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Wikidata talk:WikiProject Medicine

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LOINCEdit

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)

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

Change Detector & DiseasesEdit

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)

Drug categoriesEdit

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)

Anatomy related property template createdEdit

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)

Thanks Was a bee (talkcontribslogs) 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)

Infobox medical condition: medical specialtyEdit

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

Lots of information to harvest from French infoboxes about genetic diseasesEdit

Information about whether a gene is located within mitrochondrial DNAEdit

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)

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

Heart activityEdit

We currently have cardiac 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)

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

Wikipedia articles corresponding to 2 distinct data itemsEdit

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 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 ) 09:35, 29 January 2018 (UTC)

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 ) 09:36, 29 January 2018 (UTC)
  Comment @Seppi333: if I understood you well, I think you can use main subject (P921) on Q27156494. I mean to put beta-Hydroxy beta-methylbutyric acid (Q223081) as a main subject of Q27156494. Or to use see also (P1659) or different from (P1889). You should know that we can't link article to 2 items! --Alaa :)..! 16:16, 29 January 2018 (UTC)
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 ) 16:41, 29 January 2018 (UTC)

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

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 ) 19:55, 30 January 2018 (UTC)

Actually, I remembered that I used physically interacts with (P129) in amphetamine (Q179452) to specify the enzyme that it interacts with and its role (subject has role (P2868)) as a substrate (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 ) 20:03, 30 January 2018 (UTC)

Auto archivingEdit

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)

ReferencesEdit

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)

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

medical condition treated (P2175) mattersEdit

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), anthrax (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)

Semantically gathering studies knowledgeEdit

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 :

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 reference
+ 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)

Drug interactions (P769)Edit

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)

HospitalsEdit

Anandhisuresh (talk) 17:16, 28 February 2018 (UTC)anandhisuresh Tobias1984
Doc James
User:Bluerasberry
Wouterstomp
Gambo7
Daniel Mietchen
Andrew Su
Peter.C
Klortho
Remember
Matthiassamwald
Projekt ANA
Andrux
Pavel Dušek
Was a bee
Alepfu
FloNight
Genewiki123
Emw
emitraka
Lschriml
Mvolz
Franciaio
User:Lucas559
User:Jtuom
Chris Mungall
ChristianKl
Gstupp
Geoide
Sintakso
علاء
Dr. Abhijeet Safai
Adert
CFCF
Jtuom
Lucas559
Drchriswilliams
Okkn
CAPTAIN RAJU
LeadSongDog
Ozzie10aaaa
Sami Mlouhi
Marsupium
Netha Hussain
Abhijeet Safai
ShelleyAdams
Fractaler
Seppi333
Shani Evenstein
Csisc
linuxo
Arash
  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)

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)
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)
  • 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)

Health & healthcare by countryEdit

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)

  • 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)

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

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)

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

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

@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)

  • 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)

Price of medicationsEdit

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)

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)
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