Check if we have a vector version of the LCP logo. If not, create one.

We should add the DOI to the website somewhere. Options include the top left so that it is carried to every page (which currently lists the version number), or we could just have it on one of the data pages.

The DOI is doi:10.13026/C2XW26.

Once (/if) the website is finalized and approved by the group, what is the process for redirecting the MIMIC URL (https://mimic.physionet.org) to the new content?

We would like to share a series of tutorials on the MIMIC website. The first one will be "An introduction to MIMIC-III": http://mimic.physionet.org/tutorials/intro_to_mimic-iii/

The new tutorial could be based on the MIMIC-II version at: http://mimic.physionet.org/archive/introduction-mimic-ii.pdf

As discussed with @kepaik this might be a good task for a student, because it will be a nice introduction to MIMIC. Perhaps something for @erinhong if she is interested?

Bug reported by @kpierceHST:

it turns out that my script for approving mimic users no longer works, because it pointed to a location on the old site. ditto for the display of grantees.

Hello! So the NOTEEVENTS table obviously has a large amount of text spanning several pages sometimes. Is there an easy way to read it? On the website it states "TEXT is often large and contains many newline characters: it may be easier to read if viewed in a distinct program rather than the one performing the queries" - how exactly can I accomplish that? I mean is there a way to export the text (or query result in general) to a windows document reader? Thanks!

The front page of the website needs a logo if possible.

Is there a logo for MIMIC? If not, could we create one?

https://mimic.physionet.org/mimictables/noteevents/

Under "Links to:" I dont think there should be:
D_ITEMS on ITEMID

Since there is no column with such name.

Hello, after reading what follows, I didn't really get how can I obtain the RASS of a certain group of patients.

#185 - Three text concepts (GCS, code status, RASS) had a null linksto field in d_items, even though the data existed in chartevents. This has been corrected. Note these were the only three text concepts available for Metavision patients in MIMIC-III v1.3 (see #88).

Is it available then?

I could just find this element on d_items:
228302 CAM-ICU RASS LOC
It has yes/no values on chart events, so I guess I should look somewhere else.

PD: I don't know if this is the right place for posting this kind of questions.

In the Querying MIMIC-III tutorial, 4. Mortality and admissions section, the query uses hospital_expiry_flag field instead of expiry_flag as defined in mimic-code repo, buildmimic/postgres/postgres_create_tables.sql

@kepaik suggests that instead of listing a single page for each data table as shown in the image below, we should display the details in a single longer page (with a menu to find items within the page). I agree this would work better, so will update the template.

As noted in the following thread, some of the row counts in the documentation need to be updated:
MIT-LCP/mimic-code#31

Create tutorial on how to build MIMIC locally from CSV:

• install Postgres
• create tables
• import CSV

Probably a CSS thing.
Functionally fine.

https://mimic.physionet.org/mimictables/noteevents/

Here, there is no explanation of what this column means. :)

The following components were present in the old website, but are not currently listed anywhere on the new website:

• Research affiliates
  • BIDMC
  • Clinical Decision Making (Peter Szolovits)
  • LCP
  • RLE (Thomas Heldt)
  • Phillips Health Care
• Contact us page = issues & help which is incomplete
• Page describing most recent grant(s) funding MIMIC
• Publications
• Explorer/query builder
• Tutorial (intro to MIMIC)
• Old MIMIC II documentation
• Schema
• FAQs
• Release notes page (currently is a dummy page)

We should set up web analytics for mimic.physionet.org so that we can get an idea of things like:

• popularity of different sections of the site
• number of people looking for non-existent pages (e.g. old pages that were deleted)
• sources of inbound traffic
• broken links
• etc...

Should the website display a list of MIMIC-related articles? For example, see:
https://mimic.physionet.org/about/publications.html

If so, how should the list of articles be generated?

@kpierceHST pointed out that the font isn't particularly easy to read. Change color of text and/or background and review the font.

When a new (minor) version of MIMIC is released, we need to make a number of manual updates across several webpages. To simplify updates, the version number should be updated in a single place and the change should be reflected across the website.

The "Data" button on the front page of the website (http://mimic.physionet.org/) should link to a very clear explanation of how to get hold of the MIMIC data. At the moment, it doesn't.

