Help:Getting Started

Introduction to templates

Templates give structure to the wiki and keep the data well organized. There are several templates to choose from for various needs in describing the contents of a publication or set of experiments.

All templates are found under "Insert". The following three are currently implemened:

Literature reference

Literature reference templates allow registering literature with a DOI to the wiki database and to cite sources.

Select Literature reference, it will initially say "DOI is empty". Click on the text, select "Edit" and add in a DOI and confirm with "Apply changes". The reference will show an abbreviation in square brackets consting of the initials of the first three words in the title and the last two digits of the year of publication as follows [ABCxx]. Below is an example for the following paper: Krötzsch, Markus; Vrandečić, Denny; Völkel, Max (2006): Semantic MediaWiki. In:. International Semantic Web Conference: Springer, Berlin, Heidelberg, S. 935–942. Online verfügbar unter https://link.springer.com/content/pdf/10.1007/11926078_68.pdf .

[SM06]

Chemical formula

The chemical formula template is a way to directly draw a chemical compound (dubbed "molecule") in the wiki. It uses the Ketcher 2 editor.

Select Chemical formula. Pressing edit will open the form window and "Open Ketcher" opens the editor. Draw a chemical formula and confirm with "Apply changes". If the compound has R-groups, they need to be specified by selecting "Define R-groups". Important: Select the correct R-group from the dropdown menu, otherwise it might be an invalid entry. Ideally, the result will look something like the porphyrin ring below.

100593

Every molecule gets assigned a number upon its first registration in the wiki. Should the same molecule be drawn again, it will automatically be recognized as the previously entered structure. Molecules with R-groups will generate "Collections" and the R-groups van be viewed by clicking on [Show R-groups].

Tips

• If you have already an InchI-Key of the molecule you want to create, you can try to add it in the editor field of the chemical formula widget (other fields must be clear!). If it is known to PubChem, it will be drawn for you automatically.
• If you have already the SMILES string of a molecule, you can open the Ketcher editor, click on 'open' in the menu bar (second icon from the left), then "paste from clipboard". Now just copy&paste the SMILES string and let Ketcher draw the molecule for you.

Molecule links

Molecule links are used when the molecule that needs to be depicted already exists in the wiki and is referenced with or without image. Select the molecule link and add the ID, abbreviation, or copy the InChIKey of the molecule into the link, then select the checkbox Show image if desired.

Investigation

The investigation template is used to enter experimental data into the wiki. Note that "Investigation" designates any kind of planned process performed in a scientific study. There are two kinds of investigations: physical measurements and examinations are termed "Assay" and "Molecular process" denotes any process involving a reaction with one or more chemical compounds. Each investigation in turn consist of individual "experiments" wich are presented as rows in the table.

Selecting the template Investigation will prompt you to choose a form (e.g. Photocatalytic CO2 reduction) and give the experiments a name. Clicking on "Add experiment", then "+ Add another" will open the form in which to enter the data.

Investigation link

Investigation links are queries used on topic pages to compare all experiments in the wiki. Only experiments of the same investigation type can be compared in one query. The properties of experiments can be queried for desired characteristics, and the experiments ordered by one or more columns. The pages about SMW query syntax hold more information on how to write queries.

Selected functions

Adding tags to selected terms

Adding tags from TIB's terminology service needs to change to the edit mode, selcting a term in the description and pressing "Ctrl"