Mohammad Al-Ubaydli’s blog

Genomic electronic health records: opportunities and challenges

Posted in Articles, Medicine, My publications, Society, Technology by Dr Mohammad Al-Ubaydli on July 22, 2009

This article was originally published in Genome Medicine on 23rd July 2009 at

Mohammad Al-Ubaydli1 email and Rob Navarro2

1UCL Centre for Health Informatics and Multiprofessional Education, Archway Campus, Highgate Hill, London N19 5LW, UK

2Sapior, 16 Byron Avenue, London E18 2HQ, UK

author email corresponding author email

Genome Med 2009, 1:73doi:10.1186/gm73

The electronic version of this article is the complete one and can be found online at:

Published: 22  July  2009

© 2009 BioMed Central Ltd


There is value to patients, clinicians and researchers from having a single electronic health record data standard that allows an integrated view, including genotype and phenotype data. However, it is important that this integrated view of the data is not created through a single database because privacy breaches increase with the number of users, and such breaches are more likely with a single data warehouse. Furthermore, a single user interface should be avoided because each end user requires a different user interface. Finally, data sharing must be controlled by the patient, not the other end users of the data. A preferable alternative is a federated architecture, which allows data to be stored in multiple institutions and shared on a need-to-know basis. The data sharing raises questions of ownership and stewardship that require social and political answers, as well as consideration of the clinical and scientific benefits.

In the May issue of Genome Medicine, Belmont and McGuire [1] make the case for a ‘uniform electronic health record’ (EHR) that includes both genotype and phenotype information. By uniform they mean a single data standard across different EHR databases and user interfaces, rather than a single database or a single user interface (this has been confirmed by personal communication with the authors).

It is certainly true that a clearer picture of a patient’s health is possible when their genotype data are combined with phenotype data. The quantity and quality of these data are improving, along with the analytical tools that allow us to interpret them. Patients, clinicians and researchers can all benefit from a better understanding of these data, and Belmont and McGuire’s article [1] describes efforts in Europe and the USA to unify the datasets.

However, other parties that would benefit from better understanding include public health officials, government bureaucrats, insurance companies and employers. And in some cases, there are conflicts of interest; for example, an insurance company could use genetic information to raise premiums or deny cover, whereas a patient might use the same information to seek increased cover when they learn of the risk for future diseases.

There are ways to solve the conflicts of interest that can arise from the use and availability of patient data. First, as Belmont and McGuire [1] describe, efforts such as the Personal Genome Project [2] allow patients to opt in to fully disclose their genetic information for the benefit of researchers. [3] has an openness policy alongside their privacy policy so that participants can agree to share all their data, and tens of thousands of people from around the world have already agreed to do so. The value to researchers is currently limited because the data are self-submitted rather than independently verified, but the proof that patients are willing to share their personal information is there.

The principle must still stand, however, that data sharing begins with and is controlled by the patient. This favors a single personal health record (PHR) as a database rather than a single electronic health record. PHRs are records owned and controlled by the patient [4] , as opposed to EHRs, which are owned and controlled by health care practitioners.

Useful data standards for PHR and EHR communication should be expanded to fit the genomic vision that Belmont and McGuire [1] outline. In particular, the Continuity of Care Record (CCR) data format is the digital equivalent of a referral letter from one clinician to another about a patient [5] . It is supported by PHR providers such as Google Health and Microsoft HealthVault; pharmacies such as Walgreens and CVS; and providers such as MinuteClinic [6] . The Department of Health and Human Services at the National Cancer Institute unveiled a standard earlier this year for family history [7] . However, a single genomic data standard is not yet available or widely adopted.

Second, de-identification algorithms that work for genotype data are needed. De-identification is a better term than anonymization because the latter implies a binary process, which is misleading, while the former accurately conveys a spectrum. We know that de-identification algorithms are already in use when the public interest demands phenotype sharing but patient consent is not possible or practicable. Examples include notifiable disease surveillance, public health planning and large-scale research. In these cases, looking after the patient’s privacy requires measures that ensure they cannot be identified through illicit use of those data. But de-identification algorithms for genotype data are not mature enough.

Re-identification becomes more likely as the number of users increases. Illicit patient re-identification has three sources of risk: the research team, all other people who have access to these data and finally the inherent readability of the data itself [8] . Building a single system to be accessed by hundreds or thousands of researchers across tens or hundreds of projects is simply inconsistent with minimizing these three sources of risk. Such systems can therefore never be adequately private.

What might work, when public interest demands but consent is not possible, are schemes that separately copy just the minimum of phenotype and genotype data from various health management systems for a specific group of vetted researchers working within a highly protective legal context. Any change in project purpose would necessitate a re-assessment of the prevailing risks. A system in which highly vetted organizations were permitted to collect and link minimal data from all its various sources would be ideal.

In addition, the architecture for a single EHR or PHR is not a simple one. It is desirable and correct to view all the relevant data at the time of making a clinical decision or coming to a research conclusion. However, that does not mean all the data should be viewable.

For the person viewing the data, their storage in a single place does mean faster access and allows data normalization. But for the people whose data are viewed, such a data warehouse is ripe for abuse. Citizens have expressed their distrust of such systems on many occasions [9] , and security experts have repeatedly pointed out the risks of data warehouses [10] . Federated architectures, where data are spread across multiple sites and queried as needed, have been deployed [11] and are made easier by new approaches, such as service-oriented architecture. And knowing how much protection to put in place is made easier by couching privacy concerns in terms of the risk of illicit patient re-identification.


All of the above discussion is not to say that a single EHR is a bad idea. Belmont and McGuire [1] make a good case for the need to unify data in the service of laudable aims, including providing good patient care and advancing medical research. However, just because something can be done does not mean that it should be done, and in health care it is patients who should decide what should be done. They will be the most affected by privacy breaches, so they must be the ones who decide which of the benefits to take advantage of. The danger is when professionals confuse their convenience with the benefit of patients. The good news is that mature technologies exist that do put patients in control. As professionals we need to earn their trust by using these technologies when we ask for data sharing that makes our jobs easier.


EHR: electronic health record; PHR: personal health record.

Competing interests

MA is the CEO of Patients Know Best, a company that makes and sells personal health record software. RN is the CEO of Sapior, a company that makes and sells de-identification software for the private sharing of health data.

Authors’ contributions

MA wrote the sections on personal health records and RN wrote those on de-identification.


  1. Belmont J, McGuire A The futility of genomic counseling: essential role of electronic health records.

    Genome Med 2009, 1:48. PubMed Abstract | BioMed Central Full Text | PubMed Central Full Text OpenURL

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  2. Personal Genome Project []


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  3. PatientsLikeMe []


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  4. Markle Foundation: Connecting for Health []


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  5. Continuity of Care Record Standard []


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  6. Medpedia: Continuity of Care Record (CCR) Standard [ Standard]


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  7. Cancer Biomedical Informatics Grid []


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  8. Navarro R An ethical framework for sharing patient data without consent.

    Inform Prim Care 2008, 16:257-262. PubMed Abstract | Publisher Full Text OpenURL

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  9. McKie Robin Icelandic DNA project hit by privacy storm. [,6903,1217842,00.html]

    The Observer 2004. OpenURL

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  10. Anderson R, Brown I, Dowty T, Inglesant P, Heath W, Sasse A: []

    Database State.York: Joseph Rowntree Reform Trust; 2009. OpenURL

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  11. Gruman G Massachusetts takes a spoonful of SOA. []

    InfoWorld 2005. OpenURL

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Bahrain should Adopt Open Source Electronic Medical Records

Posted in Medicine, My publications, Peer-reviewed papers, Technology by Dr Mohammad Al-Ubaydli on December 1, 2008

This paper was published as an editorial in the December 2008 issue of Bahrain Medical Bulletin.

