Wikidata talk:WikiProject Medicine

LOINC

I know LOINC is used in at least a couple medical infoboxes (diagnostic and medical intervention) on English Wikipedia, so I was surprised when I couldn't find a property for it. Is there a reason it's not included, or has it just not been proposed yet? —ShelleyAdams (talk) 01:17, 24 September 2017 (UTC)[reply]

Created this proposal yesterday. —ShelleyAdams (talk) 13:48, 27 September 2017 (UTC)[reply]

Change Detector & Diseases

We have been working on a change detector which monitors items and generates a report of all changes over a certain time period. The change detector is very generic and can be run on any set of items over any time period. As a prototype, it has been running on a schedule now generating a monthly report of all changes to all disease items. It is running under a Jenkins system located here. You can see the latest report under the "Last Successful Artifacts" link (or for October). This is a work in progress. You can post suggestions here or on our issue tracker.

There are three tabs. The first sheet ("changes") lists everything. The "changes_filtered" lists the same information minus edits made by ProteinBoxBot and KrBot, and the "labels" sheet lists label, description, or alias changes. Each row represents one change on one statement on one item. The change can either be "ADD" or "REMOVE" (the change_type column). The qid/qid_label columns are the item the change was made to (the subject), the pid/pid_label is the property/predicate, the value/value_label is the value/object. If the statement had a reference, its in the ref_str column. Just a note, I didn't parse changes in reference statements, it is just pulling the reference if the value of the statement changes.

There has been lots of activity on diseases in the past month! There were 253 edits (not including ProteinBoxBot or KrBot) from 42 unique users, the most active being Netha Hussain, Jmarchn, Andreasmperu, Diptanshu Das, JhealdBatch. There were statements edited from 38 different properties. However, almost none of the statements contain any references. It is very important to add references so the data can be checked, updated, queried and reused effectively. Please add references. Thanks! Gstupp (talk) 21:09, 3 October 2017 (UTC)[reply]

Drug categories

Hello all, I modeled drug/chemical compound categories for 3 drugs (chlorhexidine (Q15646788), givinostat (Q426257), ansamitomicin p-3 (Q27110111)) (subclass of (P279), or 'is a' OBO edge type). All of these categories are either attached to classes in the ChEBI and/or NCI thesaurus ontologies. I post this here to get your ideas/feedback on it. Thanks, Sebotic (talk) 20:26, 9 October 2017 (UTC)[reply]

Anatomy related property template created

Though anatomy related properties have been covered by Template:Medical properties, because its number is growing recentry, I created anatomy specific template (Template:Anatomy properties) for convenience. Feel free to add, change, edit it.--Was a bee (talk) 21:51, 24 October 2017 (UTC)[reply]

Thanks Was a bee and feel free to ping me if there's anything you'd like a comment on. --Tom (LT) (talk) 01:55, 10 February 2018 (UTC)[reply]

Infobox medical condition: medical specialty

Hello everyone, if you have time, can you participate in this discussion? --Dapifer (talk) 22:52, 19 November 2017 (UTC)[reply]

Lots of information to harvest from French infoboxes about genetic diseases

Example: https://fr.wikipedia.org/wiki/Syndrome_d%27Alstr%C3%B6m

Information about whether a gene is located within mitrochondrial DNA

I'm currently interested in mitrochondrial genes. I looked at https://www.wikidata.org/wiki/Q17911652 which happens to be a mitochondrial gene but I couldn't see anything in our Wikidata item that clearly states it to be a mitrochondrial gene. Is there a good reason for that? ChristianKl (✉) 21:45, 12 December 2017 (UTC)[reply]

Hi, @ChristianKl:. That Cytochrome C1 protein works in mitrochondria (w:en:Cytochrome C1), but its gene is encoded in choromosome 8 (Q17911652#P1057). So it is autosomal gene. Not located within mitrochondrial DNA. Human mitochondrial genes (genes encoded by human mtDNA) are only these 37 (w:en:Category:Human mitochondrial genes). Although it seems that these 37 genes are not fully databasized at Wikidata, well written item page example is like this (Q14865314#P1057). --Was a bee (talk) 10:44, 14 December 2017 (UTC)[reply]

Thanks, now I get it ;) ChristianKl (✉) 13:52, 14 December 2017 (UTC)[reply]

Heart activity

We currently have heart rhythm (Q5038333), heartbeat (Q37726042), pulse (Q191733) and cardiac cycle (Q257319). It seems to me that we there's duplication in meaning and we should merge some of them. Does anybody have a good idea about what we should distinguish here and what items we want to have? ChristianKl ❪✉❫ 15:02, 24 December 2017 (UTC)[reply]

@ChristianKl: I think that heartbeat (Q37726042) is a general term that includes cardiac cycle (Q257319), pulse (Q191733). But heart rhythm (Q5038333) is different as I thought --Alaa :)..! 16:19, 29 January 2018 (UTC)[reply]

Wikipedia articles corresponding to 2 distinct data items

Is it appropriate to link a single Wikipedia article to 2 different data items when the scope of an article encompasses both topics, or are data items and Wikipedia articles supposed to be matched 1:1?

Specifically, I'm referring to en:beta-Hydroxy beta-methylbutyric acid, beta-hydroxy beta-methylbutyric acid (Q223081) (conjugate acid - aka "3-Hydroxyisovaleric acid"), and 3-hydroxy-3-methyl-butyrate (Q27156494) (conjugate base); however, this issue applies to a number of compounds that exist as a conjugate acid/base and for which there's a Wikipedia article that covers both of those. For such compounds, there's often 1 wikidata item for the conjugate acid and 1 wikidata item for the conjugate base. Seppi333 (Insert 2¢) 09:35, 29 January 2018 (UTC)[reply]

Also, I realize that this isn't the right venue to ask the more general question above, but my specific case does involve a medical article.

Seppi333 (Insert 2¢) 09:36, 29 January 2018 (UTC)[reply]

Comment @Seppi333: if I understood you well, I think you can use main subject (P921) on 3-hydroxy-3-methyl-butyrate (Q27156494). I mean to put beta-hydroxy beta-methylbutyric acid (Q223081) as a main subject of 3-hydroxy-3-methyl-butyrate (Q27156494). Or to use related property (P1659) or different from (P1889). You should know that we can't link article to 2 items! --Alaa :)..! 16:16, 29 January 2018 (UTC)[reply]

Ah. I figured it might not be possible to do that, but I didn't try. Thanks for letting me know about those alternatives! Seppi333 (Insert 2¢) 16:41, 29 January 2018 (UTC)[reply]

Are there currently any wikidata properties for specifying a metabolizing enzyme (like "substrate of X") or a drug/natural product's metabolites?

See section header. We have biological process (P682) for specifying a natural product's metabolic pathway, but I can't find any wikidata properties to specify anything more specific than that about the metabolism of a natural product; also, biological process (P682) probably wouldn't have a relevant data item to specify for most drugs. Seppi333 (Insert 2¢) 19:55, 30 January 2018 (UTC)[reply]

Actually, I remembered that I used physically interacts with (P129) in DL-amphetamine (Q179452) to specify the enzyme that it interacts with and its role (subject has role (P2868)) as a substrate (enzyme substrate (Q134167)), but I'm still unaware of what wikidata property can be used to specify the product/metabolite of the reaction catalyzed by an enzyme which is specified in physically interacts with (P129). Seppi333 (Insert 2¢) 20:03, 30 January 2018 (UTC)[reply]

Auto archiving

Hello to all! I'm an active editor on the Wikiproject Anatomy on EN Wikipedia. Having a read through this page at the moment. Any thoughts about adding auto archiving here? Not sure how one goes about it on Wikidata but it would make this page much easier to read... --Tom (LT) (talk) 01:55, 10 February 2018 (UTC)[reply]

References

I have noticed that a journal article can have its own wikidata number. Is this correct? Since I typically add references to articles on enWP, it wouldn't take much more time to create an item for each journal article on wikidata. I believe it would vastly help other language wikis find supporting content on topics. Best Regards, Barbara (WVS) (talk) 09:41, 20 February 2018 (UTC)[reply]

Yes, journal articls can have their own Wikidata items. ChristianKl ❪✉❫ 13:41, 21 May 2019 (UTC)[reply]

medical condition treated (P2175) matters

I wanted to raise issues about the "medical condition treated" property, on which I'm working as a Wikimedian in Residence.

Very many of the statements for this property are referenced to https://rxnav.nlm.nih.gov/, i.e. the National Drug File - Reference Terminology site. This is run by US Veterans Health Administration (Q6580225)[1]. According to the site "The NDF-RT API will be decommissioned in February, 2019"; but from https://rxnav.nlm.nih.gov/NdfrtAPIs.html# it seems that actually happened on 2 January.

I see that the formatter URL (P1630) for NDF-RT ID (P2115) was changed in January 2018, away from something based on mor.nlm.nih.gov/RxNav/ which it was at the time. The reference links for the NDF-RT ID are now such as http://bioportal.bioontology.org/ontologies/NDFRT?p=classes&conceptid=N0000146109, for doxycycline (Q422442). On the doxycycline item, five P2175 statements (the top five, in fact) cite NDF-RT, those for chlamydia infection (Q153356), ANTRAX (Q129104), rickettsiosis (Q646664), bacterial pneumonia (Q3776920) and gram-negative bacterial infection (Q19597369). Only those for anthrax and bacterial pneumonia are obviously supported by that Bioportal "National Drug File - Reference Terminology" page. The "May treat" section lists 13 diseases, with links based on the P2115 identifier. I've just had a look at the cholera link: the P2115 identifier was then not on the cholera item, so I have added it.

It does seem that this referencing is now tenuous and somewhat insecure. The reference links having twice been migrated from the original pages, it is not that easy, on the face of it, to track back. (I tried https://web.archive.org/web/*/https://rxnav.nlm.nih.gov/REST/Ndfrt/allInfo?nui=N0000146109 from the Wayback Machine, without anything helpful coming up).

