Wikidata talk:WikiProject COVID-19

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This project[edit]

Hello,

I love the idea of this WikiProject. There were some discussions about structuring it as a task force (see User_talk:Daniel_Mietchen#Would_you_like_to_contribute_to_a_WikiProject_COVID-19_?). And @Daniel Mietchen: has lots of experience in managing WikiProjects in Wikidata. What about we start gathering some content here and maybe move it elsewhere on Wikidata if it is a better option for the community? TiagoLubiana (talk) 01:20, 16 March 2020 (UTC)

I think the most important thing is to get going and to inform all the relevant communities/ places. --Daniel Mietchen (talk) 01:45, 16 March 2020 (UTC)

Should regional outbreaks be classified as pandemics or epidemics?[edit]

I made a wikidata list of all pandemics. See en:Talk:Pandemic#Wikidata list of pandemics. Should regional outbreaks, such as 2020 coronavirus pandemic in North Dakota (Q87746410), be considered instances of pandemics, or just epidemics and part of a specific pandemic? Tomastvivlaren (talk) 07:19, 16 March 2020 (UTC)

@Tomastvivlaren: Great point. My view is: there is only one instance of a pandemic. It is one pandemic, by definition. I guess you can classify as an instance of an outbreak, as it has been done (see 2020 COVID-19 outbreak in Brazil (Q86597695). Maybe there could be a more specific item. Something in the likes of a "local manifestation of a pandemic", a subclass of "outbreak". What do you think? TiagoLubiana (talk) 14:33, 16 March 2020 (UTC)
Up, something like local manifestation of a pandemic (Q87767992) TiagoLubiana (talk)

Mining COVID19 research using [R] and Wikidata[edit]

Project components: R, textmining, Wikidata, COVID19, open access publications, preprints, closed access publications.

A group being put together by Peter Murray Rust is looking to build an integrated open resource of current published information & data on COVID19 (see the petermr/openVirus github repo for details). It should also eventually be relevant to other topics.

A few example subgoals:

  • Immediate term: be able to edit wikidata from R via the API
  • Short term: pull all COVID19 published papers from ePMC
    • textmine for main topics and broader topics (all topics should match to wikidata items)
    • write main topics to Wikidata items for those published papers
    • publish broader topics of each paper in a separate open database
  • Medium term: as above, but for bioRxiv, medRxiv, SciElo, Redalc etc.

Medium term: as above, but for paywalled articles

  • Medium term: more in-depth text analysis
  • Long term: make process applicable to other topics

Please let us know if you'd be interested in being involved. T.Shafee(evo&evo) (talk) 08:53, 16 March 2020 (UTC)

@Evolution and evolvability: Oh, awesome that Peter is acting on this too! I will be glad to help. TiagoLubiana (talk) 14:30, 16 March 2020 (UTC)

Particularly keen to create dictionaries from Wikimedia resources. Currently

  • Links in Wikipedia pages (very noisy)
  • Categories. Often coherent lists
  • Tables in WP pages. variable
  • Templates. Look very good - writing code ATM

see https://github.com/petermr/tigr2ess Tigr2ess tutorial (will add link later) Petermr (talk) 04:09, 17 March 2020 (UTC)

For the 'edit API', a simple solution is to have the RDF generate QuickStatements. This approach has worked for me very well for years now. Of course, a Wikidata bot written in / for R would be awesome. --Egon Willighagen (talk) 07:21, 17 March 2020 (UTC)
@Egon Willighagen: Agree, making quickstatements tables should be a good intermediate solution. Is it possible to submit to quickstatements via API (the way SourceMD used to)? Will add an issue ot the repo now (link and link). T.Shafee(evo&evo) (talk) 00:55, 19 March 2020 (UTC)
There is QS Batch. Magnus has replied in both issues. I used that to submit 3M edits (only took 2 months to complete ;-) --Vladimir Alexiev (talk) 20:02, 23 March 2020 (UTC)

For dictionaries I would actually start from MeSH descriptor ID (P486). https://www.ncbi.nlm.nih.gov/mesh/2049999 (from January) and https://www.ncbi.nlm.nih.gov/mesh/2050205 (from February) are two new C-numbers (i.e. MeSH supplementary topics). The point I would make is that they each come with a list of aliases. https://www.ncbi.nlm.nih.gov/mesh/2023153 from 2018 is the relevant genus: the aliases there are not going to be so useful. https://www.ncbi.nlm.nih.gov/mesh/68018352 from 1994 likewise: but the narrower terms given on those pages deserve attention. In general reverse lookup can translate MeSH C-numbers (as for D-numbers) into the items carrying them: respectively SARS-CoV-2 (Q82069695) (added today by me), COVID-19 (Q84263196) added 17 February. (I use https://tools.wmflabs.org/wikidata-todo/resolver.php?prop=486 for reverse lookup, though there are other ways.)

Generally a good way to compile broad-based dictionaries is to extract the label and aliases for items, using a SPARQL query. A VALUES query based on a list of items would be easy to update, as things progress. Charles Matthews (talk) 16:55, 17 March 2020 (UTC)

Thanks for this! Everyone note the difference between MESH Descriptors, Concepts and Terms. Best described here https://www.wikidata.org/wiki/Wikidata:Property_proposal/MESH_Concept_ID --Vladimir Alexiev (talk) 20:06, 23 March 2020 (UTC)

For alpha users. Have written code to extract references from Wikipedia templates into dictionary form. Initial examples ``` String[] templates = {"Baltimore_(virus_classification)", "Antiretroviral_drug", "Virus_topics"}; ``` using https://github.com/petermr.ami3 will convert these Wikipedia templates into structured dictionaries. Templates of species, drugs, organizations, etc. will be useful. Please suggest templates that could be useful and I'll convert them.Petermr (talk) 09:46, 20 March 2020 (UTC)

Hello, @Petermr:. Great work! I'm with Ami the Kangaroo here cheering for us. On the Wikipedia Wikiproject on COVID19 (en:Wikipedia:WikiProject_COVID-19) there are many templates directly related to COVID19, for example, the project tempĺate (en:Template:WikiProject_COVID-19). I hope this helps somehow. Best, TiagoLubiana (talk) 18:15, 21 March 2020 (UTC)

