[DATA] Help needed for Hospital Data

[HerkulaasCombrink]

Which Dataset

health_system_za_public_hospitals.csv

Error Description

District and subdistrict data needed
Estimated population size needed for each district

Suggested fixes

1. Populating the data for the proposed file.
2. Creating an accurate dataset that is already in a computer-readable format, and not in a PDF etc.
3. Finding an updated Private and public Hospital repo for each South African province.

##Volunteer to fix the data
Choose the data you want to fix/add and volunteer to the data you want to commit to
https://docs.google.com/spreadsheets/d/1ujiuSd656BfIO3AT86GTr17oveaev-qBuYbu_v45RC4/edit?usp=sharing

[anelda]

@MikeMcMalace the humanitarian data exchange has pop size at various admin levels for SA - https://data.humdata.org/dataset/south-africa-administrative-levels-0-3-population-statistics. It was last updated in 2018 according to metadata.

I'd be interested to help with this. Also involved in https://afrimapr.github.io/afrimapr.website/blog/2020/healthsites-app/ and we've just started to work with healthsites.io as well. Let me know how I can help?

[elolelo]

@anelda we are currently working on a map visualization that is a bit similar to the one shown in your last link. For now ,most helped needed is on the data - populating the columns with

• Number of beds per identified hospital
• Number of staff members per hospital
• Geolocation of Covid19 testing centers
• Webpages of hospitals
• And just about any other incomplete info on the hospital data

The data file is the one that @MikeMcMalace has identified when he opened this issue.

[anelda]

Three questions:

1. Do you have a way to prevent different people working on the same thing for this? e.g. I can get webpages for hospitals but it would be tragic if others are working on this at the same time, duplicating effort.

2. What is the relationship between health_system_za_public_hospitals_extended_details.csv vs health_system_za_public_hospitals_contacts.csv vs health_system_za_public_hospitals.csv? Can these be merged?

3. Is there any value in contacting info@sadoctors.co.za who maintains this website - http://doctors-hospitals-medical-cape-town-south-africa.blaauwberg.net/hospitals_clinics_state_hospitals/state_public_hospitals_clinics_eastern_cape_south_africa/ (for each province with a lot of the data we need for each hospital) to hear if they can do a data dump of the data displayed on their website?

[HerkulaasCombrink]

Thank you so much for your inputs, @anelda .

1. I propose that we volunteer on this issue so that there isn't overlap. Alternatively, we can create a google doc and people can volunteer from there? - which would you think would work best?

2. Yes, they can. From the start, we needed details and information, and as time continued, the datasets expanded. We have a hospital dictionary, and I can imagine that we do not have all the IDs of all hospitals on this list. If I had to be pragmatic about it, I would propose that we update the library file, and then use that as a reference to see what we do not have.

3. Yes, there is. I have made contact with a few private hospital groups, and have reached out to provincial managers, but unfortunately, I have had little success. It is an excellent suggestion. Would you mind making contact?

[anelda]

For hospital beds, there is this study:

Geographical maldistribution of surgical resources in South Africa: A review of the number of hospitals, hospital beds and surgical beds
A J DellI; D KahnII (IBSc, MB ChB, PhD; Department of Surgery, Faculty of Health Sciences, and Groote Schuur Hospital, University of Cape Town, South Africa; IIMB ChB, FCS (SA), ChM; Department of Surgery, Faculty of Health Sciences, and Groote Schuur Hospital, University of Cape Town, South Africa)
http://dx.doi.org/10.7196/samj.2017.v107i12.12539 published 2017 with a contact email for the lead author angelajdell@gmail.com

Maybe they can share the data they collected - here is how they did it (a lot of work have gone into collecting/verifying the data)

A list of all hospitals in SA was obtained from the Provincial DoH and cross-referenced with electronic databases of hospitals in SA (Medpages and hospital websites). These were cross-referenced with the NDoH hospital list from the office of the minister of health.

The Health Systems Trust provided estimates of the total number of hospitals and hospital beds for each province for comparison among the provinces. The public hospitals were grouped according to the nine provinces in SA and were subdivided into major district municipalities.

All hospitals were contacted telephonically and by email. Either the chief executive officer, superintendent or matron (in the case of district-level facility) in each hospital was contacted to obtain the relevant data. Data were collected from 1 October to 31 December 2014. Private hospital data were readily available from the Hospital Association of SA (HASA) and included extensive data on the number of hospitals, total number of hospital beds and type of beds. Private hospitals were contacted telephonically to verify these data.