Hi,
I tried mapping ITEMID in CHARTEVENT table using
https://physionet.org/mimic2/UserGuide/UserGuide.pdf
Appendix 6.2,

But there are so many ITEMIDs that are not there in Appendix 6.2.
Is there a way that I can map every ITEMID to figure out what vital signs or lab events it shows?
I also tried matching the ITEMIDs with the Lab Event's ITEMIDs using:

It would be beneficial to have a definition table for care units and services.

The NIH require researchers of studies using MIMIC-III to include the following acknowledgment in their publications:

Research reported in this publication was supported by the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health under Award Number R01EB017205. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

There is a large community familiar with the old website and who may be looking for information such as:

• MIMIC-II SQL Querybuilder (https://mimic2app.csail.mit.edu/querybuilder/)
• MIMIC-II documentation (http://mimic.physionet.org/archive/mimic-ii-guide.pdf)
• MIMIC-II tutorial (http://mimic.physionet.org/archive/introduction-mimic-ii.pdf)

This information has been archived at: http://mimic.physionet.org/archive/mimic-ii/ but it is not immediately obvious that this is where to look.

We would like to provide a forum for the MIMIC community to discuss research questions, data extraction issues, etc. The aims of doing this include:

• openly documenting questions, answers etc for future reference;
• moving away from providing email support, reducing workload on the lab
• encouraging collaboration and idea sharing between researchers
• increasing the size of the MIMIC community in a sustainable way.

Buttons on the front page of the site have a transparent background when someone:

1. visits front page (http://mimic.physionet.org/)
2. selects a menu button and visits the content (e.g. selects 'Docs')
3. uses the browser 'back' button to return to the front page.

@kepaik suggests using a layout similar to bootstrap:
http://getbootstrap.com/

we should create a new theme on a branch then merge when ready!

Rather than rebuilding the public content manually each time updates are made, it would be good to set up automatic deployment. See: http://gohugo.io/tutorials/automated-deployments/ for a suggested method.

After installing MIMIC-III in a local Postgres database, create a test to compare dimensions of local database with online database.

There are several questions that are repeatedly sent to the mimic-support email address or to individual staff in the lab. Replying uses up lab resources, so we should explore what we can do to reduce the frequency of them (e.g. providing clearer information on the website, improving documentation, etc.). Repeated questions can be logged in this thread.

Before we begin building the MIMIC website, we need to have:

• a clear idea about what is needed
• a plan for the framework used to build the website

The description in Step 1 refers to the icustayevents table instead of icustays.

We need to create a system for making announcements on the front page of the website. Ideally it should be:

• simple to add and update announcements.
• displayed clearly on the front page

@alistairewj the website is ready for us to start adding content. Hugo was a great choice...it's really nice to work with.

Adding content is straightforward. Now the framework is there, it pretty much just involves creating new files in the content directory: https://github.com/MIT-LCP/mimic-website/tree/master/content

In case you'd like to make a start on the table descriptions, I've added a set of template files at:
https://github.com/MIT-LCP/mimic-website/tree/master/content/datatables

As we'll be providing import scripts, I'm not sure whether we need to draw out each table in the documentation? I'm undecided about whether this would be useful or not...

Hi,
I tried mapping ITEMID in CHARTEVENT table using
https://physionet.org/mimic2/UserGuide/UserGuide.pdf
Appendix 6.2,

But there are so many ITEMIDs that are not there in Appendix 6.2.
Is there a way that I can map every ITEMID to figure out what vital signs or lab events it shows?
I also tried matching the ITEMIDs with the Lab Event's ITEMIDs using:

https://github.com/MIT-LCP/mimic-code/blob/master/migrating/labid.csv

But no success!

Set up the repository on Travis CI:
https://travis-ci.org

At the moment the top left of the website reads "MIMIC-III v1.0". I think a useful improvement would be to replace this text with "The latest version of MIMIC-III is v1.1", and increment it with each version. This would make it easier for those who visit the site to notice that their version is out of date.

No response after clicking on Submit Information.

I've been trying to follow the method presented here. https://mimic.physionet.org/tutorials/install-mimic-locally-windows/. When I try to create tables with the command \i postgres_create_tables.sql, it gives me a syntax error. Screenshot attached. Please guide regarding the same. Thanks!