I see there are about 3.3K uses of the P2115 identifier here, so there would be some basis for using the "May treat" sections as they stand - would be helped by having a mix'n'match catalog effort to match more P2115 identifiers.

@Gstupp: @Magnus Manske: Right now, the information referenced to NDF-RT by MicrobeBot and ProteinBoxBot in 2016 is looking suspect. Charles Matthews (talk) 12:22, 14 February 2019 (UTC)[reply]

Semantically gathering studies knowledge

Hi,

An interesting use of Wikidata in the field of research could be to use the knowledge graph power to automatically extract trends from studies, thus orienting manual search more quickly on significant findings.

Let's take this study as an item example : Reduced Pro-Inflammatory Cytokines after Eight Weeks of Low-Dose Naltrexone for Fibromyalgia. (Q52641644)

The study concludes that :

Item : Low-dose naltrexone (Q5259325)
Action : reduce serum concentration of
Target item : TNF (Q18032037) (and others but we will keep it simple)

I imagine something like this :

Item : Reduced Pro-Inflammatory Cytokines after Eight Weeks of Low-Dose Naltrexone for Fibromyalgia. (Q52641644)

suggest that

Low-dose naltrexone

edit

reduce serum concentration of

TNF

0 references

add reference

add value

There could be other ways of doing it.

Do you have some insights or ideas about this ?

Regards

--Thibdx (talk) 19:49, 13 April 2019 (UTC)[reply]

Drug interactions (P769)

Originally posted on w:Wikipedia_talk:WikiProject_Medicine#Drug_interactions_on_Wikidata. Re-posted here as recommended more logical location.

Almost all the drug interactions listed in Wikidata appear to be from a 2012 reference: http://doi.org/10.1136/amiajnl-2011-000612. There are quite a few drug interactions that I expected to find but were missing (e.g. fentanyl x amiodarone): https://doi.org/10.3389/fphar.2018.01145. Is Wikidata missing interactions, or is there a threshold of severity required that I'm overlooking? I've updated the wikdata item for fentanyl, so please revert if I've made an error. Additionally, is there any scope to use the qaualifier field to indicate the nature or severity of the interaction? Evolution and evolvability (talk) 02:19, 20 May 2019 (UTC)[reply]

Hospitals

Notified participants of WikiProject Medicine

Hi,

Statistics

At Wikidata:WikiProject Medicine/Hospitals by country, I added a new statistics section. India tops the list. US and India have some more detailed stats. BTW it's has been 3½ years since Tobias started the lists.

Missing hospitals

There are still some countries without any hospital in Wikidata, or at least without items identified as hospitals. Try the query at Wikidata:WikiProject_Medicine/Queries#Countries_without_hospitals (currently 25). For these countries, names of hospitals can be found on Wikipedia in "health by country" articles (see w:Category:Health_by_country) - if not in Wikipedia hospital lists and categories. I made some for Micronesia and St Kitts & Nevis yesterday.

https://tools.wmflabs.org/wikidata-todo/cradle/#/subject/hospital can help create new items (log in with Widar first, see top right corner). If you want to create a larger number, QuickStatements or Openrefine are better options.

Expand items

Maybe a new "number of hospital beds"-property could help expand these items. More suggestion on how to do that are welcome. I started listing relevant properties at Q16917#P1963. Hospitals_by_country/TBD lists items that lack country statements. --- Jura 11:59, 21 May 2019 (UTC)[reply]

Hospitals in many places are defined by number of beds. @Jura1:, would you like to propose that property or could I volunteer? Blue Rasberry (talk) 14:13, 21 May 2019 (UTC)[reply]

Sure, please go ahead. w:Template:Infobox_hospital might need more properties.

Maybe we could also use a property for the health by country articles, similar to geography of topic (P2633), history, culture. It could be used to help expand information by country. --- Jura 08:30, 22 May 2019 (UTC)[reply]

To improve the items, I imported some data from the hospital infobox in various languages (Talk:Q5618337). I noticed that in addition to the linked template, some languages have additional ones, or the redirecting former name hasn't been updated in the articles. The same goes for parameters (try with or without caps). Also articles about hospitals aren't necessarily up to date. I found one about a hospital replaced ten years ago. Obviously, Wikidata isn't up to date either. In this update sequence, I will try to add the number of beds once the relevant property is created.--- Jura 09:13, 2 June 2019 (UTC)[reply]

Health & healthcare by country

At Wikidata:WikiProject Medicine/health by country, I listed various items (plenty with not much content beyond the sitelinks).

I tried to get them in a more coherent structure. Some countries had one, others the other. Languages other than English might still need sorting.

The items can be used as a basis for something more detailed. --- Jura 17:53, 26 May 2019 (UTC)[reply]

For both topics, we could try to build an infobox on Commons with some basic data. Once it works there, maybe some Wikipedias get interested. For some countries, the information in the article(s) isn't really recent and might benefit from an infobox.

BTW, it might be worth merging "healthcare" and "healthcare system" for some of the countries. --- Jura 09:13, 2 June 2019 (UTC)[reply]

Notified participants of WikiProject Medicine

The two health specific fields on the infoboxes at Commons are now live. Check any of the Commons categories on Wikidata:WikiProject Medicine/health by country. --- Jura 09:56, 21 July 2019 (UTC)[reply]

Jura: Interesting work. Excellent idea to add epidemiology support to Wikidata. However, the data should be enriched from World Health Statistics. --Csisc (talk) 10:38, 21 July 2019 (UTC)[reply]

phase IV clinical trial (Q42825046) vs postmarketing surveillance (Q7234359)

Is there a distinction between phase IV clinical trials and postmarketing surveillance? Otherwise, should they be merged? T.Shafee(evo&evo) (talk) 07:51, 19 June 2019 (UTC)[reply]

They overlap in scope but I wouldn't call them synonymous. There are mechanisms of surveillance which are outside of trials: for example, the w:Yellow Card Scheme is a form of postmarketing surveillance, but isn't a clinical trial; it's a regulatory mechanism established to monitor drug safety. It is almost true that a Phase 4 clinical trial is a subset of postmarketing surveillance, but it's sufficiently independently notable (and better-known) that I think it should be kept separate. Klbrain (talk) 06:43, 22 June 2019 (UTC)[reply]

Oppose merge, per my commentary at WP:PHARM here. ―Biochemistry🙴❤ 17:44, 23 June 2019 (UTC)[reply]

help me. How combine Q30280146 + Q16095310 (South korea hospital imfomation)

@Jura1: thanks this comment → ko:틀토론:병원 정보#number of hospital beds (P6801)

I dont know english and WIKIDATA well

I am korean wikipedian user 2011 ~

I looked Wikidata:WikiProject Medicine/Hospitals by country/South Korea today

I want combine Q30280146 and Q16095310

Q30280146 name : Bucheon St. Mary's Hospital

Q16095310 name : 가톨릭대학교 부천성모병원

new name combine, I want = The Catholic University of Korea, Bucheon ST. Mary’s Hospital

--Exj (talk) 15:09, 20 June 2019 (UTC)[reply]

Hi Exj, thanks for looking into this. It happens fairly frequently that we get two items on the same topic.

Help:Merge/ko#Gadget explains how to merge two items with a gadget. Don't hesitate to experiment, it's a wiki afterall. If needed, I can fix it afterwards or do it for you.

Once merged, you may want to edit the label of the item. I think "Bucheon St. Mary's Hospital" matches probably better the usual way of writing English labels (see Help:Label), but other ways could be an alias (see Help:Alias). --- Jura 15:18, 20 June 2019 (UTC)[reply]

Price of medications

Have begun adding pricing information for medications here aciclovir (Q147101). Basically I have added the lowest and highest wholesale price for a unit of the generic version of the medication.

We need the ability to add the "dosage". Quantity does not seem to work as it does not want to accept units. We also need the qualifier that this price is wholesale not retail. User:Bluerasberry your thoughts? Doc James (talk · contribs · email) (if I write on your page reply on mine) 02:28, 16 July 2019 (UTC)[reply]

Started the discussion Wikidata:Property proposal/Dose Doc James (talk · contribs · email) (if I write on your page reply on mine) 04:49, 17 July 2019 (UTC)[reply]

I joined in that discussion. It seems like the present problem is sorting how we model doses. If we can model doses then we can include prices, but right now, the model for doses is uncertain. I support adding prices and do think that despite global economies and the fact that we will somehow limit how much data to report, reporting a price is meaningful. Blue Rasberry (talk) 19:45, 17 July 2019 (UTC)[reply]

Notifiable diseases by country

It would be good to have a property for diseases, showing which countries they are notifiable in. For example, smallpox is classified as notifiable in Sweden, Norway, India and several other countries. I have been creating lists on Wikipedia for notifiable diseases by country (such as this one: w:en:Notifiable_diseases_in_Sweden, and I think this kind of data will fit snugly into Wikidata. --Netha Hussain (talk) 08:34, 28 August 2019 (UTC) --The US CDC also maintains such a list, so I would support such a property. Gtsulab (talk) 18:29, 23 October 2019 (UTC)[reply]

Paper on Wikidata and medicine

In case it is of interest, a paper has just been published in JBI on Wikidata's medical content:

Turki, Houcemeddine; et al. (2019), "Wikidata: A large-scale collaborative ontological medical database", Journal of Biomedical Informatics, 99: 103292, doi:10.1016/j.jbi.2019.103292
Green OA copies at Researchgate and Zenodo

It is, in part, a wikidata followup to the Heilman 2011 paper in JMIR. It aims to introduce medical researchers and practitioners to the relevance of wikidata to biomedicine, how to edit and read it, and some of its future potential. T.Shafee(evo&evo) (talk) 00:54, 1 October 2019 (UTC)[reply]

Hospital: organization vs. building

Hospital as an organization may operate in multiple buildings and it may operate in different buildings over course of time. So it should be clear that organization and building are distinct and they warrant separate items to allow meaningful classification of organizations and buildings. Similarly there are court (Q41487) (organization subclass) and courthouse (Q1137809) (building subclass), or library (Q7075) and library building (Q856584). For hospitals however the situation is messy currently: while there is separate building subclass hospital building (Q39364723), then the organization subclass hospital (Q16917) is at the same time a building subclass too.

