keys (e.g. EntryID) use the whole color scheme.
    * Overview shows the coloring by every key/axis (best seen when sorted by that axis/key).
    All other graphs (PC, SPM, KPPC, KPSP) use one single axis/key for coloring (chosen in 'PC, SPM: color by axis', 'KPPC, KPSP: color by axis').
    * Non-existent values of a chosen key can be made more prominent by separately selecting their color in 'NULL ("-") value color (for all graphs)':     Default (color scale minimum) selected
Highlighted Data:

0






Axes:


Allowing only eight (seven plus Index) visible PC axis to prevent clutter.

SPM full matrix


Height of the PC and KPPC graphs is limited to 1200px. If the graph is larger some tick clutter might appear on the axes.


Kinetic Parameter Data:



Appearance:

Color Scheme
(PC, SPM, KPPC, KPSP)


NULL ("-") value color
(for all graphs)
The "null" color is visible if the data is sorted by the key that contains the null values.

PC, SPM: color by axis

KPPC, KPSP: color by axis


Various:
Parallel Coordinates (PC) of the Entry Data
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 Brush the axis to select the data (supports multiple selections).
 Detailed numerical data values can be seen on Overview or SPM (or in the Entry View tab).
 PC visible axis/keys can be set in 'Visible PC Axes (max 8)'
 PC colored by the key (set in 'PC, SPM: color by axis'):
Scatter Plot Matrix (SPM) of the Entry Data (numerical values only -> pH, Temperature, Year; kinetic data separately)
Loading graph, please wait...

 Brush any of the scatter plots to select the data.
 SPM visible axis/keys can be set in 'Visible SPM Axes'
 SPM colored by the key (set in 'PC, SPM: color by axis'):
Kinetic Parameters
Parallel Coordinates (KPPC) of the Kinetic Parameters (plus temperature, pH) (each entry can have many parameters)
Loading graph, please wait...


 Each entry can have multiple kinetic parameters that can be explored in the two graphs (KPPC, KPSP).
 Brush the axis to select the data.
 Detailed numerical data values can be seen on scatter plot KPSP (or in the Entry View tab).
 KPPC visible axis/keys can be set in 'Visible KPPC Axes'
 Currently showing types (set in 'Used Data Types'):
 KPPC colored by the key (set in 'KPPC, KPSP: color by axis'):
 KPPC, KPSP using the color scheme (set in 'Color Scheme (PC, SPM, KPPC, KPSP)'):
 Use KPSP to see the parameter details.
 KPPC local zoom status (allows detailed parameter space exploration not possible through the search):
    Parameter data types have to be reselected on zoom out (set in 'Used Data Types'). Not all types are available when zoomed.


Search button will give you the entries with all of thier parameters.
Limit the search locally first, by zooming and then selecting for the search.
Not selecting anything before the search will give you the initial result.
Scatter Plot (KPSP) of the Kinetic Parameter Values (plus temperature, pH) (each entry can have many parameters)
Loading graph, please wait...


  Points currently colored by:
 KPSP currently showing: Start Value vs
 KPSP serves as a addition of KPPC to see the parameter details (hover over point to see the values).
 Data can be zoomed and panned, but should be selected on KPPC.
Show/hide
First three graphs represent the general information for the database entries (Overview, PC, SPM).
Since each entry can contain several kinetic parameters, data space of the kinetic parameters can be separately explored (using KPPC and KPSP).
Last two graphs offer more details about the kinetic parameters (KPPC, KPSP) belonging to the entries and an option to explore through their data space.
A number of entries is obtained as a result of a search.

Select/highlight the subset of the data on one of the graphs. Number of highlighted data and the used attributes are visible on the top right side of the visualization tab (as is the number of the selected kinetic parameters).
By clicking on "Add Selection to Search" search is performed applying the selected criteria (highlighting) on the resulting data, thus refining the search. E.g.
If the current search query is a refinement of the previous query "Use Previous Query (Go Back)" button can be used to perform the previous query again. Only one automatic step back is possible, but the query can be manually manipulated if desired.


The graphs can be manipulated and the data highlighted in the following ways:
Overview of the resulting data entries is given in the heat map:
* Sort per column (upwards, downwards) by clicking on the attribute's title, hold the "shift" key and drag the column to rearrange columns.
* Show/hide columns using Visible Overview Axes.
* Highlight individual values by clicking.
* Highlight ranges by brushing (range of the sorted column, marked with a green line).
* While brushing, the thin green line (extending from the thick one) shows the full range of the selected categories.

Parallel Coordinates (PC):
* Sort axis by double clicking on the axis title, rearrange axes by dragging.
* Show/hide axes using Visible PC Axes (maximum 7 in addition to the Index axis).
* Highlight ranges by brushing on different axes (more ranges on a single axis are possible).
* Height of the PC graph is determined by the data, but limited (has minimum and maximum height). If the graph should be larger than the maximum height some tick clutter might appear on the axes.
* Numerical axes (e.g. pH and Temperature) have their null values shown below the line unlike categorical axes (like UniprotID) that have the null value or "-" as a category on the axis.

Scatter Plot Matrix (SPM):
* Show/hide attributes (numerical ones) using Visible SPM Axes.
* Highlight range by brushing on one of the scatter plots.
* Histograms show the attribute value frequency (divided into 10 bins/columns).
* Full SPM matrix can be shown.
* Details about the point values can be seen on a tooltip when hovering above the point.
* Points with no value ("-") are shown on the left side or under the axis.
* If only points with no value ("-") are present, they are shown under or left of the zero line on the bottom/left of the respective image.
* Lower tick values are valid for the histogram graphs while ticks on the left (plus the lower ones) are only valid for the scatter plots in the matrix.
Kinetic Parameter Parallel Coordinates (KPPC):
* EntryID axis on KPPC connects the kinetic parameters with the other graphs: each parameter belongs to an entry. One entry can have more parameters.
* Sort axis by double clicking on the axis title, rearrange axes by dragging.
* Show/hide axes using Visible KPPC Axes (Type and EntryID are always visible).
* Highlight ranges by brushing on different axes (single range possible on a single axis).
* Select shown kinetic parameter data type by selecting Used Data Types (must be at least one).
     * Types are preselected on search giving types: Km, Vmax, kcat as default (if present). The user can view any other type by selecting it in the GUI.
     * Currently selected types are stated below the graph.
* Start Value Original axis shows the original values of the parameter.
* Start Value Log axis is a logarithmic axis (since the original range of the shown values can be huge). The original range can be seen in Brush Info Kinetic Parameters PC.
* Graph can be searched locally by using the Zoom in / Zoom out buttons.
* Once the desired values are narrowed down (and selected on the KPPC) they can be searched by using the "Add Selection to Search" button.
     * the kinetic parameter search query uses the selected keywords (where available) e.g. ParameterType, AssociatedSpecies.
     * where no keywords are available the kinetic parameter search query uses entryIDs.
     * the result of the search gives full entries (meaning resulting parameter data is bigger than the selection).
* Height of the KPPC graph is determined by the data, but limited (has minimum and maximum height). If the graph should be larger than the maximum height some tick clutter might appear on the axes.
* For convenience, KPPC can also show temperature and pH values and the axis can also be colored by those values.
* Numerical axes (e.g. pH and Temperature) have their null values shown below the line unlike categorical axes that have the null value or "-" as a category on the axis.

Scatter Plot of the Kinetic Parameter Values (KPSP):
* Scatter pl2000 ored (using KPPC and KPSP).
Last two graphs offer more details about the kinetic parameters (KPPC, KPSP) belonging to the entries and an option to explore through their data space.
A number of entries is obtained as a result of a search.