Wikidata talk:WikiProject Chemistry/Tools
Have a look[edit]
Notified participants of WikiProject Chemistry Please a look at these propositions: this will help to have a common structure for all chemicals and elements. Snipre (talk) 16:59, 5 April 2014 (UTC)
Items and statements[edit]
Notified participants of WikiProject Chemistry What exatly are the "pure components" mentioned in Wikidata:WikiProject Chemistry/Tools#Classification trees? I think it would be interesting to be clarified in the project as do statements for each item related to the theme, and even make a brief definition to facilitate and harmonize the work of the editors. Almondega (talk) 17:13, 20 August 2015 (UTC)
- @Almondega: Thanks to spot some details. A pure substance is more appropriated than a pure component. I will change that. To answer your question a pure substance so called a chemical compound is a compound which can be chemically characterizedand and isolated. Snipre (talk) 16:52, 26 August 2015 (UTC)
- @Snipre: You're welcome! Sorry I did not it myself, but my English is terrible! I tried to document the item chemical compound (Q11173), but not sure of the declarations to be made. I think it would be good to review them. Almondega (talk) 18:31, 26 August 2015 (UTC)
Molecular ions?[edit]
Notified participants of WikiProject Chemistry Is there a some guidance for when an item is {{P|31} chemical compound (Q11173) and/or ion (Q36496)? For example, citrate (Q1146640)? Should be be instance of both? Looking at molecular entity (Q2393187), it may be intended that many some identifier (SMILES, InChIKey) are not meant for chemical compound (Q11173) but for the molecular entity (Q2393187) as the single entity part of chemical compound (Q11173)? Second, is there a property to link to two items? --Egon Willighagen (talk) 10:48, 1 January 2017 (UTC)
- union of (P2737)
should help. author TomT0m / talk page 12:44, 1 January 2017 (UTC) - First, we should distinguish citrate (ion) from citrates (class of compounds). There were some initial discussions about it here and earlier in WikiProject Chemistry discussion page (what led to this table), but I think we're far from establishing a model for this. Lack of proper definition of chemical compound (Q11173) may lead to a situation in which this item won't be used for chemical compound items, but for now it is the best what we have. As for me: citrate and citrates should be different items, the first being an instance of ion (or of some subclass of ion like molecular ion etc.) and the latter a subclass of a chemical compound. Wostr (talk) 09:42, 27 April 2018 (UTC)
- @Egon Willighagen, TomT0m, Wostr: chemical compound (Q11173) is a subclass of chemical substance (Q79529) and the definition of chemical substance (Q79529) is "Matter of constant composition best characterized by the entities (molecules, formula units, atoms) it is composed of. Physical properties such as density, refractive index, electric conductivity, melting point etc. characterize the chemical substance. "
- Can we measure the density or the melting point of an ion only ? No, we can only measure density/melting point of salts, so ions can't be instances of chemical compound (Q11173). Snipre (talk) 10:11, 27 April 2018 (UTC)
- Interesting point... what conclusions would you like to draw from this for where Wikidata should go? Some properties are actually for single molecules... the silliest examples is the chemical structure (SMILES, for example), but also rotation constants and infra red bands (I don't think we have those yet), and arguably mass spectra (we have SPLASHes now). Do you think we should further split up the single molecules versus the bulk material? --Egon Willighagen (talk) 05:56, 28 April 2018 (UTC)
- @Egon Willighagen: Sorry I don't understand the question ? There is no problem: if a property can describe ions and chemical compounds, there is no problem: where comes the requirement that one property has to be used with only one class of items ? Even our constraint system allows to fix the use of a property for several classes of items. Just adapt the constraints to include ions. Snipre (talk) 07:21, 30 April 2018 (UTC)
- Interesting point... what conclusions would you like to draw from this for where Wikidata should go? Some properties are actually for single molecules... the silliest examples is the chemical structure (SMILES, for example), but also rotation constants and infra red bands (I don't think we have those yet), and arguably mass spectra (we have SPLASHes now). Do you think we should further split up the single molecules versus the bulk material? --Egon Willighagen (talk) 05:56, 28 April 2018 (UTC)
Building a Visualization tool using this data[edit]
Notified participants of WikiProject Chemistry Is there any possibility that a tool such as WikiGenomes is built which can help researchers visualize this data. Just so it is easier to comprehend. I am a lot more interested but I will need some help around the team. Eugene233 (talk) 09:18, 27 April 2018 (UTC)
- We started Scholia (Q45340488)... I am not sure it visualizes what you are looking for (yet) and there are some things I still want to add, but plz have a look at https://tools.wmflabs.org/scholia/chemical/ ... --Egon Willighagen (talk) 11:43, 27 April 2018 (UTC)
- @Eugene233:I have been working on something like that (I also contributed to Wikigenomes...), but then it was required to shifted the focus a bit and Wikidata wasn't the central component anymore. But I want to restart that so chem compounds in WD can be visualized, annotated, etc. Let's see how much I can get done in the coming months. Sebotic (talk) 07:45, 8 May 2018 (UTC)
- @Sebotic: Please you can get my email so that we can connect and do some stuff on the work you are looking to start. Eugene233 (talk) 21:28, 8 May 2018 (UTC)
- @Eugene233, Sebotic, Egon Willighagen: I added some visalizations based on Wikidata chemistry data here: Wikidata:WikiProject_Chemistry/Tools#Visualizations --Wiljes (talk) 12:32, 20 June 2020 (UTC)
Headlines of SPARQL queries[edit]
Notified participants of WikiProject Chemistry I would like to suggest replacing the rather technical headlines of the SPARQL queries by natural language "competency questions". This would make them easier to read, e.g.:
"instance of: chemical compound (Q11173)" → "Give me a list of all chemical compounds!"
Also, the current use of "UNION" in the headlines might be a bit misleading because the SPARQL command "UNION" equals a logical "OR", while the queries use the logical "AND".
Wiljes (talk) 14:40, 17 June 2020 (UTC)
- Which SPARQL queries? --Egon Willighagen (talk) 15:48, 17 June 2020 (UTC)
- The SPARQL queries on the Tools-page: Wikidata:WikiProject_Chemistry/Tools#Selection_SPARQL_queries --Wiljes (talk) 19:26, 17 June 2020 (UTC)
- Support, in principle. Maybe consensus on a middle way? => write both ways, but then we still need to decide which one of them is the real headline. (I would prefer "competency questions"=natural language for headlines, this looks more friendly...) --Robert Giessmann (talk) 16:51, 18 June 2020 (UTC)
- Ah, carp. Didn't notice this was on a talk page. Sorry. --Egon Willighagen (talk) 12:49, 20 June 2020 (UTC)
- The SPARQL queries on the Tools-page: Wikidata:WikiProject_Chemistry/Tools#Selection_SPARQL_queries --Wiljes (talk) 19:26, 17 June 2020 (UTC)
- I think you can just change that. You could check who wrote the headers (from the page history) and ping this person directly and ask if they agree. You can put the full narrative as text between the headline and the query. --Egon Willighagen (talk) 12:55, 20 June 2020 (UTC)
Difference between mandatory and required[edit]
What is the difference between mandatory and required?
What to do with compounds that do not have CAS, or PubChemID or Melting point or Boiling point?[edit]
How do we handle adding a compound if some of these properties are missing? Can we still do that?
- Yes, if you add a (isomeric) SMILES then other information can be added later. For melting and boiling point, most compounds miss that information, unfortunately. CAS and PubChem CID can be added automatically. --Egon Willighagen (talk) 07:18, 24 July 2023 (UTC)