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New WG - Book of OHDSI

(Seng Chan You) #61

@schuemie Recently, a publisher asked me to write a book of medical data analysis or OHDSI. (this doesn’t seem to proceed further, because I started to write online book.) So I didn’t want to use Overt FREE license. And because Hadley Wickham used this license in his book (Advanced R), I used the same license.
Briefly,I didn’t care thoroughly. :sweat_smile:

(Clark C. Evans) #62

OHDSI may want to consider CC0 for its documentation. Anything else may create unforeseen issues with the ability to update/maintain/re-purpose documentation. In particular by-nc-nd is not great on all three fronts: a) it’s unclear if publishers could make a physical book out of it or even it could be hosted, b) it prevents future initiatives from building/reusing content, and c) the attribution can make incorporating into software harder. Of the three, the attribution requirement is the least worst, but even it is tedious to get right. The thing is, most projects think they need these restrictions… but they don’t. They worry that someone would fork the effort and make a proprietary derivative or make profits from is distribution. However, the cost of the restriction is often not worth covering from what is a rather unlikely event. The more likely, and higher risk is that someone simply won’t adopt the approach.

(Martijn Schuemie) #63

Thanks @cce! I think the point of the license is to prevent obstacles, not raise them, so to your point CC0 would make most sense if I understand all this correctly.

I was personally thinking of using self-publishing to create a physical copy of the book, which it seems the CC0 license allows for.

The CommonDataModel also appears to use the CC0 license, so we would also be consistent with that.

(Seng Chan You) #64

Good, thank you @cce for the valuable comment. The book of OHDSI Korea also adopts the CC0 license.

(Martijn Schuemie) #65

Reminder: tomorrow (Tuesday June 11) we have another Book Workgroup meeting at 11am Eastern Time.

Proposed topics to discuss:

  • Face-to-face meeting summary and next steps
  • Setting a deadline for chapter drafts
  • Should we create a companion site?
  • Where should we list contributors?
  • Everyone OK with the CC0 license?

For details how to join see the Book WG Wiki.

(Hamed Abedtash) #66

Thanks @schuemie! Can you please share the Webex info?

(Martijn Schuemie) #67

Hi @abedtash_hamed! You can find the connection details on the Book WG Wiki (link posted above).

(Ellen Palmer) #69

I am unable to make the meeting, but will access the meeting notes on the Wiki to be updated on when I should have the Characterization chapter done - I’m hoping to have a complete draft available for review sometime this week.

(Martijn Schuemie) #70

A quick update: we decided yesterday that first versions of chapters should be ready 4 weeks from now, so July 9. Please reach out to me if you need help meeting that deadline.

Also, please, please, please, follow the instructions for making screenshots of ATLAS. I see a lot of screenshots of ATLAS in the Google Docs taken at the full monitor resolution, meaning the text will be too small to read in the book. Also, please use screenshots sparingly. For example, there’s no need to have a screenshot of an empty form and then another screenshot of the same form filled in. I have tried to follow both principles in this section of the estimation chapter.

(Martijn Schuemie) #71

Tomorrow we have another Book of OHDSI workgroup meeting!

Topics to discuss:

See the Book WG Wiki for the meeting details.

(Clark C. Evans) #72

One Open Science chapter topic in today’s meeting was FAIR: Findable, Accessible, Interoperable, and Reusable. It seems to me that FAIR was constructed as a response to Data-as-a-Service (DaaS) initiatives, laying out principles for what could be commercially acceptable behavior, yet preserving “open science”.

Hence, I think that FAIR applies to OHDSI’s Athena, the SaaS for distributing and browsing the Standardized Vocabularies for the OMOP CDM. It’s clear that Athena strongly meets FAIR principles, point by point.

Even so, I’m not sure that FAIR is relevant to other aspects of OHDSI since the actual CDMs are not meant to be generally accessible DaaS resources.

(Andrew Williams) #73

I’m not sure that accessibility of local CDMs is the right way to define the boundaries of what FAIR pertains to.
In addition to the OHDSI elements you name, digital objects like phenotype definitions, PLP models, study parameters and any others that affect sharability and reproducibility are within the spheres of open science that FAIR principles seek to address.

(Martijn Schuemie) #74

Today we have another Book Workgroup meeting. Here are some topics to discuss:

  • Progress report: where is everyone at?
  • Chapter summaries (see “Data Analytics Use Cases”, “SQL and R”, and “Population-Level Estimation” chapters)
  • “OHDSI Analytics Tools” chapter: add BroadSea? OHDSI-in-a-box? Others?
  • Data Quality chapter: how to proceed?

See the Book WG Wiki for the meeting details.

(Martijn Schuemie) #75

Here’s Vojtech’s paper we just discussed.

(Martijn Schuemie) #76

Please keep in mind that the deadline (July 9) for submitting full chapter drafts is less than a week away!

Chapters that are not on time may be allocated to new chapter leads.

(Martijn Schuemie) #77

Today is not only the deadline for submitting chapter drafts, we also have a Workgroup meeting!

Proposed agenda items:

  • Progress update
    • Contributors section
  • Next step: reviewing the chapters
  • Translation to other languages (see this issue)
  • Exercises using Eunomia (see this example)

See the Book WG Wiki for the meeting details.

(Seng Chan You) #78

@schuemie Sorry I cannot attend the meeting because of oncology WG meeting.
For the translation, please see the Korean one here.

(Martijn Schuemie) #79

Tomorrow we have our next Book of OHDSI Workgroup meeting (11AM Eastern Time). Topics to discuss:

  • Chapter status update
  • Update on the review process
  • Timeline until symposium
  • Middle initials of chapter leads and contributors?
  • Spread the word: still need cover designs for the competition!

(Martijn Schuemie) #80

Hi all,

Just making sure everyone is aware of our timeline. The goal is to have the book ready and printed at the OHDSI Symposium. Working back from that date:

Date Event
Sep 16 Symposium time: present the Book of OHDSI!
Aug 26 Three weeks until symposium: pens down: book should be final, going to the printer
Aug 12 Five weeks until symposium: content finalized, start proofing. (Proofing includes final language checks, checks for consistency between chapters, finalizing layout, etc.)
Aug 7 Deadline of the cover design competition
Jul 29 Seven weeks until symposium: Reviews due: chapter leads should start processing feedback

So all content should be finalized August 12, which is less than a month from now. This includes the time to review, and make changes based on the reviews.

Most chapters are perfectly on track to meet that deadline, but some are not. I hereby urge the respective chapter leads (you know who you are :wink: ) to make sure we can proudly present our work to the world at this year’s symposium!

(Christian Reich) #81


I got a good motto for the Book of OHDSI. It’s a quotation: “I have nothing to offer but blood, toil, tears and sweat”. Summarizes it pretty well, doesn’t it?