Tag Archives: data management

Count the number of discrepancies per procedure – OracleClinical (OC)

Let’s now write a quick program to count the number of discrepancies per procedure in OC/OCRDC:

Remember to comment /**/ or ***comment here*; what the program does. It is a good clinical practice to document everything so anyone can read your program and make the necessary updates, if necessary.

proc sql;
connect to oracle(path=ocpath);
create table discr as select * from connection to oracle
(Select  p.name, pd.test_order_sn detail, count(pd.test_order_sn) count, p.procedure_id procid
from discrepancy_management dm,
procedures p,
procedure_details pd
where dm.clinical_study_id=9999
and dm.procedure_id = p.procedure_id
and dm.procedure_detail_id=pd.procedure_detail_id
and p.PROCEDURE_VER_SN=pd.PROCEDURE_DETAIL_PROC_VER_SN
and dm.PROCEDURE_VER_SN=p.PROCEDURE_VER_SN
and dm.de_sub_TYPE_CODE=’MULTIVARIATE’
group by p.name, pd.test_order_sn, p.procedure_id
order by count(p.name)desc
);
/*document your code*/
proc sql;
connect to oracle(path=ocpath);
create table name as select * from connection to oracle
(select distinct p.procedure_id procid, p.name, pd.TEST_ORDER_SN detail
from  procedures p,
procedure_details pd
where p.clinical_study_id= 9999 *replace with your studyid;
and p.procedure_status_code !=’R’
and p.procedure_id=pd.procedure_id
order by procid
);
quit;

/* merge # of discrepancies with name */
proc sort data=discr;
by procid;
run;

proc sort data=name;
by procid;
run;

data discname;
merge discr (in=d) name (in=n);
by procid;
if n;
run;

proc sort data=discname ;
by descending count ;
run;

/* print out  */
proc print data=discname label;
var name numdisc percent numdcf;
label numdisc = ‘Number of discrepancies’
numdcf = ‘Number of DCFs’;
title “Number of discrepancies per Procedure”;
title2 “RA eClnica”;
run;

You could also export the report to Excel xls and have your DM / data manager review it.

Good luck and let me know if it was helpful.

To hire me for services, you may contact me via Contact Me OR Join me on LinkedIn

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Case Study 2: Supporting the Sponsor with Database Transfer Solution

Assisting the Sponsor with Database Transfer Solution

Anayansi gamboa - Data Management Support @RAeClinica

 

 
The Scenario:

The Sponsor required a large safety and data management team to assist for a submission deadline requiring the transfer of data to a new safety database for clinical trials and post-marketed products.
RA eClinica Solution:

    • RA eClinica responsible for AE/SAE reporting, safety coding, NDA submission support
    • RA eClinica collaborated with the Sponsor’s safety team to develop a functional safety alliance consisting of over 10+ team members inclusive of management, safety and data management resources
    • Ra eClinica team is responsible for managing over 5+ compounds

Ra eClinica Results:

    • RA eClinica project team exceeded the timelines, completing the tasks approximately 30-days ahead of schedule
    • RA eClinica management collaborate with the Sponsor to redefine operational workflow and processes in order to increase efficiencies across several departments (Quality Control, Pharmacovigilance)

RA eClinica is a established consultancy company for all essential aspects of statistics, clinical data management and EDC solutions. Our services are targeted to clients in the pharmaceutical and biotech sector, health insurers and medical devices.

The company is headquarter in Panama City and representation offices with business partners in the United States, India and the European Union. For discussion about our services and how you can benefit from our SMEs and cost-effective implementation CDISC SDTM clinical data click here.

WBS: Brainstorming session on Product Development

The following activities were listed during a brainstorming session on product development:

ID Task Description Task Name Duration (weeks) Predecessors
1 Organize the office: Hire manager. a 6
2 Hire personnel: The manager will recruit and hire the people needed. b 4 A
3 Train personnel: Train the people hired to sell the product to the distributors. C 7 B
4 Select advertising agency: The manager will select the agency best suited to promote the new product. D 2 A
5 Plan advertising campaign: The office and advertising agency will jointly plan the advertising campaign to introduce the product to the public. E 4 D,c
6 Conduct advertising campaign: Theadvertisingagency will conduct a “watch for” campaign forpotential customers. F 10 E
7 Design package: Have packaging engineer design the package most likely to “sell.”  G 2 F
8 Set up packaging facility: Prepare to package the products when they are received from the manufacturer.  H 10 G
9 Package initial stocks: Package stocks received from the manufacturer. I 6 H,j
10 Order and receive stock from the manufacturer:Order the stock from the manufacturer.The time given includes the time for delivery. j 13 H
11 Select distributors: The manager will select the distributors whom the people will contact to make . k 9 a
12 Sell to distributors: Take orders from the distributors for the new product, with delivery promised for the product-introduction date. If orders exceed stock, assign stock on a quota basis. l 6 K,i
13 Ship stock to distributors: Ship the packaged stock to distributors in accord with their orders or quota. m 6 l

 

anayansi gamboa AON network

AON network

The critical path starts with task “a” and follows: a-b-c-e-f-g-h-i-j-l-m. The PM cannot allow any delay in any of those tasks because that will lead to a direct delay of the whole project. This is quite long critical path so that might be one of the problems that the PM will face.

