Property talk:P699

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Disease Ontology ID
identifier in the Disease Ontology database

Description	ID in the Disease Ontology
Applicable "stated in" value	Disease Ontology (Q5282129)
Data type	External identifier
Template parameter	None yet, but being prototyped in w:Template:Infobox_disease/sandbox2
Domain	According to this template: disease According to statements in the property: class of disease (Q112193867) or disease (Q12136) When possible, data should only be stored as statements
Allowed values	DOID:([0-9]{7}|[1-9][0-9]{0,4})
Example	neuroblastoma (Q938205) → DOID:769 (RDF) Crohn's disease (Q1472) → DOID:8778 (RDF)
Source	http://disease-ontology.org
Formatter URL	http://www.disease-ontology.org/?id=$1
Tracking: usage	Category:Pages using Wikidata property P699 (Q43672558)
See also	Mondo ID (P5270)
Lists	Items with the most statements of this property Count of items by number of statements (chart) Items with the most statements Items with the fewest statements Count of items by number of sitelinks (chart) Items with the most sitelinks Items with the most sitelinks, but no link to one Wikipedia (sample: Welsh Wikipedia, cywiki) Items with the fewest sitelinks Most linked wikis 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) Usage history (main statement) Chart by item creation date Database reports/Constraint violations/P699 Map Random list
Proposal discussion	Proposal discussion
Current uses	Total 37,014 Main statement 13,402 36.2% of uses Qualifier 6 <0.1% of uses Reference 23,606 63.8% of uses
Search for values

[create Create a translatable help page (preferably in English) for this property to be included here]

Format “DOID:(0[0-9]{6,7}|[1-9][0-9]{0,4})”: value must be formatted using this pattern (PCRE syntax). (Help)

List of violations of this constraint: Database reports/Constraint violations/P699#Format, hourly updated report, 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/P699#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). Known exceptions: glucose-6-phosphate dehydrogenase deficiency (Q848343)
List of violations of this constraint: Database reports/Constraint violations/P699#Single value, SPARQL

Qualifiers “mapping relation type (P4390), reason for deprecated rank (P2241), reason for preferred rank (P7452)”: this property should be used only with the listed qualifiers. (Help)

List of violations of this constraint: Database reports/Constraint violations/P699#allowed qualifiers, hourly updated report, SPARQL

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/P699#Scope, hourly updated report, SPARQL

Item “exact match (P2888)”: Items with this property should also have “exact match (P2888)”. (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/P699#Item P2888, 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/P699#Entity types

Type “class of disease (Q112193867), disease (Q12136)”: item must contain property “instance of (P31), subclass of (P279)” with classes “class of disease (Q112193867), disease (Q12136)” or their subclasses (defined using subclass of (P279)). (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/P699#Type Q112193867, Q12136, SPARQL

This property is being used by: ru:Шаблон:Серия hy:Կաղապար:Տեղեկաքարտ Հիվանդություն, hy:Կաղապար:Տեղեկաքարտ Հիվանդություն և հիվանդագին վիճակներ en:Template:Medical resources or:ଛାଞ୍ଚ:Medical resources eu:Txantiloi:Gaixotasun infotaula zh:Template:Medical condition classification and resources, zh:Template:Medical resources fa:الگو:منابع پزشکی ta:வார்ப்புரு:Medical resources sr:Шаблон:Medical resources th:แม่แบบ:แหล่งข้อมูลการแพทย์ ar:قالب:مصادر طبية mk:Шаблон:Медицински извори, mk:Предлошка:Медицински извори vi:Bản mẫu:Medical resources si:සැකිල්ල:Medical resources sh:Šablon:Medical resources ca:Plantilla:Infotaula malaltia, ca:Plantilla:Infotaula malaltia/vell din:Macuëc:Disease ts:Template:Infobox medical condition as:সাঁচ:Medical condition classification and resources zh-yue:Template:Medical condition classification and resources pa:ਫਰਮਾ:ਮੈਡੀਕਲ ਸਰੋਤ yue:Template:Medical condition classification and resources Please notify projects that use this property before big changes (renaming, deletion, merge with another property, etc.)

