Property talk:P234

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Documentation

InChI
International Chemical Identifier
DescriptionInternational Chemical Identifier: International Chemical Identifier (Q203250) published by InChI Trust (Q6008719)
RepresentsInternational Chemical Identifier (Q203250)
Data typeExternal identifier
Domainchemical substance: chemical substance (Q79529) (note: this should be moved to the property statements)
Allowed valuesInChI=1S?/([0-9]*[A-Z][ub]?[a-z]?[0-9]*\.?) (/[0-9A-Za-z \-(),.*;?] )*
Examplebenzene (Q2270) → InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H
indoleacetic acid (Q411208) → InChI=1S/C10H9NO2/c12-10(13)5-7-6-11-9-4-2-1-3-8(7)9/h1-4,6,11H,5H2,(H,12,13)
Formatter URLhttps://chemapps.stolaf.edu/jmol/jmol.php?&model=$1
Robot and gadget jobsDeltaBot does the following jobs:
Tracking: usageCategory:Pages using Wikidata property P234 (Q26250033)
See alsoInChIKey (P235)
Lists
  • Items with the most statements of this property
  • Count of items by number of statements (chart)
  • Count of items by number of sitelinks (chart)
  • Items with the most identifier properties
  • Items with no other external identifier
  • Items with no other statements
  • Most recently created items
  • Items with novalue claims
  • Items with unknown value claims
  • Usage history (total)
  • Database reports/Constraint violations/P234
  • Map
  • Random list
    • Proposal discussion[not applicable Proposal discussion]
    Current uses
    Total1,511,557
    Main statement1,362,40890.1% of uses
    Qualifier2<0.1% of uses
    Reference149,1479.9% of uses
    Search for values
    Explanations [Edit]

    InChI exceeds the limit of character

    [edit]
    Tracked in Phabricator
    Task T154660

    Current limit of character for external-identifier datatype is set to 1500. This WikiProject Chemistry subpage collects information about items for which InChI cannot be added due to this limitation. It also provide an example on how such situation should be modelled in an item using InChI (P234) property and reason for deprecated rank (P2241) qualifier with a exact value exceeds the maximum number of characters (Q101076817) as a value.

    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). Known exceptions: 1H-tetrazole (Q58826308), 2H-tetrazole (Q58826418), 4-hydroxypyridine (Q24730939), 4-pyridone (Q230024), (2S)-2-azaniumyl-4-oxobutanoate (Q74417377), (2S)-2-amino-4-oxobutanoic acid (Q106371441)
    List of violations of this constraint: Database reports/Constraint violations/P234#Unique value, SPARQL (every item), SPARQL (by value)
    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/P234#Single value, SPARQL
    Format “InChI=1S?/([0-9]*[A-Z][ub]?[a-z]?[0-9]*\.?) (/[0-9A-Za-z \-(),.*;?] )*”: value must be formatted using this pattern (PCRE syntax). (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/P234#Format, SPARQL
    Qualifiers “reason for deprecated rank (P2241), reason for preferred rank (P7452), criterion used (P1013)”: this property should be used only with the listed qualifiers. (Help)
    List of violations of this constraint: Database reports/Constraint violations/P234#allowed qualifiers, hourly updated report, SPARQL
    Item “InChIKey (P235)”: Items with this property should also have “InChIKey (P235)”. (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/P234#Item P235, search, SPARQL
    Scope is as main value (Q54828448), as reference (Q54828450): the property must be used by specified way only (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/P234#Scope, 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/P234#Entity types
    Conflicts with “DOI (P356)”: this property must not be used with the listed properties and values. (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/P234#Conflicts with P356, search, SPARQL
    Pattern ^(1S.*)$ will be automatically replaced to InChI=\1.
    Testing: TODO list
    Properties related to chemical compound (Q11173)
    Identifiers
    Formula
    Physical properties
    Chemical properties
    Hazard classification
    Crystallography properties
    Optical properties
    Toxicological properties
    Environmental properties
    Wikidata properties related to medicine (Q11190)
    Basic
    Optional
    Databases
    Biographical
    Qualifiers
    Wikidata properties related to National Institutes of Health
    Database
    See also: WikiProject NIH

    Format constraint

    [edit]
    The following discussion is closed. Please do not modify it. Subsequent comments should be made in a new section. A summary of the conclusions reached follows.
    No answers, format constraint has been added in 2017.

    set a pattern so at least html and wiki syntax isn't alowed. should be specified for the different layers (according to en:InChI --Akkakk 23:52, 24 July 2013 (UTC)[reply]

    The above discussion is preserved as an archive. Please do not modify it. Subsequent comments should be made in a new section.