Recently I tried to clear this up by moving building related statements from hospital (Q16917) to hospital building (Q39364723), but got reverted by Jura1. After lengthy explanation to them the reason why it was reverted still remains a secret (see user talk). Now they added further layers of confusion by stating that hospital (Q16917) is institution and/or facility and not organization (Special:Diff/1029291241/1029361161), while it still is set as a subclass of (subclass of) organization. Not to mention, if it is a facility then it's also unclear how it is different from hospital building (Q39364723).

Clearing up hospital (Q16917) so that it's clearly about organization still seems like viable solution to me as that's what its instances on Wikidata are primarily about. After clearing it up this way it should be easier to find items that are specifically about buildings, but are currently set as instance of hospital (Q16917) and then correct them to be instance of hospital building (Q39364723), too. If this for some reason shouldn't work out, then is there some better solution? Should we perhaps create new class item for hospital as organization and in favour of it deprecate the use of hospital (Q16917) for classification as long as for some reason it should remain fuzzy what the latter item is about? 2001:7D0:81F7:B580:5801:674D:B5E2:CB9E 08:37, 11 October 2019 (UTC)[reply]

Currently hospital (Q16917) is a for a group of buildings. In the current setting Q39364723 isn't that useful, we could probably eliminate it entirely.
From the comments on my talk page, I understood there was some need to include information about operating, holding and property companies of hospitals. If needed, this can already be added: we have medical organization (Q4287745) and it was already done with that. If something else needs to be added, please outline what you plan to contribute.
The previous change merely disrupted the currently outlined structure. --- Jura 09:38, 11 October 2019 (UTC)[reply]

Statements/description added to hospital (Q16917) and its current usage for classification don't really support your claim that it's for a group of buildings. Also as there doesn't seem to be another item than hospital building (Q39364723) for individual hospital buildings then without it classification would be more inaccurate, and so eliminating it doesn't sound like a good idea.

There are different types of medical organization, one of them being a hospital. I don't understand why you suggest that there shouldn't be a separate item for medical organization that is a hospital.

As already explained earlier in you user talk, this is a generic classification problem, not about me wanting to contribute particular new information. So far you haven't explained in what way you believe the structure was disrupted. The current situation however quite clearly isn't sufficient for the reasons outlined above.

PS Please don't manipulate with topic title. These items listed in title according to your view of what they are about was the problem in the first place and it produces confusion. I've restored the title in more neutral form. 2001:7D0:81F7:B580:5801:674D:B5E2:CB9E 10:17, 11 October 2019 (UTC)[reply]

Also, if hospital (Q16917) was a for a group of buildings, as Jura now decided, then its statements are still wrong. As group of buildings it should be a subclass of building complex (Q1497364) or group of structures or buildings (Q18247357), and not building (Q41176) (individual building), nor institution (Q178706). 2001:7D0:81F7:B580:E45E:E230:4E9F:7428 12:41, 26 October 2019 (UTC)[reply]

Maybe you could present a usecase and type of data you want to add. We can then try to see if this can be accommodated or not.

Do you also contribute with a user account? --- Jura 17:40, 30 October 2019 (UTC)[reply]

I already replied to this above and in your user talk. This is not the issue. This issue is with the classification of data (items) that is already in Wikidata, as described above. 2001:7D0:81F7:B580:1C97:842B:5D5A:38E3 12:03, 31 October 2019 (UTC)[reply]

The appearance /physical attributes/ of drugs

Hi, I am working (with the help of members of a small non-wmf wikicommunity) on openaccess wikiarticles about various drugs. We are planning on incorporating information about various medical substances that are available through wikidata in the future. Through our project we already donated numerous photos of different drugs/drug forms to commons. For our users - medstudents, nurses and doctors alike - are information about the physical attributes of the drugs very useful and we would like to add them to wikidata and afterwards to our project. But I am not sure how to add this kind of information to wikidata, there are two barriers I would need advice with:

the physical appearance of the drug form, such as "white, round tablets" are specific per manufacturer and the drug, is it viable to set up new wikidata items for the drug by specific manufacturers /say "Metformin Teva 500mg" - an item for tablet containing 500mg of metformin produced by Teva company/?
are there any properties on wikidata already in place that could be used for the physical appearance description?

Thank you for your reply in advance. --Wesalius (talk) 17:20, 21 October 2019 (UTC)[reply]

Drug Indications

The Drug Indications Database seemed like a promising source of drug-disease relationships for inclusion in Wikidata. I mapped drug and disease items to Wikidata entities and then filtered out entries which contained drug/disease items with ambiguous mappings, entries with no predicates, and entries where the predicate did not exactly match a Wikidata property. This left <100 'has effect' relationships, <150 'may prevent' relationships, and <1800 'may treats' relationships between drugs and diseases that were sourced from NDF-RT. I would like to add these entries to Wikidata and need advice on how to best reference this data. I can reference it to DID, but DID curated it from NDF-RT. Should I just reference DID? DID and NDF-RT? Thanks Gtsulab (talk) 19:55, 25 October 2019 (UTC)[reply]

Pregnancy category

I made this change to pregnancy category (Q1057079), removing the subclass of (P279) statements to adverse drug reaction (Q45959) and drugs in pregnancy (Q5308960). I believe that those statements were incorrect (and were leading to some odd results in some SPARQL queries), but please let's discuss if anyone disagrees. Best, Andrew Su (talk) 18:54, 4 November 2019 (UTC)[reply]

Medical encyclopedias

Hi All,

Just wanted to let you know that there are many new medical encyclopedias, databases in Mix'n'match to work on, take a look: https://tools.wmflabs.org/mix-n-match/#/group/medical Also, if there are any others you'd like to add to the list of catalogues but don't know how, you can suggest it on the list here: https://meta.wikimedia.org/wiki/Mix'n'match/Catalogues Best, Adam Harangozó (talk) 17:07, 8 November 2019 (UTC)[reply]

Modeling Adverse Drug Reactions

FDA Structured Product Labels (SPLs) have information on adverse drug reactions. I am interested in adding adverse drug reactions from FDA SPLs to Wikidata and have seen an example of modeling adverse effects in the property proposal discussions for Risk Factors. Is this how I should add FDA SPL ADRs to Wikidata or is there another way ADRs should be modeled? Gtsulab (talk) 20:02, 13 November 2019 (UTC)[reply]

It could be a sensible way to encode it, however it looks to be used in the reverse direction to what you're talking about. It is used on the item for the reaction, not for the drug (e.g. myocardial infarction (Q12152) has the risk factor (P5642) of smoking (Q662860)). Perhaps a reciprocal property would be more useful for this case (e.g. 'has adverse effect', or 'increases risk of', or some quality modifier of has effect (P1542))? A somewhat similar scenario is that currently (RS)-warfarin (Q407431) has effect (P1542) warfarin exposure (Q21175420). T.Shafee(evo&evo) (talk) 00:07, 14 November 2019 (UTC) ping @Csisc, Okkn, MaynardClark, Soupvector, Yair rand, Doc James: @مصعب, علاء, Bluerasberry, Jura1: @Pigsonthewing, Egon Willighagen, Thibdx, ArthurPSmith: [reply]

Thanks for the input, T.Shafee(evo&evo). I planned to model the ADRs exactly as I saw in the risk factor property: eg- ADR has risk factor (drug name), with qualifiers: criterion used (P1013) treatment (Q179661) and has effect (P1542) incidence (Q217690). I really liked the way the NIOSH folks modeled the chemical - chemical intoxication - symptoms, but I didn't see it used on drugs until your example. Would love more input on this. Gtsulab (talk) 16:51, 14 November 2019 (UTC)[reply]

Foundational Model of Anatomy ID

Why Foundational Model of Anatomy ID (P1402) is a string-datatype and not external-id? Is it intentional? Wostr (talk) 03:20, 12 December 2019 (UTC)[reply]

Manuscript: Wikidata as a FAIR knowledge graph for the life sciences

Notified participants of WikiProject Medicine

Dear all: You may have seen that we recently published a preprint entitled "Wikidata as a FAIR knowledge graph for the life sciences". This manuscript was primarily spearheaded by the Gene Wiki team, which has been active in data modeling and data ingestion for a variety of biomedical resources.

Our goal was to write a manuscript that educated the general biological community about Wikidata and to drive more growth and participation. To do this, we selected and described a series of scientific vignettes -- identifier translation, integrative biomedical SPARQL queries, crowdsourced curation, Wikidata-backed application development, and phenotype-based disease diagnosis. Those vignettes were based on our own areas of interest as well as our guess at what would appeal to our target audience.

Of course, there are many possible vignettes that could fit under the broad title we chose. As a matter of practicality, we could not include them all while still creating a final product of reasonable length and focus.

However, upon further reflection and discussion with colleagues, we realized that while the selection of vignettes needed to be somewhat limited, the manuscript should reflect a more complete and inclusive representation of the people behind the larger movement, including those that worked on aspects that weren't directly highlighted as vignettes. Therefore, we'd like to invite anyone to add their name to the author list or acknowledgements by adding their name to Wikidata:WikiProject Molecular biology/FAIR_knowledge_graph. Note that due to journal policies, all authors must still meet the ICMJE standards, but interpreted according to the broadly-defined title of the manuscript. (That broader scope might also be summarized by the class-level diagram shown at right, which is included as Figure 1 in the manuscript.)

Finally, this message is being cross-posted to many places. We will monitor replies at Wikidata_talk:WikiProject_Molecular_biology, or please {{Ping}} me to notify me of replies or discussion elsewhere. Best, Andrew Su (talk) 22:51, 18 December 2019 (UTC)[reply]

Is it time for a Wikiproject Coronavirus?