[HerkulaasCombrink]

Brilliant, brilliant study - and this is the data we need. It is a shame that this is 2017, but, it does have the data we require. Thank you for your insight @anelda. I do not personally know the authors, but I do know the department. Would you mind making contact?

[HerkulaasCombrink]

@elolelo , what is your idea of the websites? I am trying to find the geo-locations of the testing centres but I am picking up something that exponentially might complicate things, that labs/pathologists might be referring samples. This means that we need to track down core testing facilities. I can ask for this.

[anelda]

Thank you so much for your inputs, @anelda .

1. I propose that we volunteer on this issue so that there isn't overlap. Alternatively, we can create a google doc and people can volunteer from there? - which would you think would work best?

2. Yes, they can. From the start, we needed details and information, and as time continued, the datasets expanded. We have a hospital dictionary, and I can imagine that we do not have all the IDs of all hospitals on this list. If I had to be pragmatic about it, I would propose that we update the library file, and then use that as a reference to see what we do not have.

3. Yes, there is. I have made contact with a few private hospital groups, and have reached out to provincial managers, but unfortunately, I have had little success. It is an excellent suggestion. Would you mind making contact?

1. Let's start a Google Doc - great suggestion. This thread may become quite long and people might miss stuff if they have to read through everything. I can do it and share unless you have a covid19 Google Folder already where you want to keep things together?

2. Which one is the library file? I can do a compare and merge on the files unless either of you have a script ready to do that? I'll probably do it in R and can share the merged file in the next hour or so

3. I can reach out to the website owners. Fingers crossed that the email is still functional and that they're checking it.

[anelda]

Brilliant, brilliant study - and this is the data we need. It is a shame that this is 2017, but, it does have the data we require. Thank you for your insight @anelda. I do not personally know the authors, but I do know the department. Would you mind making contact?

I'll email them.

[HerkulaasCombrink]

@elolelo @anelda the link to the doc is below.

https://docs.google.com/spreadsheets/d/1ujiuSd656BfIO3AT86GTr17oveaev-qBuYbu_v45RC4/edit?usp=sharing

Choose an item, then update accordingly.

There are five hospital files:

• health_system_za_hospital_id (which contains the ID and hospital name as they appear in the other four files)
• health_system_za_private_hospitals
• health_system_za_public_hospitals
• health_system_za_public_hospitals_contacts
• health_system_za_public_hospitals_extended_details

The idea is to gather, create the complete files, then merge at the end.

I used Python for the merging, but any basic inner join will do - since the current ID's are already linked to the files.

[anelda]

For hospital beds, there is this study:

Geographical maldistribution of surgical resources in South Africa: A review of the number of hospitals, hospital beds and surgical beds
A J DellI; D KahnII (IBSc, MB ChB, PhD; Department of Surgery, Faculty of Health Sciences, and Groote Schuur Hospital, University of Cape Town, South Africa; IIMB ChB, FCS (SA), ChM; Department of Surgery, Faculty of Health Sciences, and Groote Schuur Hospital, University of Cape Town, South Africa)
http://dx.doi.org/10.7196/samj.2017.v107i12.12539 published 2017 with a contact email for the lead author angelajdell@gmail.com

Great news! Angela responded within 25 minutes to my email. She shared her thesis in PDF (also available from http://hdl.handle.net/11427/22796) and is busy looking through her spreadsheets to find the most recent one. She'll share that as soon as she's found it.

We have to make sure people who share their hard collected open datasets receive due credit!

[HerkulaasCombrink]

@anelda I echo your request and acknowledge your statement. Thank you.

[anelda]

@anelda I echo your request and acknowledge your statement. Thank you.

I'll create an issue about this. It's important for data provenance as well

[anelda]

@anelda I echo your request and acknowledge your statement. Thank you.

I'll create an issue about this. It's important for data provenance as well

See #117

[anelda]

@elolelo @anelda the link to the doc is below.

https://docs.google.com/spreadsheets/d/1ujiuSd656BfIO3AT86GTr17oveaev-qBuYbu_v45RC4/edit?usp=sharing

@MikeMcMalace good morning! I can't access this file? Can you help please?

