Intern:Advanced retrieval tool

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ART stands for Advanced Retrieval Tool and is a data mining tool written in Java to retrieve individually configured subsets of data from all tables of the relational data model. With ART the user is able e.g. to compare time series from different sites, parameters from different profiles, plotted on a common axis versus time or space or even allows to extract slices in time and/or space for a specific parameter. The use of ART needs some training but provides a powerful tool for the scientific work with data. A context sensitive help system is supplied. ART should only be used by experienced users with knowledge about the Pangaea data model !

The default screen of ART to access the different tables shows a graphic of the simplified data model. Each box in the data model reflects a table of the relational system. Clicking on the box of choice will open a retrieval window, which is configured for this specific type of information. The number of cards shown depends on the tables context. An example is given to retrieve analytical data. After clicking on Data, the user interface opens a window containing five tabs:

(1) ‘Retrieval’ – to define the query; (2) ‘Config’ – onfiguration of the output table; (3) ‘List’ – listing of data in a table; (4) ‘Map’ – data related sites plotted on a geographical map; (5) ‘Plot’ – visualization of data versus space.

Figure 12. ART retrieval card. The upper area displays the edited search expression (1). In the lower left field - subscribed ‘Criteria’ - the card shows the list of search criterions (2) that you can use in this specific context. This list will vary depending on the object that you selected in the data model. In the middle lower part a list of operators is displayed (3) and on the right are shown the values (4), that you typed in or selected from choices. If you click on a row of the search expression (1), the components from which it is made of are highlighted resp. displayed in the lower fields. You might then change this row by selecting different items in the lower fields. Different rows of the search expression are combined by the Boolean operators ‘AND’ and ‘OR’, thus giving you the possibility to do complex retrievals. The operators are located on the left side (5). You can delete rows of the search expression by clicking on that row and subsequently clicking on the ‘Delete line’ button (6). Values (4) are normally typed in. However, in many cases you can also use choice lists, or both, or only choices. Choice lists are useful, if you do not have an idea on how the value could be written. You can enter choices for a search criterion, if the choices button is highlighted or the add choices button is displayed. There are search criterions for which you will get immediately the complete list of choices after clicking the choices button. Other criterions, though, would result in hundreds or thousands of choice items. In this case you will get a further retrieval window, where you can first reduce the choices list by a subretrieval. If you are using the object ‘DATA’ you can press the ‘Add’ button to add parameters to the ‘Criteria’ list (2). You will get another retrieval window, where you can do a subretrieval for the parameters that you want to retrieve data for. The subretrieval window tries to reflect the previously defined search, thus confining the parameter retrieval to what can be expected in this context. E.g., if you have defined ‘Reference is equal to publication xy’, the subretrieval window will show the same search expression and clicking on the ‘Fetch’ button brings back exactly those parameters which are relevant to this publication. Search expressions can be saved and reloaded (7). In the ‘Options’ panel (8) you can set up the number of items to fetch (rows for metainformation, data items for DATA retrievals). On the lower part find the ‘Fetch’ button (9) to start a retrieval.

￼ Figure 13. ART list configuration card for Event retrievals. The configuration card presents a choice list of items to be displayed on the ‘List’ card as the final result of a search. On the left you find a choice list subscribed ‘Metainformation’ with all items that are available for display in the current context (1). On the right a default configuration is shown - named ‘Columns to display’ (2). The lists will vary depending on the object that you selected in the data model. You can add items to the default configuration either by clicking on the item and using the arrow (3) or by double clicking on an item in the left list. Items can also be removed (4). Items in the default configuration can be rearranged through the buttons ‘Up’ and ‘Down’ (5). Each item in the default list is associated with a specific format. Text items can not be configured. For numerical items the total number of digits, the precision, and leading zeros can configured. For date/time choose between a variety of formats (6). Use the ‘Save’ and ‘Load’ buttons (7) for custom configurations. ￼ Figure 15. ART list configuration of a Data retrieval. When using the retrieval for data there are two more fields to select ‘Parameters’ and ‘Geocodes’. Use the ‘Add’ button (8) to add parameters to the ‘Parameters’ list. A second retrieval window, will allow to extract the parameters of interest from the parameter dictionary. The subretrieval window may reflect the previously defined search expression on the ‘Retrieval’ card, thus confining the parameter retrieval to what can be expected in this context. From the list of ‘Geocodes’ you can choose the type of geocoding of your data. The special geocode ‘Age calculated’ can be used for data from geological profiles, which are related to an age model. Using Agem calculate the age is calculated as part of the retrieval, based on an existing age model. The ‘Split by events’ option (9) will return data laterally grouped by events, thus allowing a comparison of profiles between events (max 255 columns). Checking the ‘Split by versions’ option will split different versions of the same parameter. A retrieval is started by using the ‘Fetch’ button (10).