Notified participants of WikiProject Medicine

Hello, Given the efficiency and success of the Wikidata:WikiProject_Zika_Corpus, I wonder if we shouldn't create a Covid19 corpus to gather the information around coronavirus. It is going to be around at least for a few months and I think Wikidata can help to organize the information around that.

What do you think? TiagoLubiana (talk) 11:39, 13 March 2020 (UTC)[reply]

That WikiProject is now up at Wikidata:WikiProject COVID-19. --Daniel Mietchen (talk) 02:58, 16 March 2020 (UTC)[reply]

Just a note about organisation: I realise that things are done differently over in wikidata, but in Wikipedia it's been more long-term successful to keep larger wikiprojects together to keep discussions consolidated, and to make dead wikiprojects not give the feel of a ghost town. Obviously not the highest priority currently, but making these taskforces as subpages of a larger project can help longer-term. T.Shafee(evo&evo) (talk) 08:45, 16 March 2020 (UTC)[reply]

Mining COVID19 research using [R] and Wikidata

For people interested in [R], textmining, Wikidata, COVID19 and open access data: project posted over at Wikidata_talk:WikiProject_COVID-19. T.Shafee(evo&evo) (talk) 08:57, 16 March 2020 (UTC)[reply]

Is it OR to state that novel Coronavirus can be transmitted by common communion cup?

Please see discussion at noticeboard [2]. Cinadon36 (talk) 15:20, 16 March 2020 (UTC)[reply]

I made or improved wikidata queries of endocrinologists.

endocrinologist: named syndrome
Gerald Swyer (Q88262504): XY gonadal dysgenesis (Q957751)
S. Douglas Frasier (Q88559284): Frasier syndrome (Q5493754)
Pierre Denys (Q88246461): Denys-Drash syndrome (Q774016)

They are dicoverers of named syndromes. In Wikidata, there are many queries about their academic articles. Please link these queries about their academic articles to these authors. --Sharouser (talk) 01:52, 27 March 2020 (UTC)[reply]

Which P31 for a prepublication article version

Sorry for crashing the medicine project, but you seem an active group. What is the right P31 for a Prepublication article version? The examples I'm referring to are those which are reviewed and commented on. See:

Thanks for your recommendations. Trilotat (talk) 13:19, 20 April 2020 (UTC)[reply]

diseases are mostly not human-specific

I'm afraid you will need to reconsider the description "human disease" on all disease items because, de facto, the items are used for other animals, as well. These edits are done by bot by the thousands. Example: https://www.wikidata.org/wiki/Q28588205#P921. Human-centricity is a futile notion, anyway. --SCIdude (talk) 07:30, 23 June 2020 (UTC)[reply]

I agree there should be items for the human diseases that subclass the general concept. ChristianKl ❪✉❫ 23:54, 14 December 2020 (UTC)[reply]
That would be a good idea. There are a few diseases that don't appear in non-humans (e.g., smallpox), and many that affect plants or non-human animals. WhatamIdoing (talk) 21:42, 27 December 2020 (UTC)[reply]

External identifiers for medical items

Hi All,

I've made a Mix'n'match query where it is easy to add the missing IDs to illnesses, conditions, etc. from a wide number of databases. Feel free to use it.

Best, Adam Harangozó (talk) 13:10, 20 November 2020 (UTC)[reply]

Notified participants of WikiProject Medicine

VEXAS = VEXAS syndrome

Hallo, I've been advised that this is the place to raise this, which I previously posted in en.wiki on Wikiproject Medicine talkpage.

Copying most of that post:

I am not a regular medical editor but ... created a stub for the new autoinflammatory disorder VEXAS on 17 November ...

I wasn't sure then whether its article title should be "VEXAS" or "VEXAS syndrome" (I made a redirect from the latter). Some sources use one, some the other. The NIH News release uses "VEXAS". I've just found it in OMIM, where both names are given. But I now find that Wikidata has two separate entries, one at VEXAS (created 20 Nov by an editor who apparently first edited Wikidata on 19 Nov)) linking to the en.wiki article, and one at VEXAS syndrome (created on 24 Nov by a bot), linking to the DOID record. I am not a Wikidata expert. But I'm confident they both refer to the same entity so presumably there should only be one Wikidata record.

So I have two questions for expert medical editors, especially those well versed in Wikidata:

Is the article at the right title?
Could someone please do what's needed in Wikidata so that there is just the one entry, with the alternative name included?

...

Thanks in advance for any help on this article and its Wikidata. PamD 21:53, 13 December 2020 (UTC)[reply]

So, could someone please fix the Wikidata duplicate entries? Thanks. PamD (talk) 22:56, 13 December 2020 (UTC)[reply]

The en.wiki article is now at the title "VEXAS syndrome": I moved it after feedback from a couple of medical editors. PamD (talk) 23:45, 14 December 2020 (UTC)[reply]

inception (P571) of surgical mask (Q10282403)

Could somebody please check this property resp. the consistency of the item with the respective Wikipedia articles? The dates in the version history range from 1300, 1960s and 2004 (reverted). None has references. Does this item describe this normed mask (de.wp), a general surgical mask (en.wp - 19th century, 1960s) or maybe sth. else even more historical? I could not find the 1300 reference, it might be arabic medicine history? I have no idea how to figure this out (not to mention modeling the data) so I place it here, maybe somebody likes these kinds of riddles ;-) Thanks. --Elya (talk) 16:06, 16 January 2022 (UTC)[reply]

I wonder whether the 1300s is a reference to a plague doctor costume (Q2063050), which was seen by at least the 1600s. (Black plague is the most widely known disease of the 1300s.)

IMO this item would, ideally, by about the modern/normed mask, and that there would be a more general "category" item that encompassed and connected all the things that healthcare providers wear over their mouths for protection (e.g., plague doctor costumes from the 17th century, cloth masks from the 19th century, modern surgical masks, N95 respirators, etc.). WhatamIdoing (talk) 19:05, 20 January 2022 (UTC)[reply]

Mapping inflammatory bowel disease to Orphanet ID

There are some inconsistencies between how Orphanet ID (P1550) and Disease Ontology ID (P699) treat subclasses of inflammatory bowel diseases (Q917447), and I opened a discussion for that over at WikiProject Ontology. Your comments would be appreciated. –Rainforest80 (talk) 09:33, 28 January 2022 (UTC)[reply]

How to model medical indications?

I started a discussion about this at Wikidata:Property proposal/medical indication. --Daniel Mietchen (talk) 21:55, 20 February 2022 (UTC)[reply]

The property medically indicated in case of (P10630)

has since been created, so I also started Wikidata:Property proposal/contraindication. --Daniel Mietchen (talk) 00:06, 30 April 2022 (UTC)[reply]

congenital adrenal hyperplasia (Q366868) and adrenogenital disease (Q13368382)

Some sitelinks of congenital adrenal hyperplasia (Q366868) actually mean adrenogenital disease (Q13368382) Sharouser (talk) 03:59, 17 April 2022 (UTC)[reply]

Can you fix it? WhatamIdoing (talk) 06:44, 17 April 2022 (UTC)[reply]

WikiProject Clinical Trials for Wikidata - the paper

See Wikidata:WikiProject Clinical Trials. Care about this because

We presented it as a model WikiProject in this new preprint - https://doi.org/10.1101/2022.04.01.22273328
It is a tidy cool WikiProject which coordinated the import of ClinicalTrials.gov (Q5133746) to Wikidata
I and others will continue to develop this project and further integrate it with Wikidata for medicine, universities, biographical records of medical researchers, and meta:WikiCite

Comments requested here or at the WikiProject talk page.

THANKS TO ANYONE WHO COMMENTS! Bluerasberry (talk) 19:23, 19 April 2022 (UTC)[reply]

We should create individual medical procedures in Wikidata

There are a lot of medical procedures which are mentioned in multiple scholarly articles but not notable in any Wikipedia. Vecchietti procedure is an example. Sharouser (talk) 13:08, 15 June 2022 (UTC)[reply]

I think this is the "tomato" problem: Should you have an article about the tomato plant, or the tomato that you eat? Many Wikipedias write a single article about both the plant and the food it produces. Wikidata needs the plant and its fruit separated. When a topic is merged together in Wikipedia, then please feel free to create separate Wikidata items. WhatamIdoing (talk) 15:45, 15 June 2022 (UTC)[reply]

I created Vecchietti procedure (Q114270203). We should also create cohorts such as GAZEL cohort. Sharouser (talk) 15:28, 29 September 2022 (UTC)[reply]

Intravenous

Resolved at w:Wikipedia_talk:WikiProject_Medicine#Intravenous Utfor (talk) 16:20, 20 August 2022 (UTC)[reply]

Originally posted at w:Wikipedia_talk:WikiProject_Medicine#Intravenous and copied here

Items d:Q640448 and d:Q1369403 seem to overlap or cover the same or similar topics. Could a WikiProject member please look into this, and check whether they should be merged, splitted, cleaned up or something else? Utfor (talk) 19:15, 19 August 2022 (UTC)

Wikidata_talk:WikiProject_Medicine is also a good place to post IMO--Ozzie10aaaa (talk) 11:52, 20 August 2022 (UTC)

It can't easily be merged. Enwiki has a sitelink for both. Dewiki also has a sitelink for both. Unfortunately, it's quite messy. To untangle the situation we need first think about what different concepts are involved, than see whether we have items for those concepts and than move all the sitelinks to the correct item. ChristianKl ❪✉❫ 21:30, 20 August 2022 (UTC)[reply]

User:ChristianKl Thank you for your answer! Utfor (talk) 17:51, 21 August 2022 (UTC)[reply]

How to link clinical trials to the main subject of the research?

