OHDSI Home | Forums | Wiki | Github

LAERTES Team Meeting Agenda

Developers
#1

Agenda for December 17th 2014 (telecon information below)

  • Help requests

  • Erica - Pivot Table review

  • Christoph - Code project from a new developer’s perspective

  • Rich - addressing RDF issues raised by Michel

  • Christian and Rich - requesting input on pitch to FDB

  • Rich suggests delaying until v0.5 of LAERTES is released

  • Rich to provide edits to written bullets drafted by Christian

  • Milestone: Funding seeking

  • Milestone: Stabilize a v1 of LAERTES in incremental versions

    • Migrating to v5 of the Schema

  • EU SPC

  • SPLICER

  • PubMed

  • API develoipment

  • Milestone: Make progress on hard problems with important datasets

TELECON INFO

Call in Number: 1-877-5659999 (US)

Attendee access code: 283 060 06

Show global numbers

WebEx: https://jjconferencing.webex.com/jjconferencing/j.php?ED=234815742&UID=0&RT=MiMxMQ%3D%3D

#2

@rkboyce

Is there a time for this call?

Thanks,
Bill

#3

sorry for forgetting that: 12 PM Eastern

#4

Dear LAERTES Team, No meeting today because of the holiday. As for updates, please note the following:

Data updates:

Please post any other updates as a reply on this forum topic.

Happy New Year,
-Rich

#5

Dear LAERTES Team,

Here is the agenda for today’s meeting:

Milestone: Stabilize a v1 of LAERTES in incremental versions

  • SPLICER update
  • progress on PubMed (MeSH)
  • progress on SemMed - update needed
  • progress on PV Signals
  • VigiBase API
  • representing evidence at various levels
  • WebAPI

Milestone: Make progress on hard problems with important datasets

  • Questions about PubMed and SemMed

Milestone: Funding seeking

  • setting a meeting schedule

TELECON INFO

Call in Number: 1-877-5659999 (US)

Attendee access code: 283 060 06

Show global numbers

WebEx: https://jjconferencing.webex.com/jjconferencing/j.php?ED=234815742&UID=0&RT=MiMxMQ%3D%3D

#6

SORRY FOR THIS CHANGE — UPDATED TELECON INFO:

  1. Please join my meeting.
    https://global.gotomeeting.com/join/530277469

  2. Use your microphone and speakers (VoIP) - a headset is recommended. Or, call in using your telephone.

Dial +1 (646) 749-3122
Access Code: 530-277-469
Audio PIN: Shown after joining the meeting

Meeting ID: 530-277-469

GoToMeeting®
Online Meetings Made Easy®

Not at your computer? Click the link to join this meeting from your iPhone®, iPad®, Android® or Windows Phone® device via the GoToMeeting app.

#7

Dear Team,

We are scheduled to meet tomorrow. Please note the revised telecon information below. Here is what I propose for our agenda:

Milestone: Stabilize a v1 of LAERTES in incremental versions

  • representing evidence at various levels (i.e., “Roll Up queries”)
  • Web API
  • progress on SemMed
  • progress on PV Signals
  • VigiBase API

Milestone: Make progress on hard problems with important datasets

  • Questions about CT.gov, PubMed, SemMed

Milestone: Funding seeking

  • setting a meeting schedule

Telecon info
WEB: https://global.gotomeeting.com/join/530277469
PHONE:
Dial +1 (646) 749-3122
Access Code: 530-277-469

Meeting ID: 530-277-469

#8

Dear Team,

We are scheduled to meet Wednesday 2/11. Here is what I propose for our agenda:

Milestone: Stabilize a v1 of LAERTES in incremental versions

  • representing evidence at various levels (i.e., “Roll Up queries”)
  • Web API
  • SemMed now loaded
  • progress on PV Signals
  • CT.gov
  • VigiBase API

Milestone: Make progress on hard problems with important datasets

  • Discussion of drug and hoi mappings from each source to the Standard Vocab

Milestone: Funding seeking

  • meeting schedule set

Telecon info
WEB: https://global.gotomeeting.com/join/530277469
PHONE:
Dial +1 (646) 749-3122
Access Code: 530-277-469

Meeting ID: 530-277-469

1 Like
#9

Dear Team,

We are scheduled to meet today. Here is what I propose for our agenda:

Milestone: Stabilize a v1 of LAERTES in incremental versions

  • Source updates: Vigibase, CT.gov, PV Signals, CT.gov
  • Web API: progress
  • Planning for AMIA
  • Negative controls

Milestone: Make progress on hard problems with important datasets- Discussion of drug and hoi mappings from each source to the Standard Vocab

  • Source drugs and HOIs

Milestone: Funding seeking- meeting schedule set

  • general idea

Telecon infoWEB:
https://global.gotomeeting.com/join/530277469
PHONE:
Dial +1 (646) 749-3122
Access Code: 530-277-469

Meeting ID: 530-277-469

#10

Dear Laertes Team - I am canceling the telecon for this coming week to give me more time to work on tidying up the evidence base and WebAPI in preparation for the AMIA CRI presentation. I will follow up by email with folks working on specific items. Also, I plan to email out some slides for the presentation for feedback.

best,
-R

#11

Dear Team,

The agenda and telecon for today’s meeting at Stanford are copied below. The meeting will start at 11:15 PST (2:15 Eastern).