Mohammad Al-Ubaydli, MB, BChir, MA, Cantab. Honorary Senior Research Associate, University College London, UK. E-mail

Bahrain should Adopt Open Source Electronic Medical Records

As Bahrain begins the switch to electronic medical records the use of open source software becomes increasingly important. Without it, the country’s public health data is at the mercy of private companies, local young innovators are unable to contribute solutions, and the citizens’ fears about how data is used will lead to patients withholding information from their doctors.

However, with open source software, the country gains the accountability from its vendors, locally-led solutions to our health problems can emerge, and all of us as patients can trust the health care system with the safety of our records.

Open source software is software for which the source code is openly available for inspection and reuse. Inspection of the source code in software development is equivalent to peer review in medicine and science. It is the best way to critique software, ensure honesty and improve quality.

The reusability of the software also decreases costs. This is not just because the software is available free of charge but rather because the creators of closed source software keep on reinventing the wheel. They keep on spending money to write parts of their new software that have already been written by other programmers around the world. In addition, they pass on those costs to the end customer.

Perhaps the best illustration for why Bahrain should adopt open source software is Britain’s experience with closed source software in the National Health Service. The government’s aim was to bring the benefits of electronic medical records to all UK citizens.

Starting in 2002 the UK government began what was arguably the most complex and best-funded IT project in the world. Companies from all over the world were keen on winning the contracts because of their size and prestige. Richard Granger was recruited and became the most highly paid civil servant, earning £100,000 more than Prime Minister Tony Blair does. The government did this because it wanted the best possible controls over the delivery of the software by the private contractors.

Moreover, the government remains at the mercy of the contractors. Initially only iSoft won three of the five regions in England, and General Electric (GE) won two. Soon, problems with GE’s deployment meant that it had to give up one of its regions and Cerner took over that contract. Of course each company brings its own proprietary closed source software and reusing existing software is not possible. Meanwhile problems and delays continue. The government is unlikely to get other companies to fix future problems because the pool of companies is so small and the problems have been so large. How would the Bahraini government be able to avoid these problems?

It is noteworthy that most of the contracts have been won by American companies. Microsoft, Cerner, Accenture, GE, CSC are but few, and British companies like BT and iSoft are in the minority, until iSoft itself was bought by an Australian company. It is right for the government to demand the best software from the best companies around the world but the insistence on large contracts of closed source software has locked out much of Britain’s previously vibrant health care IT industry. Companies like EMIS publicly expressed their frustration at their inability to participate even though they had the largest market share of software for General Practitioners.

Meanwhile many start-ups in the UK had to refocus their efforts on selling outside the UK as they are barred from integrating their software to the closed source of the winners of the large contracts. How would the Bahraini government be able to support local innovators?

Finally, the transparency in the governance of medical records is crucial. In the UK original plans were to allow medical records to travel from any doctor’s medical record’s system to the central database, and then to any NHS doctor. Patients felt that they had lost control over the data, and letters to newspapers expressed citizens’ distrust of the security controls. After all there was no way of inspecting the source code of the software that transferred the data to ensure that it does so securely, much less give the patient control over the transfer of the data. Some patients began refusing to tell their doctors about some of their illnesses because they feared the loss of control. A key part of patient-doctor confidentiality had been broken. How would the Bahraini government reassure its citizens?

Open source software offers a simple and cost-effective solution. Open source electronic medical records software tools are available free of charge. For example, VistA (the Veterans Health Information Systems and Technology Architecture) was created by the U.S. Department of Veterans Affairs (VA) as far back as 1982 to support the care of U.S. veterans and is the world’s most widely deployed and carefully tested Electronic Health Record systems (EHR)1. Versions of this system are in active use in the U.S. Department of Defense Military Health System, the U.S.

Department of Health and Human Services Indian Health Service, and internationally as well, e.g., Mexico – Instituto Mexicano del Seguro Social, Berlin Heart Institute of Germany, and National Cancer Institute of Cairo University in Egypt.

Using the software would transform Bahrain’s efforts. Contractors could bid for how well they deploy and support the software. If there are problems, as there were with closed source software contractors in the UK, it would be easy to replace them by others who would provide better services. Local innovators would also be encouraged. First, Bahraini programmers could learn from the best in the world because they could study the source code free of charge. Second, they would be able to build solutions on top of VistA without needing the permission of contractors. A suite of localized solutions could emerge, and Islamic-friendly software could be exported to other Muslim countries that have the same aspects to the delivery of medical care. Finally, the problem of transparency would be solved. When a government minister in the UK says that NHS software is safe, there is no way to confirm the accuracy of his or her statements. Nevertheless, open source software could be inspected and tested for these claims. Not every citizen has to be a programmer for this to be the case, but the programmers in our midst could carry out the tests for their fellow citizens.

Surely we all deserve these benefits as we embrace the future with open source arms.


1. VistA ( is open source medical software made by the U.S. Department of Veterans Affairs (VA), as opposed to Windows Vista the closed source operating system software made by Microsoft.

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Using Ajax for Cleaner Software

Posted in Articles, Medicine, My publications, Technology by Dr Mohammad Al-Ubaydli on November 22, 2008

Published in UK Health Informatics Today Autumn 2008 edition.
Mohammad Al-Ubaydli, MB BChir Cantab
Founder, Patients Know Best –

Ajax is a new web programming technology that solves an old conflict between CIOs and clinicians and eases the use of innovative devices in large organizations.

For IT staff, managing a single server with web browser-based clients is much easier than installing client software on every single computer that clinicians use. But for clinicians, web browser client software is too slow and simple: only clients installed locally on a Windows machine provide the responsive and rich user interface needed for consultations with patients.

Traditionally, this conflict was settled in favour of the clinician. Staff from the IT department had the Sisyphean task of installing software onto every computer, and no sooner had they completed one round before the next one began with a newer version of the software. Furthermore, local software stored data locally, requiring strong security protocols on each computer.

Ajax can end this cycle. It allows web browser-based clients that are fast and powerful in their response to server software, which the IT department may now focus on managing. Ajax is an acronym for Asynchronous JavaScript and XML. XML is the data that is exchanged between client and server, and JavaScript is the browser-based programming language that is powerful enough to support complex user interfaces.

Asynchronous is the clever and recent innovation; it allows the browser to only update the part of the screen that is relevant to the user’s most recent interaction. In other words, rather than redrawing the entire page in response to a user’s click, the web browser can redraw only the relevant part in an Ajax-driven page. The rest of the page can continue to function asynchronously as the XML arrives for the part that the JavaScript is changing.

The release of Google Maps in 2005 was a watershed event in showing the world what Ajax could do. The technology had been in place since 1999 when Microsoft introduced the XMLHttpRequest programming object for asynchronous communication in Internet Explorer, and soon afterwards Mozilla and Opera followed suit with support in their own web browsers. However, few sites made use of the technology and few users understood its significance. But with Ajax, maps on Google’s website loaded quickly and scrolled even more quickly. By contrast, existing map sites had to reload the entire page with each click by the user.

Slowly, mainstream healthcare software developers are integrating this approach into their products. Naturally, it is startups that are first to do so, companies like Tolven Health and Net.Orange. From my conversations with the executives of larger, more entrenched companies, they too are making the switch.

Just as significantly, it is easier to deploy innovative devices because most of them support Ajax in their web browser. Apple’s iPhone, for example, was notorious among developers because the first version only accepted Ajax software. The web browsers of most new smartphones also support Ajax.

This means that clinicians can use operating systems other than Microsoft Windows, something that has so far held back deployments in the NHS.