I want to make links to male circumcision and mogen clamp from Evaluation of the ShangRing vs. Mogen Clamp for Early Infant Male Circumcision (EIMC) in Sub-Saharan Africa (Q64789667). Sharouser (talk) 10:17, 9 October 2022 (UTC)[reply]

Maybe described by source (P1343) on the trial item? --SCIdude (talk) 15:55, 9 October 2022 (UTC)[reply]

My intention was the opposite case. But thank you for your answer. Sharouser (talk) 14:04, 11 October 2022 (UTC)[reply]

main subject (P921) seems to me like the most straightforward choice. ChristianKl ❪✉❫ 17:28, 11 October 2022 (UTC)[reply]

missing diseases or syndromes

I found that there are no wikidata item about GLUT1 deficiency. I want to add a link in A Family With a Complex Phenotype Caused by Two Different Rare Metabolic Disorders: GLUT1 and Very-Long-Chain Fatty Acid Dehydrogenase (VLCAD) Deficiencies (Q97520872). Sharouser (talk) 04:40, 17 November 2022 (UTC)[reply]

I suggest that we should make a subpage of this WikiProject for missing diseases or syndromes. Sharouser (talk) 04:43, 17 November 2022 (UTC)[reply]

I would expect it to be very similar to w:en:Wikipedia:WikiProject Missing encyclopedic articles/Missing diseases. WhatamIdoing (talk) 04:09, 18 November 2022 (UTC)[reply]

US-Drug_Master_file_ID

Given that we currently don't have a property for the id of US drug master files I created Wikidata:Property proposal/Natural science#US-Drug Master file ID I'm happy about any support votes. ChristianKl ❪✉❫ 13:00, 3 December 2022 (UTC)[reply]

Medicinal plant : how to link with a class of medications?

Hello :) I have a question about standarts to tag medicinal plant swith their respectives proprieties. Example, plantago major is astringent. Should I entre astringent in the Property:P366, or I should add a qualifier inside the medicinal plant item ? Or another thing ? Thx ! :) Haymillefolium (talk) 17:26, 17 January 2023 (UTC)[reply]

In many cases a plants used for medical purposes, there's an extract that's used instead of the whole plant. Having a separate item for that extract would be good. ChristianKl ❪✉❫ 20:02, 22 January 2023 (UTC)[reply]

For me its another information, we could do both :

tag the medicinal proprieties of the pant : still the question how ? (we could create a propriety "has medicinal use" ?)
tag what extracts that are produced from the plan : also how ? (has use seem to general, maybe creating a specific propriety would be better, like "extract to")

We could also add

what diseases it can be used for, associating a posology and a method of use (infusion, extract, etc)

Haymillefolium (talk) 15:23, 23 January 2023 (UTC)[reply]

Clinical guideline data model

Hi,

Could anyone knowledgeable help me with creating a data model for clinical guidelines, please ?

https://w.wiki/6Leq - only 50+ medical guidelines so far.

Kpjas (talk) 13:24, 15 February 2023 (UTC)[reply]

Value-type constraint of route of administration (P636)

In Property talk:P636, Wostr and I now discuss (1) the class constraint on the value of property route of administration (P636) and (2) the inconsistency of the current route of administration (Q621636) (route, anatomical structure) and drug administration (Q29914073) (method, procedure) ontologies. We need community discussion and consensus as major changes will be required, so we would appreciate your comments. Thank you, --Okkn (talk) 23:40, 9 June 2023 (UTC)[reply]

Some_UMLS_CUI_(P2892)_concerns

https://www.wikidata.org/wiki/Property_talk:P2892#Some_UMLS_CUI_(P2892)_concerns Vladimir Alexiev (talk) 14:26, 21 June 2023 (UTC)[reply]

Medical treatment class hierarchy

It seems to me that medical procedure (Q796194) and medication (Q12140) should be subclasses of medical treatment (Q179661). What should be the parent class of medical treatment (Q179661)?

I also think the English description of medical treatment (Q179661) is perhaps too restrictive. It currently reads "attempted medical remediation of a health problem, usually following a diagnosis" which could be interpreted to exclude preventative interventions. Thoughts? Daask (talk) 19:03, 15 July 2023 (UTC)[reply]

I'm not sure that I'd personally use the word treatment to describe a preventive action (it just wouldn't occur to me to use that word), but I believe that prevention is a valid form of treatment.

It might help to think of the more generic understand of treatment, e.g., "I don't like their treatment of you; they seem rather selfish and inconsiderate". So anything you do to/for a patient is a type of "treatment", even what we would call the bedside manner. That makes me think that the parent class is going to be very generic – some sort of human–human interaction, perhaps. WhatamIdoing (talk) 18:18, 20 July 2023 (UTC)[reply]

Schemas for medical entitites

I have started Wikidata:WikiProject Medicine/Schemas to keep track of schemas related to medicine. Daniel Mietchen (talk) 12:52, 26 July 2023 (UTC)[reply]

diseases and rare diseases

@TiagoLubiana

Is disease (Q12136) in the scope of this project? If not, is there a project for diseases?

I am investigating problems with the Wikidata ontology and ran into a lot of problems with diseases. class of disease (Q112193867) is the class of diseases, with actual diseases, such as primary organ-specific lymphoma (Q55786911), as instances of class of disease (Q112193867) and subclasses of disease (Q12136).

But many diseases, such as cone dystrophy (Q147270), have ontological issues, being an instance of (P31) both class of disease (Q112193867) and rare disease (Q929833). rare disease (Q929833) is itself an instance of (P31) class of disease (Q112193867). This doesn't make any sense, but I'm not sure what the remedy should be. One way to go is to make rare disease (Q929833) be a subclass of class of disease (Q112193867). The other way to do is to make a disease class that was an instance of (P31) rare disease (Q929833) a subclass of (P279) rare disease (Q929833) instead. Any suggestions on the way to go?

Other diseases, such as measles (Q79793), are neither an instance of class of disease (Q112193867) nor disease (Q12136). although it is a subclass of viral infectious disease (Q1928978), which is an instance of class of disease (Q112193867) and a subclass of disease (Q12136). What can be done about these diseases? Peter F. Patel-Schneider (talk) 16:44, 1 September 2023 (UTC)[reply]

@Peter F. Patel-Schneider: I think here is the most adequate place! There are many issues with these multilevel relations on Wikidata. Here is some old considerations on that (done outside of Wikidata):

Wikidata is made by the community, so reaching ontological rigor is not always easy
Wikidata has no intention of being completely coherent, as sources of information might provide contradicting statements (https://www.wikidata.org/wiki/Help:Statements#Plurality%20and%20consensus and https://blog.wikimedia.de/2013/02/22/restricting-the-world/, https://blog.wikimedia.de/2013/06/04/on-truths-and-lies/
There are a lot of cases of conceptual disarray on Wikidata (Dadalto et al. 2021)
Even with such issues, Wikidata is incredibly useful for the biology community. (Waagmeester et al. 2020)
Improving the modeling of biological entities may increase even more the value of Wikidata for scientists.
The modeling of diseases is a clear example, with ~5000 classes being, as of June 2022, at the same time, “instance of” and “subclass of” disease (Q12136) on Wikidata: https://w.wiki/5D4M
This mixture can be seen as an example of ontological punning (https://www.w3.org/TR/owl2-new-features/#F12:_Punning)
One solution is to consider disease (Q12136) as punning/mix of two “pure” classes:

disease (class): A new item to be used at the root of the P279 hierarchy

disease (metaclass): A new item to be used as the value of P31

The current entry for disease (Q12136) is left as a subclass of both disease (class) and disease (metaclass)
The proposal aims at a balance between flexibility for the community, backwards interoperability of current structure, and a move towards improving the ontological modelling of biological entities.
While it increases triples, it also leads to more efficient SPARQL queries, avoiding costly P279* paths, now currently needed for comprehensively querying diseases.
The proposal might be implemented manually for a subset of current diseases as a live test for the community feedback
After some level of agreement, a bot could employ the modeling to update the disease items, without removing any previous triples.

This was done in June 2022, and I haven't come back and analysed that in detail. Your post is a motivation to come back to it. Thanks! TiagoLubiana (talk) 16:59, 1 September 2023 (UTC)[reply]

Also, I think it is okay to have multiple P31 values if needed, it really helps query performance and is not wrong in an ontological sense. TiagoLubiana (talk) 17:01, 1 September 2023 (UTC)[reply]

I agree that multiple instance of (P31) (or multiple subclass of (P279)) are not a problem. But the kind of order-mixing that results from having disease (Q12136) have as instances both types of disease (e.g., measles) and occurrences of diseases (e.g., the measles that I had as a child) needs to be carefully documented and supported, which does not appear to be the case.

As far as I can tell, some types of disease are (potentially indirect) subclasses of Rigel (Q12126) some are (direct) instances of disease (Q12136). So to retrieve diseases one has to find both the instances and the subclasses of disease (Q12136). Peter F. Patel-Schneider (talk) 17:26, 1 September 2023 (UTC)[reply]

@TiagoLubiana One problem with making Rigel (Q12126) a "mixed" class is that it makes class of disease (Q112193867) not be a second-order class, violating a claim there. Peter F. Patel-Schneider (talk) 17:10, 1 September 2023 (UTC)[reply]

While I agree with you in principle, as Wikidata allows inconsistencies, this imperfection is maybe useful.

As disease (Q12136) is a punned class, one can argue that it can be considered both a first-order and second-order class. And thus, when it is a subclass of "class of disease" it is acting as a second order class, and a first-order class in the other case. Again, not super clean, but arguably useful.

What complicates the issue is that there are reusers of Wikidata that leverage the "P31 - Q12136" statements, and others that leverage the "P279* - Q12136" statements. This proposal is a way of trying to fix the issue on one hand and provide some backwards compatibility on the other. TiagoLubiana (talk) 17:21, 1 September 2023 (UTC)[reply]

The problem with this view of class order is that it makes finding and fixing errors very difficult. If a class is a first-order class then it should only have individuals as instances and it does not make sense to make it be a second-order class as well. Peter F. Patel-Schneider (talk) 17:30, 1 September 2023 (UTC)[reply]

Here are some counts for class of disease and disease:

Direct instances of class of disease 16820

Indirect instances of class of disease 16820

Direct instances of disease 2816

Indirect instances of disease 12264 (10 seconds, with labels)

Subclasses of disease 30982 (12 seconds, with labels)

Intersection of previous two times out

So it appears that it is better to retrieve instances of class of disease, rather than instances of disease, but neither appears to be comprehensive.