Agenda:

  • Summary of progress on loading sources

  • WebAPI calls and demo

  • Evidence of negative drug-HOI signals from the loaded data

  • Publications in progress

  • Grant and other resource opportunities

Telecon:

(WG Laertes)

  1. Please join my meeting.

https://global.gotomeeting.com/join/530277469

  1. Use your microphone and speakers (VoIP) - a headset is recommended. Or, call in using your telephone.

Dial +1 (646) 749-3122

Access Code: 530-277-469

Audio PIN: Shown after joining the meeting

Meeting ID: 530-277-469

#12

Dear Team,

The agenda and telecon for today’s meeting at 12 Eastern is pasted below:

Agenda:

Telecon:

(WG Laertes)

Please join my meeting.

https://global.gotomeeting.com/join/530277469

Use your microphone and speakers (VoIP) - a headset is recommended. Or, call in using your telephone.

Dial +1 (646) 749-3122

Access Code: 530-277-469

Audio PIN: Shown after joining the meeting

Meeting ID: 530-277-469

#13

Dear Laertes Team,

The agenda and telecon for today’s (5.6.2015) meeting at 12 Eastern is pasted below:

Agenda:

  • Spring update of sources SPLICER, PubMed, SemMed, EU SPC, PV counts and signals
    – progress and current issues

  • WebAPI : integration into the public facing version and view for Hermes

  • Vigibase integration and collaboration with UMC

  • Progress on prospective papers responsive to the BioMed Research CFP : http://www.hindawi.com/journals/bmri/si/706947/cfp/

Telecon:

(WG Laertes)

Please join my meeting.

https://global.gotomeeting.com/join/530277469

Use your microphone and speakers (VoIP) - a headset is recommended. Or, call in using your telephone.

Dial +1 (646) 749-3122

Access Code: 530-277-469

Audio PIN: Shown after joining the meeting

Meeting ID: 530-277-469
[/quote]

#14

All - sorry for the last minute change. I need to cancel this week’s meeting because of travel to ISPOR other concerns. Let’s plan for the next meeting to be June 3rd. The topics to discuss then will be the UI scenarios for Laertes and use cases. Please think about and comment on the following:

From Tomas:

  • Would it be possible to extend the API to allow counts by grouping on something else than the SNOMED concept ids, since our source data (the spontaneous reports in VigiBase) use MedDRA we would like the statistics to correspond to that terminology. If things are counted based on SNOMED the counts will not be representative if the counts themselves have to be aggregated to a MedDRA term from several different SNOMED terms.

  •  For another use case  that we have we would be interested in knowing the aggregated statistics (drug, condition, source_counts) for all combinations of drugs and conditions in LAERTES. Such a query would only have to be used very  rarely but otherwise we would face the same problem as you have  experienced with extracting information from the VigiBase API.

Scenarios:

  1. Pharmacovigilance investigator

  • Katrina is trained as an epidemiologist and works full time at a center that monitors the safety of newly released drugs and old drugs that have received new indications. She typically receives suspected adverse drug events from spontaneous case reports that she evaluates using a structured algorithm like the Naranjo scale (you can see one in the last page of the attached). The first question the scale asks is “Are there previous conclusive reports on this reaction?”. Her current process is to look in a local database of spontaneous reports, review the ADR sections of the product label, and do a query of the published literature in Medline for case reports. She might also look at clinicaltrials.gov to see if any studies with the drug have recorded the adverse event and see if she can contact the PIs of those studies to learn more about the context.

  • Katrina would like her search to be more organized and simple to execute. She heard about the evidence base in OHDSI and decided to try it out. She uses Hermes one of two ways:

    • to identify the concept id for the HOI and then goes to the
      evidence tab to see if the specific drug she is interested in has
      been reported as potentially associated with the HOI. When she looks
      at the tab, she is especially interested in the following:

    — finding the drug quickly in the list of all drugs for which the
    AE has been reported

    — Identifying if the report is at the clinical drug or ingredient
    level

    — Identifying from which source the association was noted. She
    cares mostly about product labeling, case reports from the
    literature, and spontaneous reports. She would like to see a summary
    of the evidence across these sources and then be able to click on a
    link and review a bit more information about each. For the labeling,
    she would like to see the source SPL and the section with the
    adverse event highlighted. Literature, the abstract with (possibly
    only for SemMed) the sentence mentioning the AE highlighted. For
    Spontaneus reports, the counts and PRR (i.e., strength of signal),
    and then when the reports came in, where from, and some demographics
    on the cases

    • alternately, she might want to identify the concept id for the
      drug and then goes to the evidence tab to see if the specific HOI
      she is interested in has been reported as potentially associated
      with the drug. Similar use cases apply.
  1. quality improvement director for a health system

  • Eileen is a nurse with some training (certificate level) in
    epidemiology. She is in charge of ensuring that certain health
    quality measures QM are are at optimal levels in the health system
    she serves (which currently has five NH facilities). She typically
    receives QM reports each quarter. The current report shows that
    anemia is at a very rate and she would like to determine what sort
    of intervention is needed. Her typical process is to raise the issue
    with her colleagues after looking in the literature for evidence of
    what can be associated with the QM and if other clinical
    interventions have been tested.