The switch to Ajax does have security implications. On the one hand, Ajax-powered thin client software is more secure than locally installed thick-client software because the data is only stored on one central server for which security can be maximized. But the ubiquity of the web means developers must abandon previously tolerated but inherently insecure practices.

Most significantly, state data must only be stored on the server, not the clients. Examples of state data include the fact that the end user is a doctor or the identification number of the patient they are looking; these must be maintained centrally even if they are temporarily displayed on a local web browser. Programs that do not have this architecture leave themselves open to manipulation at the local computer level. For example, a malicious end user may easily identify and manipulate their state data by editing the local cache file to identify him- or herself as a doctor.

Such vulnerabilities were always possible with old, thick-client computing models. Security through obscurity made this tolerable because each program had its own security model and fragmented market share. By contrast, the web is much more transparent and information about vulnerabilities is shared
quickly and comprehensively.

If you are working with an experienced programmer who is new to Ajax, the risk is that such a programmer would assume that programming in the web environment is the same as working with Windows. A simple explanation of this vulnerability is typically enough to enable a change in programming habits.

Such changes in habits are well worth the effort. The end results are software that is cleaner to deploy and manage as well as increases in the productivity of IT staff –things from which we can all benefit.

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BabelMeSH and PICO Linguist in Arabic

Posted in Arabs and Arabic, Medicine, My publications, Peer-reviewed papers, Technology by Dr Mohammad Al-Ubaydli on November 10, 2008

For AMIA 2008, Dr. Paul Fontelo and colleagues presented this poster.

BabelMeSH is a multilanguage search for MEDLINE/PubMed. We created a database of Arabic translations of MeSH terms and other medical terms using MySQL and developed a Web interface for searching MEDLINE/PubMed in Arabic. We evaluated the accuracy of BabelMeSH using a list of medical terms from BMJ Clinical Evidence.  The accuracy was 58% (machine scoring) and 65% human review.) The result obtained may be explained by variations in expressing medical terms in Arabic.

My name is down as one of the authors but my contribution is minor relative to those of the others, especially Paul’s, as he has created and championed BabelMeSH for some time now. At any rate, I highly recommend the Arabic language BabelMeSH.

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Working as a doctor in the USA

Posted in Lectures, My publications by Dr Mohammad Al-Ubaydli on October 4, 2008

Many doctors are attracted to working in the States for at least part of their careers. A UK doctor who has worked in the States for over five years shares his experiences.

View slides – presented by Mohammad Al-Ubaydli at the BMJ Careers Fair, London, on 4 October 2008.

Smartphone Computing Moving Into Docs’ Offices

Posted in Articles, Medicine, My publications, Technology by Dr Mohammad Al-Ubaydli on March 31, 2008

Published 2008-03-31 in iHealthBeat.

More and more doctors are using smartphones — essentially PDAs that can make phone calls — in their daily lives, yet few of them are integrating the devices into their clinical practice. New clinical software designed specifically for smartphones is helping to overcome some barriers, yet there are other roadblocks preventing smartphones from becoming much more common in medicine than they are now.

As the average cell phone becomes “smarter” and telecommunications companies aggressively expand mobile networks, consumers in both developed and developing countries increasingly have a wireless computer in their pockets, according to Joel Selanikio, a pediatrician in Washington, D.C. Selanikio’s not-for-profit company makes open-source public health data collection software for PDAs and cell phones. The software is used by the World Health Organization, the World Bank and other organizations around the globe.

Unlike laptops and tablet PCs, smartphones are small enough to carry everywhere, their battery life lasts longer than a clinical shift and they have no standby or hibernation waiting times.

Yet, however convenient, many physicians are reluctant to carry and learn how to use smartphones in their medical practice. Others find it difficult to enter data into the devices using handwriting recognition. A further barrier is that hospital IT departments must provide support for doctors using the devices.

Vendors Step Up to the Plate

The medical software sector has seen a flurry of activity surrounding the smartphone market in the last few months. Epocrates recently announced the availability of its drug reference software for BlackBerrys, while Skyscape announced the release of all its medical textbooks for the BlackBerry platform. Thomson Healthcare has been providing medical software for BlackBerry devices since 2006.

The publicity surrounding the release of Apple’s iPhone prompted yet another wave of companies pledging support for its platform. eClinicalWorks practice management software is designed for Web browsers, including those operating on iPhone, as is the American Academy of Family Physicians’ CEND Personal Health Record Web site and Life Record’s electronic health records software.

Unbound Medicine, a provider of evidence-based medicine content, announced in July 2007 that its clinical references Web site works on iPhones. Meanwhile, Epocrates announced the availability of iPhone software at an Apple press conference in February.

All of this is in addition to the existing products from medical software vendors for handheld computers and smartphones running the Palm, Pocket PC and Windows Mobile operating systems.

The technology advances come at a time when sales of nonsmartphone handhelds continue to fall. IDC estimates that worldwide sales in the third quarter of 2007 were just under $730,000, a 40% drop from the 1.2 million units sold during the same quarter in 2006.

Rises in smartphone sales are much greater than this drop. In-Stat estimates double-digit growth every year for the next five years by traditionally PDA-centric vendors like Palm, as well as newer smartphone vendors like BlackBerry and the most recent and famous entrant, Apple.

Hospitals Integrating Smartphones Into Clinical Workflow

At Virginia Commonwealth University Medical Center, a pilot study with emergency department physicians has been successful enough to justify providing smartphones to each physician in the hospital.

The devices access data from a central EHR system run by Cerner. Physicians also can use their smartphones to search textbooks and the Internet, send and receive e-mails, and make and receive telephone calls with hospital staff. The hospital’s investment largely is covered by the increased charge capture from enabling billing by the bedside with the same PatientKeeper software that provides the Cerner medical records for patient care.

IT teams are still learning how to get the best value from technology like smartphones. At VCU, two earlier pilots uncovered problems with nonsmartphone PDAs, as wireless connectivity was not reliable enough for clinicians, and certain smartphones could not meet clinicians’ need to use several applications simultaneously.

Barriers to More Widespread Use

The spread of methicillin-resistant Staphylococcus aureus infections is leading to questions about hospitals’ hygiene policies for clothing and devices, including smartphones. Infections associated with handheld computers are less significant than those spread by not washing hands, explained Anatole Menon-Johansson, a U.K.-trained physician completing a master’s degree in public health at Harvard University.

“Hands are by far the most important, then white coats, shirt cuffs, stethoscopes, ties, rubber hammers, ophthalmoscope, whatever else is in your white coat pocket, and only then cell phones and PDAs,” Menon-Johansson said.

The cost of integration can also be significant for hospitals. However, if hospitals do not make an investment in supporting smartphone technology, physicians using smartphones either have to double-document, entering data into both their own handheld computers and the central medical records system, or they fail to reap the advantages of up-to-date information by patients’ bedsides.

70% Penetration Predicted by 2011

Getting accurate data on how many physicians use smartphones in their practice is difficult because the term “use” can be defined in a broad range from taking practice-related phone calls to data storage, computing and Internet research.

According to Thomson Healthcare research, about 31% of physicians in this country use smartphones in their practice. The Diffusion Group, a consulting firm specializing in IT, estimates higher — that nearly half (49%) of U.S. doctors used smartphones in 2006.

Leaders in both the medical and information industries predict smartphone use in physicians’ practices will grow rapidly across the globe. Selanikio of DataDyne predicts African countries will be among the most rapid adopters of wireless smartphone technology because of the relative dearth of land-based computing options.

In the United States, according to research by the Diffusion Group, smartphone use by physicians will increase to 70% over the next three years.