Note that not all subclasses of disease are necessarily (named) diseases. For example, there might be a subclass of disease that consists of some of the disease occurences that President Kennedy had. Similarly under the mixed view of disease not all instances of disease are necessarily (named) diseases. For example, there might be an instance of disease that represents the case of coeliac disease that President Kennedy had. As far as I can tell the only way to get the right answers is via something like class of disease. Peter F. Patel-Schneider (talk) 18:44, 1 September 2023 (UTC)[reply]

I generally agree with your point.

To make it clear, I am against using disease (Q12136) as an ontologically consistent term due to legacy issues, as you noticed first hand. Cleaning it up is a sysyphean task, requiring tech skills and political brilliance.

As an alternative, I've created two terms for the cases you mention, with clearer names and definitions:

disease of a particular individual (Q112193769) --> first order class
class of disease (Q112193867) --> second order class

IMO that is a good enough alternative for the time being. TiagoLubiana (talk) 17:49, 6 September 2023 (UTC)[reply]

One problem that I see with this state of affairs is that there is no guidance on how to model new diseases. Someone modelling a disease is very likely to just use disease (Q12136). I think it would be much better if there was easy-to-find guidance telling modellers to use the other two classes. (Unfortunately, I don't know how this could be done in Wikidata.) Peter F. Patel-Schneider (talk) 15:36, 7 September 2023 (UTC)[reply]

As evidence that disease is likely still capturing items that should go in the other classes, there are currently no instances of disease of a particular individual (Q112193769). Peter F. Patel-Schneider (talk) 15:47, 7 September 2023 (UTC)[reply]

I'm not sure what those two classes are supposed to represent. Is measles a "disease of a particular individual" in this scheme? WhatamIdoing (talk) 16:10, 8 September 2023 (UTC)[reply]

Measles is an instance of class of disease (Q112193867). Take a look at the description and commentary for both class of disease (Q112193867) and disease of a particular individual (Q112193769). Peter F. Patel-Schneider (talk) 17:53, 8 September 2023 (UTC)[reply]

When I think of a "class" of a disease, I'm thinking of something like "cancer" (there are hundreds of types). I would never describe a single clinical manifestation of a single virus as a "class of diesase". WhatamIdoing (talk) 04:48, 11 September 2023 (UTC)[reply]

There is always a tension between using a short label and something that better describes the concept. I agree that "class of disease" isn't a great label but I don't know of something much better. The place to put a longer description is in the value of Wikidata usage instructions (P2559), I think. A related problem here is that "disease" might be a better name, but it isn't being used because that item is already used for something somewhat different. One possibility would be to rename disease (Q12136), but even just renaming disease (Q12136) is difficult because of it current usage. (I am of the opinion that untangling disease (Q12136) is the best option, but I realize that this would have to be done only after getting agreement from the people who are using it as is.) Peter F. Patel-Schneider (talk) 15:17, 11 September 2023 (UTC)[reply]

If measles is a "class of disease", then what should we call cancer? WhatamIdoing (talk) 00:55, 13 September 2023 (UTC)[reply]

This is another place where natural language is problematic. You could think of instances of "class of disease" as "sets of illnesses that share enough characteristics to be given a short description". So cancer is an instance, as is the common cold, as is pneumonia, as is double pneumonia, as is viral pneumonia, as is measles.

As you indicate, it is possible to define "class of disease" in a different manner so that illnesses caused by a single organism or cause working in a single manner (so as to distinguish between chicken pox and shingles) are an extra instance level down. That does have the problem that diseases are (or were) often described as a complex of symptoms and thus would start out at a higher level would have to be moved down a level if they were subsequently found out to be caused by a particular organism or cause. A recent example of this is AIDS. Peter F. Patel-Schneider (talk) 01:20, 13 September 2023 (UTC)[reply]

Okay, in nosological terms, measles is "a" disease. That is, it has one (1) cause with one (1) typical clinical manifestation. Cancer, on the other hand, is not "a" disease. Cancer is more than 100 diseases. I'd like a hierarchy that would let us say:

Cancer > Breast cancer > Paget's disease of the breast

What this does is more like:

Cancer, Measles, Breast cancer, Paget's – eh, they're all the same. WhatamIdoing (talk) 15:58, 13 September 2023 (UTC)[reply]

Yes, but what is the > relationship? It can't be instance because then you could get Paget's disease of the left breast is an instance of Paget's disease of the breast is an instance of Breast cancer is an instances of Cancer of women is an instance of Cancer of humans is an instance of Cancer of animals is an instance of Cancer. What > is is subclass of (P279). So what you get is measles (Q79793) subclass of (P279) viral infectious disease (Q1928978) subclass of (P279) infectious disease (Q18123741) subclass of (P279) disease (Q12136). Peter F. Patel-Schneider (talk) 18:54, 13 September 2023 (UTC)[reply]

The subclass system makes sense to me. Declaring both cancer and measles to be a (i.e., the same) "class of disease" does not make sense to me. WhatamIdoing (talk) 04:18, 17 September 2023 (UTC)[reply]

Cancer and measles are both intensional sets of illnesses that can be naturally described, cancer as "illnesses caused by abnormal development of cells" (more or less) and measles as "illnesses caused by infection by the measles virus". So the two are, in some sense, the same and can be considered to both belong to a class. (Of course, they are in many senses different but that's also a feature of instances of a class.) So what doesn't make sense? If it is the label or description of "class of disease" then a solution would be to relabel or re-describe the class (except that perhaps the most natural label is already taken). Peter F. Patel-Schneider (talk) 09:14, 18 September 2023 (UTC)[reply]

Measles is a single disease with a single cause. It is not a "set of illnesses". It is one. Cancer, by contrast, is 200 different diseases with thousands of different causes. Cancer is a "set of illnesses". WhatamIdoing (talk) 01:38, 20 September 2023 (UTC)[reply]

These are the labels–reality pairs that make sense to me:

Class of disease–a group of related diseases, e.g., cancer, infectious disease
Disease–a single nosological entity, e.g., Paget's, measles
Instance of someone having a disease–an event involving one (usually named) individual who has a disease, e.g., Stephen Hawking had ALS, my friend has a cold this week, etc.

I don't think that cancer and measles should be in the same group. I think the general rule should be that you shouldn't call anything "a class of _____" unless you can name other things that belong inside the class. Therefore cancer is a class (entities inside the class: cancer of the lung, breast, colon, skin, etc.), but measles is not. WhatamIdoing (talk) 02:35, 20 September 2023 (UTC)[reply]

That is only one way of thinking about class of disease (Q112193867). I described another way, where instances of class of disease (Q112193867) are a class of illnesses, so cancer contains all the illnesses that are described as cancer and measles contains all the illnesses that are described as measles. Which way is the Wikidata way? That depends on the intent of the person or group that created the class and how the class is being used.

Consider disease (Q12136) itself. Cancer is a subclass of disease but so is measles. Neither is an instance of disease. Instances of disease include

running injury (Q30314084). Is this good modelling? I say absolutely not, and I think it should be changed. class of disease (Q112193867) is, in some sense, an attempt to change how diseases are modelled in Wikidata and, in my opinion, it would be much better if it took over completely from {Q|12136}}.

But is there an even better way? I think so, and I think it would fit into your view of diseases but it requires even more changes to the current state of affairs. The basic idea is to have two metaclasses, one for groupings of diseases (including singular groupings) and one for individual diseases. This works well for constructed objects like ships. There is ship (Q11446) which contains individual ships like the Titanic (Q25173), ship type (Q2235308) which contains general groupings of ships like steamship (Q12859788), and ship class (Q559026) which contains groupings of ships with the same design like Olympic-class ocean liner (Q767166). The analogous classes in the medical domain could be illness (Q814207), class of disease (Q112193867), and disease (Q12136).

Is it worth trying to move to a better way of modelling illness and disease? There could be a lot of resistance. Peter F. Patel-Schneider (talk) 12:01, 20 September 2023 (UTC)[reply]

I do not understand why you keep talking about "all the illnesses that are described as measles". There is only one illness that is (correctly/accurately) described as measles. The fact that measles is only one illness is why measles cannot be a "class" of disease/illness. The fact that cancer is hundreds of diseases is why cancer can be a "class" of disease. WhatamIdoing (talk) 04:59, 21 September 2023 (UTC)[reply]

To use your shipping-related analogy:

Ship > Steamship > Olympic-class ocean liner > Titanic
Disease > Infectious disease > Viral disease > Measles
Disease > Cancer > Breast cancer > Paget's disease of the breast

The key point that I want you to understand is that, no matter what the overall scheme is, cancer and measles should not be at the same level.

(Please ignore illness; when that word isn't just a synonym for disease, it's about your emotional experience of a medical condition – not "I have a fever and a rash", but "I feel ashamed that I caught a loathsome infection".) WhatamIdoing (talk) 05:24, 21 September 2023 (UTC)[reply]

I disagree that cancer and measles should not be on the same level. If you have a class whose instances are individual diseases and you define measles as and individiual disease and cancer as a group of diseases then you want to put cancer and measles on different levels, for that class. But if you have a class whose instances are cases of disease, like the case of measles I had when I was young, then both cancer and measles are classes. This way of organizing disease has advantages, particularly that any disease can be further subdivided, perhaps as the result of new discoveries.

A problem with putting cancer and measles on separate levels is the need for a distinction between the levels. It may be obvious that measles is on the lower level and cancer is on the upper. Then where do particular cancers go? Each kind of cancer has to be placed on either the upper level or the lower level. And any disease on the lower level cannot be specialized like cancer can.