Numeric data[edit]

There are various data that can be represented on Wikidata or in the Tabular Data format on Wikimedia Commons, see, e.g., [1]. It is somewhat difficult to collect. Hospitalizations are apparently not available from Danish authorities, but scattered in the news media; longitudinal Danish data is hard to get because the page where it is presented is overwritten daily. I suppose that is the same problem for other countries. — Finn Årup Nielsen (fnielsen) (talk) 14:31, 16 March 2020 (UTC)

Great point. The fact that the page is overwritten everyday might be good. Perhaps we can get legacy pages from a service such as webarchive [2] and standardize the refs? TiagoLubiana (talk) 14:41, 16 March 2020 (UTC)
Yes, exactly! I recommend using the Wayback Machine (Q648266) too, and in fact was doing that for 2020 coronavirus outbreak in the Netherlands (Q86756826) already. --Egon Willighagen (talk) 09:44, 17 March 2020 (UTC)
For the numeric data in Austria (Q40) on 2020 coronavirus pandemic in Austria (Q86847911) i am starting to use the following structure of references including data published by the Federal Ministry of Health (Q1006381):
* reference URL (P854)https://www.sozialministerium.at/Informationen-zum-Coronavirus/Neuartiges-Coronavirus-(2019-nCov).html
* publisher (P123)Federal Ministry of Health (Q1006381)
* publication date (P577) → 2020-03-17
* archive URL (P1065)[3]
* archive date (P2960) → 2020-03-17
* retrieved (P813) → 2020-03-17
* language of work or name (P407)German (Q188)
--Mfchris84 (talk) 14:33, 17 March 2020 (UTC)
There is a similar discussion on the English Wikipedia. --Daniel Mietchen (talk) 10:53, 17 March 2020 (UTC)
An option for standardized, global source of information are the WHO Novel Coronavirus (2019-nCoV) Situation Reports, at least for number of cases (P1603) and number of deaths (P1120). You can easily find them (at least now) in this Scholia page: for the COVID-19 pandemic. I have made a few python scripts to parse the WHO table and convert them to quickstatements (WHO to Wikidata on GithHub). For now, it is something like:
If you have any contributions, please feel free to make either there or here. I can already send the batch for the yesterday numbers, but I thought about consulting you first. TiagoLubiana (talk) 18:14, 17 March 2020 (UTC)

Collection SPARQL queries as a book[edit]

Hi all, some time ago I started playing with SPARQL embedded in Markdown, to create an online book. Since someone was asking about queries for the virus, I started this book: https://egonw.github.io/SARS-CoV-2-Queries/ --Egon Willighagen (talk) 19:38, 16 March 2020 (UTC)

Capturing Special Announcements in a Wikibase[edit]

Following the announcement of schema.org of their release version 7.0, I took the liberty to set up a wikibase where I tried to follow the same schema. The special announcement schema was created to deal with the CORVID-19 Pandemic

The Wikibase is running on WBStack and still very much an early prototype. I was not able to fully following the schema proposed by schema.org, since Wikibase only accepts one datatype per property, but I was able to solve that by using wikibase items, where the items will capture the other possible data types.

I am reaching out to this group for scrutiny. Please feel free to test run. I will also continue working on it, but if the model is mature, I will try set up a Wikibase that can be used to collect these special announcements for real. --Andrawaag (talk) 21:49, 17 March 2020 (UTC)

@Andrawaag: I took a look at it, and it looks quite useful. I'm not able to give technical feedback on it, but I liked the idea and the implementation. Collecting those announcements can be super informative, indeed. TiagoLubiana (talk) 14:19, 18 March 2020 (UTC)

I made a second prototype of a Wikibase for specialAnnouncement, this time with a wikibase property for each data type included in a schema.org property. e.g isBasedOnUrl (http://schema.org/Product as item) and isBasedOnUrl (url).

To move forward it would be nice to have a set of special announcements to see which approach fits best. Who has examples? --Andrawaag (talk) 08:03, 19 March 2020 (UTC)

Semantic Scholar's COVID-19 Open Research Dataset[edit]

News from Semantic Scholar (Q22908627):

Semantic Scholar has partnered with several leading research groups to prepare the COVID-19 Open Research Dataset (CORD-19), a unique resource of over 29,000 scholarly articles about COVID-19, SARS-CoV-2, and related coronaviruses.

Do be aware of the associated licence.

I have a contact there, if anyone needs something that is not already publicly available. Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits 12:21, 18 March 2020 (UTC)

How the CORD dataset was made. And they'll keep it up to date https://www.whitehouse.gov/briefings-statements/call-action-tech-community-new-machine-readable-covid-19-dataset/. Many people are working off that dataset. I know of 2 RDF representations. So is it a goal to mirror CORD in Wikidata and link it to the rest of WD? Only makes sense if we can keep it up to date. Vladimir Alexiev (talk) 20:15, 23 March 2020 (UTC)

biological processes[edit]

This is a heads up on my personal project to import papers on the molecular biology of SARS-Cov-2 replication in humans. These will have a common main subject claim added, so that they can later be searched. The ultimate goal is to provide a collection of references for statements on the biology, practically the base of biocuration. --SCIdude (talk) 07:53, 19 March 2020 (UTC)

@SCIdude: That is awesome. Do you want to document what you are doing (so more people can help) somewhere around this project? For example, what do you think about a new tab about scholarly research? TiagoLubiana (talk) 23:27, 19 March 2020 (UTC)
The result is continously visible in the query https://www.wikidata.org/wiki/Wikidata:WikiProject_COVID-19/Queries#with_main_subject_molecular/structural_biology_of_any_SARS-related_strain. --SCIdude (talk) 14:03, 20 March 2020 (UTC)
@SCIdude:, please take note of this project: https://covid.pages.uni.lu/map_curation Let's try to coordinate all our work. --Egon Willighagen (talk) 13:22, 21 March 2020 (UTC)

wirvsvirushackathon[edit]

