Manual for the FunCat Database Tool
Manual for the Search- and Update Interface of the FunCat Database
- Search function
- A simple search can be performed, selecting a column of the database, in which to search and entering a search term in the appropriate field. The software tolerates so called whitespace characters (Space, Tab) an the beginning and end of the search term. A error message is displayed when either the search term or the column, which to search, is missing.
The entered search terms are expanded to the right only, if they are numbers and to the left and right in all other cases. The search is not case sensitive.
- The search can additionally be extended or restricted, using the boolean operators AND or OR. Selecting Exact (standard preselection) searches for exact matches with the entered search term. The boolean operators are not useable for a number search.
- The search result is displayed as a list of clickable FunCat numbers and their description.
- Clicking on the FunCat number of interest in the overview table leads to a detailed view of the dataset assigned to this FunCat number.
- The content of the fields funlink and reference_PMID are (when present) clickable and lead either to the corresponding dataset (funlink) or to the Homepage of the NCBI to the PubMed database. The reference_PMID number leads to the abstract of interest. The link overview leads to an overview page for the PMID's in the dataset.
- The column GO Mapping contains a mapping of the Gene Ontology consortium's categories to the FunCat categories.
- The update link leads to the update function for this dataset (administrative task).
- Update function (only internal)
- Clicking on the update link in the detailed view of the dataset leads you to a page where all editable columns of the set are displayed in form fields and can be altered. The columns number and description are not editable.
- You can enter all sorts of information into the fields but please consider the following suggestions:
- Only values entered into the funlink field are checked for correctness. All other fields cannnot be checked, due to technical reasons. Please be very careful with the data you enter!
- Multiple entries in the fields reference_PMID and funlink have to be divided with simple commas.
- In the fields reference_PMID, funlink, EC_number and tag, all whitespace characters will be removed automatically. In the field reference_PMID additionally semicolons, colons and full stops will be substituted with commas automatically.
- If you want to delete all your changes and the update button has not been clicked, please use the clear button to get rid of only your changes to the dataset.
- A click on update writes your changes to the MySQL table permanently. You are beeing presented a summary of the new dataset. Please proof-read it and use the back button of your browser to correct the data. After a correction press update again.
- From the summary view of the changed dataset, a link leads to the detailed view of this dataset.
- Viewing species specific annotations
- On the detailed results page you can choose a species from the Drop Down Menue, which leads you to an webpage displaying all proteins with code, description and all annotated FunCat categories, that are annotated in the FunCat categorie you have been viewing.
- The different proteins are divided by a line.
- Manual and auto refer to the mechanism or the annotation. Automatically annotated proteins have been classified into the FunCat categories, depending on sequence similarity via the Pedant system. Manual annotated proteins have been manually revised and corrected.
- The search frame is permanent on top and stays with you the whole time you work with the FunCat database.
- If you use the back button of your browser, you may not be presented with the newest modified dataset, depending on your browser preferences. So please use the links to navigate the functions whenever possible.
- If a mistake did occur and you don't know how to correct it, please contact the email address in the left frame. A daily backup is availiable, so don't be frightened.
- Suggestions and critics are always welcome!
Last modified: Fri May 14 09:52:59 CEST 2004