DOID prefix

Are there any arguments pro or contra adding the prefix DOID: to the identifier? --Pasleim (talk) 10:05, 28 April 2015 (UTC)

I do not see any arguments pro or contra. Both variants are equals as I see. Wikidata does not have standard policy about database name prefixes. ID without DOID: was used by historical reasons. I think it is better to continue this practice until we does not have some other arguments. — Ivan A. Krestinin (talk) 18:50, 27 July 2015 (UTC)

I would argue in favor of adding the prefix "DOID:" to all disease ontology identifiers for two reasons. First, on the original source the prefix is an intrinsic part of the identifier (e.g. [[1]]). Secondly, external resources such as the miriam registry also include the prefix DOID in its pattern for Disease Ontology. So it seems more common to include the DOID prefix to an identifier from the Disease Ontology. Andrawaag (talk) 20:17, 27 July 2015 (UTC)

I support these arguments. In addition, IDs with prefix are easier to recognize if one is outside of its Wikidata web page. Also, practically all other biology and chemistry identifiers are imported to Wikidata with their prefixes, retaining the prefix for the disease ontology ID therefore adds to consistency. Sebotic (talk) 21:02, 27 July 2015 (UTC)

Andrawaag: You removed the prefix. --Succu (talk) 21:58, 27 July 2015 (UTC)

Succu I indeed did, but that was basically to include the prefix in the claims. With the DOID prefix in the formatter URL, the resulting URL in the P699 claims would resolve in a URL with two prefixes "DOID" Andrawaag (talk) 22:23, 27 July 2015 (UTC)

The prefixes are an integral part when working with ontologies, they are part of the URI of each term. In OWL when importing a term to a new/different ontology it is standard practice to do that according to the MIREOT principles. The prefixes are essential for referencing. They should not be removed.Emitraka (talk) 22:14, 27 July 2015 (UTC)

This rule doesn't seem to be applied consistently; for example the IDs for Uberon are unprefixed: https://www.wikidata.org/wiki/Q23640 - I prefer prefixing but note that it seems impossible to expand this to the OBO PURL using the current system which assumes that the complete ID can be affixed to a base URL. This is because OBO shortform IDs should be understood as CURIEs, and some limited level of CURIE awareness should be built into the URL expansion system on wikidata and wikipedia. This confusion frequently arises, see some of the entries in identifiers.org and see also this discussion which recapitulates the same issues: https://github.com/ga4gh/schemas/issues/165 Cmungall (talk) 15:28, 26 August 2015 (UTC)

We have a number of arguments pro DOID: prefix now. Minor argument about historical reasons is not important in this situation. So I am starting migration process. — Ivan A. Krestinin (talk) 22:17, 1 August 2015 (UTC)

There is now another service which uses IRI that are different from DOID:\d+ scheme, see, e.g., https://www.ebi.ac.uk/ols/ontologies/doid/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_10652# This also presents symptoms, e.g., for paralysis: http://purl.obolibrary.org/obo/SYMP_0000030 — Finn Årup Nielsen (fnielsen) (talk) 20:01, 29 January 2018 (UTC)

I propose not having the prefix be part of the ID:

• There is the practical argument of simply defining a "concept base URI" of "http://purl.obolibrary.org/obo/DOID_", or, in Wikidata terms, a formatter URI for RDF resource (P1921) of "http://purl.obolibrary.org/obo/DOID_$1".
• The argument has been made the on some websites (example), one sees "DOID:769". However, such websites also things like "MESH:D009447", "NCI:C3270", ...; in general, this looks like a listing of "property:value" pairs. This just means that a number is only useful in a given context, given by the property ("identifier type") to which this number pertains.

Toni 001 (talk) 12:07, 26 March 2020 (UTC)

Constraints

With over 7000 exceptions already for each the Single and Distinct constraints, I wonder if these should simply be removed. For example, I would like to annotate biological pathways with DOIDs, using the "mapping relation type" of "related match" to express the fundamental relationship between particular pathways and particular diseases. This is often not a one-to-one mapping however (breaking Single) and multiple pathway items will relate to the same DOID (breaking Distinct). Should I ignore this oft violated constraint? Should the constraint be removed? Or should I not annotate Wikidata items with this information? Thanks for feedback and advice. - AlexanderPico (talk) 19:55, 27 September 2019 (UTC)

After further consideration and discussion with other wikidata curators, I'm going to try annotating biological pathways with wikidata items representing diseases which are themselves identified by DIODs. This way we can help fix the exceptions and not contribute further to the problem. This requires a new property, e.g., something like "pathway annotation" to capture many-to-many associations between pathway instances and diseases (see proposal for new property). --AlexanderPico (talk) 17:04, 9 October 2019 (UTC)