Hello,

at the Weekend starting on tomorrow there is a hackathon. Maybe it is possible and you are interested in attending. More information you can find on that page. https://wirvsvirushackathon.org/ I have seen it a few minutes ago and I think maybe it is interesting for you. --Hogü-456 (talk) 21:55, 19 March 2020 (UTC)

Here you can add the project if you want. I think it could help the other people. [4] --Hogü-456 (talk) 21:59, 19 March 2020 (UTC)
@Hogü-456: Awesome! Good contribution. I was not able to add the project to the list. If someone wants to use Wikidata, great, I can make myself available to help any way possible. Just leave a message at my talk page. TiagoLubiana (talk) 17:55, 21 March 2020 (UTC)

How to represent putative treatments?[edit]

There are some drugs that appear in the scientific literature as putative treatments for COVID-19. For example, in the english Wikipedia page is said:

"Authorities recommend chloroquine[108] and the Chinese 7th edition guidelines include interferon, ribavirin, chloroquine, or umifenovir.[109]."

Do you think that using drug used for treatment (P2176) with these drugs is suitable? TiagoLubiana (talk) 17:47, 21 March 2020 (UTC)

New branch of the project: statements![edit]

TiagoLubiana (talk) 01:35, 16 March 2020 (UTC) Daniel Mietchen (talk) 01:42, 16 March 2020 (UTC) Jodi.a.schneider (talk) 02:45, 16 March 2020 (UTC) Chchowmein (talk) 02:45, 16 March 2020 (UTC) Dhx1 (talk) 03:38, 16 March 2020 (UTC) Konrad Foerstner (talk) 06:02, 16 March 2020 (UTC) -Netha Hussain (talk) 06:19, 16 March 2020 (UTC) Bodhisattwa (talk) 06:56, 16 March 2020 (UTC) Neo-Jay (talk) 07:04, 16 March 2020 (UTC) John Samuel (talk) 07:31, 16 March 2020 (UTC) KlaudiuMihaila (talk) 07:53, 16 March 2020 (UTC) Salgo60 (talk) 09:11, 16 March 2020 (UTC) Andrawaag (talk) 10:12, 16 March 2020 (UTC) Whidou (talk) 10:16, 16 March 2020 (UTC) Blue Rasberry (talk) 15:07, 16 March 2020 (UTC) TJMSmith (talk) 16:15, 16 March 2020 (UTC) Egon Willighagen (talk) 16:49, 16 March 2020 (UTC) Nehaoua(talk) 20:32, 16 March 2020 (UTC) Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits Peter Murray-Rust (talk) 00:00, 17 March 2020 (UTC) Kasyap (talk) 02:45, 17 March 2020 (UTC) Denny (talk) 16:21, 17 March 2020 (UTC) Kwj2772 (talk) 16:56, 17 March 2020 (UTC) Joalpe (talk) 22:47, 17 March 2020 (UTC) Finn Årup Nielsen (fnielsen) (talk) 10:59, 18 March 2020 (UTC) Skim (talk) 11:45, 18 March 2020 (UTC) SCIdude () 15:15, 18 March 2020 (UTC) T.Shafee(evo&evo) (talk) 01:23, 20 March 2020 (UTC) Susanna Ånäs (Susannaanas) (talk) 07:05, 20 March 2020 (UTC) Mlemusrojas (talk) 15:30, 20 March 2020 (UTC) Yupik (talk) 20:23, 20 March 2020 (UTC) Csisc (talk) 23:05, 20 March 2020 (UTC) OAnick (talk) 10:26, 21 March 2020 (UTC) ❙❚❚❙❙ JinOy ❚❙❚❙❙ 12:28, 21 March 2020 (UTC) Jjkoehorst (talk) 14:27, 21 March 2020 (UTC) So9q (talk) 08:58, 22 March 2020 (UTC) Nandana (talk) 14:58, 23 March 2020 (UTC) ·addshore· talk to me! 15:56, 23 March 2020 (UTC) Librarian lena (talk) 18:19, 24 March 2020 (UTC) Jelabra (talk) 19:19, 24 March 2020 (UTC) AlexanderPico (talk) 23:34, 27 March 2020 (UTC) Higa4 (talk) 02:51, 29 March 2020 (UTC) JoranL (talk) 19:56, 29 March 2020 (UTC) Alejgh (talk) 11:04, 1 April 2020 (UTC) Will (Wiki Ed) (talk) 17:36, 1 April 2020 (UTC) Ranjithsiji (talk) 04:47, 2 April 2020 (UTC) AntoineLogean (talk) 07:35, 2 April 2020 (UTC) Hannolans (talk) 17:22, 2 April 2020 (UTC) Farmbrough21:15, 3 April 2020 (UTC).
Ecritures (talk) 21:26, 3 April 2020 (UTC)
Pictogram voting comment.svg Notified participants of WikiProject COVID-19

Hello,

I am quite excited about this new branch of the project called statements (Wikidata:WikiProject_COVID-19/Statements). The idea is to gather the statements behind core publications and Wikipedia articles. Why doing that?

  • Check which core informations can and cannot be currently represented in Wikidata.
  • Identify missing items and properties.
  • Update Wikidata items so they capture the core informations of Wikipedia.
  • Start to work on templates for, in the future, automatically create pages in Wikipedia for projects/languages that do not have pages for those items (See en:Wikipedia:Mbabel).

I hope you like the idea and contribute! It is still experimental, so new ideas of how to organize that are super welcome.