The Doctor’s PDA and Smartphone Handbook: Medical records

Posted in Medicine, My publications, Peer-reviewed papers, Technology by Dr Mohammad Al-Ubaydli on April 18, 2006

The ability to store patient records on a handheld computer is perhaps the feature that clinicians want the most, yet it also is perhaps the hardest to provide. If you are buying a device for yourself simply so that you can use it for medical records, then you should abandon the purchase and save your money.

Let us explain why we say this. It is relatively easy to store information about your patients in your personal database. Buy HanDBase, create your forms and start entering patient data. The difficulty comes when you have to share information with other clinicians. Beaming may be enough for small teams, but for any more than five clinicians, you will need to synchronize your devices with a central computer… and that requires the help and support of the IT department.

The practice of medicine means that you almost always have to share information with your colleagues. Whether you do it in the paper notes or your institution’s electronic medical records system, you must document what you do to the patients so your team can provide appropriate care.

Thus, if you decide that you do not want to share the patient notes on your device because of the complexity of involving the IT department, you will have to duplicate your writing: once for your device and again for the institution’s notes. You will soon get tired of this; we are all too busy to be duplicating work.

On the other hand, in institutions around the world, and increasingly with the support of national governments, IT departments are switching to electronic medical records. In many cases, handheld computers are part of that switch—or at least they are planned as the next stage. In such institutions, the doctors will be provided with handheld computers as part of good clinical care.

If you are in such an institution—congratulations, make use of your good fortune and enjoy your equipment!

If you are not, then you can change the institution and convince its decision makers of the investment, but this is a long process and requires sustained effort. In the meantime, do not buy a handheld computer for yourself in the hope that you will get the support for medical records software. It will not come soon.

Of course, you should still buy the device for all the other advantages, and we hope that we have convinced you of their value. The rest of this article will discuss the options you have as you move your institution to electronic medical records.

Medical records systems for small individuals and small teams

The easiest way to begin managing your patient’s records at the start is to buy software like Patient Tracker [], which includes a handheld computer version and a PC version. This makes it easy to enter most of a patient’s information at your clinic desk but to add more details with the handheld computer at the patient’s home or to read those details on the device while away from your desk. The data are encrypted.

The software is designed for American clinicians and is ideal for small practices. It is not suitable for general practitioners in the UK, as more than 95% of their practices already have an electronic medical records system—and their complementary handheld computer versions are better. For doctors in hospitals in the UK that do not yet have a such a system, however, Patient Tracker could be a useful purchase for each small team.

If for any reason you do not like Patient Tracker’s interface, however, you cannot modify it. This is why so many clinicians like HanDBase: each team can create the exact forms they need for their workflow. The effort of designing and implementing the forms is not trivial though and will take some time for experimentation.

Whatever you decide, one risk to think about is losing data. You can consider buying a backup SD card for your handheld from companies like MDM []—for around $50 (£29), the card allows a complete backup of your device. Should you lose the data for any reason, you can restore it within a few minutes after inserting the card into the device. More dangerous is losing the device itself through theft or forgetfulness. This is why encryption is so important.

Bespoke medical recrods systems

With the financial and managerial support of your institution, you can consider a medical records system tailored to your team’s needs. Scotland has wonderful examples of this, as the government has standardized data formats (which means that medical software designers can more easily share patient data between their products) and has provided budgets for software investments and target dates for implementation. Unlike the government in England, however, Scotland’s government has not been involved in micromanaging implementation.

This has led to many new companies creating innovative products and tailoring them to clinicians’ needs. For example, Extramed [] and Kelvin Connect [] both created software that allowed hospital clinicians to read information on their patients during the ward round. The information is synchronized automatically between the handheld computer on the ward round, the PCs of the nurses in the medical assessment unit and the workstations of the radiologists in their offices.

What is interesting about these examples is the new working habits that they support and the planning that the team must go through. For example, in Lanarkshire, the software is a small part of the innovation of the night time hospital emergency care teams. A small team of two nurses and five doctors triages and treats the hospital’s inpatients overnight. In the morning, the nurses provide a report on each patient they treated, because it was the nurses that prescribed many of the drugs and the nurses that had the handheld computers.

For these habits, the doctors, nurses, managers and software developers worked together and decided on how to best to proceed for their patients. When you understand the information in this book, you will be one of the best people in your institution to help guide the decision-making for handheld computers. Find out about the committees involved in such planning and contribute to them.

Off-the-shelf systems

Even if you cannot contribute to the design of a custom system for your team, you can still play an important role if your institution chooses an off-the-shelf medical records system. This is happening in England, where the government has designated specific medical records system providers for each region. Furthermore, in many institutions, including the practices of all general practitioners in England, complete medical records systems already exist. You will not be able to switch to a different provider, but you still can buy the handheld computer version of their software. For example Inchware [] makes impressive PDA versions for the existing products of EMIS, iSoft, Torex and Vision in the UK, while IDX and McKesson in the USA also have had their own mobile software for several years.

Even after the purchasing decision has been made, and even if the product is fixed and not customized, you still will play a crucial role. For example, you can take part in the early testing. This will mean that you can advise on the rate of deployment—which wards should come first—and will be ideally placed to provide training for your colleagues.

Such work is good for your career. For many clinicians, such satisfying work has prompted a switch to medical informatics as a specialty. In the end, of course, it will be the patients that benefit. Medical errors are many, expensive and dangerous. To reduce these and improve care governments around the world are investing billions of dollars in solutions. Electronic medical records are a vital part of these, and handheld computers are already making their mark. We hope that these articles help you bring the benefits to your patients.

Clinical vignette of medical records

Impressed by the work of Dr Cochrane in her general practice surgery, Dr Snow bought a handheld computer. It greatly improved his organization, and they designed a database to store audit information about their patients with diabetes for audits.

Soon, their seven colleagues wanted to make the same investment. In a practice meeting, they decided that each doctor should buy their own device to suit their tastes. Because the practice had an EMIS medical records system, the clinicians with Palm Powered devices could use the EMIS PDA software, while those with Pocket PCs could get EMIScompatible PDA software from Inchware.

This allowed Dr Snow to take the records of the patients he would see on a home visit, refer to the prescriptions and past medical history while with the patient and make notes on the visit on the handheld computer. Once back in the practice, the new notes would synchronize back to the central computer and become available to the PCs and PDAs of the other doctors and nurses.

The software did not do everything the team required, however, so Dr Snow wrote a business case for the purchase of custom software to monitor the progress of patients with cardiological conditions and diabetes. He received funding from his primary care trust and found a small company in the area. They collaborated on the design of the software and made sure that it integrated into the existing EMIS system.

The product was so well suited to the management of the patients’ conditions that he was able to coauthor several papers that documented the improved control of hypertension, and several practices in the surrounding area also invested in the software.

By this time, Dr Snow was hooked on the benefits of handheld computer for good clinical practice. He started a long-distance course in medical informatics, supported by a scholarship from his primary care trust, and searched for other areas in which he could improve patient care.


This is the fifth in a series of extracts from a forthcoming book by M Al-Ubaydli and C Paton. The website [] includes video tutorials to accompany this text.

Citation: Paton C, Al-Ubaydli M. The Doctor’s PDA and Smartphone Handbook Medical records. J R Soc Med. 2006 Apr;99(4):183-4.

The Doctor’s PDA and Smartphone Handbook: Medical references

Posted in Medicine, My publications, Peer-reviewed papers, Technology by Dr Mohammad Al-Ubaydli on March 18, 2006

A handheld computer smaller than a paperback can carry the equivalent of several bookshelves of text, and you have whole libraries from which to choose. For many doctors, the ability to carry and refer to their own favourite books on a handheld computer is the best reason for investing in a device.