    Missing prefix

    [edit]
    The following discussion is closed. Please do not modify it. Subsequent comments should be made in a new section. A summary of the conclusions reached follows.
    InChI prefix has been added to all statements, format constraint has been updated accordingly.

    benzene (Q2270) currently lists InChI (P234) as "1S/C6H6/c1-2-4-6-5-3-1/h1-6H". This seems to be missing the "InChI=" part. Justification:

    Personally I don't yet have enough experience with InChI to judge whether embedding the name of the identifier in the identifier is a good thing. But for interoperability I propose that Wikidata follows the common scheme and adds the InChI= prefix. Toni 001 (talk) 15:40, 6 September 2019 (UTC)[reply]

    Now that some time has passed and I repeatedly stumbled over this little issue, I now have the following opinion: For compatibility with other systems, "InChI=" should be part of the ID. As a general rule regarding identifiers I suggest: "The identifier name should not be part of the identifier." The case of InChI should be considered an exception to this rule (the only exception that I found justified after reviewing hundreds of Wikidata external ID properties). Notified participants of WikiProject Chemistry Toni 001 (talk) 11:39, 16 March 2020 (UTC)[reply]
    The "InChI=" is indeed part of the InChI. That said, the property is not the only one where a fixed prefix part is left out for space considerations. I understood the leaving it out is just a pragmatic choice. --Egon Willighagen (talk) 12:25, 16 March 2020 (UTC)[reply]
    I don't think there were any other reasons for omitting 'InChI=' rather than the fact that this is a fixed prefix. The 'DrugBank' property is an another example. This creates more problems than it solves (wait, does it solves anything?), every time I had to do something with this property I had to either add the prefix manually or to delete the prefix from an InChI (if I needed to compare two IDs). Fixed prefixes should not be deleted from any ID, especially since we are very inconsistent with this in WD and sometimes similar databases have different method (ex: DrugBank without 'DB' prefix; HMDB with prefix). Wostr (talk) 13:40, 16 March 2020 (UTC)[reply]
    Please note that the property has formatter URLs and the third party formatter URL may be the reason why the "InChi=" is left out. In other words there may be URLs that can only be built using the shortened version of the key. --SCIdude (talk) 15:03, 16 March 2020 (UTC)[reply]
    I see no such thing here or in some other properties for IDs where fixed prefix is omitted. Even using InChI in chemical search engines (like in PubChem), you have to add the prefix manually, because search doesn't work without prefix. Wostr (talk) 17:28, 16 March 2020 (UTC)[reply]
    For big molecules, we can't save the whole string due to length limitation. Omitting the prefix allows to reduce the number of chemicals with truncated InChI. Snipre (talk) 19:47, 16 March 2020 (UTC)[reply]
    Tracked in Phabricator
    Task T154660
    It was changed once (cf. phab ticket), but there will be always a problem (practical or only theoretical) for a small fraction of InChIs unless there is no length limit at all, so a few more symbols ('InChI=') are not really an argument for me now as we have a limit of 1500. How many InChIs we have in WD that exceeds that limit and how many would have to be deleted after addition of 'InChI=' prefix? Wostr (talk) 21:40, 16 March 2020 (UTC)[reply]
    Yes, InChI= should always be a part of the InChi and while we do that for InChIs directly on the EPA CompTox Chemicals Dashboard we do NOT prefix the InChIKey with anything as the format suffices as is for searching.--Antony Williams 23:57, 26 July 2020 (UTC)
    Do I read correctly in the comments that we think it should be included? --Egon Willighagen (talk) 05:24, 17 September 2020 (UTC)[reply]
    I think yes. However, I asked how many InChIs we have in WD is now truncated as a reason of 1500 character limit and how many would be truncated after addition of 'InChI=' prefix. Wostr (talk) 08:29, 17 September 2020 (UTC) PS If the number is not so low, we should ask for an increase of the limit first. Wostr (talk) 08:31, 17 September 2020 (UTC)[reply]
    Currently the longest InChI string is 1486 characters (Avicatonin). --Stuchalk (talk) 09:14, 17 September 2020 (UTC)[reply]

    Okay. I have temporarily replaced the format string to avoid errors during the change. --SCIdude (talk) 14:49, 17 September 2020 (UTC)[reply]

    Next step is stopping KrBot from fixing InChis that have the prefix. Done. --SCIdude (talk) 04:35, 18 September 2020 (UTC)[reply]
    Bot is running now. Expect finish in November. --SCIdude (talk) 14:49, 18 September 2020 (UTC)[reply]
    @SCIdude: Pubchem uses "InChI=" instead of "InChi=".--GZWDer (talk) 22:00, 19 September 2020 (UTC)[reply]
    That's right. Thank you. --SCIdude (talk) 04:32, 20 September 2020 (UTC)[reply]

    Thanks all for moving forward with the proposal. I updated examples and formatter URLs (though I'm wondering when the latter will take effect). Toni 001 (talk) 17:49, 24 September 2020 (UTC)[reply]

    The bot is done, earlier than thought, the effective edit rate over the whole timespan was 37 / min. I have reset the format strings. The bot fixing the InChI strings is also no longer needed. Thanks from me too for the rational discussion of the decision. --SCIdude (talk) 17:06, 5 October 2020 (UTC)[reply]

    @SCIdude: From this edit it seems that the bot does not account for multiple values of the same property. Ungurinis (talk) 11:21, 24 September 2021 (UTC)[reply]

    The above discussion is preserved as an archive. Please do not modify it. Subsequent comments should be made in a new section.
    Retrieved from "https://www.wikidata.org/w/index.php?title=Property_talk:P234&oldid=2242352774"