One of the advantages for the PM might be the handling of tasks “d” and “k”.

Those are non-critical path tasks and they can be delayed. Task “d” has a slack of 15 weeks (LFT-EFT=17-2=15). Task “l” has a lot larger slack of 40 weeks (LFT-EFT=62-9=53). The PM can use the two slacks and complete the tasks “d” and “l” later that they require so that the PM can use the resources needed for those two tasks to complete tasks from the critical path. This is one of the ways to complete the project earlier, if the interconnections of the different tasks are not taken into account.

What managerial problems and opportunities do you see as a result of your work? what can you tell about the slack?

Comments? Join us at {EDC Developer}

Anayansi Gamboa, MPM, an EDC Developer Consultant and clinical programmer for the Pharmaceutical and Biotech industry with more than 13 years of experience.

Available for short-term contracts or ad-hoc requests. See my specialties section (Oracle, SQL Server, EDC Inform, EDC Rave, OpenClinica, SAS and other CDM tools)

As the 3 C’s of life states: Choices, Chances and Changes- you must make a choice to take a chance or your life will never change. I continually seek to implement means of improving processes to reduce cycle time and decrease work effort.

Subscribe to my blog’s RSS feed and email newsletter to get immediate updates on latest news, articles, and tips. I am available on LinkedIn. Connect with me there for technical discussions.

OpenClinica: Printing subject casebooks, blank casebooks and blank CRFs

Wanna print subject casebooks using OpenClinica? This article is an extract from a video demo from the OpenClinica blog website. Click the link below now.

Source: http://blog.openclinica.com/2014/10/06/video-demos-printing-subject-casebooks-blank-casebooks-and-blank-crfs/

Happy Printing!!!

 

Fair Use Notice: This video contains some copyrighted material whose use has not been authorized by the copyright owners. We believe that this not-for-profit, educational, and/or criticism or commentary use on the Web constitutes a fair use of the copyrighted material (as provided for in section 107 of the US Copyright Law. If you wish to use this copyrighted material for purposes that go beyond fair use, you must obtain permission from the copyright owner. Fair Use notwithstanding we will immediately comply with any copyright owner who wants their material removed or modified, wants us to link to their website or wants us to add their photo.

The EDC Developer blog is “one man’s opinion”. Anything that is said on the report is either opinion, criticism, information or commentary, If making any type of investment or legal decision it would be wise to contact or consult a professional before making that decision.

Disclaimer:De inhoud van deze columns weerspiegelen niet per definitie de mening van {EDC Developer}.

Society of the Sojourner

Dear Readers,

Please accept our apologies for having ”dropped off the planet earth” during the last 6 months, with not producing any new posts on this blog.

Due to circumstances beyond our control, we here, at EDC Developer, do hope that you have not given up on reading us…

Actually, in some ways…we did go ”off road”…

More details about this will be coming very soon …

In the meantime, please accept, a small ”heads-up” :

Somewhere within, and, underneath …one of SWITZERLAND`S Mountains … :

Fair Use Notice: This video contains some copyrighted material whose use has not been authorized by the copyright owners. We believe that this not-for-profit, educational, and/or criticism or commentary use on the Web constitutes a fair use of the copyrighted material (as provided for in section 107 of the US Copyright Law.) If you wish to use this copyrighted material for purposes that go beyond fair use, you must obtain permission from the copyright owner. Fair Use notwithstanding we will immediately comply with any copyright owner who wants their material removed or modified, wants us to link to their website or wants us to add their photo.

Disclaimer: The EDC Developer blog is “one man’s opinion”. Anything that is said on the report is either opinion, criticism, information or commentary. If making any type of investment or legal decision it would be wise to contact or consult a professional before making that decision.

Disclaimer:De inhoud van deze columns weerspiegelen niet per definitie de mening van {EDC Developer}.

