Wikidata:WikiProject Chemistry/Tools
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Classification trees
[edit]In order to optimize the use of wikidata several classifications have to be applied on each chemical compounds:
- All pure components are defined by the property instance of (P31) with value chemical compound (Q11173).
- All pure components are defined by their elemental composition (properties still missing).
- All pure components are defined by their functional groups (property and list of functional groups used in that classification still missing).
Chemical element
[edit]- Mandatory classification:
- Each element is an instance of (P31) chemical element (Q11344).
- Each element is part of a group (Q83306).
- Each element is part of a period (Q101843).
- Each element is a subclass of isotope (Q25276).
- Mandatory properties:
- ..
Monitor changes
[edit]- List of chemical elements and their isotopes, generated by listeria : List of chemical elements on Wikidata. Also lists half-life, atomic number, numbre of neutrons. Can be added to your watchlist to monitor change on these data (they are vandalized sometimes).
- To follow the recent changes on elements and isotopes item, there is an associated watchlist : Special:RecentChangesLinked/Wikidata:WikiProject Chemistry/Elements. You can check this periodically.
- The page of the constraint violations for Complex constraint violations for “neutron number” also lists some consistency checks to monitor vandalisms. You can also add this to your watchlist. Consistency checks implemented :
- The "rank" of isotopes (currently coded as a qualifier of instance of (P31) should be the sum of their number of protons and neutrons
- The english label of isotopes seems to be normalized as
[elementname]-[number of nuclides], will be listed if something breaks the pattern.
Chemical compound
[edit]- Chemical compound and mineral form have to be splitted into 2 different items.
Definition
[edit]- chemical compound: each instance of chemical compound (Q11173) is a class of molecules of identical atomic structure.
- isotopic compound: each instance of isotopic compound (Q22332141) is a class of molecules of identical isotopic structure.
Examples
[edit]amyl alcohol (Q248797) — subclass of (P279): chemical compound (Q11173)
- 1-pentanol (Q151733), 3-pentanol (Q590622) — instance of (P31): chemical compound (Q11173); subclass of (P279): amyl alcohol (Q248797)
- 2-pentanol (Q210479): — subclass of (P279): amyl alcohol (Q248797)
- (R)-2-pentanol, (S)-2-pentanol — instance of (P31): chemical compound (Q11173); subclass of (P279): 2-pentanol (Q210479)
water (Q283) — instance of (P31): chemical compound (Q11173)
- heavy water (Q155890) — subclass of (P279): water (Q283); instance of (P31): isotopic compound (Q22332141)
Properties
[edit]- Mandatory properties:
- CAS Registry Number (P231): Only one value per chemical compound. Don't mix different numbers representing different compounds in the same item:
- For drugs: only the CAS number of the active substance in the organic form. Salt forms have to be described in other items.
- For hydrates: only the CAS number for the hydrate defined in the label of the item. Other hydrates have to be described in other items.
- PubChem CID (P662): Only one number per item and only the CID number.
- chemical formula (P274): Different ways are possible to describe the formula but put always the w:en:Hill formula and after other formulas based on other rules.
- canonical SMILES (P233): Use the canonical version of the SMILES identifier: this ensures an unique version of the SMILES.
- InChI (P234): Use the standard version of the InChI identifier like 1S/C2H6O/c1-2-3/h3H,2H2,1H3 and not 1/C2H6O/c1-2-3/h3H,2H2,1H3
- InChIKey (P235): Use the standard version of the InChIKey identifier has a single character at the end of the identifier (in the following example this is an N): BQJCRHHNABKAKU-KBQPJGBKSA-N.
- CAS Registry Number (P231): Only one value per chemical compound. Don't mix different numbers representing different compounds in the same item:
- Required properties:
- melting point (P2101): Important for solid at room temperature
- boiling point (P2102): Important for liquid at room temperature. Always indicate the pressure at which the meaure was done by using under pressure (P2077) as qualifier.
- Optional properties:
- Identifiers:
- Physical properties:
- Safety properties:
- Identifiers:
SPARQL queries
[edit]...
Visualizations
[edit]CDK Depict
[edit]Toolforge has an running CDK Depict functionality at https://cdkdepict.toolforge.org/
It can be used via a Wikidata gadget with https://www.wikidata.org/wiki/User:Egon_Willighagen/cdkdepict_gadget.js
Image gallery of all elements (ordered by atomic number)
[edit]#defaultView:ImageGrid
SELECT DISTINCT ?element ?elementLabel ?pic ?atomicNumber
{
?element wdt:P31 wd:Q11344 ; # element
wdt:P1086 ?atomicNumber . # atomic number
OPTIONAL { ?element wdt:P18 ?pic } # picture
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en,de" }
}
ORDER BY ASC(?atomicNumber)
Bubble chart of all elements by atomic mass
[edit]#defaultView:BubbleChart
SELECT DISTINCT ?element ?elementLabel (SAMPLE(?mass) AS ?oneMass)
{
?element wdt:P31 wd:Q11344 ; # element
wdt:P2067 ?mass . # mass
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en,de" }
}
GROUP BY ?element ?elementLabel
ORDER BY DESC(?oneMass)
Timeline of the elements by the time of their discovery
[edit]#defaultView:Timeline
SELECT DISTINCT ?element ?elementLabel ?pic ?discoveryDate
{
?element wdt:P31 wd:Q11344 ; # element
wdt:P575 ?discoveryDate . # date of discovery
OPTIONAL { ?element wdt:P18 ?pic }
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en,de" }
}
ORDER BY ASC(?discoveryDate)
Birthplaces of Chemistry Nobel Prize laureates (as a map)
[edit]#defaultView:Map
SELECT DISTINCT ?person ?geo ?personLabel
WHERE {
?person wdt:P166 wd:Q44585 ; # Nobel Prize
wdt:P19 ?birthplace .
?birthplace wdt:P625 ?geo .
SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en,de" }
}
Ions and corresponding salts families
[edit]Chemical element and corresponding simple substance
[edit]- Wikidata overview: