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CABRI Search Information The CABRI Search is designed to allow a user to interrogate the CABRI catalogues via a simple, single entry interface and to order materials after searching. The steps involved in searching and ordering are as follows - Selecting the catalogue(s) Entering a query Including synonyms in a search Submitting the query Manipulating the results Using the shopping cart 1. Select the catalogue(s) to search The list of catalogues which are available is located at the top of the search page, divided into subsets as defined by the type of material in each catalogue, e.g. Human & Animal Cell Lines and Bacteria. Animal & Human Cell Lines Catalogues DSMZ ECACC ICLC All Catalogues ECACC HLA ECACC Hybridomas Bacteria Catalogues BCCM/LMG CABI CBS CIP NCCB DSMZ All Catalogues Fig. 1.1 - Example of Catalogue list To select the catalogue(s) of your choice, simply click in the checkbox beside catalogue name. To deselect it, click in the checkbox a second time. Animal & Human Cell Lines Catalogues DSMZ ECACC ICLC All Catalogues ECACC HLA ECACC Hybridomas Fig. 1.2 - Example of selection of "ECACC" catalogue from "Human & Animal Cell Lines" subset. Clicking on the name of the catalogue will return a page with more information on that catalogue, including reference contacts and a sample record. In many subsets, is a checkbox labeled "All Catalogues". Clicking in this checkbox will automatically select all the catalogues listed above it and to its left side. Clicking a second time will automatically deselect all those catalogues. Animal & Human Cell Lines Catalogues DSMZ ECACC ICLC All Catalogues ECACC HLA ECACC Hybridomas Fig. 1.3. - Clicking in the "All Catalogues" checkbox selects (and deselects) all catalogues in the subset above and to its left side (try it out!). It is also possible to select more than one catalogue in more than one subset. Simply click in the checkboxes beside whichever catalogues are desired. Remember of course that searching across disparate subsets could result in very few and/or meaningless results. Animal & Human Cell Lines Catalogues DSMZ ECACC ICLC All Catalogues ECACC HLA ECACC Hybridomas Bacteria Catalogues BCCM/LMG CABI CBS CIP NCCB DSMZ All Catalogues Fig. 1.4 - The "ECACC HLA" and "CABI Bacteria" catalogues correctly selected. If no valid selection of a catalogue is made, any attempts to submit a search will return an error as follows :- no catalogue was selected or no search term was entered 2. Entering a query The CABRI Search page has three fields for entering your query. The first field is the Unique Identifier which is usually the accession number unique to an entry within each individual catalogue. The second field is the Name, which is the designated name of an organism or cell type. The third field is Other Fields which will search on all other areas of a catalogue besides the accession number and the name. Each of these three headings is a hypertext link to a file which will inform which fields from each individual catalogue are catagorised under each heading. Unique Identifier Name Other Fields Fig. 2.1 - The CABRI Search entry fields. To search CABRI, simply type in your search term(s) in one or more of these search fields. Searches are not case sensitive (i.e. there is no distinction between upper and lower case characters). Name Fig. 2.2 - Search for the cell line named "HELA" More than one term can be entered. In this case, the resulting hits will be those entries that contain both terms. Other Fields Fig. 2.3 - Search for the cell lines whose description contains the words "human" and "liver". NB However, there are some factors to remember! Sometimes you may wish to search for a term which includes a space, e.g. the whole term "Bacillus subtilis". It is possible to do this by simply enclosing such terms in double quotes. Name Fig. 2.4 Searching for the complete term "Bacillus subtilis". It is important to remember that in general in CABRI, entries are indexed as single words and not entities containing spaces, except for searches on the name and Unique Identifier fields! NB When searching for a Unique Identifier it is not necessary to use the double quotes. When searching for a name, however, it is necessary to utilise the double quotes to search for correct names. Unique Identifier Fig. 2.5 Searching for the accession number 'iclc al96001'. Since it is a unique identifier, no double quotes are required. When searching using the double quotes, all other operators (see below), e.g. the wildcard, *, can be used. However, it is important to remember that the wildcard must be contained within the double quotes for it to be valid (to do otherwise may cause an error!) but boolean operators (such as ! and |) can occur outside them. Name Fig. 2.6 Valid use of a wildcard when searching with double quotes. Name Fig. 2.7 Invalid use of a wildcard when searching with double quotes. Name Fig. 2.8 Valid use of a boolean operator when searching with double quotes to find all Bacillus except subtilis. Name Fig. 2.9 Equally valid use of a boolean operator when searching with double quotes to find all Bacillus except subtilis. When entering a query, it is important to remember the function of the wildcard *. The wild card can be appended to a search term for more general searches. For example, entering the search term "rat*" will not only find all entries with the word "rat" in them, but also all entries with any word which begins with "rat" e.g. "rate", "ratify" etc. Thus, the wildcard essentially stands for "plus everything else". NB Wildcards