The investment can be expensive, however, so you should consider your options before buying. The first consideration is storage. Although some devices today can carry a lot of data—measured by the amount of random access memory (RAM)—they still store less than 10% of the storage capacity of the biggest secure digital card. Furthermore, the cost of storage on a secure digital card is less than 10% of the cost of a handheld computer’s built-in RAM. In other words, it is far better to buy a $200 (c.£114) handheld computer with modest RAM and a $100 (c.£57) high-capacity secure digital card than to buy a $300 (c.£171) handheld computer with more RAM. Even if you buy a $600 (c.£340) device, you will still not come close to the capacity of the $100 (c.£57) card. This capacity is impressive. A 1 gigabyte card can store around 600 000 pages of text. Pictures take up far more space than text, but you will still be able to carry several anatomy textbooks on a 1GB card, along with hours of music and scores of photographs.

The second consideration is that a lot of reference texts are available free of charge, and many are perfectly good for your needs—even if the lack of advertising budget means that they are not as easy to find. Furthermore, for most doctors, the most valuable and important reference texts are generated locally—your own Word documents, your clinic’s guidelines, your hospital’s protocols or the local government’s social services documentation. For around $30 (c.£17), you can create handheld computer versions of all of these and share them with your team.

Finally, if you do decide to buy commercial textbooks for your device, consider that each costs at least $60 (c.£34)—and many cost much more. Choose carefully and take your time in doing so, because so many excellent offerings are available. It is easy to be tempted by all of these.

Free references

The National Library of Medicine (NLM) in the US makes several resources available free of charge at []. These include two versions of the Medline database which allows you to search the medical literature and read abstracts of most modern biomedical papers on your device. The Wireless System for Emergency Responders (WISER) software provides differential diagnoses and treatment guidelines for clinicians who suspect their patients have encountered hazardous materials.

Finally, the National Center for Biotechnology Information Bookshelf has handheld computer versions of several textbooks (Figure 1). These include Clinical Methods (a comprehensive guide to clinical examination), Genes and Disease (a primer on many common hereditary diseases) and Medical Microbiology (with encyclopaedic discussions of common microbes). The NLM’s own AHRQ Evidence report summaries is well worth downloading, because it lists protocols for the management of many conditions and even clinicians outside of the USA will appreciate the depth of the content.

Textbooks are not the only valuable references—laboratory result normal ranges, Spanish medical dictionaries and lists of medical abbreviation also can be useful. Such information is stored in databases, which was covered in more detail in the January issue. The advantage of using a database rather than an electronic book for storing this information is the ability to categorize data and run sophisticated searches. You can find all these data files on portals such as [], but if you follow our recommendation to buy the HanDBase database software, you should look through the HanDBase website [] in the `Free Downloads’ section.

Finally, ePocrates [] makes a USA formulary, Epocrates Rx, available free of charge (Figure 2). British, German and Spanish versions exist for clinicians outside the USA. The software’s ability to identify drug interactions already has prompted one medical indemnity company to subsidize the purchase price of handheld computers for its residents because it could reduce prescription errors. In many cases, however, the most important references are local ones.

Making your local references available

Your local references are available in several formats, and it is unusual for these to be suitable for the small screen of your handheld computer. Paper is the worst format, of course, because you have to retype the information into your computer before you can use it. Someone somewhere in your institution, however, has the original file from which the paper version was printed. Find that person and ask for that file.

The three most common formats are Microsoft Word documents, Adobe Reader documents and web pages. Each of these has its problems.

Although most devices include software that is compatible with Microsoft Word, the compatibility is not perfect. Ironically, Microsoft’s own Pocket Word is rather poor, losing a lot of the formatting that you may depend on to read the text correctly and coping poorly with tables.

Far more significantly, all of these software tools allow the user to edit the Microsoft Word document. This means it is possible to for you to write a protocol that includes drug dosages, but for a colleague then to accidentally delete a decimal point in one dosage—worse still, they can beam that incorrect document to other colleagues.

Reference information on handheld computers should not be editable

A great alternative is to use RepliGo’s software []. This comes in two versions: the desktop version costs $30 (c.£17) and can convert your Word documents into uneditable RepliGo documents. Buy one copy for your team. The second version works on handheld computers and can read RepliGo documents. Install it on all of your colleagues’ devices, because it is available free of charge.

RepliGo is also good for Adobe Reader documents. These documents cannot be edited, and Adobe makes Adobe Reader software for Palm Powered and Pocket PC devices. The software adjusts poorly to the small screen size, however, which makes for a frustrating experience for the user.

RepliGo’s desktop software converts Adobe Reader documents into RepliGo documents. On your handheld computer, you have two options for reading the document. The first is to look at the document as it was originally designed for Adobe Reader, which preserves the layout, columns of text, pictures and tables. This is good for getting an overview of the pages originally designed for printing (Figure 3). The second option, which you will find most useful most often, is the text reflow view. By clicking the `REFLOW icon’ button, RepliGo will reflow the text of the page so that it is in just one column the same width as your device. This means you can comfortably read the document from start to finish by pressing the up and down buttons on your device. Adobe Reader, by contrast, can force you to scroll right every few words to read more of the line, as it tries to preserve the original formatting of the page.

To see an example of this, visit [] where a RepliGo version of PLoS medicine is stored. This is the leading open access clinical journal, and its funding means that all its issues are available free of charge. The RepliGo handheld computer version of the issues combines the great illustrations of PLoS with the illuminating text of its authors.

RepliGo is not useful for webpages, however, because useful websites usually are composed of many webpages, with rich links between those pages. A single RepliGo document, by contrast, cannot contain more than one webpage and certainly does not allow linking between webpages. Instead, you should use Plucker []. As with RepliGo, a desktop version of Plucker creates Plucker documents and a handheld computer version reads them. Unlike RepliGo, both versions are available free of charge, as they are examples of high-quality, open-source software. Plucker is capable of downloading entire websites, including your hospital’s internal webpages, and compressing the pages for efficient storage on your device but optimizing the presentation for the small screen.

Finally, HanDBase is good for storing local data, such as the appropriate blood tube for each blood test.

Converting a document to RepliGo format

After you have installed RepliGo onto your PC and handheld computer, the software can convert any document that can be printed. For example, to convert a Microsoft Word document that details your hospital’s protocol for patients with febrile leukaemia:

  1. Open the document in Microsoft Word
  2. From the `File’ menu, select `Print…’
  3. To the right of the printer’s `Name:’, select `RepliGo’ from the drop-down menu (Figure 4)
  4. Click the `OK’ button
  5. Enter the name you want for the document on your handheld computer
  6. Select from the drop-down list to the right of `Location:’. `Handheld’ means the file will be stored on your device, which means it is fast but will occupy precious space. `SecureDigital (SD) Card’ is a little slower, but it is preferable as you have a far bigger storage area
  7. Click the `OK’ button
  8. Synchronize your handheld computer
  9. Open RepliGo on the device to read the document.

Converting a document to Plucker format

After you have installed Plucker onto your PC and handheld computer, the software can convert any webpage or website into a single file. Your connection to the Internet must be working at the time of conversion, but after that you can read all the webpages on your device without the connection. For example, to convert the website of the government’s driving regulations for medical conditions:

  1. Use your web browser to go to the main webpage for that website. This will be the starting point for Plucker on your device
  2. Copy the address of that webpage from you web browser
  3. Open Plucker
  4. From the `File’ menu select `Add new channel using wizard…’
  5. Enter a name for the channel and click the `Next’ button
  6. Paste the address you had copied and click the `Next’ button
  7. Type a number to the right of `Retrieve linked pages to a depth of’. A good number is `2′. The higher this is, the less likely that you will miss out a copy of a page from the site, but the much greater the storage space on your handheld computer. Click the `Next’ button
  8. Confirm that the channel’s content will be sent to your handheld computer and click the `Next’ button then the `Finish’ button
  9. From the `Update’ menu, select `Update all channels’ to get the latest copy of the websites
  10. Synchronize your handheld computer
  11. Open Plucker on the device to read the website.

