Enhanced stock searching facilities and direct linking to sequence databases in AIMS via the World Wide Web

Randy Scholl and Jin Kim

ABRC, Ohio State University; and Dept. of Computer Science, Michigan State University, respectively.


A large volume of information is available on the Internet relating to genetics and molecular biology of Arabidopsis. However, this exists in different locations, and the most effective terms to enter when executing searches for information for these sources are sometimes uncertain. Hence, two new features have been added to the Web version of AIMS. These are automatic links to the sequence databases (including EST Sequence Analysis Database at the University of Minnesota and to EST Sequence and GenBank databases of NCBI) and a structured phenotypic searching tool for seed stocks which is based on a fixed, systematic set of categories. These system enhancements are described below, and examples of their use are included. This is part of the continued adaptation of AIMS to the Web, in which we have previously implemented a number of improvements including stock ordering and searching(see AIMS menu).


A. Description

Locating items of interest in a large database can sometimes be difficult and becomes a greater challenge when the user is unfamiliar with the terminology of the subject. Also, use of terminology can differ between individual scientists, and the database user is thus faced with the challenge of ascertaining the terms that individuals entering the data may have been employing. If there is any inconsistency of terminology in data entry, these difficulties are magnified. Hence, we have developed a series of categories for AIMS in which all mutants (seed stocks) can be classified and the classification system then employed as a stock-locating tool. This new addition is referred to as "structured phenotypic searching" and has just been added to the AIMS Web server - as a link from the seed stock searching page (the address of the structured phenotype search page is http://genesys.cps.msu.edu:3333/phenotype.html).

The logical base of this tool is an hierarchical classification scheme developed as a collaboration between members of the Chris Somerville lab and AIMS personnel. In this scheme, mutant stocks are assigned at least one category in the structure. The four main headings of the classification are I. Development, II. Cytogenetics, III. Biochemistry and IV. Environmental Interaction. To see the subcategories of any of these groups, you may click on the appropriate category name. While the categories are arranged into an outline format, there are also assigned sequence numbers which are shown at the left of each line. These exist simply for convenience of the user, and are designed to assist in keeping track of one's location in the outline at any point in time (or to flag a location of a category for future use)

The logic of the category structure is that main headings represent very widely based searches, subheading are more specific and sub-subheadings still more specific. Searching for the item "rosette leaf" will find any stock affecting size, shape, color or pubescence of the leaf (which are subheadings of "rosette leaf"). A stock which has been classified as possessing a characteristic that is general (e.g., the "Fertility" subsection (#61) of Development) will not be found in searches specifying more specific subsections (e. g., "Male sterility" (#62)).

For stocks which have complex phenotypes and/or multiple effects, more than one of the categories may be appropriate and are assigned. Hence, different search choices may find the same stock. In this sense, the category system also becomes a tool for identifying different stocks affecting single aspects of development or metabolism.

A search for stocks affecting silique development can be used as an example of a simple category search. The actions required to execute the search are; a) click on "roots" (line #5 ), and then click on "Search." The resulting page with the list of stocks, including choices for additional stock details, stock ordering, viewing and comparing of images operates exactly the same way as the similar page of the standard stock search. (Click here to connect to the search page and work the example.) Note that, as previously, single or multiple stocks can be highlighted for simultaneous viewing of details or order placement.

More complex or concise structured phenotype searches can be formulated using the structured phenotypic search screen by executing joint searches among different categories. For example, highlighting only "rosette leaf color" (item #14) finds a very large number of stocks. If, however, one suspects that a mutant of interest affects both leaf color and shape, these two categories can be simultaneously highlighted to achieve a joint search. (Highlighting of multiple categories is achieved on the Macintosh by clicking sequentially on the desired categories while depressing the "Apple" key; in other systems the action is similar with keys such as "control" being used instead of "Apple.") Note that this search will find multiple mutants which have genes cumulatively affecting all of the selected categories as well as stocks with single loci having multiple effects.

