Property talk:P703

Documentation

found in taxon
the taxon in which the item can be found

Description

taxon in which the molecule or substance can be found

Represents

natural product (Q901227)

Data type

Item

Domain

According to this template: types of protein (Q8054) (but instances gene (Q7187) as well ??)

According to statements in the property:
enzyme (Q8047), chromosome (Q37748), anatomical entity (Q27043950), type of chemical entity (Q113145171), genome (Q7020), cell (Q7868), anatomy (Q514), protein complex (Q420927), biological pathway (Q4915012), ion (Q36496), polymer (Q81163), biological process (Q2996394), protein domain (Q898273), protein family (Q417841), protein-containing complex (Q22325163), group or class of chemical substances (Q17339814), cell type (Q189118), gene (Q7187), missense mutation (Q2656896), chemical substance (Q79529), group of stereoisomers (Q59199015), animal shelter created by an animal (Q56656227), leaf mine (Q27493024), gall (Q224107) or egg (Q17147)

When possible, data should only be stored as statements

Allowed values

taxon (Q16521) (note: this should be moved to the property statements)

Example

RELN (Q414043) → human (Q5)
elytron (Q658398) → beetles (Q22671)
fur (Q197204) → mammal (Q7377)
erysodine (Q27265641) → Erythrina americana (Q5837303)

Tracking: usage

Category:Pages using Wikidata property P703 (Q116025424)

See also

anatomical location (P927), individual of taxon (P10241), natural product of taxon (P1582), this taxon is source of (P1672), host (P2975), has natural reservoir (P1605), produced by (P2849)

Lists

Proposal discussion

Current uses

Total	7,245,646
Main statement	2,883,653	39.8% of uses
Qualifier	4,361,989	60.2% of uses
Reference	4	<0.1% of uses

Search for values

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

Type “enzyme (Q8047), chromosome (Q37748), anatomical entity (Q27043950), type of chemical entity (Q113145171), genome (Q7020), cell (Q7868), anatomy (Q514), protein complex (Q420927), biological pathway (Q4915012), ion (Q36496), polymer (Q81163), biological process (Q2996394), protein domain (Q898273), protein family (Q417841), protein-containing complex (Q22325163), group or class of chemical substances (Q17339814), cell type (Q189118), gene (Q7187), missense mutation (Q2656896), chemical substance (Q79529), group of stereoisomers (Q59199015), animal shelter created by an animal (Q56656227), leaf mine (Q27493024), gall (Q224107), egg (Q17147)”: item must contain property “instance of (P31), subclass of (P279)” with classes “enzyme (Q8047), chromosome (Q37748), anatomical entity (Q27043950), type of chemical entity (Q113145171), genome (Q7020), cell (Q7868), anatomy (Q514), protein complex (Q420927), biological pathway (Q4915012), ion (Q36496), polymer (Q81163), biological process (Q2996394), protein domain (Q898273), protein family (Q417841), protein-containing complex (Q22325163), group or class of chemical substances (Q17339814), cell type (Q189118), gene (Q7187), missense mutation (Q2656896), chemical substance (Q79529), group of stereoisomers (Q59199015), animal shelter created by an animal (Q56656227), leaf mine (Q27493024), gall (Q224107), egg (Q17147)” 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/P703#Type Q8047, Q37748, Q27043950, Q113145171, Q7020, Q7868, Q514, Q420927, Q4915012, Q36496, Q81163, Q2996394, Q898273, Q417841, Q22325163, Q17339814, Q189118, Q7187, Q2656896, Q79529, Q59199015, Q56656227, Q27493024, Q224107, Q17147, SPARQL

Value type “taxon (Q16521)”: This property should use items as value that contain property “instance of (P31)”. On these, the value for instance of (P31) should be an item that uses subclass of (P279) with value taxon (Q16521) (or a subclass thereof). (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/P703#Value type Q16521, 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/P703#Entity types

Scope is as main value (Q54828448), as qualifier (Q54828449): 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/P703#Scope, SPARQL

This property is being used by:

Please notify projects that use this property before big changes (renaming, deletion, merge with another property, etc.)

Widening scope

I propose to open up the scope. In particular for anatomical structure (Q4936952). But allowing all chemical compound (Q11173) seems to make sense to allow substances like ylang-ylang essential oil (Q251104) as well. ChristianKl (talk) 13:06, 9 July 2016 (UTC)[reply]

I support opening it up to anatomical structures, but also to biological processes, diseases, phenotypes. In OBO we include taxon links for a variety of ontologies, in particular anatomy ontologies. Cmungall (talk) 00:59, 8 October 2016 (UTC)[reply]

Has this been accepted? The description of the property suggests it applies to molecules and substances, but the domain is (still?) more restrictive. --Egon Willighagen (talk) 21:25, 13 December 2016 (UTC)[reply]

Opening this up to "chemical substances" broadly speaking, makes this property so broad as to be useless. See edits from today here and here. Having entries that list "morphine" and "nicotine" as "found in taxon" human, like variants of BDNF Q24381815 is "found in taxon" rat and Q14863330 is "found in taxon" human and Q14863331 is "found in taxon" mouse - makes no sense. And humans have millions of chemicals in them, everything from metabolites of endogenous reactions like, oh, NADP+ to contaminants like bisphenol a to recreational drugs like nicotine to actual drugs given for medical treatment like morphine. You really want to put all those things in a) one field, and b) the same field that we put endogenous genes and proteins into? That makes no sense to me. btw on the nicotine entry, i changed the "found in taxon" field to Solanaceae because nicotine is endogenously made by those plants but even that seems a stretch and I am not sure it should stand. Jytdog (talk) 21:52, 13 December 2016 (UTC)[reply]