TiagoLubiana (talk) 02:04, 20 March 2020 (UTC)

Wikidata/Wikipedia related work at Hack the Crisis Finland hackathon this weekend[edit]

I am participating in Hack the Crisis hackathon initiated by the the Finnish government and startups. I would like to reach out to this group for collaboration. I can introduce resources that Wikidata offers to the participants or propose ways in which they can contribute to it. Please help me focus on the most essential needs. You can also join the hackathon if you have the time. Cheers, Susanna Ånäs (Susannaanas) (talk) 07:19, 20 March 2020 (UTC)

@Susannaanas: I only saw that now, I am sorry! The project is still organizing itself. I would say that a dire need is a trustable and updated source of number of number of cases (P1603) and number of deaths (P1120) for auto updating thee items for the specific locations of the pandemics. Infos on the Wikidata:WikiProject_COVID-19/Items#Genes,_genomes_and_proteins would also help a lot. Also, the queries here Wikidata:WikiProject_COVID-19/Queries can be interesting for the hackathon participants. If you think of any other ways this project can colab with hackathons, that would be great, and please let us know. If there is time, I might even write a page about this integration. I wish you a great hackathon! TiagoLubiana (talk) 18:03, 21 March 2020 (UTC)

How to indicate someone being the index case (Q1639798) in their country?[edit]

As the title says. --Trade (talk) 12:43, 20 March 2020 (UTC)

subject --> part of --> national epidemic; qualifier: subject has role --> index case. --SCIdude (talk) 13:56, 20 March 2020 (UTC)
@Trade:, @SCIdude:. Good question and ideas. Adding to the discussion, it seems that there is a different solution already modelled. See for example Thomas Eric Duncan (Q18249266) index case of (P1677) Ebola virus disease in the United States (Q17486597) and the property has index case (P1660). TiagoLubiana (talk) 17:46, 21 March 2020 (UTC)

Basic terminology[edit]

Hi all! I'm collecting basic terminology that people would need in order to be able to write articles about this pandemic as part of the same hackathon that Susanna Ånäs (Susannaanas) was talking about above this. If you'd like to add items to the table, all you need to do is add in the qid from Wikidata for the concept. If the concept doesn't have a qid, it can be added to the list below the table. I appreciate any and all help! -Yupik (talk) 07:42, 21 March 2020 (UTC)

@Yupik: Awesome dashboard! I saw that most concepts were already "QIDed". Amazing. I have added your dashboard to Wikidata:WikiProject_COVID-19/Items. I am also trying to convert the Wikipedia pages to a "structured format", so to identify the concepts and relations used in such pages. Many of the concepts are already in your list, but perhaps you will enjoy taking a look at this page for example. TiagoLubiana (talk) 17:40, 21 March 2020 (UTC)
@TiagoLubiana: Thank you, that is a great page! Susannaanas (talkcontribslogs) has made wonderful visualization of COVID-19-related topics, which should help out with the structured format. Would you be interested in helping us translate some hygiene-related bits and piece into Portuguese btw? -Yupik (talk) 18:23, 21 March 2020 (UTC) 
@Yupik: Sure, great! I have added it to my today's todo list. TiagoLubiana (talk) 19:06, 21 March 2020 (UTC)
@TiagoLubiana: Thank you! -Yupik (talk) 19:35, 21 March 2020 (UTC)

Be careful when adding values from WHO via quickstatements[edit]

Hi, I recently discovered that quickstatements has what I believe is a bug that makes it ADD qualifiers and references to an EXISTING value if it already exist. This is very unfortunate.

Please check the pages you do not:

  1. add conflicting point-in-time statements
  2. lump references that refers has different dates under the same value statement

Please ensure that you remember to:

  1. add "refine time" qualifiers (for WHO 00:00)
  2. add timezone information (for WHO CET=UTC+1)

Details here: https://www.wikidata.org/wiki/User_talk:TiagoLubiana#Messy_edits_to_Q84081576 Thanks in advance for your attention to details.--So9q (talk) 19:50, 21 March 2020 (UTC)

Warning: Wrong_numbers_from_WHO_suspected[edit]

https://www.wikidata.org/wiki/Talk:Q84104992#Wrong_numbers_from_WHO_suspected --So9q (talk) 10:53, 23 March 2020 (UTC)

Hello @So9q:. Apparently the WHO reports are quite messy themselves. It is surprising to me, as I would expect them to be a reliable source. I will avoid using WHO information to update Wikidata pages. If possible, could explain the problems you are locating in detail? WHO numbers report confirmed case numbers that are sent by local health organizations to WHO. TiagoLubiana (talk) 18:04, 23 March 2020 (UTC)
The latest case numbers from Italy seem way off. So much that I suspect they are equivalent to the total cases. I therefore marked them with determination method=unknown. I trust the national sites over WHO, but not all countries have published their statistics, e.g. I just cannot find the numbers from Bosnia Hercegovina and the sources in WP are bogus with numbers newer than the retrieval date.--So9q (talk) 21:14, 23 March 2020 (UTC)
I misinterpreted the italian source it seems. WHO numbers for Italy are correct, but lack behind.--So9q (talk) 11:01, 25 March 2020 (UTC)
I don't think there is any problem with including the numbers reported by WHO as long as the statements specify they come from WHO. ·addshore· talk to me! 12:20, 24 March 2020 (UTC)
Update: also wrong numbers from WHO reported for India, see https://www.wikidata.org/wiki/Wikidata:WikiProject_India/COVID-19_task_force. --So9q (talk) 09:43, 25 March 2020 (UTC)

WikiProject Clinical Trials[edit]

I am writing to invite anyone here to join in developing Wikidata:WikiProject Clinical Trials.

There are already COVID-19 clinical trial studies in progress. There will be increasing interest in gaining information about these studies from Wikidata.

Wikidata already has items for 320,000 trials with a ClinicalTrials.gov Identifier (P3098), which is 99% of all the trials. Right now I would like to request review and support for these property proposals:

If we can stay on top of COVID-19 trials then we can have a really interesting complete collection. Thanks. Blue Rasberry (talk) 17:30, 23 March 2020 (UTC)

Redundancy on 2019–20 COVID-19 pandemic (Q81068910)[edit]

Hello,

There is some redundancy in how the {{Q|Q81068910}] page is currently modeled, and that is annoying me a little bit.

We have country (P17) and has part (P527) modelling the same cases, i.e. local instances of the global pandemic. I suggest that we remove all the country (P17) statements from the page, leaving only the links on has part (P527), as these are clearer.

Do you Symbol support vote.svg Support or Symbol oppose vote.svg Oppose to that change?

