[Obi-devel] competency questions

[Fostel, Jennifer (NIH/NIEHS) [C]]

these are questions that i have had from our community for similar studies

 

Study information:

where was the study held (institution / location)?

who was the PI?

what were the study factors?

was this a parallel study or cross over design?

when was the study done / when did the study start?

 

Dosing:

what was the purity of the fucoidan used?

what was the nominal dose given in each administration?

what was the actual amount of active substance given in each administration?

what amount was given in total?

what was the frequency of dosing?

what was the duration of dosing?

what was the route of administration?

was a positive control used?

was a negative control used?

what was the negative control?

 

Subject characteristics:

what exclusion criteria were used for subjects?

what is gender? age? ethnicity? medical history?

was subjects' diet controlled during the study?

was additional medication given to subjects during study?

was the dose administration monitored by study personnel?

were any adverse events noted during the study?

 

Data and conclusions:

how many subjects were in each group?

What were study conclusions?

what assays were performed?

what assays had statistically significant results?

did all assay results support the conclusion?

what hypothesis/es did the authors support?

what further hypotheses did this paper produce?

 

Questions with answers missing from the paper:

if we could distinguish individual subjects on the basis of data presented

which subjects were in the control group / treatment group?

 

can we (legally) use the data for additional analysis?

 

what inter-subject variability was observed in the assay data?

did n=10 provide sufficient statistical power to support the conclusion?

were the assay results of control group within historical range for lab?

 

were doses given with food?

did assay results from subjects given negative control deviate from control range?

what was the dosing regimen (eg, did they deviate for weekends / holidays, etc.)?

 

 

Jennifer Fostel, Ph.D.

CEBS Scientific Administrator

Global Health Sector, SRA International, Inc

 

Laboratory of Respiratory Biology

NIEHS, NIH

PO Box 12233 Mail Drop F1-05

111 Alexander Drive

Research Triangle Park NC 27709-2233

 

phone 919 541 5055

fax 919 541 1460

 

 

[Bjoern Peters]

My personal bias would be to consider the following questions most important:
 

Study information:

where was the study held (institution / location)?

who was the PI?

was this a parallel study or cross over design?

when was the study done / when did the study start?

 

Dosing:

what was the actual amount of active substance given in each administration?

what was the duration of dosing?

what was the frequency of dosing?
what was the route of administration?

was a positive control used?

was a negative control used?

what was the negative control?

 

Subject characteristics:

what is gender? age? ethnicity? medical history?

Data and conclusions:

how many subjects were in each group?

What were study conclusions?

what assays were performed?

what assays had statistically significant results?

what hypothesis/es did the authors support?

what further hypotheses did this paper produce?

I am not sure about what this question means:

what were the study factors?

Would consider the remaining questions lower priority: 

what was the purity of the fucoidan used?

what was the nominal dose given in each administration?

what amount was given in total?

what exclusion criteria were used for subjects?

was additional medication given to subjects during study?

was the dose administration monitored by study personnel?

were any adverse events noted during the study?

did all assay results support the conclusion?

----- Original Message -----
From: "Jennifer Fostel (NIH/NIEHS) [C]" <fos...@niehs.nih.gov>
To: "OBI Developers" <obi-...@lists.sourceforge.net>
Sent: Wednesday, September 30, 2009 7:44:43 AM GMT -08:00 US/Canada Pacific
Subject: [Obi-devel] competency questions

 

Jennifer Fostel, Ph.D.

CEBS Scientific Administrator

Global Health Sector, SRA International, Inc

 

Laboratory of Respiratory Biology

NIEHS, NIH

PO Box 12233 Mail Drop F1-05

111 Alexander Drive

Research Triangle Park NC 27709-2233

 

phone 919 541 5055

fax 919 541 1460

 

 

------------------------------------------------------------------------------ Come build with us! The BlackBerry® Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9-12, 2009. Register now! http://p.sf.net/sfu/devconf
_______________________________________________ Obi-devel mailing list Obi-...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/obi-devel

--
Bjoern Peters
Assistant Member
La Jolla Institute for Allergy and Immunology
9420 Athena Circle
La Jolla, CA 92037, USA
Tel: 858/752-6914
Fax: 858/752-6987
http://www.liai.org/pages/faculty-peters

[Fostel, Jennifer (NIH/NIEHS) [C]]

 

my community all wants to know the nominal dosage given + purity.  from this we calculate the actual active dose (see what was reported in the abstract -- no one computes / reports the 2.25 grams, just 3 grams / 75% pure). 

 

no problem for the others; the reason to include woudl be as follows....

 

some points impact the conclusions, for example aspirin and green veggies contribute to coagulation time, the endpoint in this study.  if some subjects were eating cole slaw / aspirin then the study is difficult to interpret.  people are notoriously noncompliant and so having them supervised is importantto the interpretation as well

 

exclusion criteria point to considerations made by the study scientists, which will impact the scope of the results, for example, if they did not exclude / note heart conditions then this will impact the conclusions (however they do say healthy volunteers, so we can assume things are all ok)

 

thanks for help in proritizing

 

cheers!