Commercial references

Few commercial textbooks are available for less than $60. High-quality publishers include Skyscape [], Franklin [] and Lippincott Williams & Wilkins []. They make available such famous general textbooks as the Oxford Handbook Of Clinical Medicine,2 Griffith’s 5 Minute Clinical Consult3 and Harrison’s Principles Of Internal Medicine,4 as well as excellent texts for each specialty.

InfoRetriever takes a different approach, providing the text of InfoPOEMs []. This consists of Patient-Oriented Evidence that Matters (POEM), which means that the authors have scanned the literature for evidence that affects your clinical management. Furthermore, they have condensed it significantly so that accessing the information while the patient is surprisingly quick.

You should, however, choose carefully before paying the prices that publishers charge. In particular, try to install a trial version of any book you are interested in, because this will give you an idea of the complication of the publisher’s digital rights management software. This is the software that the publisher uses to stop you making copies of its textbook. While it is important to make sure that the publisher does not lose money from piracy, it can punish honest customers. The more complicated the software, the more likely that a problem will arise in the future that stops you from reading a book for which you have paid good money.

Stay away from publishers with complex installation software. One notable exception is MedHand []. The company sells subscriptions to its textbooks of 1 year’s duration. In return you get four secure digital cards per year. Each contains the latest version of the British National Formulary, as well as more than 20 textbooks, including the Oxford Handbook Of Clinical Medicine and an astonishing anatomical atlas. No installation is necessary—you simply insert a card into your device and it is ready to use. The downside to this is the cost. At the time of writing, one year’s subscription cost more than £300. Institutional discounts are available, which is why some hospitals are buying the cards for their clinicians. One irritating aspect is that each card stops working after a certain date. The company explains this by saying that out-of-date prescription information must not be made available, but old paper copies of the British National Formulary and other formularies still are available in most wards and clinic and are perfectly useful.

That computer technology is used to produce greater restrictions at a greater price than with paper texts is unfortunate. The reverse should be true, and you should direct your money to publishers that understand this best.

Reading for fun

The fondness we had for our first PDAs was because the device allowed us to reclaim reading time. Clinical school meant spending a lot of time in the hospital. We had plenty of spare moments, but few paper books that we could carry. The PDA, however, could store novels and biographies as electronic books, and eventually Mohammad would also buy audio books to listen to while walking.

Project Gutenberg [] provides free digital versions of books that are in the public domain. For the most part, this means old texts that are out of copyright, but we all could benefit from a classical education. Each book is available in any of several formats—usually simple text or a single webpage. Use RepliGo or Plucker to convert it into something suitable for your device.

For the latest books, you will have to pay money, and one of the best sites is eReader []. Each electronic book costs about the same price as the hardback edition on That means a 10-30% discount, but it is still more expensive than the paperback version. The freely available software for reading these books, however, is wonderfully unobtrusive. A lot of thought went into providing a good interface that helps reading.

Most importantly, of all the companies that produce electronic books, this one treats its customers with the greatest respect. To unlock a book, you simply need the name and credit card number of the person who bought the copy in the first place. This simplicity is why Mohammad still has the library of 30 books he bought from them and why we recommend the company to colleagues and friends.

Audible [] is the other company that we recommend – this time for audio books. If you sign up for the $15 (c.£9) a month deal, you can get one book and one radio programme per month for your handheld computer, while their $20 (c.£11) deal gets you two books. You can interrupt and restart your subscription whenever you want. Once you get a book, though, it is yours forever—regardless of subscription status—and the company allows you to download it as many times as you want in the future. Mohammad has been subscribing on and off since medical school and has gone through several PCs, handheld computers and countries in the process.

He still has access to more than 50 audio books that he bought and can make CD versions to lend to friends and family. It is not quite as simple as beaming but is still a wonderful way of sharing.

Clinical vignette of a junior doctor’s shift

In his prime, Dr Avicenna was a skilled surgeon and an expert in his specialty. He liked to carry around general medical textbooks that he could refer to for knowledge outside his specialty. For £30, he bought Saunders Pocket Essentials Of Clinical Medicine [], which included the paperback version and a handheld computer version. He knew that the medical team in the hospital was provided with subscriptions to MedHand, but for his team he just used ePocrates Rx to spot any drug interactions.

Dr Avicenna stored all these books on a $200 4GB secure digital card that he bought for his smartphone. This card also allowed him to store his entire classical music collection. By connecting a speaker to his device, he could play his favourite symphonies in theatre while operating. For his car, he had a $20 connector from his cassette player to his smartphone. He could play the same music through his car’s speaker, but he preferred to listen to audio books from Audible for his morning commute.

Finally, on nights that he had to stay in the hospital, Dr Avicenna appreciated having the books he had bought from eReader. He could switch off the light in his room and yet read comfortably through the brightness of his smartphone’s screen. Two minutes after he fell asleep, the screen would switch off, saving the page he had been reading till the next time he wanted to resume the novel.


This is the fourth in a series of extracts from a forthcoming book by M Al-Ubaydli and C Paton. The website [] includes video tutorials to accompany this text.


  1. Al-Ubaydli M, Paton C. The Doctor’s PDA and Smartphone Handbook: Databases. J R Soc Med2006; 99:20 -23
  2. Longmore M, Wilkinson I, Rajagopalan S. Oxford Handbook Of Clinical Medicine. Oxford: Oxford University Press,2004
  3. Dambro MR. Griffith’s 5-minute Clinical Consult. Philadelphia: Lippincott Williams & Wilkins,2005
  4. Kasper DL, Braunwald E, Fauci AS, Hauser SL, Longo DL, eds. Harrison’s Principles Of Internal Medicine. New York: McGraw-Hill Professional, 2004

Citation: Paton C, Al-Ubaydli M. The Doctor’s PDA and Smartphone Handbook Medical references. J R Soc Med. 2006 Mar;99(3):120-4.

The Doctor’s PDA and Smartphone Handbook: The task list

Posted in Medicine, My publications, Peer-reviewed papers, Technology by Dr Mohammad Al-Ubaydli on February 18, 2006

A good house officer is an organized house officer; and keeping track of the jobs to be done for each patient is arguably the most important skill for doctors beginning their career. Your handheld computer’s task list will not make you organized, but it will provide you with the tools you need to be organized.

Like the diary and address book, the task list’s importance means that most handheld computers include a button that takes you straight to the program. This is usually in the bottom right-hand corner, second from the right. Alternatively, on Palm Powered machines, tap on the HOME icon and then the icon labeled To Do List. On Pocket PCs, tap on the START icon and then Tasks.

The tasks are given in a list, with a tick box next to each task (Figures 1 and 2). Tap on a tick box if you have completed its task, and tap again to remove the tick from the box. Tapping on a task allows you to look at the task’s related text, priority and due date. The priority and due date are what you really need to manage your tasks for the day.

Creating a task

To add a task about setting up a chest computed tomography scan for a patient with hospital ID ABC123456:

  1. Tap on the New button on a Palm Powered device or the New menu item on a Pocket PC
  2. Write ‘CT scan ABC123456’
  3. 3. On a Pocket PC, tap the OK button.

It is important to make the text for each task short yet explanatory. As you look at the list of tasks during the day, you will mostly rely on this writing to give you the information you need at a glance.