Thanks TiagoLubiana (talk) 16:32, 24 March 2020 (UTC)

Symbol support vote.svg Support--So9q (talk) 09:37, 25 March 2020 (UTC)
Symbol support vote.svg Support--AntoineLogean (talk) 09:48, 28 March 2020 (UTC)

APIs for COVID-19 Data[edit]

Hi. I'm the PM for APIs at Wikimedia Foundation in the Core Platform Team. One thing I've noticed is that we're building up a big corpus of geographical data for COVID-19 cases and deaths. I've seen a couple of data analysts using the data on various WPs and Wikidata. I wonder if it would be helpful to tabulate that data and make it available as JSON or CSV feeds. Is this happening? Worth doing? --EProdromou (WMF) (talk) 16:46, 24 March 2020 (UTC)

Hello, @EProdromou:, and thanks for your message. As of today, data about COVID-19 cases and deaths on Wikidata are still far from standardized. There are 3 main sources of numbers that seem to be used here and on Wikipedia, WHO situation reports, which are official but delayed, the Johns HOpkins dashboard and worldometers. There isn't a consensus on how this knowledge should be represented in Wikidata too. An API that gave fully referenced information on cases, deaths and recoveries (including location, source of information, specific time to which it refers to) would be quite useful for automatic, reliable updating of Wikidata items for when we reach such a consensus. The data is kind of already available at the Johns Hopkins dashboard github. What would be the source of the API you are thinking about? Thanks again! TiagoLubiana (talk) 22:03, 24 March 2020 (UTC)
One thing that may be useful re: APIs, if you could give any advice over at openVirus I-15 on APIs to deposit from [R] to wikidata, since none of us over at that project have much experience with the wikidata API. T.Shafee(evo&evo) (talk) 03:12, 25 March 2020 (UTC)

GIFs[edit]

Hello to all,

I started translating some of the GIFs about this topic to Portuguese. I think content is better absorbed if it is in the reader's language. I uploaded the .psd files to a folder in Github, so anyone (with Photoshop) can download them and translate the texts to their language without the task of cleaning the rasterized text in each frame. Let me know if you need help with them. Good contributions, Ederporto (talk) 16:51, 24 March 2020 (UTC)

droplet spread transmission[edit]

I tagged three potentially identical items (I'm the one who "said to be the same as") that may warrant merging: Q15304517, droplet infection (Q871752), and Q1557568. I'm not a health care expert, nor a data ontology enthusiast, so I invite others to take a look and see if they can be straightened out, merged, and/or clarified. Cheers, -Animalparty (talk) 21:11, 24 March 2020 (UTC)

@Animalparty: I would think these three items can be merged, as they are wiki pages of different languages (fi/de/sv/cs/hu/pl) of the same mechanism. --Zhenqinli (talk) 21:43, 24 March 2020 (UTC)
@Animalparty: Thanks for pointing that out. I believe all but Q15304517 can be removed. They have different names from other languages, true, but the instanciation and other relations seem weird. I have made the requests for deletion at Wikidata:Requests_for_deletions, but I would not oppose merging and fixing (as per @Zhenqinli:). TiagoLubiana (talk) 21:47, 24 March 2020 (UTC)

How are we standardizing the deaths by SARS-CoV-2[edit]

How are we standardizing the deaths by SARS-CoV-2? I am using for cause_of_death=COVID-19 and I am also adding "significant_event=2020 COVID-19 pandemic in the United States". Is this what we are standardizing on? See Orlando Staton (Q88505446) and Q88584577. How many deaths entries have we recorded so far? --RAN (talk) 21:29, 25 March 2020 (UTC) ‎

@Richard Arthur Norton (1958- ): So far, I haven't seen any standardization per se. It seems that cause of death (P509) COVID-19 (Q84263196) does the job. [Wikidata:WikiProject_COVID-19/Queries#Image_grid_of_individuals_who_have_died_from_COVID-19_ordered_by_Wikidata_item_completeness This SPARQL query] might be of interest to you. This other query points to around 100 people in Wikidata that have died from COVID-19:

The following query uses these:

  • Properties: cause of death (P509) View with Reasonator View with SQID
    1 SELECT ?item ?itemLabel WHERE {
    2   ?item wdt:P509 wd:Q84263196.
    3   SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
    4 }
    

. TiagoLubiana (talk) 02:09, 26 March 2020 (UTC)

This is complicated as people can die of other complications because they are weakened by the infection. Does this mean they die from the virus? Maybe not. Maybe we should model it something like: cause_of_death=COVID-19_or_during_COVID-19_infection which is broader.--So9q (talk) 10:38, 26 March 2020 (UTC)
I believe that if people die from complications that arose due to COVID-19, both things could be related as cause of death (one is more proximal, and other more distal, but both sound to me like causes). There is a further insteresting aspect about this: what about COVID-19 negative deaths that happened during the pandemic? I bet that many deaths are happening (or will happen) due to the collapse of healthcare system. Something to represent that the pandemic contributed to their death, albeit not directly. I would endorse any modelling of that kind. TiagoLubiana (talk) 19:46, 26 March 2020 (UTC)
Wikidata shouldn't be an endless spiral of reductionism. Practicality should trump technicality. I think a convention of "disease died from" = "cause of death" is most sensible. If someone is shot to death, is cause of death the bullet? The blood loss? The organ failure? Are cancer deaths due to cancerous cells, tumors, organ failure, or simply cancer (Q12078)? With COVD-19 deaths, the proximate (and practical) cause of death is COVID-19 (Q84263196), even if the ultimate cause of death is pneumonia (Q12192) (which in turn causes pulmonary aspiration (Q737510) which causes asphyxia (Q193840) which causes brain death (Q223867)...). Add qualifiers if needed. -Animalparty (talk) 22:23, 26 March 2020 (UTC)
See below for how AIDS was handled to take care of such a problem with "AIDS" and "AIDS related death", which needs to harmonized. I am not sure two were needed but it does cover the problem under discussion. There are two causes now at AIDS and we need to standardize on one. --RAN (talk) 02:11, 27 March 2020 (UTC)
See this question about U07.1 vs U07.2 usage on en.Wikipedia. These two codes are temporary emergency ICD-10 codes. U07.1 is for lab-confirmed COVID-19 and U07.2 is for clinically or epidemiologically defined COVID-19. The Polish medical authorities presently only classify U07.1 deaths as COVID-19 deaths; U07.2 deaths are excluded. It seems to me that it would probably be best to have two separate wikidata items for U07.1 and U07.2 (which at some time in the future - months? - will be renamed to standard ICD-10 codes), which are subclasses of COVID-19 (Q84263196). Some health agencies/medical sources may separate these, some (at least one) ignore U07.2, and some may give just the two together. Boud (talk) 15:55, 1 April 2020 (UTC) (Update: the Polish health agency issuing the instructions for disease classification added U07.2 as a COVID-19 classification as of 1 April 2020. The main Polish centrist newspaper said that there has been a lot of fuss about the issue. See the article for details and a ref.) Boud (talk) 00:22, 2 April 2020 (UTC)