    • She heard about the evidence base in OHDSI and decided to try it
      out. She wants uses Hermes because the QM “anemia” is not very
      specific. She would like to see what sub-types of anemia there are
      and if there is any evidence of drug assocation. She finds “anemia”
      concept and goes to the evidence tab. When she looks at the tab, she
      is especially interested in the following:

    ---- Is there evidence for drug association with the general concept
    “anemia”?

    ---- How does that evidence apply when looking at the sub-concepts
    of “anemia”

    ---- What is the list of drugs for which there is evidence for the
    sub-concept of anemia she cares about?

    — Identifying from which source the association was noted. She
    cares mostly about product labeling, case reports, and clinical
    studies in the literature. She would like to see a summary of the
    evidence across these sources and then be able to click on a link
    and review a bit more information about each.

    ---- She would like to use other OHDSI tools to determine with of
    the drugs are prescribed at her sites and then design and
    characterize the cohort of individuals who are exposed to anemia and
    the drugs at her facilities to get a rough idea if the potential for
    the intervention to work (see http://www.slideshare.net/boycer/piloting-acomprehensivepharmacovigilanceknowledgebase2015v2)

#15

Dear Laertes Team,

The agenda and telecon for tomorrow’s (6.2.2015) meeting at 12 Eastern is pasted below:

Agenda:

  • progress and current issues

Telecon:
(WG Laertes)

Please join my meeting.

https://global.gotomeeting.com/join/5302774692

Use your microphone and speakers (VoIP) - a headset is recommended. Or, call in using your telephone.

Dial +1 (646) 749-3122

Access Code: 530-277-469

Audio PIN: Shown after joining the meeting

Meeting ID: 530-277-469

#16

All - I made a mistake in sending out the telecon info - here is the correct telecon - we are on the call now if you can still join. Sorry about this!

  1. Please join my meeting.

https://global.gotomeeting.com/join/530277469

  1. Use your microphone and speakers (VoIP) - a headset is recommended. Or, call in using your telephone.

Dial +1 (646) 749-3122

Access Code: 530-277-469

Audio PIN: Shown after joining the meeting

Meeting ID: 530-277-469

#17

Dear Laertes Team,

Here is the agenda for today’s (6.17) telecon at 12 Eastern. Telecon info is pasted below:

Agenda:

TELECON
https://global.gotomeeting.com/join/530277469

  1. Use your microphone and speakers (VoIP) - a headset is recommended. Or, call in using your telephone.

Dial +1 (646) 749-3122

Access Code: 530-277-469

Audio PIN: Shown after joining the meeting

Meeting ID: 530-277-469

#18

Dear Laertes Team,

Here is the agenda for today’s (7/1) telecon at 12 Eastern. Telecon info is pasted below:

Agenda:

  • WebAPI : integration into the public facing version and view for Hermes

– Indications, contra-indications, HOI concept similarity

  • Planning for the next revision

  • Vigibase integration and collaboration with UMCCT

Progress on prospective papers responsive to the BioMed Research CFP: http://www.hindawi.com/journals/bmri/si/706947/cfp/
Architecture paper: https://docs.google.com/document/d/1Yn0kV6bxdQtrvwglr0vCp040yNbmWiUF5idY8C78ez8/edit

TELECON

https://global.gotomeeting.com/join/530277469

Use your microphone and speakers (VoIP) - a headset is recommended. Or, call in using your telephone.

Dial +1 (646) 749-3122

Access Code: 530-277-469

Audio PIN: Shown after joining the meeting

Meeting ID: 530-277-469

#19

Dear Laertes Team,

Here is the agenda for today’s (7/15) telecon at 12 Eastern. Telecon info is pasted below:

Agenda:

  • Planning for the next revision

  • Vigibase integration and collaboration with UMCCT

  • Publication - one down, one to go!

  • JSM talk in August

TELECON

https://global.gotomeeting.com/join/530277469

Use your microphone and speakers (VoIP) - a headset is recommended. Or, call in using your telephone.

Dial +1 (646) 749-3122

Access Code: 530-277-469

Audio PIN: Shown after joining the meeting

Meeting ID: 530-277-469

#20

FYI, today’s meeting 8/11 is canceled. I sent out an email, if you did not receive it let me know.

t