Buliding MIMIC-III Waveform Database

[waqaraziz123]

Hi,
I have downloaded and build the MIMIC-III clinical database. I am just wondering how to build the MIMIC-III waveform database as there is no information available on the website. Is there a way I can build it just like the way clinical database is being set up. ?

Thanks

[alistairewj]

There's no build process for the matched waveform database as it's not as well suited to traditional relational database management systems - you can view individual records via LightWave, or download the database locally if you plan on using it extensively.

[waqaraziz123]

Thank you for your quick response. I have already downloaded the waveform database (7 TB). However, I am just wondering how to extract some specific patients data. Its really hard to search entire data individual file wise to find patients having a specific disease.

Thanks

[alistairewj]

Indeed! I don't have a good answer for this. We are considering adding waveform related tables to the next release to simplify connecting the two resources, and would be grateful for suggestions of what would be useful.

At the moment, your best bet is to identify the subjects who interest you using the clinical data, then identify the subset of those patients who are available in the matched waveform database.

[waqaraziz123]

Thank you.
Is there a way through which I can automate this process ? I guess it will be difficult to manually cross check each matched record from the whole WFDB with the clinical data. And is there any published literature on the usage of MIMIC-III WFDB ? It might help.

Thanks

[alistairewj]

Could you be more specific on which part of the process you think would require manually going through records?

[waqaraziz123]

Hi,
I have identified 2416 patients of septic shock using ICD-9 code and have their Subject_ID's. Now I want to fetch the waveform records of these 2416 patients, if available in the matched subset. I am unable to figure out how can I look for specific Subject_ID's relating to septic shock in the matched subset waveform data through some automated process. Or do I need to manually check each Subject_ID ?

Thanks

[alistairewj]

You can cross-reference it with the RECORDS-waveforms or RECORDS-numerics file in the matched database.

More specifically, let's say you are specifically interested in the waveforms (125+ Hz signals), and not the numerics (1/minute obs like HR, BP, etc). You can look at all available waveform records here: https://physionet.org/physiobank/database/mimic3wdb/matched/RECORDS-waveforms

Here are the top 5 lines from that file:

p00/p000020/p000020-2183-04-28-17-47
p00/p000030/p000030-2172-10-16-12-22
p00/p000033/p000033-2116-12-24-12-35
p00/p000033/p000033-2116-12-25-13-11
p00/p000052/p000052-2191-01-10-02-21

So, to get a list of subject IDs for the waveform database, we just need to pull out the middle folder name. Which can be done with something like cut -d/ -f2 RECORDS-waveforms (cut gets us the 2nd column using / as the delimiter). Joining your list to this list will get you the subset of patients with matched waveforms.

[waqaraziz123]

Thank you. I will try this and will get back to you in case of any issue.

Thanks

[alistairewj]

Good luck!

[waqaraziz123]

Hi,

I somehow managed to sort out patients of interest in the matched subset (The count is 770). I guess it will be sufficient for the analysis.

Thank you again for your help.

[waqaraziz123]

Hi,
I am analysing the waveform database (WFDB) and there is one confusion about matching time infomation of WFDB with clinical database? Like, If I am viewing a record of a septic shock patient in waveform database then how can I see the exact time at which it was diagnosed?
In short, I want to sync the time of both databases for better analysis.

Thanks

[alistairewj]

The timestamp of matched waveform records should match the timestamp of the clinical database.

…

On Thu, Jan 18, 2018 at 6:15 PM, waqaraziz123 ***@***.***> wrote: Hi, I am analysing the waveform database (WFDB) and there is one confusion about matching time infomation of WFDB with clinical database? Like, If I am viewing a record of a septic shock patient in waveform database then how can I see the exact time at which it was diagnosed? In short, I want to sync the time of both databases for better analysis. Thanks — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#350 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ABOSdNKKQ-7J6bpRU3lHUB_1C6GqSsB4ks5tL9CQgaJpZM4Q-Alu> .

[waqaraziz123]

Is there a possiblity that for a single waveform at a particular timestamp, there can be multiple clincal records?

[alistairewj]

No, a single waveform cannot be associated with multiple clinical records, since that would imply that the waveform corresponded to multiple patients simultaneously.

[marciofreire]

Hello!

I've been trying to identify the onset time of septic shock of the patients in MIMIC III Database, but I couldn't find a way to do that. Could you help me with that?

Thank you very much.