[HerkulaasCombrink]

Please try link @anelda @elolelo

[HerkulaasCombrink]

@anelda @elolelo Good morning!

[anelda]

Please try link

Thanks @MikeMcMalace . It's view only mode though?

[elolelo]

@anelda @MikeMcMalace Good morning, @anelda , in this #117 issue, do you suggest that @MikeMcMalace should create another sheet to add the details about sources of data ?

[anelda]

in this #117 issue, do you suggest that @MikeMcMalace should create another sheet to add the details about sources of data ?

Good morning @elolelo. Hmmm... I wonder if it may be worth our while to have a quick online meeting to chat about the data and where we want to go with it? I received hospital bed data from Angela this morning and am busy cleaning it up. What do you think @MikeMcMalace

[elolelo]

@anelda - I think the meeting may be worth our while. I should be available from 11 am and onwards today .
Wow!! sounds like you've recieved valueable data - I just saw now that 87 000 beds in the public sector are available for Covid19 patients - I wondered where (in which hospitals) are those beds - so hopefully your data could answer this question.

[anelda]

If you send me your email addresses and times when you're available, I can set up a meeting in Zoom or Hangouts. Don't want to share meeting link here as there's been problems with trolls crashing open online meetings. anelda@talarify.co.za. Thanks!

[HerkulaasCombrink]

Love the idea of a meeting! Yes. Currently, I see a gap at 12:00? Would that suffice?

Can we invite @vukosim to this meeting, please?

[Yeshara]

Hello!
Will do this soon.

[IneffableKoD]

Hello!
Will do this soon.

Great! Let me know in case you need help.

[IneffableKoD]

Has anyone checked/transcribed the data from this video? https://sacoronavirus.co.za/2020/04/03/johannesburg-covid-19-testing-centres/

[elolelo]

Has anyone checked/transcribed the data from this video? https://sacoronavirus.co.za/2020/04/03/johannesburg-covid-19-testing-centres/

I have checked it out but haven't transcribed the data ,as yet. To avoid duplicating efforts - should I leave you to it ?

[IneffableKoD]

I am very busy the next few days. Would be happy if someone could help. ‐‐‐‐‐‐‐ Original Message ‐‐‐‐‐‐‐

…

On Thursday, April 16, 2020 1:55 PM, Nompumelelo ***@***.***> wrote: > Has anyone checked/transcribed the data from this video? https://sacoronavirus.co.za/2020/04/03/johannesburg-covid-19-testing-centres/ I have checked it out but haven't transcribed the data ,as yet. To avoid duplicating efforts - should I leave you to it ? — You are receiving this because you were mentioned. Reply to this email directly, [view it on GitHub](#115 (comment)), or [unsubscribe](https://github.com/notifications/unsubscribe-auth/AIJTRDCFYVYJM2SZ4R3S5SLRM3W3LANCNFSM4LX5LHZA).

[Yeshara]

I would be able to help @elolelo, if you are busy.

[elolelo]

I would be able to help @elolelo, if you are busy.

Thanks @Yeshara ,I am busy with these testing centers right now. There is about 21 or just less clinics showning in this video. You could help by confirming that I got all the details corrently or as shown in the video. The reason for the confirmation is because the video quality from my side is not optimal, some numbers I might not get right. So, once I am done ; I will upload to the repo and then you may start double checking.

[IneffableKoD]

Thank you both @Yeshara and @elolelo!

[anelda]

Thanks @Yeshara ,I am busy with these testing centers right now. There is about 21 or just less clinics showning in this video. You could help by confirming that I got all the details corrently or as shown in the video. The reason for the confirmation is because the video quality from my side is not optimal, some numbers I might not get right. So, once I am done ; I will upload to the repo and then you may start double checking.

@elolelo @Yeshara you can use https://www.kapwing.com/tools/caption-video to automatically get access to a transcription and extract the info from there. It's free and you don't have to sign up for an account to get the transcript. There are other tools too but I found this one to probably be okay for what you need?

[anelda]

I've been doing more work on understanding the process of merging facility lists and working with Andy South who is the project lead from afrimapr to see how we can help to automate some of those tasks. I updated the data readme with the new link. Here it is too - http://afrimapr.org/blog/2020/merging-health-facility-lists-part1/. We don't have a solution yet and I can't offer you a more complete, cleaner data set yet, but we are working on it and will share here once there is progress.