Central Designer – Troubleshooting Tips

If an edit check or function fails to behave as expected, it is time to use your ‘troubleshooting’ skills. The following tips may help you when you are troubleshooting rules in InForm:

Rules:

  • check if rules are running
  • check the rule logic
  • check Rule Dependencies: a rule on a form has access to items on that form, but not other forms or other visits
  • check InForm machine’s Application Event Log

Though some vendors will correct major problems with their products by releasing entirely new versions, other vendors may fix minor bugs by issuing patches, small software updates that address problems detected by users or developers.

Check the release notes for Central Designer for known problems. The release notes provide descriptions and workaround solutions for known problems.
Remember that there is a report available you can run “Data Entry Rule Actions Report”. This report outputs all data entry rules in CSV format and can be formatted into an edit check specification documentation for QA testing.
A rule can be written in more than one way, which makes it difficult to impose any restrictions:
Scenario: Route item has 3 choices. OP, SC and IV. Query should fire if the user does not choose either OP or SC. This rule could be written in many ways:

–Value = route.Value

If (value == 3)

–Value = route.Value == 3

If (value == true)

–Value = !(route.Value == 3)

If (value == false)

–Value = (route.Value == 1 || route.Value == 2)

If (value == false)

–Value = route.Value !=1 && route.Value != 2

If (value == true)

Keep it consistent across the trial. Do not overuse the conditional statements when a simple range check should be program.

Note: Be aware that if you want to reuse a rule that uses data from a logical schema in another study, the other study must also contain the logical schema.

If you have explored most of the obvious possibilities and still
cannot get your rule / edit check to work, ask someone in your team to peer review the build.

 

  • unit test your code
  • context available for defining test cases
  • Site name, date/time, locale; Form associations; Empty values; Unknown dates; Repeating objects
  • test case results: Pass or Fail based on expected results
  • perform formal QA / QT

Remember to check the Event log via Control Panel -> Administrative Tools -> Event Viewer

Reference Document : Central Designer – Rule Troubleshooting.pdf

Your comments and questions are valued and encouraged.
Anayansi Gamboa has an extensive background in clinical data management as well as experience with different EDC systems including Oracle InForm, InForm Architect, Central Designer, CIS, Clintrial, Medidata Rave, Central Coding, OpenClinica, Open Source and Oracle Clinical.

Data Management Plan in Clinical Trials

 

The preparation of the data management plan (DMP) is a simple, straightforward approach designed to promote and ensure comprehensive project planning.

The data management plan typically contains the following items. They are:

  1. Introduction/Purpose of the document
  2. Scope of application/Definitions
  3. Abbreviations
  4. Who/what/where/when
  5. Project Schedule/Major Project Milestones
  6. Updates of the DMP
  7. Appendix

The objective of this guidelines is to define the general content of the Data Management Plan (DMP) and the procedures for developing and maintaining this document.

The abbreviation section could include all acronyms used within a particular study for further clarification.

e.g. CRF = Case Report Form
TA = Therapeutic Area

The Who/What/Where/When section should describe the objective of the study specific data management plans for ABC study. This section provides detail information about the indications, the number of subjects planned for the study, countries participating in the clinical trial, monitoring guidelines (SDV) or partial SDV, if any CROs or 3rd party are involved in the study (e.g. IVRS, central labs), which database will be used to collect study information (e.g. Clintrial, Oracle Clinical, Medidata Rave or Inform EDC).

The Appendix provides a place to put supporting information, allowing the body of the DMP to be kept concise and at more summary levels. For example, you could document Database Access of team members, Self-evident correction plan, Data Entry plan if using Double-data entry systems or Paper-Based clinical trials systems.

Remember, this is a living document and must be updated throughout the course of the clinical trial.

If problems arise during the life of a project, our first hunch would be that the project was not properly planned.

Reference: Role of Project Management in Clinical Trials
Your comments and questions are valued and encouraged.
Anayansi Gamboa has an extensive background in clinical data management as well as experience with different EDC systems including Oracle InForm, InForm Architect, Central Designer, CIS, Clintrial, Medidata Rave, Central Coding, OpenClinica, Open Source and Oracle Clinical.

To hire me for services, you may contact me via Contact Me OR Join me on LinkedIn

Disclaimer: The legal entity on this blog is registered as Doing Business As (DBA) – Trade Name – Fictitious Name – Assumed Name as “GAMBOA”.