 

...jennfier

---

From: Bjoern Peters [mailto:bpe...@liai.org]
Sent: Wednesday, September 30, 2009 12:30 PM
To: Fostel, Jennifer (NIH/NIEHS) [C]
Cc: OBI Developers
Subject: Re: [Obi-devel] competency questions

[Turner, Jessica]

I was figuring that

what were the study factors?

 

Means what were the experimental design factors or structure: eg subject groups, drugs being tested, level of dosing, timing of dosing, etc.  It should follow from the hypotheses being tested (though representing the hypotheses of the study is not one of the competency questions?).

 

Exclusion criteria are critical for interpreting the results of a clinical study, so I would definitely put that question at least at the same level of importance as who the PI was (if not more important).

 

Thanks,

Jess

 

From: Bjoern Peters [mailto:bpe...@liai.org]
Sent: Wednesday, September 30, 2009 9:30 AM
To: Jennifer Fostel (NIH/NIEHS) [C]
Cc: OBI Developers
Subject: Re: [Obi-devel] competency questions

 

My personal bias would be to consider the following questions most important:
 

---

This message contains confidential information and is intended only for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail by mistake and delete this e-mail from your system. E-mail transmission cannot be guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain viruses. The sender therefore does not accept liability for any errors or omissions in the contents of this message, which arise as a result of e-mail transmission.

[Helen Parkinson]

This is how I think these map to the file after discussing this with
Alan. We will do some work on this.
--------------------------------------------------------------------------

Study information:
where was the study held (institution / location)? - n/a - to add
who was the PI? - ok
was this a parallel study or cross over design? - n/a to add
when was the study done / when did the study start? - is a date range
expected? Is this in the paper?

Dosing:
what was the actual amount of active substance given in each

administration? - ok, tho adminsistration still needs to be modelled
what was the duration of dosing? - what dose this mean?
what was the frequency of dosing? - n/a to add once per day
what was the route of administration? - ok
was a positive control used? - this is not explicit in the paper, and
the answer is no.
was a negative control used? - ok
what was the negative control? - ok

Subject characteristics:
what is gender? age? ethnicity? medical history?

- not all in the paper, some of these are known only at aggregate level
- AR/HP think this should not be modelled at the aggregate level. Again,
what is the scope.

Data and conclusions:
how many subjects were in each group? n/a - to add as class=10 homo
sapiens instances
What were study conclusions? - n/a - no anticoag in vivo and there is in
vitro?
what assays were performed? - n/a antithrombin assay needs modelling -
but JF suggested we model only 1, and in this case we can't answer for
all assays
what assays had statistically significant results? - n/a we did model
plan to model all assays
what hypothesis/es did the authors support? n/a
what further hypotheses did this paper produce? n/a

I am not sure about what this question means:
what were the study factors?

HP: does this mean what are the study variables?

> Come build with us! The BlackBerry® Developer Conference in SF, CA is

> the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and
> stay ahead of the curve. Join us from November 9-12, 2009. Register
> now! http://p.sf.net/sfu/devconf
> _______________________________________________ Obi-devel mailing list
> Obi-...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-devel
>
> --
> Bjoern Peters
> Assistant Member
> La Jolla Institute for Allergy and Immunology
> 9420 Athena Circle
> La Jolla, CA 92037, USA
> Tel: 858/752-6914
> Fax: 858/752-6987
> http://www.liai.org/pages/faculty-peters

> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA

> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay

> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
> http://p.sf.net/sfu/devconf
> ------------------------------------------------------------------------

>
> _______________________________________________
> Obi-devel mailing list
> Obi-...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-devel
>

------------------------------------------------------------------------------
Come build with us! The BlackBerry&reg; Developer Conference in SF, CA

is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay

ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;

[Frank Gibson]

HI,

You have probably discussed this, so I may just be echoing what has already been said, but once you decide on the competency questions your going to test for it may be helpful to write out what you think that answers should be, why you are asking the questions in the first place, and then query the ontology and see if the answers match up, and evaluate accordingly. You could also have some more slightly generic questions, such as "Does the ontology have a clinical trial process",  for example.

Frank

--
Frank Gibson, PhD
http://peanutbutter.wordpress.com/

[Helen Parkinson]

Hi Frank

Alan and I did discuss this, we'd like Jennifer to provide these, and
yes the generic questions is a good point as well,

Helen

> <mailto:Obi-...@lists.sourceforge.net>

> <mailto:Obi-...@lists.sourceforge.net>

> > https://lists.sourceforge.net/lists/listinfo/obi-devel
> >
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year.
> Jumpstart your
> developing skills, take BlackBerry mobile applications to market
> and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register
> now&#33;
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Obi-devel mailing list
> Obi-...@lists.sourceforge.net

> <mailto:Obi-...@lists.sourceforge.net>

[Fostel, Jennifer (NIH/NIEHS) [C]]

this is not the priority that most members of my community would assign the questions. we are very interested in the dosing regimen, the item given and the subject characteristics.

i will provide a map and answers at the next call. cheers!

