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This page will guide you in adding a new publication, set of experiments or dataset to the wiki. | This page will guide you in adding a new publication, set of experiments or dataset to the wiki. | ||
== | == Guidelines to style pages in this wiki == | ||
'''Auto generated pages according to templates (no edits possible):''' | |||
- literature page (generated from DOI),<br> | |||
- investigation (generated from investigation template input on publication page),<br> | |||
- molecule page (only add abbreviation) | |||
=== Publication pages === | |||
How to generate a new publication page: Authoring → Create a new Publication: enter title (default publication title, check formatting in the wiki), DOI, topic(s) it belongs to → Create publiction<br> | |||
This leads to the new publication page with auto-generated infobox (About) from the DOI-generated literature page | |||
Page titles cannot contain brackets [] or slashes /, or hashtags #. For a full list, see: | |||
https://www.mediawiki.org/wiki/Manual:Page_title | |||
'''Publication pages (and topic pages) are the only ones that can be freely edited! Any changes to molecules or investigations must be made on the publication page. Only exception is adding an abbreviation to a molecule, this happens on the molecule page.''' | |||
'''How to select suitable publications/papers that are added to the Wiki?'''<br> | |||
The most important point for a selection of a publication to be represented in the Wiki as a novel article is that the publication deals with the scientific content of one of the (sub)topics. Further, the publication needs to contain data to be used for filling the investigation tables. This data can be given in the manuscript or the SI but it needs to be given with the original publication. If a publication does not contain data (or insufficient data) for the required information in the investigation, the publication would be out of scope for the Wiki. | |||
Publication pages show legally available data and information from published papers, e.g. | |||
I) The investigations: Tables with data<br> | |||
II) Molecules used in the publication | |||
III) Key findings of the original publication in brief | |||
Currently, the pages are structured by the headlines: | |||
1) Catalyst<br> | |||
2) Photosensitizer<br> | |||
3) Investigation<br> | |||
4) Sacrificial electron donor<br> | |||
5) Additives (optional)<br> | |||
Each headline is formatted as sub-heading 2 | |||
The investigations are named: currently Table 1, Table 2 | |||
The appropriate molecules for 1), 2), 4), 5) are drawn under their respective title. Solvents or gas atmosphere don’t need to be drawn, as do small (inorganic) additives. | |||
The | |||
=== Molecule Drawings === | |||
To draw molecules in Ketcher 2:<br> | |||
Bonds between ligands and metal are '''hydrogen bonds''' by default, unless this adds surplus hydrogens to the structure and those hydrogens cannot be removed by an appropriate charge. In this case, use an '''any bond'''. | |||
Remember to add charges on the molecule, especially on metal centers in complexes with counter ions.<br> | |||
Position ligands with aromatic rings correctly around the center metal atom. Try to avoid using the clean-up function, as this distorts the aromatic rings. | |||
Molecule collections with R-groups: Add R-groups when multiple rests are mentioned in literature. Use different (R1, R2, R3…) groups for different positions on the molecule, unless two positions are always substituted with the same rest. Specify the R-groups in the Ketcher “Define R-groups” menu.<br> | |||
R-groups can also be used for counter ions: add an unconnected R-group on the top right of the molecule drawing and specify one or multiple counter ions in the “Define R-groups” menu.<br> | |||
Small organic molecule ligands: draw individually instead of abbreviation<br> | |||
CO: triple bond, negative charge on C, positive charge on O | |||
(example: https://pubchem.ncbi.nlm.nih.gov/compound/139130150) | |||
'''Drawing molecules correctly is important to generate the right identifiers (InChIKey) and find molecule information in PubChem!''' | |||
=== Investigations === | |||
Columns with free text but guidelines: | |||
Additives: free text; gases according to list (…)<br> | |||
Solvent ratio: e. g. 4:1<br> | |||
Irradiation wavelength: number, “dark” (or empty), description of source<br> | |||
Columns with numbers: Leave empty when number is not given or zero | |||
=== Comment banner === | |||
Several comment banners can be found under “Templates” | |||
[[Test MissingTemplates|MissingTemplates]] | |||
[[Test MissingItems|MissingItems]] | |||
Latest revision as of 14:32, 20 March 2025
This page will guide you in adding a new publication, set of experiments or dataset to the wiki.
Guidelines to style pages in this wiki[edit source]
Auto generated pages according to templates (no edits possible):
- literature page (generated from DOI),
- investigation (generated from investigation template input on publication page),
- molecule page (only add abbreviation)
Publication pages[edit source]
How to generate a new publication page: Authoring → Create a new Publication: enter title (default publication title, check formatting in the wiki), DOI, topic(s) it belongs to → Create publiction
This leads to the new publication page with auto-generated infobox (About) from the DOI-generated literature page
Page titles cannot contain brackets [] or slashes /, or hashtags #. For a full list, see: https://www.mediawiki.org/wiki/Manual:Page_title
Publication pages (and topic pages) are the only ones that can be freely edited! Any changes to molecules or investigations must be made on the publication page. Only exception is adding an abbreviation to a molecule, this happens on the molecule page.
How to select suitable publications/papers that are added to the Wiki?
The most important point for a selection of a publication to be represented in the Wiki as a novel article is that the publication deals with the scientific content of one of the (sub)topics. Further, the publication needs to contain data to be used for filling the investigation tables. This data can be given in the manuscript or the SI but it needs to be given with the original publication. If a publication does not contain data (or insufficient data) for the required information in the investigation, the publication would be out of scope for the Wiki.
Publication pages show legally available data and information from published papers, e.g.
I) The investigations: Tables with data
II) Molecules used in the publication
III) Key findings of the original publication in brief
Currently, the pages are structured by the headlines:
1) Catalyst
2) Photosensitizer
3) Investigation
4) Sacrificial electron donor
5) Additives (optional)
Each headline is formatted as sub-heading 2 The investigations are named: currently Table 1, Table 2
The appropriate molecules for 1), 2), 4), 5) are drawn under their respective title. Solvents or gas atmosphere don’t need to be drawn, as do small (inorganic) additives.
Molecule Drawings[edit source]
To draw molecules in Ketcher 2:
Bonds between ligands and metal are hydrogen bonds by default, unless this adds surplus hydrogens to the structure and those hydrogens cannot be removed by an appropriate charge. In this case, use an any bond.
Remember to add charges on the molecule, especially on metal centers in complexes with counter ions.
Position ligands with aromatic rings correctly around the center metal atom. Try to avoid using the clean-up function, as this distorts the aromatic rings.
Molecule collections with R-groups: Add R-groups when multiple rests are mentioned in literature. Use different (R1, R2, R3…) groups for different positions on the molecule, unless two positions are always substituted with the same rest. Specify the R-groups in the Ketcher “Define R-groups” menu.
R-groups can also be used for counter ions: add an unconnected R-group on the top right of the molecule drawing and specify one or multiple counter ions in the “Define R-groups” menu.
Small organic molecule ligands: draw individually instead of abbreviation
CO: triple bond, negative charge on C, positive charge on O
(example: https://pubchem.ncbi.nlm.nih.gov/compound/139130150)
Drawing molecules correctly is important to generate the right identifiers (InChIKey) and find molecule information in PubChem!
Investigations[edit source]
Columns with free text but guidelines:
Additives: free text; gases according to list (…)
Solvent ratio: e. g. 4:1
Irradiation wavelength: number, “dark” (or empty), description of source
Columns with numbers: Leave empty when number is not given or zero
Comment banner[edit source]
Several comment banners can be found under “Templates” MissingTemplates MissingItems
