identifier from database and ontology of molecular entities focused on 'small' chemical compounds
|Description||ChEBI (Q902623): Chemical Entities of Biological Interest, also known as ChEBI, is a database and ontology of molecular entities focused on 'small' chemical compounds, that is part of the Open Biomedical Ontologies effort.|
|Represents||ChEBI (Q902623), Chemical Entities of Biological Interest (Q55118295)|
|Applicable "stated in" value||ChEBI (Q902623)|
|Data type||External identifier|
|Template parameter||Template:Infobox drug (Q6033882) ChEBI , Template:Chembox (Q52426) ChEBI|
|Domain||term (note: this should be moved to the property statements)|
|Allowed values||\d+ (Only digits, without the prefix "CHEBI:")|
|Usage notes||Only primary CHEBI identifiers (from "CHEBI ID" field) should be present in items; secondary identifiers (from "Secondary ChEBI IDs" field) should not be added.|
|Example||dimethyltryptamine (Q407217) → 28969 (RDF)|
acetylene (Q133145) → 27518 (RDF)
ethylene (Q151313) → 18153 (RDF)
|Tracking: usage||Category:Pages using Wikidata property P683 (Q26249995)|
|See also||IEDB Epitope ID (P4168)|
|Proposal discussion||Proposal discussion|
|Search for values|
|Database reports/Constraint violations/P683#Format, hourly updated report, SPARQL|
Single value: this property generally contains a single value. (Help)Exceptions are possible as rare values may exist. Exceptions can be specified using exception to constraint (P2303).
List of violations of this constraint: Database reports/Constraint violations/P683#Single value, SPARQL
Distinct values: this property likely contains a value that is different from all other items. (Help)Exceptions are possible as rare values may exist. Exceptions can be specified using exception to constraint (P2303).
List of violations of this constraint: Database reports/Constraint violations/P683#Unique value, SPARQL (every item), SPARQL (by value)
Scope is as main value (Q54828448), as reference (Q54828450): the property must be used by specified way only (Help)List of violations of this constraint: Database reports/Constraint violations/P683#scope, hourly updated report, SPARQL
Allowed entity types are Wikibase item (Q29934200): the property may only be used on a certain entity type (Help)Exceptions are possible as rare values may exist. Exceptions can be specified using exception to constraint (P2303).
List of violations of this constraint: Database reports/Constraint violations/P683#allowed entity types
Required qualifier “mapping relation type (P4390)”: this property should be used with the listed qualifier. (Help)Exceptions are possible as rare values may exist. Exceptions can be specified using exception to constraint (P2303).
List of violations of this constraint: Database reports/Constraint violations/P683#mandatory qualifier, SPARQL
Canonical capitalization and OBO prefixEdit
Although CHEBI frequently uses a lowercase h it is more common to use a fully capitalized prefix 'CHEBI' when constructing database identifiers. For example:
- GO prefix registry
- OBO Entry - the OBO purls are of the form $OBO/CHEBI_nnn, and rendered as CURIEs CHEBI:nnnnn
Is there a way we can denote this as a property here so that we can harmonize our registries?
Name of property is gone?!Edit
Tried to add a ChEBI ID for a compound I added to Wikidata (https://www.wikidata.org/wiki/Q2756638). Unfortunately, I could not search ChEBI as an identifier... After checking another compound; I saw the name of the property was not displayed, it just reads P683. Why is this? @Egon_Willighagen: @andrawaag:
There is a problem with current constraint and the presence of secondary identifiers. One way is to delete secondary ids, the other way is to change the constraint. You can comment on this topic here (WikiProject Chemistry). Wostr (talk) 18:59, 14 July 2018 (UTC)
- @Wostr: I have added a Modified single value constraint on the top of this page that does not have these shortcomings. I propose to use that and remove the general single value constraint. --SCIdude (talk) 15:42, 4 April 2021 (UTC)
How am I supposed to use the constraint? And what is the purpose? For example, carbon dioxide (Q1997) uses skos:exactMatch (exact match (Q39893449)) but this results in conflicting properties: how is the relation between Wikipedia and Wikidata defined? While it attempts to introduce semantic meaning, it does it wrongly. The ontological model in ChEBI is not skos:exactMatch of what Wikidata uses:
- ChEBI has every chemical as a subclass not an instance
- things like gas are not associated with the chemical compound (ChEBI does not have a CO2 for gas and one for the solid; ChEBI goes wrong here itself)
- Wikipedia often is about slightly different things (this is a larger problem, I know)
- things like refrigerant (Q266790) are roles in ChEBI, not types
So, should I convert this to skos:closeMatch (close match (Q39893184))?
Second, is this also how we are going to link Wikidata neutral forms of compounds to the corresponding ions in ChEBI, e.g. with related match (related match (Q39894604))? --Egon Willighagen
- This is most useful for MeSH IDs, because in case of that database, there are many situations of not 1:1 relationships between entries. In case of ChEBI I started adding these in items about classes and groups of chemical compounds to indicate whether item in WD is an equivalent to ChEBI entry (and maybe in the future that would allow to check our classification tree and ChEBI). In case of chemical compound, I think most of WD items should have an exactMatch. About the problems mentioned: (1) WD should have every chemical compound to be a subclass, (2) instance of gas was an incorrect statement that was imported from ru.wiki, (3) Wikipedia is not a problem to anything in WD, it does not define an item, it does not affect any statements in an item; Wikipedia sitelink should be associated with the most similar concept in WD (ideally it should be a 1:1 relationship, but in the case of chemistry, usually it is not 1:1), (4) I think all statements involving roles and uses should be moved to more specific properties like has use (P366) and subject has role (P2868); just like CO2 is not a preservative, it is used as preservative, it is not a vasodilator agent, it acts as vasodilator agent. I tried to do this with food additives, but we need a more general approach to this preceded by a discussion, (5) neutral forms should be linked to neutral forms, ions should be linked to ions; relations other than exactMatch should be used only when there is no an exactMatch item. Wostr (talk) 17:00, 1 January 2021 (UTC)
- @Egon Willighagen: Wostr has correctly removed instance-of gas. The irritation comes from "greenhouse gas". As to "ChEBI has every chemical as a subclass" I think we are coming to this conclusion in Wikidata too. --SCIdude (talk) 15:54, 4 April 2021 (UTC)
- Also, don't use ChEBI Id to connect organic ion with base, use conjugate acid (P4147) and conjugate base (P4149). However for anorganic ions skos:related is certainly fine as long as there is no WD property. --SCIdude (talk) 16:03, 4 April 2021 (UTC)