[elolelo]

Here are the testing sites, @Yeshara if you still can please confirm the accuracy. The source for the geocoordinates and some addresses is the National Department of Health's Data Dictionary. I will mention this on the README.

@anelda The tool is useful it's only that the audio from the video does not mention all the necessary details that I want to hear therefore the transcript does not give perfect information as seen on the screen. One last drawback is that the tool gets some words spelled wrong (mostly African Names and other words that are just based on the presenter's pronunciation). But it has helped greatly with the numbers . Thank you

[anelda]

The tool is useful it's only that the audio from the video does not mention all the necessary details that I want to hear therefore the transcript does not give perfect information as seen on the screen. One last drawback is that the tool gets some words spelled wrong (mostly African Names and other words that are just based on the presenter's pronunciation). But it has helped greatly with the numbers . Thank you

@elolelo yes, African language speech to text is a field under development. If you have more needs like this, we should reach out to https://sadilar.org. Their people might know of a tool that is better with South African names and pronunciation. Not too convinced that we'll find something that will work 100%, but it's worth a try if it will save you time.

[Yeshara]

@elolelo I have looked at your data and the video and it seems to be accurate! Just saw that entry 9 doesn't have coordinates?

[elolelo]

@Yeshara That clinic on entry 9 has an address (one shown on the video ) that does not correspond with the geo-coordinates and the address shown in the Data Dictionary (source for geo-coordinates). So, l will check on google maps a bit later what geo codes to use. Thanks.

[vaibhavijames]

Hello! I saw that help is wanted for this project, and I was wondering if there's anything I can help out with? I have experience with data analysis and some intermediate programming as well. Let me know what I can do!

[elolelo]

Hello @vaibhavijames

Thanks for offering to help. I suggest that you start by getting a sense of where we are going with this issue from this blog post.

Right now the main thing that we are still working on is data collection, so we can complete atleast this main dataset. I think your analysis and development skills will still be needed just not immediately.

Putting in webpages of hospitals in this file is one thing that I think you can do. Another thing could be filling in details about field hospitals in this file.

@anelda , @MikeMcMalace , @vukosim could suggest other tasks

[vaibhavijames]

Sounds good! I can work on that. Glad I can help!

[ghost]

Hello everyone, I am Nelisiwe currently working on ‘updating the population of districts per province’, Nompumelelo referred me to the necessary csv files. I am also supporting HSRC with data collection on a broader context.

[vukosim]

Welcome @DevNelz.

[ghost]

@vukosim thank you.

[vukosim]

@DevNelz @elolelo Do we have specific tasks you will be focusing on or sources we have not thought about?

[elolelo]

I don't think we have specific tasks. Since @DevNelz offered to help, I though it would be a good start to help by filling up that first dataset by populating population estimates of district based on this source from statssa.
I thought it could be meaningful on the PWA to have a population estimate accompanying the number of hospitals on each district.

So, No - we don't have new sources or tasks, yet.

Welcome, @DevNelz

[Sarapsis]

Hi,

If you would like a central place to edit and add more hospitals to a dataset and visualize it on a map. I have used the data you created and added it to HERE Studio. https://studio.here.com/viewer/?project_id=181b1c1e-649f-4b56-a229-5d00024532e8

If it is something you are keen on using let me know and we can develop it further.

Thanks,
Clint

[elolelo]

Hi Clint,

Thanks for show casing what you did with the hospitals data.

I took a quick look at your map but was unable to edit . Do you maybe have a readme writing somewhere showing how one can make edits to the data on the map?

Also, is it ok that the map gets added to the projects showcased at the end of this page?

[Sarapsis]

Hi @elolelo,

I can create another account and add the data to it, everyone can access that account and make edits as needed.

I will have a look for a little readme/instructions on how to edit/add data, it is a relatively easy interface to use.

Feel free to add the map, wherever you need to. Also the DB and visualisations can be added to a potential app via the API's using a token.

Thanks
Clint

[elolelo]

@Sarapsis OK, so for the account whose details you'll allow access - please use this data as there are many maps that have already been built using the data that you have used on your first map.

To add your first map on the list - the following details are needed from you

Project Name | Project Description | Project Demo | Project owner | Country

[HerkulaasCombrink]

We are about to close this issue