It is not the case that Ship > Steamship > Olympic-class ocean liner > Titanic. Instead Ship > Steamship > Olympic-class ocean liner / Titanic, where / is dropping down a level. This is analogous to Disease > Infectious disease > Viral disease > Measles / my case of measles, or, maybe better, Disease > Infectious disease > Viral disease > Infection by chicken pox virus > Primary infection by Chicken pox / my case of chicken pox and Disease > Infectious disease > Viral disease > Infection by chicken pox virus > Secondary infection by chicken pox virus / John's case of shingles. Peter F. Patel-Schneider (talk) 19:10, 22 September 2023 (UTC)[reply]

┌────────────────────────────────────────────────────────────────────────────────────────────────────┘ It sounds like you aren't thinking of these as diseases. You are thinking of them as experiences that individual humans have.

You had measles; therefore, all the human experiences of measles is a group.

While you were sick with measles, did you simultaneously have the experience of Disease, Infectious disease, and Viral disease? Or did you only have Measles? WhatamIdoing (talk) 00:32, 23 September 2023 (UTC)[reply]

I think of them as more than an experience, but, yes, disease is something that organisms experience. How can it be otherwise - the identity of disease is fundamentally concerned with experience. And, yes, when I experienced measles I also experienced Viral Disease, etc. Peter F. Patel-Schneider (talk) 15:53, 27 September 2023 (UTC)[reply]

So you think that measles == disease == infectious disease == viral disease; they are all equivalent, and therefore they should all be considered disease of a particular individual (Q112193769).

I think that disease, infectious disease, and viral disease are class of disease (Q112193867), that measles is disease (Q12136), and that your personal experience is disease of a particular individual (Q112193769). WhatamIdoing (talk) 15:03, 29 September 2023 (UTC)[reply]

Measles, viral disease, infectious disease, and disease are not equivalent, but they can be considered to be a disease of a particular individual. Consider how diagnosis works. Initially the diagnosis may be something general, like pneumonia. Then it might be specialized to viral pneumonia. Finally it might be further specialized to pneumonia caused by one or more of a particular group of viruses. And that's where it might end, with no particular identification of what species of virus caused the pneumonia. All of these are diseases, with none of them infection by a particular species of organism. Should there be a level distinction between these? I say no, and I say that this can be considered to be the same situation as with measles, even though there is a particular species of virus that causes measles. Peter F. Patel-Schneider (talk) 12:46, 30 September 2023 (UTC)[reply]

I don't think that a less-than-precise diagnosis is a reason for Wikidata to say that these are all equivalent.

TiagoLubiana, perhaps you can help. Peter here seems to think that (e.g.,) measles or cancer is a disease of a particular individual (Q112193769) (because individual people get sick). Looking at it, I wonder if you meant for this to be a way to say, in the entry for (e.g.,) measles (Q79793) that Maureen McCormick (Q454374) famously had measles in 1969. WhatamIdoing (talk) 16:29, 30 September 2023 (UTC)[reply]

I've been following this discussion for some time, it seems to me that you're both partly right, but you're not entirely talking about the same thing. So, first thing first, which items here are classes and which are entities from the examples below:

hypothetical item about a disease of an individual (e.g. my case of measles (Q79793) in 1998 or Stephen Hawking's case of ALS etc.) — I couldn't find any such item, but it cannot be ruled out that there is an item like this or will be created in the future. Here we have (hierarchically) the lowest possible example of a disease. There cannot be any more specific items here — it is an entity; an instance of a disease.
measles (Q79793) — is a class. There may be instances of measles (Q79793) (like above, e.g. my case of measles (Q79793) in 1998), but there are no subclasses of measles (Q79793) (no subtypes of this disease, no more specific diseases that can be broadly described as measles (Q79793) etc.).
cancer (Q12078) – is a class, but a different one from measles (Q79793). There may be several sybtypes of cancer (Q12078) like adenoid cystic carcinoma (Q356005), spindle cell cancer (Q18975358) or invasive cancer (Q111796831); some of these subtypes may have its own subtypes, some may have no subtypes, only instances.

In this discussion you have mentioned two metaclasses: class of disease (Q112193867) and disease of a particular individual (Q112193769). It may be enough, but it may not be; basically determining the number of these metaclasses depends on the discussion. For the #1 (hypothetical item about a disease of an individual) disease of a particular individual (Q112193769) is a proper metaclass. The class of disease (Q112193867) could be used for both #2 and #3, but that's not necessarily what you have to do. You can choose to use different metaclasses for these two. An example from chemistry:

2-methylheptane (Q2493733) (class) has a instance of (P31)type of chemical entity (Q113145171) (metaclass) and subclass of (P279)octane (Q58623289) (class)

octane (Q58623289) (class) has a instance of (P31)group of isomeric entities (Q15711994) (metaclass) and subclass of (P279)alkane (Q41581) (class)

alkane (Q41581) (class) has a instance of (P31)structural class of chemical entities (Q47154513) (metaclass) and subclass of (P279)aliphatic hydrocarbon (Q47165582) (class) ... etc.

In this example we have three classes, each with different metaclass depending on the nature (specific attributes) of the described class. All three could be described as a class of chemical entities metaclass, but it wouldn't be feasible, because these classes differ very much. So you could also choose to describe measles (Q79793) and cancer (Q12078) with different metaclasses, not by the same class of disease (Q112193867) (both are classes of diseases, but it does not mean that both should have the same metaclass, especially if the differences are significant).

To sum up, you could establish a system in which:

hypothetical item about a disease of an individual would have a metaclass added via P31 being disease of a particular individual (Q112193769).
measles (Q79793) would have a metaclass added via P31 like type of a disease (metaclass that would indicate that there are no subclasses of this disease).
cancer (Q12078) would have a metaclass added via P31 like group of diseases (metaclass that would indicate that it is a collective name for a certain group of more specific diseases; in other words: that there are subclasses of this disease).

In #2 or #3 class of disease (Q112193867) could be used as a metaclass. However, I find the English language very limited in such situations and it lacks certain linguistic nuances that would enable to distinguish such concepts like type, class, group, set etc. effectively. Wostr (talk) 20:19, 3 October 2023 (UTC)[reply]

@Wostr, in this model, would an iPhone 14 Pro Max (Q113816991) be "an entity" or "a class"? WhatamIdoing (talk) 21:53, 3 October 2023 (UTC)[reply]

@WhatamIdoing: A class of course. Just as it is modelled now. Wostr (talk) 21:58, 3 October 2023 (UTC)[reply]

Is the specific iPhone 14 Pro Max in someone's pocket is the "entity"? WhatamIdoing (talk) 22:22, 3 October 2023 (UTC)[reply]

Yes, that's right. Wostr (talk) 22:28, 3 October 2023 (UTC)[reply]

Is a book an "entity", or is it a class, and only "the copy owned by this person" is the entity? WhatamIdoing (talk) 02:15, 5 October 2023 (UTC)[reply]

I'm not sure where this discussion is going. Books have a more complicated data model in WD (and not only in WD) based on FRBR with two (instead of four) concepts. We have items about individual copies of a book (like Q70783217) linked via P31-like property (exemplar of (P1574)). At this point, I cannot say whether such a different data model could in any way be properly translated into the discussed problem with diseases. Probably one could say that a disease of an individual person is some sort of manifestation of a concept of a specific disease. However, even this does not solve the problem with disease items. I suspect that you are trying to argue that diseases such as 'measles' (which are at the very bottom of the classification tree) should be treated as 'entities' (because they don't have any subtypes). I believe that this will not work properly in WD, such a model will be inconsistent, even taking into account medical classifications (ICD, DSM), they may not be accurate enough (unlike e.g. biological taxonomy) to avoid some classification problems in WD. Wostr (talk) 18:02, 5 October 2023 (UTC)[reply]

In the real world, we speak of things like measles as "a disease entity" (e.g., https://academic.oup.com/jmp/article/39/6/609/2743604). The concept is fundamental to nosology, and differentiating disease entities from (e.g.,) symptoms and risk factors is an important part of medicine. It would be strange to have Wikidata declare that "a disease entity" is not actually an entity. WhatamIdoing (talk) 19:19, 6 October 2023 (UTC)[reply]

┌────────────────────────────────────────────────────────────────────────────────────────────────────┘ It is always good to base WD data model on established ontologies. However, most often there are problems when trying to accurately reproduce them in WD. They are created for specific, limited areas of knowledge, and in WD we try to combine all these areas into one whole.
It seems to me that there will be no contradiction with nosology here. Classification is not the same as ontology. The latter describes the relationships between many aspects in a field, not only the classification (of diseases). In other words: treating 'measles' as a class in WD does not contradicts with a 'disease entity' term. I don't think there is a problem in this discussion with defining concepts or with classifying diseases as such. The problem I see here is to apply a specific model to this data and to select the appropriate metaclasses for diseases in such a way that the whole thing is coherent. If two separate metaclasses are chosen for cases such as 'measles' and for cases such as 'cancer', it will still be possible to distinguish such cases based on the metaclasses used. Otherwise, if we treat 'measles'-like items as instances of specific classes of diseases, there will be a problem with how to treat potential items about cases of measles in individuals. You can't have an instance of an instance. It seems easier and more consistent to me to have all diseases modelled as classes, linked via subclass of (P279) and differentiate them based on metaclasses used. It is also consistent with medical ontologies I found: there is only one type of relation between diseases on different classification level (either is_a or subclass_of).
It seems to me that it is largely my fault that this discussion has moved to topics that are less and less related to the problem, so:

right now there are no guidelines on how to use instance of (P31) and subclass of (P279) in items about diseases;
items like disease (Q12136) are used as both classes and metaclasses;
my comments mainly aim to specify that instance of (P31) should only be used for metaclasses and all relationships between diseases should be modeled using subclass of (P279)
- while modeling all diseases via subclass of (P279) also means indicating that 'measles'-like items are classes in WD, this does not mean that they have to have the same metaclasses if there is no agreement or there are other reasons for such a division (see examples below):

measles (Q79793)

instance of (P31)

	type of a disease (Q...)	edit

	0 references add reference

name of this metaclass is irrelevant, it can be named in any way

add value

subclass of (P279)

	Morbillivirus infectious disease (Q18975514)	edit

	0 references add reference

going up subclass of you will reach disease (Q12136)

add value

cancer (Q12078)

instance of (P31)

	class of disease (Q112193867)	edit

	0 references add reference

add value

subclass of (P279)

	neoplasm (Q1216998)	edit

	0 references add reference

	tumor (Q133212)	edit

	0 references add reference

	disease of cellular proliferation (Q18554796)	edit

	0 references add reference

going up subclass of you will reach disease (Q12136), while going down subclass of you will reach diseases like choroid spindle cell melanoma (Q18557115)

add value

Wostr (talk) 21:49, 6 October 2023 (UTC)[reply]

If we model all diseases (e.g., measles) as classes, then measles is disease (Q12136), which should be a (plain/simple/ordinary) class, and cancer should be (if I understand correctly) a meta-class and class of disease (Q112193867).