1918-1920 flu pandemic deaths needs some TLC[edit]

We only have 285 1918 flu pandemic deaths formatted so they show up in a search, any ideas how to find the missing ones to harmonize them? --RAN (talk) 19:21, 26 March 2020 (UTC)

The following query uses these:

  • Properties: cause of death (P509) View with Reasonator View with SQID
    1 SELECT ?item ?itemLabel WHERE {
    2   ?item wdt:P509 wd:Q178275.
    3   SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
    4 }
    
@ Richard Arthur Norton (1958- ): Hmm, good question. Maybe query for dead people in that time that cause of death is influenza (Q2840). Finding a reliable database would me, in my opinion, the best approach. Also, cause of death (P509) 1918-1920 flu pandemic (Q178275) does not seem super precise. If it is to be consistent with the current pandemic modelling, we would need an item for the flu itself, and another for the pandemic. TiagoLubiana (talk) 19:55, 26 March 2020 (UTC)
I was just running the very query you suggested! Eventually we can harmonize all disease agent deaths the same way, I was just looking at HIV deaths too. --RAN (talk) 20:16, 26 March 2020 (UTC)
We could also try to peruse relevant Wikipedia categories or perhaps mine relevant Wikipedia articles directly with queries like these:
The following query uses these:
  • Properties: instance of (P31) View with Reasonator View with SQID, date of death (P570) View with Reasonator View with SQID, cause of death (P509) View with Reasonator View with SQID
     1 SELECT 
     2   DISTINCT ?item ?itemLabel ?dod ?cod ?codLabel
     3 WHERE {
     4   {   
     5    SELECT DISTINCT ?item  WHERE {
     6     SERVICE wikibase:mwapi {
     7       bd:serviceParam wikibase:endpoint "en.wikipedia.org" .
     8       bd:serviceParam wikibase:api "Generator" .
     9       bd:serviceParam mwapi:generator "search" .
    10       bd:serviceParam mwapi:gsrsearch "\"Spanish flu\"" .
    11       bd:serviceParam mwapi:gsrlimit "max" .
    12       ?item wikibase:apiOutputItem mwapi:item .
    13     }
    14   } LIMIT 100
    15  }
    16 
    17   ?item wdt:P31 wd:Q5.
    18   
    19   OPTIONAL {?item wdt:P570 ?dod .}
    20 
    21   OPTIONAL {?item wdt:P509 ?cod .}
    22 
    23   SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". }
    24 }
    25 ORDER BY ASC(?dod)
    
--Daniel Mietchen (talk) 02:55, 29 March 2020 (UTC)

Death from AIDS-related complications[edit]

While we are working on pandemic death data, can someone help me with the AIDS deaths. I know this is tangential, but people will be comparing notable people death rates. Currently the cause of death for is split between "AIDS" and "death from AIDS-related complications", I think we can switch the 200 with "AIDS" to the more specific "death from AIDS-related complications", which has about 500. See Keith Haring (Q485635) as an example to get the property numbers. Can someone help with the switch. I do not know how to automate something like this. --RAN (talk) 01:44, 27 March 2020 (UTC)

@Richard Arthur Norton (1958- ): What you say seems correct to me but before doing this at scale I think it would be worthwhile to propose this as a data model for biographies. I started this at Wikidata:WikiProject_COVID-19/Data_models#Biographies. Perhaps for Keith Haring medical condition (P1050) should be AIDS (Q12199), the cause of death (P509) should be death from AIDS-related complications (Q4651894), and manner of death (P1196) should be natural causes (Q3739104). What do you think? How would the comparable situation work for COVID-19? Blue Rasberry (talk) 13:34, 28 March 2020 (UTC)
  • I agree 100%! Is there a way to automate the task, I am not familiar with the tools for making changes on a large scale. I also have a list of 1918-1920 flu deaths that need to be harmonized. --RAN (talk) 18:40, 28 March 2020 (UTC)
@Richard Arthur Norton (1958- ): The automation is the easy part. Either someone can help you with it, or you might be surprised at the options for trying it yourself. The much more difficult part of Wikidata is learning enough to have the conversations which are supporting evidence to justify harmonization. You are spot on with the HIV/AIDS comparison and we could ping Wikidata:WikiProject LGBT into a discussion. That might be enough, or additionally, we could also do an example for the 1918 flu pandemic. If you have like 3 similar cases, have an example for each, and can recruit someone to speak about each one and agree, then that makes the argument to reconcile them all. In general, people hesitate to do anything large scale without supporting evidence that the proposed massive change is worthwhile. I have done this before and I myself am not so sure about how to do things right in this case, but in general, having a greater number of examples and feedback from multiple communities of editors makes a stronger case. Thoughts? Blue Rasberry (talk) 20:16, 31 March 2020 (UTC)

Need two new property for "number of hospitalized cases" and for "number of home cases"[edit]

Hi all,

France (SpF) will no longer give, from 26 March 2020, the number of "total cases" (hospitalised + home) by region every day, but probably only once a week.

while waiting France (SpF) only give every day the number of "hospitalized cases" (number of people hospitalized in hospital).

what do I use as a property in "number of cases" P1603 to attach them?

quantity (P1114) with criteria used (P1013) ?