￼ Figure 15. ART List card showing the result of a data retrieval. List card This card displays the result of your retrieval as a text matrix, formatted as give on the ‘List config’ card. button have the functionality (1) to save the list, (2) to open the results in a browser window, (3) to select all rows in the list, (4) to gain more details on list items. Just click on single rows or SHIFT click to select multiple rows. Then click the ‘Details’ button and a further window shows cards with detailed information for each selected row. Sorting of a specific column by values is enabled through clicking in the header row above that column; dragging the delimiters between columns lets you change the horizontal size of the columns. ￼ Figure 16. ART Map card displaying the position of the retrieved data sets. Map card This card gives you an overview on the geographical context of the retrieved information; only available for objects having geographical coordinates. (1) zoom in, (2) geographical retrieval mode’ to define a geographical selection as an added constraint to the ‘Retrieval’ card with latitudes/longitudes as search criterions, (3) detail info opens a card with detailed information for each selected point, (4) zoom out, (5) back to global view, (6) map properties button opens a configuration to choose projection and center, (7) save grafic as Postscript, (8) save as pixel grafic ￼ Figure 17. ART plot card for displaying data columns in a line or scatter graph. Plot card If the first column of a result set contains numerical values and there is at least one further numerical column the ‘Plot’ card displays x-y-plots for each pair of numerical columns. If the values in the first column are continuously increasing or decreasing a line graph is drawn, otherwise a scatter plot. The detail info window ￼ Figure 18. ART detailed info window. The detail info window shows cards with detailed information for each selected. Only one card is displayed, the others are in the background as indicated by tabs. Bring other cards in front by clicking on its tab. Click on the ‘Save’ button to download the information of all cards to your harddisk. Global buttons are "Fetch": To start a retrieval. It is highlighted as soon as the search expression and the configuration is valid, "Close": to close the retrieval window, "?": to switch on context sensitive help. Metadata example ART retrieval example for metadata: finding gravity cores in the Mediterranean Sea: click on EVENT in the data model; click on list config tab; configure your table in ‘Columns to display’. You can select the searched criterions by double clicking on them and you can sort them by the up and down options. (e.g. include ‘Elevation’ and ‘Recovery’ from the metainformation menu, exclude ‘Gear type’ in columns to display); click on map card; click on rectangle in the tools bar; select the derived area by dragging the cursor in the global map keeping the mouse button pressed (e.g. Mediterranean Sea). The coordinates of the selected area are shown in the status line below the the map; click on retrieval tab (the search area is now defined); click on new line click on and click on ‘Gear type’ in the criteria menu and on ‘is equal to’ in the Boolean operator table; choices gives you a list of all gear types defined in the system; select gravity corer - wait until this field is inverted, then click ok; the retrieval is defined. Click on fetch; the list card gives the results, the map card shows sites; select i and click on one of the dots to get a more detailed information. Save the list from the list card localy by clicking on the disk symbol in the tool bar. Data example Retrieving data for a specific publication (sediment surface data from Pflaumann et al. 1996) click on DATA in the data model on the Retrieval card enter ‘Reference’ as search criteria click on Add choices. A choices window for Reference opens. Here you enter ‘Author(s) begins with Pflau’ and press the Fetch button. switch to the List card in the choices window and choose (after the download is complete) ‘Pflaumann, U, Duprat, J ...’ from the list and click on OK. The choices window closes and the choices list is filled with your selection (the retrieval is now defined). now click on the List config card. In contrast to the metainfo level there is no default configuration here. This is obvious, if you imagine that there are several thousands of parameters to choose from. You have to make a configuration: click the Add button above the Parameters field. A new window named Add parameter opens. In this window you can make now a subretrieval for the desired parameters. The little trick here is that the retrieval expression from the underlying DATA  window is replicated, so the only thing to do is push the Fetch button. Switch to the List card, which will show all parameters which are specific for the selected publication. Choose ‘Globigerina bulloides’ and ‘Globigerina quinqueloba’ from the list (with shift click) and click OK. The Add parameter window closes and your selection is displayed in the Parameters field. Now you can compose your configuration. Choose for display (with double click or use arrows): ‘Event label’ as metainformation, both ‘Globigerina’ as parameters, and ‘Latitude’,’Longitude’ as Geocodes. push the Fetch button - average download time is 30 sec. result are shown in the List card and an overview on related locations is given in the Map card. If you switch to the Map card, enable the detail info mode from the tool bar on the left side, and click on a specific point or group of points, a new window opens, displaying a detail info for each location. Variation (fast download - also the way for users of some browser platforms (see retrieval entry page) to save data on disk): on the Retrieval card enter ‘Fetch max. 1 data items’ and select ‘Complete results as textfile’. push the Fetch button again - after the download is complete, the List and Map cards will be empty, instead the results are displayed in a browser window.

Retrieval example for events in ART: Looking for gravity cores in the Mediterranean Sea

This example explains the way how to define a retrieval with ART (Advanced Retrieval Tool). Any retrival in one of the tables of the data model works in a similar way.

> start on http://www.pangaea.de
 * click on Data
 * click on ART (the data mining tool of PANGAEA is a Java applet which is now loaded to the local computer; if using ART for the first time, accept requester for the certificate)
 * click on Event (the Event table includes all samples/observations with its metadata)
 * click on the List config card
 * configure your table in Columns to display. You can select the searched criterions by double clicking on an item; sort with the up and down options. (e.g. include elevation and recovery from the "Meta Information" menu, exclude gear type).
 * click on the Map card.
 * select Geographical retrieval mode in the tool bar; select the derived area by dragging the cursor in the global map keeping the mouse button pressed (e.g. Mediterranean Sea). The coordinates of the selected area are shown in the status line below the map.
 * click on Retrieval card (the search area is now defined)
 * click on new line
 * click on and
 * click on gear type in Criteria and on is equal to in the Operator list
 * Choices... gives you a list of all gear types defined in the system.
 * select Gravity corer and click ok
 * click on Fetch - the job is beeing processed.
 * the List card shows the results
 * the Map card shows the sites; use the Zoom mode to zoom in
 * select the Detail info mode i and click on one of the dots to get detailed information.

You may save the list from the List card to your harddisk by clicking on the disk symbol in the tool bar or open the results in a new browser window which can also be saved to disc.

You can import the results into the program PanMap to draw your individual map. This implies that you have Latitude and Longitude in the first two columns of the list.