Help:Getting Started: Difference between revisions

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== Guidelines to style pages in this wiki ==
== 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.


'''Auto generated pages according to templates (no edits possible):'''
All templates are found under "Insert". The following three are currently implemened:
[[File:WikiTemplate open-book.png|left|frameless]]


- literature page (generated from DOI),
==== Literature reference ====
- investigation (generated from investigation template input on publication page),
Literature reference templates allow registering literature with a DOI to the wiki database and to cite sources.
- molecule page (only add abbreviation)


=== Publication pages ===
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 <nowiki>https://link.springer.com/content/pdf/10.1007/11926078_68.pdf</nowiki>    .
How to generate a new publication page: Authoring → Create a new Paper: enter title (default publication title, check formatting in the wiki), DOI, topic(s) it belongs to → Create paper
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:
{{#literature:|doi=10.1007/11926078_68}}
https://www.mediawiki.org/wiki/Manual:Page_title
[[File:WikiTemplate chemistry.png|left|frameless]]
'''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.'''


Publication pages show the legally available data from published papers. These are
==== Chemical formula ====
I) The investigations: Tables with data
The chemical formula template is a way to directly draw a chemical compound (dubbed "molecule") in the wiki. It uses the [https://lifescience.opensource.epam.com/ketcher/ Ketcher 2] editor.
II) Molecules used in the publication


Currently, the pages are structured by the headlines
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.
1) Catalyst
2) Photosensitizer
3) Investigation
4) Sacrificial electron donor
5) Additives (optional)


Each headline is formatted as sub-heading 2
<chemform smiles="N1=C2/C=C3/C=C/C(=C/C4C=C/C(=C/C5=CC=C(/C=C\1/C=C2)N5)/N=4)/N/3" inchi="1S/C20H14N4/c1-2-14-10-16-5-6-18(23-16)12-20-8-7-19(24-20)11-17-4-3-15(22-17)9-13(1)21-14/h1-12,21,24H/b13-9-,14-10-,15-9-,16-10-,17-11-,18-12-,19-11-,20-12-" inchikey="RKCAIXNGYQCCAL-CEVVSZFKSA-N" height="200px" width="300px" float="none">
The investigations are named: currently Table 1, Table 2
  -INDIGO-11142210272D


The appropriate molecules for 2) to 5) are drawn under their respective title. Solvents or gas atmosphere don’t need to be drawn, as do small (inorganic) additives.
  0  0  0  0  0  0  0  0  0  0  0 V3000
M  V30 BEGIN CTAB
M  V30 COUNTS 24 28 0 0 0
M  V30 BEGIN ATOM
M  V30 1 N 5.98871 -4.54988 0.0 0
M  V30 2 C 4.56202 -3.74634 0.0 0
M  V30 3 C 4.99445 -4.63645 0.0 0
M  V30 4 C 5.30731 -3.08612 0.0 0
M  V30 5 C 6.17466 -3.60897 0.0 0
M  V30 6 N 8.34186 -4.56114 0.0 0
M  V30 7 C 8.96423 -3.06908 0.0 0
M  V30 8 C 8.11464 -3.60828 0.0 0
M  V30 9 C 9.71958 -3.68546 0.0 0
M  V30 10 C 9.35762 -4.57836 0.0 0
M  V30 11 N 6.135 -6.34275 0.0 0
M  V30 12 C 5.55175 -7.86269 0.0 0
M  V30 13 C 6.38821 -7.30514 0.0 0
M  V30 14 C 4.75198 -7.23278 0.0 0
M  V30 15 C 5.10199 -6.32714 0.0 0
M  V30 16 C 9.24382 -7.72002 0.0 0
M  V30 17 N 8.49132 -6.30084 0.0 0
M  V30 18 C 8.34354 -7.24092 0.0 0
M  V30 19 C 9.47357 -6.17938 0.0 0
M  V30 20 C 9.93544 -7.0252 0.0 0
M  V30 21 C 7.13942 -3.14551 0.0 0
M  V30 22 C 9.89232 -5.35675 0.0 0
M  V30 23 C 7.4039 -7.75203 0.0 0
M  V30 24 C 4.53491 -5.48916 0.0 0
M  V30 END ATOM
M  V30 BEGIN BOND
M  V30 1 1 1 5
M  V30 2 1 2 3
M  V30 3 2 3 1
M  V30 4 2 4 2
M  V30 5 1 5 4
M  V30 6 1 6 10
M  V30 7 2 7 8
M  V30 8 1 8 6
M  V30 9 1 9 7
M  V30 10 2 10 9
M  V30 11 1 11 15
M  V30 12 1 12 13
M  V30 13 1 13 11
M  V30 14 2 14 12
M  V30 15 1 15 14
M  V30 16 2 16 20
M  V30 17 2 17 18
M  V30 18 1 18 16
M  V30 19 1 19 17
M  V30 20 1 20 19
M  V30 21 2 5 21
M  V30 22 1 21 8
M  V30 23 1 10 22
M  V30 24 2 22 19
M  V30 25 1 18 23
M  V30 26 2 23 13
M  V30 27 2 15 24
M  V30 28 1 24 3
M  V30 END BOND
M  V30 END CTAB
M  END
</chemform>


=== Molecule Drawings ===
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]'''.
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.
;Tips
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.
* 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 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.
==== Molecule links  ====
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.
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.
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!'''
[[File:WikiTemplate experiment.png|left|frameless]]


=== Investigations ===
==== Investigation ====
Columns with free text but guidelines:
The investigation template is used to enter experimental data into the wiki. Note that "[https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000066 Investigation]" designates any kind of planned process performed in a scientific study. There are two kinds of investigations: physical measurements and examinations are termed "[https://www.ebi.ac.uk/ols/ontologies/obi/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FOBI_0000070 Assay]" and "[https://www.ebi.ac.uk/ols/ontologies/mop/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMOP_0000543 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.
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 ===
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.
 
Several comment banners can be found under “Templates”
{{#experimentlist:|form=DemoExperiment1|name=batch1}}
[[Test MissingTemplates|MissingTemplates]]
 
[[Test MissingItems|MissingItems]]
==== 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 [https://www.semantic-mediawiki.org/wiki/Help:Semantic_search 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"

Latest revision as of 12:05, 22 November 2024

Introduction to templates[edit source]

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:

WikiTemplate open-book.png

Literature reference[edit source]

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]

WikiTemplate chemistry.png

Chemical formula[edit source]

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[edit source]

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.

WikiTemplate experiment.png

Investigation[edit source]

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.

Experiment 'Getting Started/batch1' does not exist.

Investigation link[edit source]

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[edit source]

Adding tags to selected terms[edit source]

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

Literature

[SM06] Semantic MediaWiki. Markus Krötzsch, Denny Vrandečić, Max Völkel, Lecture Notes in Computer Science 2006, Pages 935-942. DOI2: 10.1007/11926078_68
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