Worm Breeder's Gazette 14(1): 20 (October 1, 1995)
These abstracts should not be cited in bibliographies. Material contained herein should be treated as personal communication and should be cited as such only with the consent of the author.
|1||The Sanger Centre, Cambridge CB10 1RQ|
|2||Dept.Biology, The University of Leeds LS2 9JT|
Descriptions of 55 gene expression patterns (Class: Expr_pattern) have been included in the worm release of ACEDB (4-8). 37 digitised images of worms were also included, which can be fetched from within the corresponding textual gene expression objects (Expr_pattern). The pictures are currently only realised on UNIX systems with an external viewer. Any external viewer that can read jpeg files will do, but we recommend using XV, which can be provided by us upon request. If you are not using XV, you must replace the command "xv" in the file wscripts/display_script with your own viewer command. (Note that the current system won't work on Macintosh, but this should be released soon.) The pictures are accessed in two stages, leading from Expr_pattern text objects to a Picture text object to the image itself. First select an Expr_pattern which contains a Picture field. Click on the name of any picture to call up the text window associated with a specific Picture; clicking on the words Pick_me_to_call will produce a worm picture in an XV window after some delay. Current pictures show worms with darker stains representing lacZ activity. To remove the image, click with right mouse button anywhere on the picture. This brings up the XV menu window in which one can click on quit. As well as the new class Expr_pattern, it was necessary to create Class Picture. Two other classes : Life_stage and Cell_group have been added to maximise the utility of the data and give both temporal and spatial qualities to gene expression. The presence of both Cell and Cell_group gives a more coherent structural hierarchy. In consequence, some of the so-called "Cells" in the Cell class have been moved into Cell_group (such as vulvaD). Other Cell_groups represent tissue-types (such as muscle) and organs (such as pharynx) but others are less well-defined. An injection of more data would help with the refinement of the current pragmatic rules for defining suitable objects in these classes. The classes Picture, Life_stage and Cell_group are not visible on the main class menu but they can be examined by clicking with the left mouse button on the triangle next to the words <In class.>, then selecting the class wanted. Small changes have been made to some classes (Paper, Sequence, Clone, Protein, Locus, Cell) to permit cross-referencing with the new text-based Expression patterns. Those of you willing and able to submit expression data, please note that the following data fields are additional to those listed when we requested expression pattern data previously [wbg13.5p89] :- Laboratory : as usual the two letter code if listed in ACEDB Remark : almost anything you like. Picture : a name for the picture file which needs to be in jpeg, gif or tiff format. Life_stage : as specific as possible e.g L2 larva, postembryonic, post L3, adult male etc. If expression ceases during development, please indicate when. Cell_group : a group of cells, either currently in database, or a new term embracing the cells affected e.g. tail ganglia, dorsal muscle. e.g. Cell_group e2 Cell e2DL Cell e2DR Cell e2V e.g. Cell_group rectal epithelium Cell rect_VR Cell rect_D Cell rect_VL This makes it clear to which Cell_group cells belong. If you send in a picture you may wish write a brief summary of the most cogent data from the Expression pattern under the heading DESCRIPTION. This text will appear on the 'record card' called by clicking on the Picture field from within an Expr_pattern window. Description should include keywords, in particular the gene/clone/sequence in question and the type of stain used, such as lacZ activity. Further refinement will take time and requires constructive input from the worm community : comments on the current presentation are sought, also new data and pictures. Please send contributions directly to firstname.lastname@example.org in the future.