can also be used at the start of a term e.g. "*ate" would locate everything which ends in "ate" such as "surrogate". Other Fields Fig. 2.10 - By appending the wildcard * to "rat", all terms containing words beginning with "rat" will be searched. Additional symbols which may be included in searching are boolean terms such as an exclamation mark, ! ("not") and a single verticle line or pipe, | ("or"). For example, the ! symbol could be used to find all rat cells that are not liver cells. Other Fields Fig. 2.11 - Find all entries that contain the word "rat" but not the word "liver". Equally, the | symbol could be used to find all rat or liver cells. Here, the result is (unlike with ! above) cumulative as all rat cells and all liver cells will be located and returned. Other Fields Fig. 2.12 - Find all entries with either the word "rat" or "liver" in them. More than one symbol can be used in a search, so combinations of these operators can be used to build quite complex expressions. Other Fields Fig. 2.13 - Find all cells that contain both "rat" and "liver" but not "hepatoma". When searching on more than one term, the default is for entries containing the first and the second (and subsequent) terms to be returned. You can explicitly state to use one and another using the ampersand, &. This may be useful in complex expressions when you want clarity of expression. Other Fields Fig. 2.14 - Find all cells that contain both "rat" and "liver" but not "embryonal". If no query is entered in the query box, an error will be returned. no catalogue was selected or no search term was entered Fig. 2.15 - Error message when a blank query is submitted. If the search term you entered is not present in the database, a message will inform you of this. Information: no entries found, query: "[ecacc_cell-AllText: rat liver*] " Fig. 2.16 - Error message generated when a search term is not found. 3. Including synonyms in a search To the right of the search fields, there is an optional checkbox labelled "Include synonyms of Name in search" Unique Identifier Name Other Fields Include synonyms of Name in search Fig. 3.1 Display showing Synonym checkbox. When searching on a name, checking this checkbox and then searching will perform a preliminary search of that name on a database of synonyms. If it is found that the name entered is in fact a synonym or, in the case of fungi, an alternate state (or indeed a synonym of an alternate state), then the correct name will be extracted from the synonym database and included in the search along with the original term entered and any results will be returned as normal. At present, the following catalogues have synonym data: BCCM/LMG Bacteria BCCM/MUCL Yeasts and Fungi CABI Bacteria CABI Filamentous Fungi CABI Yeasts CBS Bacteria CBS Filamentous Fungi CBS Yeasts DSMZ Bacteria DSMZ Fungi NCCB Bacteria Upon performing a search, the name of the organism returned from the above catalogues will contain a link to the relevant synonym database. If a synonym is present, clicking on the link will display it; however, if no synonym information is present, the link will be an invalid one and return an error. Information: no entries found, query: "[bccm_lmg_synonyms-name:Bacillus subtilis]" Fig. 3.2 Error returned when name "Bacillus subtilis" is clicked on after searching BCCM/LMG database as synonym data for this organism is unavailable in the associated synonym database. 4. Submitting the query To submit the query, click on the "Do Query". Clicking the "Reset" button will reset all the search details to blank, removing any search terms entered and unselecting all catalogues. NB It is imperative that the search is submitted by clicking the "Do Query" button and not by hitting the return key! Submitting a search by hitting the return key will result in an error. no catalogue was selected or no search term was entered Fig. 4.1 Error generated when search is submitted with the return key. 5. Manipulating the results Once a search has been performed, results (if any) will be displayed. All results returned are equally valid for the search terms entered and are merely listed in alphabetical order by catalogue searched. The resulting information can be manipulated in several ways. By default entries are returned in chunks of 30. If your search returns more than 30 entries, then subsequent chunks can be viewed by clicking in the "go to entries in chunk" section at the bottom of the results page. To change the number of entries displayed per chunk, alter the "View entries in chunks of" dropdown menu at the top left of the results page and click on the "view" button. To select particular entries to view or save, click on the checkbox beside their name. If you want to view or manipulate these, ensure that the radio button "Selected" is clicked in the "Perform a "view" operation on" section on the top left hand side of the results page. Perform a "view" operation on Selected All but selected View entries in chunks of 5 10 20 30 40 50 100 200 500 1000 2000 5000 10000 Fig. 5.1 Option to change chunk size and view selected or non selected items. You may alter the view of the results by choosing a new view in the dropdown box (which defaults to "SIMPLE") and clicking the view button. To view an entry in its entirety, simply click on the highlighted unique identifier beside the checkbox. If the catalogue searched has a synonym database associated with it, the name of the entry will be a hypertext link to any synonym information which may exist. If no such synonym data is available for a particular name, the link will return an error. 