Using the patient’s hospital ID rather than their full name is doubly important. First, tasks are not encrypted, so they are not secure enough to include identifying information about your patients. Second, as you fill out the computerized tomography request form later on, the ID is the most important detail you will need.

This works fine if you are already in the habit of attaching a sticky label from your patient’s notes onto your white coat. Combine this with the hospital number on your task list and you have a convenient system that still maintains confidentiality and complies with data protection rules.

Adding notes to a task

For some tasks, it is necessary to include extra information about the task. In the chest computerized tomography example, you might want to include a clinical summary of the patient and the question you want the radiologist to answer. Use the task’s notes to do this. On a Pocket PC:

  1. Tap on the task you want to edit
  2. Tap the Edit menu item
  3. Tap on the Notes tab
  4. Write the note
  5. Tap the OK button

On a Palm Powered device:

  1. Tap on the task you want to edit
  2. Tap on the Details… button
  3. Tap on the Note button
  4. Write your notes
  5. Tap the Done button.

Again, remember that the notes part of the tasks list is not encrypted, so you should not include any information that could identify your patients.

tasks.pocketpc.gif tasks.palm.gif
Figure 1 Pocket PC’s Tasks Figure 2 Palm Powered device’s To Do list

Priority and due dates

The key to being organized is to make sure that every task has a priority and a due date. Then you can begin your day’s efforts with the tasks that are most important or urgent. Once these are complete, you can focus your attention on the other tasks.

To change the priority and due date on a Pocket PC:

  1. Tap on the task to edit it
  2. Tap to the right of Priority:
  3. Select from Low, Normal and High. Normal is the default, while High priority tasks appear with a red exclamation mark in the tasks list
  4. Tap to the right of Due:
  5. Select the date by which the task needs to be completed.

On a Palm Powered device:

  1. Tap on the task to edit it
  2. Tap on the Details… button
  3. Select from 1 to 5 to the right of Priority: 1 is the default and is also the highest priority
  4. Tap to the right of Due:
  5. Select the date by which the task needs to be completed. You can quickly choose from Today, Tomorrow, One Week Later and No Date or you can tap on Choose Date… to get a calendar from which to choose another date.

Sorting and the satisfaction of purging

  1. Tap on Sort By in the top right corner
  2. Select Due Date instead.

By default, Palm Powered devices sort first by due date and second by priority. To change this:

  1. Tap on the Show… button
  2. Tap to the right of Sort by:
  3. Select Priority, Due Date to sort first by priority and second by due date
  4. It is worth also unticking the box to the left of Show Completed Items
  5. Tap the OK button.

To untick the Show Completed Items box is optional but very useful. The result is that whenever you tick a task to signal it has been completed, it will disappear from the list. To do the equivalent on a Pocket PC:

  1. Tap on the Show menu in the top left corner
  2. Tap on Active Tasks….

It is satisfying to see your list of tasks gradually getting shorter during the day as you go about your work.


As with the address book, categories are useful. Good categories to create include the names of the wards of your patients and the names of the consultants for whom you work. On a Pocket PC:

  1. Tap on the task to edit
  2. Tap the Edit menu item
  3. Tap to the right of Categories:
  4. Tick the box next to each category you want
  5. If you do not find the category you need, tap on the Add/Delete tab and add the name of your new category
  6. Tap the OK button.

On a Palm Powered device:

  1. Tap on the task to edit
  2. Tap on the Details… button
  3. Tap to the right of Category:
  4. Select the category you want
  5. If you do not find the category you need, tap on Edit Categories… and add the name of your new category
  6. Tap the OK button.

Categories are particularly helpful for beaming.


To beam a task on a Pocket PC:

  1. Tap and hold on the task
  2. Select Beam Task… from the menu that appears.

On a Palm Powered device:

  1. Tap on the task
  2. Tap on the MENU icon
  3. Tap on Beam Item from the Record menu.

To beam all the tasks within a category on a Pocket PC:

  1. Select the category from the list of categories in the top left-hand corner
  2. Tap and hold on the first task in the category
  3. Drag down to the last task in the category. You can tell when all of the tasks in the category are selected because they will switch to white writing over a blue background
  4. Select Beam Task… from the Tools menu.

On a Palm Powered device:

  1. Select the category from the list of categories in the top right corner
  2. Tap on the MENU icon
  3. Tap on Beam Category from the Record menu.

Advanced uses

Two types of additional software are available. The first type is useful because it allows you to link a task to a person. For example, you can link each of your referral tasks to the consultant the patient needs to see. When you meet the consultant, their name in the address book will list all the referral tasks for that consultant. You can discuss all the relevant patients with that consultant. Examples of software in this group include Agendus [] for Palm Powered machines and Agenda Fusion [] for Pocket PCs.

The second type of software allows hierarchical tasks. For example, the main task for a patient might be setting up a referral to a neurologist, but this would depend on the completion of two other tasks: scheduling a computerized tomography scan of the patient’s head and putting the radiology report in the notes for the neurologist to use. It is best to set up one task with the title `refer to neurologist’ and give it three subsidiary tasks: `CT head’, `add CT head report to notes’ and `write referral letter’. Hierarchical software, such as ThoughtManager [] for Palm Powered devices and TreNotes for Pocket PCs [], allows correct sequencing for the subsidiary tasks and tracks the progress of each of these.

Sadly, no software allows linking to both addresses and hierarchical tasks, so you will have to choose which feature matters to you most. If you are already using Agendus or Agenda Fusion, it is best to stick to it for your tasks. If you end up using ThoughtManager for its note-taking skills, you should use it for your tasks as well. Otherwise, you should try both types of software, as they include free trial versions that will allow you to decide which best suits your habits.


This is the third in a series of extracts from a forthcoming book by A Al-Ubaydli and C Paton. The website [] includes video tutorials to accompany this text.

Clinical vignette of a junior doctor’s shift

Tuesday mornings were Dr Charcot’s busiest, as they began with her consultant’s ward round. During the round, she would keep track of every job for the patients on her handheld computer’s task list. From each patient’s notes, she attached a sticker to her coat pocket. For each task, she included the patient’s hospital number. For the more complex tasks, she added a note with extra information.

Dr Charcot categorized the tasks by the ward on which the patient was present. She also included the priority and due date for each task.

After the round, Dr Charcot carried out the most urgent and highest priority tasks before going for lunch. After lunch, she could go through the other tasks at her leisure. It was satisfying to see her list get shorter as she ticked off each task as completed.

The stickers on Dr Charcot’s coat provided her with each patient’s identifying information. Combined with the patient number on each task, she could keep track of who needed what without compromising patient confidentiality on her handheld computer.

At the end of Dr Charcot’s shift, she would beam the categories with tasks that she had not yet completed to the night shift’s junior doctor. The next morning, she would confirm that the junior doctor had completed all the tasks overnight. As Dr Charcot left the hospital, she made use of the `shopping’ task list category. She ticked off every item as she went down the supermarket’s aisles. Soon it would be time to relax over dinner.

Citation: Paton C, Al-Ubaydli M. The Doctor’s PDA and Smartphone Handbook Databases. J R Soc Med. 2006 Feb;99(1):73-6.

The Doctor’s PDA and Smartphone Handbook: Databases

Posted in Medicine, My publications, Peer-reviewed papers, Technology by Dr Mohammad Al-Ubaydli on January 18, 2006

A database is the computer equivalent of a filing cabinet full of forms. Like a filing cabinet, a database can store a lot of information, and by using forms, the information is structured, which paves the way for statistical analysis and audits.