Or do I have to apply for two new properties :

thanks for answers--Viruscorona2020 (talk) 05:43, 27 March 2020 (UTC)

TiagoLubiana (talk) 01:35, 16 March 2020 (UTC) Daniel Mietchen (talk) 01:42, 16 March 2020 (UTC) Jodi.a.schneider (talk) 02:45, 16 March 2020 (UTC) Chchowmein (talk) 02:45, 16 March 2020 (UTC) Dhx1 (talk) 03:38, 16 March 2020 (UTC) Konrad Foerstner (talk) 06:02, 16 March 2020 (UTC) -Netha Hussain (talk) 06:19, 16 March 2020 (UTC) Bodhisattwa (talk) 06:56, 16 March 2020 (UTC) Neo-Jay (talk) 07:04, 16 March 2020 (UTC) John Samuel (talk) 07:31, 16 March 2020 (UTC) KlaudiuMihaila (talk) 07:53, 16 March 2020 (UTC) Salgo60 (talk) 09:11, 16 March 2020 (UTC) Andrawaag (talk) 10:12, 16 March 2020 (UTC) Whidou (talk) 10:16, 16 March 2020 (UTC) Blue Rasberry (talk) 15:07, 16 March 2020 (UTC) TJMSmith (talk) 16:15, 16 March 2020 (UTC) Egon Willighagen (talk) 16:49, 16 March 2020 (UTC) Nehaoua(talk) 20:32, 16 March 2020 (UTC) Andy Mabbett (Pigsonthewing); Talk to Andy; Andy's edits Peter Murray-Rust (talk) 00:00, 17 March 2020 (UTC) Kasyap (talk) 02:45, 17 March 2020 (UTC) Denny (talk) 16:21, 17 March 2020 (UTC) Kwj2772 (talk) 16:56, 17 March 2020 (UTC) Joalpe (talk) 22:47, 17 March 2020 (UTC) Finn Årup Nielsen (fnielsen) (talk) 10:59, 18 March 2020 (UTC) Skim (talk) 11:45, 18 March 2020 (UTC) SCIdude () 15:15, 18 March 2020 (UTC) T.Shafee(evo&evo) (talk) 01:23, 20 March 2020 (UTC) Susanna Ånäs (Susannaanas) (talk) 07:05, 20 March 2020 (UTC) Mlemusrojas (talk) 15:30, 20 March 2020 (UTC) Yupik (talk) 20:23, 20 March 2020 (UTC) Csisc (talk) 23:05, 20 March 2020 (UTC) OAnick (talk) 10:26, 21 March 2020 (UTC) ❙❚❚❙❙ JinOy ❚❙❚❙❙ 12:28, 21 March 2020 (UTC) Jjkoehorst (talk) 14:27, 21 March 2020 (UTC) So9q (talk) 08:58, 22 March 2020 (UTC) Nandana (talk) 14:58, 23 March 2020 (UTC) ·addshore· talk to me! 15:56, 23 March 2020 (UTC) Librarian lena (talk) 18:19, 24 March 2020 (UTC) Jelabra (talk) 19:19, 24 March 2020 (UTC) AlexanderPico (talk) 23:34, 27 March 2020 (UTC) Higa4 (talk) 02:51, 29 March 2020 (UTC) JoranL (talk) 19:56, 29 March 2020 (UTC) Alejgh (talk) 11:04, 1 April 2020 (UTC) Will (Wiki Ed) (talk) 17:36, 1 April 2020 (UTC) Ranjithsiji (talk) 04:47, 2 April 2020 (UTC) AntoineLogean (talk) 07:35, 2 April 2020 (UTC) Hannolans (talk) 17:22, 2 April 2020 (UTC) Farmbrough21:15, 3 April 2020 (UTC).
Ecritures (talk) 21:26, 3 April 2020 (UTC)
Pictogram voting comment.svg Notified participants of WikiProject COVID-19--- Jura 00:50, 28 March 2020 (UTC)

Enter covid-19 affected and death cases for Switzerland at the canton level[edit]

As part of the HackZurich hackathon (https://codevscovid19.slack.com) I would like to make use of the open data provided by the canton of Zurich and enter the time development of infected and death cases for each Swiss canton. To start, I would do this manually so that I get a good understanding of the underlying metamodel. Then it would be nice to have a bot.

If I take as model the case of China, from the page https://www.wikidata.org/wiki/Q83872271 they have added an "includes" statement that links national outbreak with local outbreak instances. So I would need to create first for each canton a page "2019-2020 coronavirus outbreak in Swiss canton XX" and then, on this new page enter the time development via the property "number of cases" and "number of death". Is it correct ?  – The preceding unsigned comment was added by AntoineLogean (talk • contribs).

Feedback on data model for countermeasures/strategies against the outbreak[edit]

Hello, I have been trying to make a data model for documenting the countermeasures/strategies that different actors, such as governments, implement against the outbreak. I now hope to get some feedback in this forum about if it is a useful model and what can be improved.

(I read on Wikidata:WikiProject_COVID-19/Data_models that Wikidata:WikiProject Policies has a role, but I do not think it serves any purpose for what I am trying to do; that project seems to deal with policies in the sense of a written document, not as strategies)
If you want to have a look, countermeasures in Sweden during the 2020 coronavirus pandemic (Q88807626) is probably the best way to start.

I am quite new to Wikidata, any advice would be helpful and appreciated! JoranL (talk) 21:23, 29 March 2020 (UTC)

@JoranL: Hello and thanks for your contributions. That is some modelling work going on regarding countermeasures at the property proposal Wikidata:Property_proposal/countermeasure. Your opinion there would be of great value, as you already gave some thought into this issue. It is still very open, so I think every idea matters. TiagoLubiana (talk) 15:08, 30 March 2020 (UTC)
@TiagoLubiana: Many thanks, I hadn't seen that, I will join the discussion there.

Talk on Wikidata, COVID-19 and Education[edit]

Hello everyone,

Tomorrow there will be a talk discussing the Wikimedia projects and how they can help the efforts to tackle the current pandemic.

I will copy the Facebook communication ipsis litteris here.