CDISC Clinical Research “A” Terminology

acronym: A word formed from the beginning letters (e.g., ANSI) or
a combination of syllables and letters (e.g., MedDRA) of a name or phrase.
admission criteria:Basis for selecting target population for a clinical trial.
Subjects must be screened to ensure that their characteristics match a list of admission criteria and that none of their characteristics match any single one of the exclusion criteria set up for the study.
algorithm: Step-by-step procedure
for solving a mathematical problem;
also used to describe step-by-step
procedures for making a series of
choices among alternative decisions to
reach a calculated result or decision.
amendment: A written description
of a change(s) to, or formal clarification
of, a protocol.
analysis dataset:An organized collection of data or
information with a common theme arranged in rows and columns and
represented as a single file; comparable to a database table.
analysis variables: Variables used
to test the statistical hypotheses
identified in the protocol and analysis
plan; variables to be analyzed.
approvable letter:An official communication from FDA to an
NDA/BLA sponsor that lists issues to be resolved before an approval can be issued.
[Modified from 21 CFR 314.3;Guidance to Industry and FDA Staff

arm: A planned sequence of elements,
typically equivalent to a treatment
group.

attribute (n): In data modeling,
refers to specific items of data that can
be collected for a class.
audit:A systematic and independent
examination of trial-related activities
and documents to determine whether
the evaluated trial-related activities were
conducted and the data were recorded,
analyzed, and accurately reported
according to the protocol, sponsor’s
standard operating procedures (SOPs),
good clinical practice (GCP), and the
applicable regulatory requirement(s).
[ICH E6 Glossary]
audit report: A written evaluation by
the auditor of the results of the audit.
[Modified from ICH E6 Glossary]
audit trail. A process that captures
details such as additions, deletions,
or alterations of information in an
electronic record without obliterating the original record. An audit trail
facilitates the reconstruction of the
history of such actions relating to the
electronic record.

Source:Applied Clinical Trials

Anayansi Gamboa has an extensive background in clinical data management as well as experience with different EDC systems including Oracle InForm, InForm Architect, Central Designer, CIS, Clintrial, Medidata Rave, Central Coding, OpenClinica Open Source and Oracle Clinical.

Assigning Libraries to Access and Store SAS® Data

Use SAS learning software to learn how to assign libraries to access and store SAS data.

-FAIR USE-
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Source: http://support.sas.com/learn/ondemand/professionals

Clinical Trials Terminology for SAS Programmers

Entry Level SAS Programmers

Statistical Programmer:requires him to program using the SAS language to analyze clinical data and produce reports for the FDA

Bioanalyst, Clinical Data Analyst, Statistical Programmer Analyst and SAS Programmer: same as Statistical programmer.

Biotechnology:companies which is a general term used to explain a technique of using living organisms within biological systems to develop micro-organisms for a particular purpose.

protocol:outlined all the procedures and contained detailed plans of the study.

controlled experiment: the clinical trial had patients grouped into different groups such as those in the placebo controlled group which had no active drug. This is how comparisons are made within the controlled clinical trial CFR Part 11:Code of Federal Regulations set by the FDA to regulate food, drug, biologics and device industries. The part 11 specifically deals with the creation and maintenance of electronic records.
Case Report Form or CRF:forms to collect information such as demographic and adverse events. Source Data or the information collected:which include important documents because they contain the core information required to reconstruct the essential capital of the study.
sponsor:company who is responsible for the management, financing and conduct of the entire trial. randomized: subjects that are randomly assigned to groups so that each subject has an equal chance to be assigned to the placebo control
baseline: subjects are assigned to their drug change from baseline:analyses that measure differences between baseline and current visit
placebo or sugar pill:is an inactive substance designed to look like the drug being tested. blinded:they do not know if the drug that they are taking contains the active ingredient.
open-label study:all was out in the open, the drug the subject is assigned to. Pharmacokinetics or PK:analysis of that study showed that with that dosing level, there were high levels of toxicity in the subject.
informed consent: described all the potential benefits and risks involved. TLGs: Tables, Listings and Graphs
trade name:drug name that is collected from the patient and recorded into the source data. For example: Tylenol generic name: refers to its chemical compound. For example: Acetaminophen.
WHO-DRUG: list all the drug names and how they matched to the generic drug names.This dictionary is managed by the World Health Organization MedDRA:This is short for Med (Medical), D (Dictionary), R (Regulatory), and A (Activities).
SAP: Statistical Analysis Plan ANOVA: analysis of variable
confidence interval:gives an estimated range of values being calculated from the sample of patient data that is currently in the study. null hypothesis:lack of difference between the groups in a report
pilot study:perform the same analysis upon an older. DIA: Drug Information Association
CBER: Center for Biologics Evaluation and Research (medical device) CDER: Center for Drug Evaluation and Research (drug)

Source:CDER Acronym List


Anayansi Gamboa has an extensive background in clinical data management as well as experience with different EDC systems including Oracle InForm, InForm Architect, Central Designer, CIS, Clintrial, Medidata Rave, Central Coding, OpenClinica Open Source and Oracle Clinical.