When rebuilding the website, old pages don't seem to be deleted. For example, IOEVENTS has been removed and replaced with a few tables, e.g. INPUTEVENTS_CV:

http://mimic.physionet.org/mimictables/inputevents_cv/

And on the left, it's clear that IOEVENTS is no longer listed:

But, you can still type in the URL for the old table: http://mimic.physionet.org/mimictables/ioevents/

Which brings you to an obsolete page describing IOEVENTS:

The table of contents for pages with lots of header items extends beyond the bottom of the page, and it isn't possible to reach the lower items:

For example, see the following screenshot (table of contents shown on the right side):

Add a citation for MIMIC-III to acknowledgements.md. I believe the current in-press citation is:

Johnson A, Pollard T, Shen L, Lehman L, Feng M, Ghassemi M, Moody B, Szolovits P, Celi LA, Mark R. Medical Information Mart for Intensive Care (MIMIC-III): the public access critical care database. Scientific Data 2016 (In press).

I'm currently running MIMIC-III on PostgreSQL through pgAdmin III on a windows installation, and I just tried going through the last part of the 'Patient age and mortality' tutorial. I noticed a couple of things that didn't work on my installation of MIMIC.

The main thing was the 'months_between' function, supposedly it doesn't exist on PostgreSQL. I think the query on the website could be for an Oracle installation.

Here is the full query I ran that resulted in what I was looking for (changed lines marked with %):

WITH first_admission_time AS (
SELECT 
    p.subject_id, p.dob, p.gender, 
    MIN (a.admittime) AS first_admittime
%FROM mimiciii.patients p
%INNER JOIN mimiciii.admissions a
ON p.subject_id = a.subject_id
%GROUP BY p.subject_id, p.dob, p.gender, a.hadm_id
ORDER BY a.hadm_id, p.subject_id
),
age AS (
SELECT 
    subject_id,  dob, gender, first_admittime, 
%    age(first_admittime, dob) 
        AS first_admit_age, 
    CASE
%       WHEN age(first_admittime, dob) > '89 years'
%            THEN '>89'
%        WHEN age(first_admittime, dob) >= '15 years'
            THEN 'adult'
%        WHEN age(first_admittime, dob) <= '1  year'
            THEN 'neonate'
        ELSE 'middle'
        END AS age_group
FROM first_admission_time
ORDER BY subject_id
)
SELECT *
FROM age;

This query gives the age in years, months, days, and hours so there could be a more relevant function depending on what you need age for. The reasons behind these changes are outlined below:

• on pgAdmin, the schema (in this case - mimiciii) needs to be identified before the table when selecting data
• hadm_id had to be placed in the 'GROUP_BY' section in order to run the query
• 'months_between' function had to be replaced by the 'age' function, and the WHEN condition had to be changed to compare interval arguments
• another age group '>89' was added as a personal preference to keep anyone with a computed age of 300+ separate from other patients.

Since the tutorial page says that the tutorial should be run on a PostgreSQL installation I'm concerned that maybe my set-up or query is incorrect. I also have limited programming/sql knowledge so something else may have gone wrong along the way.

Another interesting note is that there were no patients in the database with an age between 5 months and 14 years. Is this because there is no data from the paediatric ICU?

Thanks

Hi,

I am getting ready to build a data dictionnary for mimic descibing things like https://mimic.physionet.org/mimictables/callout/ . This data dictionnary will be machine exploitable. For my use case, it will be a basis to align my database on mimic and document it. But it could be usefull too for you:

1. autobuild ansible scripts to generate mimic build in many databases kinds
2. autogenerate documentation, by eg mimic-website documentation
3. autogenerate yaml file for by eg anonimyse

I uselly use an excel spreadsheet, robust & multiplateform. Do you have any thing to start with other than the website flat documentation ?

Thanks,

Aaron pointed out that these instructions

"...You can avoid browser warnings by installing
our certificate authority file which can be obtained from: http://mimic.physionet.org/certs/lcpca.crt"

failed because of a broken link. I copied the certs directory from old site to new and asked him to try again.

A PDF of the documentation should be automatically generated from the web content. One option is to use Pandoc, as we did previously.

I noticed that there is a tutorial for installing MIMIC-III on Windows here on GitHub, but it hasn't yet been added to the mimic website.

It is a fairly similar install but a few of the commands differ. As a beginner I got a little bit lost trying to translate the Ubuntu instructions to work on Windows until luckily, I stumbled across the Windows readme here on GitHub (thanks for posting @alistairewj !)
https://github.com/MIT-LCP/mimic-code/blob/master/buildmimic/postgres/README-windows.md