...jennifer

-----Original Message-----
From: Helen Parkinson [mailto:park...@ebi.ac.uk]
Sent: Wednesday, September 30, 2009 5:00 PM
To: Bjoern Peters
Cc: Fostel, Jennifer (NIH/NIEHS) [C]; OBI Developers
Subject: Re: [Obi-devel] competency questions

> -------- Come build with us! The BlackBerry&reg; Developer Conference

[Philippe Rocca-Serra]

Hi Frank,

I guess OBI has no clinical trial process due to the fact OCI was being
developed in parallel, we were probably thinking to rely on this effort.
Now things have moved on so it is certainly time to reorganize some of
the resource.
During a recent call, this topic was brought up and resources such as
OCRE should also be evaluated.
OBI needs to be able to tell when a study falls in the realm of clinical
trial or not, and what makes a study a clinical trial.

Jennifer, thanks for putting together these competency questions, these
are spot on. I am with you on the dose regimen, this is critical. We
need to be able to understand whether it was a single dose treatment or
repeated administration. Talking of which, having access to the
quantitative dose is one thing but does not tell the whole story.

how can we efficiently answer the following questions also matters to me.
What is the intended toxic/subtoxic doses,
What are the high, medium and lose dose?
Was it a chronic toxicity study ?
Was as is acute toxicity study ?

great work.

P

> <mailto:Obi-...@lists.sourceforge.net>

> <mailto:Obi-...@lists.sourceforge.net>

> > https://lists.sourceforge.net/lists/listinfo/obi-devel
> >
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year.
> Jumpstart your
> developing skills, take BlackBerry mobile applications to market
> and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register
> now&#33;
> http://p.sf.net/sfu/devconf
> _______________________________________________
> Obi-devel mailing list
> Obi-...@lists.sourceforge.net

> <mailto:Obi-...@lists.sourceforge.net>

> https://lists.sourceforge.net/lists/listinfo/obi-devel
>
>
>
>
> --
> Frank Gibson, PhD
> http://peanutbutter.wordpress.com/

> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
> is the only developer event you need to attend this year. Jumpstart your
> developing skills, take BlackBerry mobile applications to market and stay
> ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
> http://p.sf.net/sfu/devconf
> ------------------------------------------------------------------------
>
> _______________________________________________
> Obi-devel mailing list
> Obi-...@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/obi-devel
>

--
Philippe Rocca-Serra, PhD

Technical Coordinator
www.ebi.ac.uk/net-project

The European Bioinformatics Institute email: ro...@ebi.ac.uk
EMBL Outstation - Hinxton direct: +44 (0)1223 492 553
Wellcome Trust Genome Campus fax: +44 (0)1223 492 620
Cambridge CB10 1SD, UK room: A3-141
--

[Fostel, Jennifer (NIH/NIEHS) [C]]

Thanks, Philippe!

i totally agree about the intended dose range; the competency questions i developed were those related to this paper, which had only one dose, and i did not see a dose justification but will look for it again.

i think we should develop general competency questions for a tox study, and yours would be important to include.

re OCI -- Richard and I were nominally co-chairing an effort to add clinical terms on a structure parallel to OBI, but the effort dwindled as Richard and others stopped attending the calls. OCRE sounds like a good alternative, and Richard is involved in that as well, i understand.

-----Original Message-----
From: Philippe Rocca-Serra [mailto:ro...@ebi.ac.uk]
Sent: Friday, October 02, 2009 1:34 PM
To: Frank Gibson
Cc: OBI Developers
Subject: Re: [Obi-devel] competency questions

Hi Frank,

great work.

P

> -------- Come build with us! The BlackBerry&reg; Developer Conference

> in SF, CA is the only developer event you need to attend this year.
> Jumpstart your developing skills, take BlackBerry mobile applications
> to market and stay ahead of the curve. Join us from November 9&#45;12,
> 2009. Register now&#33; http://p.sf.net/sfu/devconf
> ----------------------------------------------------------------------
> --
>

[Bjoern Peters]

Just a reminder to all: Our goal is to complete the modeling of this use case this week. Everything else is ready, or could be dealt with in the clean up meeting. So I want to ask everyone to distinguish in their suggestions if they believe we need to model this specifically for the paper, or if they are requirements we should be able to deal with in a future version of OBI.

- Bjern

[Fostel, Jennifer (NIH/NIEHS) [C]]

i plan to use the call today to decide which aspects of this use case we can model with OBI today, and which will be deferred for future versions.  we are already deferring "assays involving measureing time for something to happen" (in the queue along with "assays to determine number of things" such as cell counts)

 

in the original presentation of the use case we showed (1) planning the study (2) enrolling volunteers (3) measuring baseline values of AT-III (4) taking the treatments daily for 12 days (5) colelcting assay data on day 12 from each subject (6) carrying out data transformations to produce a summary for each group (7) drawing a conclusion (8) publishing the paper.  it would be great if we could achive modeling this progression using OBI.

---

From: Bjoern Peters [mailto:bpe...@liai.org]

Sent: Monday, October 05, 2009 11:23 AM
To: Fostel, Jennifer (NIH/NIEHS) [C]
Cc: OBI Developers; Philippe Rocca-Serra; Frank Gibson