I don't think the meaning would broaden, but this property would just be used more. However, looking at the note above about the "type" constraint, it confirms me the widening was already accepted (overlooked that last night) and it can be used for chemical compound (Q11173)}. Regarding the number of statements this will result in: there are currently maybe 60 thousand chemicals known in human, much more (secondary metabolites) expected in plants. However, for few of them we have experimental knowledge to back that up. To me, that defines the scope to the extend it should be used. Some metabolites can be linked to species, like water. Such info does not sounds to be useful to me either. I like your suggestion very much to figure out a way to annotate the found in taxon (P703) link with further information, like nocitine: "found in taxon homo sapiens because of smoking", "found in taxon Solanaceae (Q134172) because of biosynthesis". --Egon Willighagen (talk) 06:08, 14 December 2016 (UTC)[reply]

Look at the history. The OP just went and did that shortly after proposing it. Jytdog (talk) 08:06, 14 December 2016 (UTC)[reply]

OP? What is that short for? --Egon Willighagen (talk) 08:32, 15 December 2016 (UTC)[reply]

So what do you all do here in WD when there is a disagreement like this? The OP went ahead and broadened the definition at the same time they asked about it. dif. Is that actually what you all do here? And again, how are disagreements like this handled here? (and please note that the kind of thing the OP wants to include, ylang-ylang essential oil (Q251104), is "Ylang-ylang essential oils" which is apparently used as perfume. This opens this property to zillions of kinds of things. Oy. Jytdog (talk) 07:23, 15 December 2016 (UTC)[reply]

See https://www.wikidata.org/wiki/Wikidata:Community_portal For clarity, I support the current practical implementation. Anything can go wrong, but that does not mean we should not do anything. BTW, oils are not compounds but substances. Your example does not work. The way to resolve the potential unlimited use, is to create a guidance page in the Chemistry Project, where we outline what we do and do not want. For example, (and that's my expectation), it is only used of there is published experimental data backing it up (from a trustable resources, discussed as default thing in many Wikimedia projects; no difference here). --Egon Willighagen (talk) 08:31, 15 December 2016 (UTC)[reply]

"taxon in which the molecule or substance can be found" - how about carbon (Q623)? --Fractaler (talk) 14:08, 15 December 2016 (UTC)[reply]

Carbon is an element and would be part of, say, glucose, and yes, is found in humans. Can you indicate carbon is part of any organic compound? Yes, and this is actually done in Wikidata. No, I don't think it is a good idea to widen the scope to chemical elements. There is the aforementioned mechanism for that, and you can use that with query.wikidata.org to query which elements are found in humans. --Egon Willighagen (talk) 20:20, 15 December 2016 (UTC)[reply]

You can use this query:

SELECT DISTINCT ?element ?elementLabel WHERE {

 ?element wdt:P31 wd:Q11344.
 ?entity wdt:P527 ?element.
 ?entity wdt:P703 wd:Q15978631.
 SERVICE wikibase:label { bd:serviceParam wikibase:language "en". }

} --Egon Willighagen (talk) 21:06, 15 December 2016 (UTC)[reply]

It isn't my example, it was the example of the OP -- their intention when they actually broadened the scope of this property. Unclear why WD:CHEM should own this property, as it seemed to start from the molecular biology people. Are the projects the only place where DR takes place in WD? Jytdog (talk) 23:01, 15 December 2016 (UTC)[reply]

No, does not have to be the Chemistry project, and no, any project is not the only route. But you already found the community page. If you want to make complain about a decision made by someone, that community page will probably give you pointers. (@Jytdog: Did you see my question above about what OP is?) --Egon Willighagen (talk) 08:18, 16 December 2016 (UTC)[reply]

carbon dioxide (Q1997) - molecule --Fractaler (talk) 09:07, 16 December 2016 (UTC)[reply]

"OP" = "original poster", the person who opens a thread. common in english online discussions. sorry for the jargon. Jytdog (talk) 17:47, 16 December 2016 (UTC)[reply]

Ah, makes sense. I've been in online english discussions for some time now, but did not make this link... thanks! --Egon Willighagen (talk) 06:13, 17 December 2016 (UTC)[reply]

if i may, one more question. in my experience with databases, field definitions are something that people put a lot of work and thought into, because the kinds of queries you can run depends on the kinds of fields you have, and because a lot of work goes into populating the fields, and because it is a lot of work to fix it (and really fix it), if you decide later that the field definitions were not OK. I wrote above that i am really surprised that this field was broadened so casually. i was surprised again, and even more, by how casually you accepted this. I really find this baffling. Can you explain a bit, why there is no "master plan" for field definitions? Why does this not matter here? (big question i know). Maybe there is something i fundamentally don't understand about WD or about this kind of database.... thanks. Jytdog (talk) 18:21, 16 December 2016 (UTC)[reply]

I think the original intention for this property was more like "naturally found in taxon" but the proponents didn't imagine other uses. So why not add "naturally" to the definition? --SCIdude (talk) 07:48, 28 August 2019 (UTC)[reply]

Semantics

I think this property corresponds to http://purl.obolibrary.org/obo/RO_0002162 - can we mark this somehow? Cmungall (talk) 00:59, 8 October 2016 (UTC)[reply]

User:Cmungall I added it as a equivalent property (P1628). We should talk about generating a more complete mapping of RO properties to wikidata properties. Gstupp (talk) 19:52, 24 January 2017 (UTC)[reply]

Property talk:P703

Documentation

Widening scope

Semantics

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