But couldn't we accomplish approximately the same thing by saying that measles is an instance of disease (Q12136) (making that not be a class), and handling the individual cases, like Maureen McCormick (Q454374) getting measles, through exemplar of (P1574)? WhatamIdoing (talk) 16:54, 17 October 2023 (UTC)[reply]

Probably through manifestation of (P1557) or more specific property, exemplar of (P1574) does not seem to be correct here, but yes, that is possible. I'm not so sure though that this approach would be easier. 'Measles' is a good example in this discussion as a type of disease with no subtypes etc., but with neoplasm (Q1216998) and the approach of using instance of (P31) for the lowest-level subtypes, I'd expect problems. Where should one draw the line and use instance of (P31) and where should one use subclass of (P279)? There is an ICD classification, but even such a detailed classification does not take into account the even more detailed division in WD. Upon finding or creating more detailed item (subtype), one would have to be careful and change instance of (P31) to subclass of (P279), and as a result, items describing diseases on similar level of detail could be at different levels (instance of (P31) or subclass of (P279)).

From my perspective it seems easier to put all the classification in subclass of (P279) and use instance of (P31) for metaclasses only; then determine what metaclasses can be used for diseases and what level of detail in the disease description in an item should be to assign a given metaclass. Wostr (talk) 17:36, 17 October 2023 (UTC)[reply]

One should draw the line wherever the sources do, which is usually pretty straightforward. Neoplasm is a very big group. Measles is a single thing.

Are you involved in Wikidata:Events/Data Modelling Days 2023? It sounds like the kind of event in which this could be discussed. WhatamIdoing (talk) 18:43, 22 November 2023 (UTC)[reply]

Merge systemic inflammation (Q7663815) and chronic inflammatory response (Q3798557)?

There is no intersection between those items wiki sitelinks languages, and I'm under the impression that they refer to pretty much the same concept, or is there a difference I'm missing? Maxlath (talk) 19:30, 2 October 2023 (UTC)[reply]

Can't systemic inflammation be acute? WhatamIdoing (talk) 23:52, 2 October 2023 (UTC)[reply]

Removing inactive participants

Wikidata's default ping system does not send alerts to more than 50 people at once. Since currently more than 50 people are signed on for the default WikiProject Medicine alert system, no one can use it for general project alerts until we get the group under 50 people.

I removed the following people who have not made Wikidata editors in more than 2 years. If any of you are around, feel free to sign back up.

Bluerasberry (talk) 19:49, 3 October 2023 (UTC)[reply]

That is a good idea. Thanks, Lane! TiagoLubiana (talk) 17:16, 26 November 2023 (UTC)[reply]

Representation of notifiability of diseases

Hello!

I am thinking about how to model notifiable diseases on Wikidata. There are some Wikipedia pages on the topic, and some Wikidata items like notifiable diseases in the United States (Q55625522).

I was considering maybe using the list items themselves to catalog the diseases. Currently some diseases have it as instance of (P31) properties, but that seems unsustainable. For example, see the multiple instance of values for tularemia with applies to jurisdiction (P1001) and valid in place (P3005) values describing the places where they are notifiable.

Usually "Wikimedia list items" do not have much semantic associated, but it seems to be the cleanest way to represent that.

Adding places to disease items or diseases to country items would lead to too many items for each.

Maybe a decent modelling would be transforming "list of notifiable diseases" (Q6630849) in "set of notifiable diseases in a particular location" and have listings for the different jurisdictions.

Bringing it here to see if anyone has thoughts about it! Cheers, TiagoLubiana (talk) 17:22, 26 November 2023 (UTC)[reply]

Are you more interested how Wikidata handles the list pages (e.g., notifiable diseases in the United States (Q55625522)), or in how to mark each the individual disease (e.g., measles (Q79793)) to say that this individual disease is notifiable in the US? WhatamIdoing (talk) 17:18, 27 November 2023 (UTC)[reply]

hyperlipidemia (Q1079120), dyslipidemia (Q66291209), and lipid metabolism disorder (Q1476525)

Over at WikiProject Conflation (which has more medical-related listings too), we have hyperlipidemia (Q1079120), dyslipidemia (Q66291209), and lipid metabolism disorder (Q1476525) that need to be untangled. The item for hyperlipidemia had quite a few references to dyslipidemia, but I've moved those over to the other item. But I'm stuck on dyslipidemia and lipid metabolic disorder; are these the same or not? MESH says no[3][4], Disease ontology says yes. I would think not, that dyslipidemia is one type of lipid metabolic disorder, but I have no medical training, so I'm turning to all of you on this project for help. - Yupik (talk) 14:53, 2 September 2024 (UTC)[reply]

In the specific case, I think that MeSH is sensible. If you have high cholesterol (very common), then the classification runs like this:

Lipid Metabolism Disorders (big category)
- Dyslipidemias (an in-between category; having the wrong amount of lipids is one of five ways of having problems with lipids)
  - Hyperlipidemias (an in-between category; having too much lipids is one of three ways of having the wrong amount of lipids)
    - Hypercholesterolemia (the bottom category; having too much cholesterol is one of the four ways of having too much lipids)

I tentatively suggest that, as a principle, splitting will be more useful to Wikidata than lumping. I suggest this approach because medical practice varies by country/culture, so doctors in one country might say "Oh, X and Y are basically the same" and doctors in another country might say "We use X for these cases and Y for those cases". WhatamIdoing (talk) 19:22, 2 September 2024 (UTC)[reply]

My apologies, I forgot to thank you for explaining these in a way that I could understand it! I will try to work on these before the end of the year if no one else does it first. If you don't mind, I'd like to paste your text with a link back to it at the conflation project under these items there. - Yupik (talk) 17:34, 16 September 2024 (UTC)[reply]

You're welcome, @Yupik. Feel free to copy/paste my comments to any discussion. WhatamIdoing (talk) 21:53, 16 September 2024 (UTC)[reply]

Modelling internship, residency, fellowship of physicians

How shall we model internship, residency, and fellowship of physicians on Wikidata? I'm not familiar with the American medical training practices, but I frequently provide identifying information on items of authors on Wikidata. To be precise, is the appropriate property is educated at (P69), affiliation (P1416), or employer (P108)? Is there a suitable qualifier for that statement to specify medical internship (Q349015), residency (Q256698), fellowship (Q2912722), such as subject has role (P2868), position held (P39)? Perhaps there are other ways of modeling that these more precise questions don't consider.

For example, this official record describes James Alan Thorp (Q131194660). Daask (talk) 21:06, 15 November 2024 (UTC)[reply]

Wikidata talk:WikiProject Medicine

LOINC

Change Detector & Diseases

Drug categories

Anatomy related property template created

Infobox medical condition: medical specialty

Lots of information to harvest from French infoboxes about genetic diseases

Information about whether a gene is located within mitrochondrial DNA

Heart activity

Wikipedia articles corresponding to 2 distinct data items

Are there currently any wikidata properties for specifying a metabolizing enzyme (like "substrate of X") or a drug/natural product's metabolites?

Auto archiving

References

medical condition treated (P2175) matters

Semantically gathering studies knowledge

Drug interactions (P769)

Hospitals

Health & healthcare by country

phase IV clinical trial (Q42825046) vs postmarketing surveillance (Q7234359)

help me. How combine Q30280146 + Q16095310 (South korea hospital imfomation)

Price of medications

Notifiable diseases by country

Paper on Wikidata and medicine

Hospital: organization vs. building

The appearance /physical attributes/ of drugs

Drug Indications

Pregnancy category

Medical encyclopedias

Modeling Adverse Drug Reactions

Foundational Model of Anatomy ID

Manuscript: Wikidata as a FAIR knowledge graph for the life sciences

Is it time for a Wikiproject Coronavirus?

Mining COVID19 research using [R] and Wikidata

Is it OR to state that novel Coronavirus can be transmitted by common communion cup?

I made or improved wikidata queries of endocrinologists.

Which P31 for a prepublication article version

diseases are mostly not human-specific

External identifiers for medical items

VEXAS = VEXAS syndrome

inception (P571) of surgical mask (Q10282403)

Mapping inflammatory bowel disease to Orphanet ID

How to model medical indications?

congenital adrenal hyperplasia (Q366868) and adrenogenital disease (Q13368382)

WikiProject Clinical Trials for Wikidata - the paper

We should create individual medical procedures in Wikidata

Intravenous

How to link clinical trials to the main subject of the research?

missing diseases or syndromes

US-Drug_Master_file_ID

Medicinal plant : how to link with a class of medications?

Clinical guideline data model

Value-type constraint of route of administration (P636)

Some_UMLS_CUI_(P2892)_concerns

Medical treatment class hierarchy

Schemas for medical entitites

diseases and rare diseases

Merge systemic inflammation (Q7663815) and chronic inflammatory response (Q3798557)?

Removing inactive participants

Representation of notifiability of diseases

hyperlipidemia (Q1079120), dyslipidemia (Q66291209), and lipid metabolism disorder (Q1476525)

Modelling internship, residency, fellowship of physicians

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