"The board of the Wikipedia & Education User Group invites you to attend our user group's next Open Meeting, one week from today, on Thursday, April 2, at 15:00 UTC, as always via Zoom. We'll be discussing the Wikimedia & Education community's response to the COVID-19 pandemic. Guest speakers include:

  • User:TiagoLubiana, a graduate student in Computational Biology from the University of São Paulo, and a leading editor at Wikidata:WikiProject COVID-19, will discuss Wikidata's work around COVID-19 and how the Wikimedia and education community can help. (https://www.wikidata.org/wiki/Wikidata:WikiProject_COVID-19)

Per usual, the board will provide an update on user group activities, and we'll offer an opportunity for others to briefly share what they've been up to in light of the COVID-19 pandemic. Join us!

What: Wikipedia & Education User Group Open Meeting When: Apr 2, 2020 15:00 UTC

Where: https://zoom.us/j/759620545 Meeting ID: 759 620 545" This is the facebook post made by (@LiAnna_(Wiki_Ed):) [Facebook post] I am going to present a little bit about this project, and share a few ideas on how the Education community might help. If anyone has insights or tips, I can add anything you feel might be important to the presentation. Best, TiagoLubiana (talk) 03:13, 2 April 2020 (UTC)

I have joined the call at 15h00 (Zürich time) but I was alone ☹️ Antoine Logean (talk) 18:20, 2 April 2020 (UTC)

@AntoineLogean: Sorry about the confusion. The time was 3:00 PM Coordinated Universal Time (UTC) which is

5:00 PM in Zürich, Switzerland. TiagoLubiana (talk) 20:06, 2 April 2020 (UTC)


A logo for this wikidata project ?[edit]

Covid19WikidataGroupLogo.jpg
@AntoineLogean: Nice idea and cool logo! Is this the final version? Maybe we could leave this open for some days, so people can share their thoughts and perhaps bid other logos. What do you think? TiagoLubiana (talk) 14:14, 2 April 2020 (UTC)

Sure. It is just a draft anyway. Antoine Logean (talk) 18:12, 2 April 2020 (UTC)

Wikipedia templates[edit]

Hello,

One thing that would greatly aid the effort for updating Wikipedia on the COVID situation in languages other than English would be to have proper templates so this information shows up there.

Anyone interested in leading a task force for building such templates? I could try and start it, but I have no previous experience with templates.

Here are some links that might be interesting for the matter:

TiagoLubiana (talk) 01:24, 5 April 2020 (UTC)

Full individual Singapore cases table proposed for deletion[edit]

The table of all individual Singapore SARS-CoV-2 cases at en.Wikipedia has been proposed for deletion:

I don't have a strong opinion on this particular table, but if Wikidata people want the data, then probably now is the time to get involved, rather than trying to undelete the page later.

I do worry that this might set a precedent for deleting other COVID-19 related template tables on en.Wikipedia.... Boud (talk) 12:05, 3 April 2020 (UTC)

@Boud: Thanks for your comment. I do not have a strong opinion on that. I saw that the sources would be there anyway, so if the Wikipedia community decides to remove it, we could build it from the sources in Wikidata later. And I hope this won't set a precedent too. Maybe other people here in the project will have different visions on the matter. TiagoLubiana (talk) 17:26, 3 April 2020 (UTC)
@TiagoLubiana: By "the sources would be there anyway", do you mean that the Singapore Ministry of Health has well-organised static web pages with the info and there's a fair chance of them remaining stable for a long time? I noticed that the refs in the template proposed for deletion are all repeat refs, so deleting the template will clearly not delete the sources. I seem to remember that using repeat refs only is what I encouraged many many weeks ago - but checking now, I couldn't find or remember where the sources of the refs are, in the sense of full {{cite web|...}} type references. Did you notice where the full wikified sources are? Boud (talk) 00:06, 4 April 2020 (UTC)

Structuring effects and impacts of the pandemic[edit]

I am trying to recreate / mimick the enwiki COVID-19 template 2019–20 coronavirus pandemic with Wikidata. The template lists issues and impacts. Wikidata has at least facets and effects. They are a mixed bag of items both. Is anyone working on these, do you have suggestions for structuring them? – Susanna Ånäs (Susannaanas) (talk) 00:44, 4 April 2020 (UTC)

@Susannaanas: Hello, what exactly you are trying to recreate? Would it be some way to link 2019–20 COVID-19 pandemic (Q81068910) and template items such as Human rights issues during the 2019–20 coronavirus pandemic (Q87796964) and Media coverage of the 2019–20 coronavirus pandemic (Q88293962)? TiagoLubiana (talk) 01:49, 5 April 2020 (UTC)
I am preparing to make a dashboard of COVID-19 topics for translation and editing purposes, see here: https://wikidocumentaries.wmflabs.org/wiki/COVID-19_Global_Dashboard. Translators find the enwiki template a useful overview. I am thinking how to regenerate something similar by querying Wikidata. For that purpose many topics would need more structure in Wikidata. Arranging topics can be a purpose that this dashboard could also serve. – Susanna Ånäs (Susannaanas) (talk) 07:32, 5 April 2020 (UTC)

Wikidata is one of the topics on the Biohackathon covid-19-bh20[edit]

The biohackahton is an annual hackathon with editions in Japan and Europe. Given the COVID-19 pandemic, there will be a virtual edition from April 5th until April 11th, specifically aimed at tackling the COVID19. The program is similar to the usual wikimedia hackathons where in idea's are pitched and then progress is self-organise and regularly reported to the wider audience. Amoung the different topics, there is a one on. Wikidata and Wikibase, which will give us the opportunity to align many other resources with Wikidata. You can join this hackathon by adding your name to [5] and joining Slack and the #wikidata channel there.

The program start with the 2-minute introductions on Sunday, after which different subprojects, sometimes together with other groups, will emerge. --Andrawaag (talk) 06:01, 4 April 2020 (UTC)

Graphs from queries[edit]

Just to let you know, User:Abbe98 is showing some potential in this video of how the results from a query could be used in a graph. Ainali (talk) 17:57, 4 April 2020 (UTC)