6. Using the shopping cart The shopping cart can be used to submit or format orders for purchase of materials from the various collections in CABRI. NB! For the shopping cart to work correctly, you must have a Javascript enabled browser which accepts cookies. Most modern browsers will have both of these set on by default, but it will not work with a browser below Netscape 3 or Internet Explorer 4. To add one or more items to the shopping cart, after performing a search, simply check the checkbox(es) beside the desired item(s) and click on the "Add to Cart" button at the top of the results page. NB! If there is more than one page of results, items must be added from each page separately. A new window will pop up with the items you have selected listed. Items you are adding will be highlighted in green and will be listed as either new items, or items already in the cart depending on whether you have previously added any. The quantity of items already in the cart will be listed and defaults to "1" for all new items being added. The items themselves will be hypertext links to pricing information. Item Quantity Items already present in Cart DSMZ_MUTZ:ACC 132 DSMZ_MUTZ:ACC 208 New items to be added to Cart DSMZ_MUTZ:ACC 297 Fig. 6.1 Addition of two items to the shopping cart (in green), one of which (ACC 132) has already been added to the cart previously. You may change the quantity of any item (both those being added or those already in the cart) simply by changing the value in the "Quantity" column. To completely remove an item from the cart, simply change the value in the "Quantity" column to zero and update the cart (using the "Add to Cart" or the "Update Cart" button, depending on which is available). If you are happy with the selection in your cart, click on the yellow "Add to Cart" button in the shopping cart window. NB! You must click on the yellow "Add to Cart" button in the cart window to actually add any items or change the quantities! If you wish to empty the cart completely, simply click on the "Empty Cart" button and upon answering "OK" in the ensuing confirmation box, your cart will be emptied. Once you have added items to your cart, you will then have the option of ordering them via the "Order" button. Doing so will display the items you have selected and the quantity. It may also, depending on the collection, allow you to select the type of distribution medium. Order Details Item Quantity Distribution DSMZ_MUTZ:ACC 132 1 Frozen Growing DSMZ_MUTZ:ACC 208 1 Frozen Growing DSMZ_MUTZ:ACC 297 1 Frozen Growing Fig. 6.2 Example of summary of items being ordered and choice of distributions There will also be a Personal Details form which has to be completed. This form requires standard information such as name, address etc. and may also require specific information for each collection such as Customer Number. Some of the information on this form is mandatory and the user will be informed if he tries to submit the form without completing these fields. Personal Details Name Institute Delivery Address Telephone Email Invoice Address (If different from Delivery Address) Fig. 6.3 The Personal details form Once the form has been completed, it may be submitted via email to the centres or formatted for printing and sending via postal mail. If submitted via email, the order details will be split and the centres who own the collections being ordered from sent the information relevant to them. A copy of the order form will also be sent to the orderer themselves at the email address entered in the "Email" field of the order form. There will be a CABRI Order Number displayed which is unique to this order and should be quoted if any subsequent query on the matter is required. There will also be a contact address for each centre ordered from. If the "Print" button is selected instead of the "Email" button on the order page, the information will be presented as a series of hypertext links for each centre being ordered from. Clicking on these links will display an order form which can be printed via the browser's print function and sent via normal postal mail. At the bottom of both the email and print pages, there are three buttons which can be used to save some information should you desire to do so. You have the option of saving your Order Details (i.e. the last contents of your cart), your Personal Details (i.e. Name, Address, etc) or both. It is possible to retrieve information you have saved by clicking on the "Retrieve Previous Order" button on the main CABRI search page. When you retrieve your cart, it allows you to confirm that overwriting your current cart is OK and if you agree, the saved cart is restored and can be added to or altered in the normal manner, or indeed simply submitted for order again. NB! If you choose to store information, you should be aware that cookies will be set on your own machine with some of this information. Therefore you must use the same machine again in order to retrieve this information. Also, if this machine can be accessed by another person, they may be able to retrieve the stored information. NB! In the case of both emailed and printed orders, the cart is automatically emptied when either is chosen. You may alter your personal details (if you have any stored) without going as far as ordering anything by simply clicking on the "Change Personal Details" button on the initial "Add to Cart" screen. Top of Page © The CABRI Consortium 1999-2020. This work cannot be reproduced in whole or in part without the express written permission of the CABRI consortium. Site maintained by Paolo Romano. Last revised in January 2020.