B. Comments

Some categories of this structure presently have large numbers of assigned mutants and others are more sparsely populated. Categories representing easily identifiable phenotypes, such as rosette leaf color, have large numbers. Searches utilizing such categories work correctly, although they may be slow - requiring up to several minutes to produce the found list of stocks. To minimize long searching times, we have classified the Feldmann T-DNA lines and recombinant inbred lines as Type = "lab strains" as opposed to the "mutant" classification utilized for individual mutant lines. Hence, choosing "mutant" using the button labelled "Type:" at the bottom of this screen eliminates these relatively large groups from the search pool and speeds the process. It is hoped that this scheme will assist researchers in locating desired stocks among the rapidly increasing array of mutants and other stocks of Arabidopsis. The present categories were designed to be comprehensive but not overly complicated. Undoubtedly there are neglected areas, and aspects which could have been constructed more logically. While alteration of the AIMS Sybase data structure to accommodate major changes would require substantial effort, it should be possible to make some changes in the categories, as warranted. A few such changes have been accomplished during the data entry by ABRC, as deficiencies of the structure were identified. Comments and suggestions on the structure are welcome as are suggestions regarding category assignments of specific stocks. We will do everything possible to make the category structure most useful.

If you have any questions, comments or suggestions regarding this database feature, feel free to contact ABRC or the AIMS manager.


Several important resources relating to Arabidopsis DNA sequences are now available via the World Wide Web. Links among all of these databases have been in existence for some time so that transfer among them is simple. However, AIMS and the sequence databases at NCBI and the Arabidopsis cDNA Sequencing Project deal with different data relating to the same entities - namely sequenced DNA clones, especially ESTs. AIMS maintains clone data, stock center availability of clones and histories of orders placed for clones. The sequence databases maintain sequence information and a very useful variety of similarity analysis results. Hence an opportunity exists to create direct links between corresponding data items. Linkages at both individual clone levels and general search pages have been created in AIMS and are described below. These links should complement the similar links that exist between the Minnesota cDNA sequence database and GenBank and between dbEST and GenBank.

A. Description of AIMS clone-to-remote sequence linkages

One potentially useful link of this type is a link from a clone in AIMS (with associated stock data) to the up-to-date sequence information available in GenBank, dbEST and the Arabidopsis cDNA Sequence Analysis Project. This has now been implemented in AIMS. Clone searches in AIMS are executed from the DNA search page, and in the resulting report page details of clones are accessed, orders initiated and the corresponding sequence similarity information from any of these three databases can be automatically accessed. Here is an example which can be worked through starting with a click on the hypertext "Start" below; 1) After the hypertext link is executed, the AIMS DNA search page should appear, and you then enter a clone number (e.g., 124f20t7) in the clone name field; 2) Click on "Submit Query"; 3) Examine the table at the bottom of the resulting search results page, and select appropriate hypertext items to initiate automatic searches in any of the three database. Click Start if you wish to initiate this search. If ***** is found in a cell of the table, the corresponding database cannot be accessed. These links should work for all AIMS EST entries to both dbEST and the Minnesota analysis database. In the latter case, an entry will only be seen if similarity results exist for the sequence in question. For all clones of AIMS having sequence entries in GenBank, the automatic link will be functional.

B. Description of AIMS main search-page links

Linkages from the main search page of AIMS to GenBank, dbEST, the Arabidopsis cDNA Analysis Project and ATGC at the University of Pennsylvania also have been created. This is similar to existing links among a number of the databases possessing Arabidopsis data. In the case of these links, the transfer is to the main search pages, where possible. Hence, searches within each of these databases can be launched directly from this location.

C. Comments

The principle for database linking and the level at which clone-sequence links are created pose several choices. The linking principle to the Minnesota database and dbEST is clone name, and GenBank accession number is employed in GenBank. These are items that are reliably associated with the correct sequence in the respective database and have produced consistent results in our initial testing. The level of linking is aimed at producing the same list of items that would be initially found by a search for clone name or identification number in the respective database. A clear alternative to this would be to target the specific sequence associated with the clone/stock. However, the former was chosen since the correct clone is usually the first item on the report list, and the additional choices represent potentially very useful information (e.g., as alternate or additional choices for study). It is thus hoped that the most useful possible link has been generated. Any suggestions for improvement of these new linkages are welcome.

The contacts for questions or comments regarding these or any other features of AIMS are: aims-manager@aims.cps.msu or arabidopsis+@osu.edu. All comments are welcome.