A database on a handheld computer has many advantages over a filing cabinet. First, you can carry all the forms you need. This is great for audits, because you can enter data about patients at any time, including while you are with the patient during the ward round or when you can get hold of the patient’s notes from the consultant’s secretary.

Second, you can carry all the information you have filled out in the past. Not only is the handheld device orders of magnitude smaller than a filing cabinet, the sorting and searching tools are very fast. For example, if you have a list of patients, it only takes a few seconds to sort it by each patient’s name and then to sort it again by consultant’s name. You can quickly search for a patient whose date of birth is before a certain year and whose blood results are within a certain range.

Finally, you can share the information with colleagues. Beaming makes this quick and easy to do as you meet with colleagues during the day. It takes more effort and expertise to do this with synchronization, but it means you can get the information without needing a face-to-face meeting.

Choice of database

Many database programs are available to choose from. For the palm powered devices, you can use Pilot-DB [], which is free of charge but lacks encryption and is not very user friendly. JFile is well worth the US$25 [], as is Sprint DB Pro for pocket personal computers [].

For most users, however, HanDBase is the most appropriate database software. First, it is available for both palm powered and pocket PC devices, which makes sharing data with your colleagues easier. Second, it has the most example databases available, both free of charge and for sale, which means that you can use someone else’s work
rather than design your own database forms.

Using someone else’s database

Freshly installed database software has no forms for you to enter data, so you must either spend the time creating your own forms or use someone else’s. Many doctors prefer creating a form that is perfectly suited to their habits and work, and this has its advantages. For the novice user, however, creating a form can be daunting. Furthermore, it is more efficient to use someone else’s work and customize it than to create a brand new form. Finally, standardization can be a good thing, especially if you would like to share data with colleagues. In other words, if you use a different form to your colleagues, you cannot share the data in each other’s forms.

This is why so many medical institutions make database forms available to their members. For example, the Association of Surgeons of Great Britain and Ireland [] has created a surgical logbook built on HanDBase, which you can download free of charge from []. What is particularly impressive is the ability to transfer the data from your handheld computer to the association’s website so you can back up and view it over the web.

The Royal College of Anaesthetists’ logbook is available at [] and is also built on HanDBase. The author’s own website [] makes other databases that you can customize and share with colleagues available free of charge. The next few examples will use the surgical logbook HanDBase database from this site.

Entering data

To open HanDBase on pocket PCs, tap on the ‘Start’ icon, then ‘Program Files’ and then the icon labelled ‘HanDBase’. On palm powered machines, tap on the ‘Home’ icon and then the icon labelled ‘HanDBase’. You will see a list of the databases you have installed. Tap on ‘Surgical logbook’ for this example (Figure 1).

palm.handbase.png palm.handbase.logbook.png
Figure 1 HanDBase lists the databases you have installed Figure 2 Tap the ‘New’ button to enter a record in your database. This example is from the surgical logbook database.

For security, this database is encrypted. The default password is blank, so just tap the ‘OK’ button, but you will have to change this when you finish entering data.

You will see a list of column headings across the top, including ID, Date, Patient ID, DOB, Sex and Age. As you add data about your operations, a row will appear for each operation (Figure 2).

To enter data:

  1. Tap the ‘New’ button
  2. By default, the date of the operation is today’s date.
  3. Tap to the right of ‘Date’ to select a different one
  4. Write the patient’s hospital identification number to the right of ‘Patient ID’
  5. Tap to the right of ‘DOB’ to select the patient’s date of birth
  6. Select the patient’s sex by tapping to the right of ‘Sex’
  7. Write the patient’s age to the right of ‘Age’
  8. By default, the current time is used for the operation’s starting and ending times. Tap to the right of ‘Start’ and ‘End’ to select different times
  9. Tap on ‘Operation’ to select the operation from the list of operations. If the operation you want is not in the
    list, tap ‘Edit Popup List’ to add its name
  10. By default, the priority is ‘Routine’. Tap on ‘Priority’ to select an alternative, such as ‘Day case’, ‘Emergency’ or ‘Urgent’
  11. By default, your role is ‘1st assistant’. Tap on ‘Role’ to select a different one, such as ‘Performed alone’
  12. This should be enough information to enter about the patient at the start. It is useful for your own records and for submission to your surgical college, however, to enter more information. For example, further down the form, you can document the patient’s past medical history (tap to the right of ‘PMH’) and complications at 24 hours, 1 month and in the long term
  13. Tap on the ‘Down’ icon button to go down and the ‘UP’ icon button to go up
  14. When you are finished, tap the ‘OK’ button.


In each database, the records usually are listed in the order you entered them. To choose a different method, tap on a column name. For example, to sort by date, with the latest operations appearing at the top:

  1. Tap on the column titled ‘Date’
  2. Tap ‘Sort Reverse’

You can sort using multiple criteria. For example, to sort your operations first by your role and then by the date of the operation:

  1. Tap on the ‘Tools’ button
  2. Tap on the ‘Sort’ button
  3. Tap to the right of ‘Primary Sort’ and select ‘Role’
  4. Tap to the right of ‘Secondary Sort’ and select ‘Date’
  5. Underneath ‘Secondary Sort’, tap on ‘Reverse’
  6. Tap the ‘OK’ button.


Filtering allows you to find a particular group of patients. For example, to find all the patients between the age of 30 and 40 years who had diabetes in their past medical history:

  1. Tap on the ‘Tools’ button
  2. Tap on the ‘Filter’ button
  3. Tick the box labelled ‘Filter 1 Enabled’
  4. Tap to the right of ‘Select Field’ and select ‘Age’
  5. Write ‘30’ to right of ‘Lower Limit’ and ‘40’ to the right of ‘Upper Limit’
  6. Tick the box labelled ‘Filter 2 Enabled’
  7. Tap to the right of ‘Select Field’ and select ‘PMH’
  8. Write ‘diabetes’ to the right of ‘Must Contain’
  9. Tap on the ‘Down 2’ icon button to go down and the ‘Up 2’ icon button to go up and add any other filters
  10. When you are finished, tap the ‘OK’ button.

The list of operations now will include only those that meet the criteria of these filters.

To remove the filter:

  1. Tap on the ‘Tools’ button
  2. Tap on the ‘Filter’ button
  3. Untick the boxes labelled ‘Filter 1 Enabled’ and ‘Filter 2 Enabled’
  4. Tap the ‘OK’ button

The list will return to showing all of the operations.

Running a report

You can do simple statistical analyses of your data. To find the average age of your patients on a palm powered device, tap on the ‘Menu’ icon. Then, on this device or a pocket PC:

  1. Tap on the ‘Actions’ menu and select ‘Run Report’
  2. Tap on ‘Select Field’
  3. Tap on ‘Age’
  4. Tap the ‘Go’ button.

You will see the average age to the right of ‘Average’, as well as the minimum (‘Min value’) and maximum (‘Max value’) ages. The ‘Sum’ is not useful in this case, but it would be important for adding up the cost column in a database that tracked the purchases made by your department.

Designing a database

It is technically fairly easy to design your own database, but coming up with a good design can be hard. It certainly takes experience and a little thinking in advance. It is worth trying the example databases with your patients for a few days to note which parts of the design you would like to change.

To change the design of an existing database on your pocket PCs, tap on the ‘Start’ icon, then on ‘Program Files’ and then on the icon labelled ‘HanDBase’. On a palm powered device, tap on the ‘Home’ icon and then the icon labelled ‘HanDBase’. Then:

  1. Tap on the name of the database you want to edit
  2. Tap on the ‘Details’ button
  3. If the database is encrypted or password protected, enter the password and tap the ‘OK’ button
  4. Tap on the ‘Fields’ button.

You will see a list of fields. Each field is the equivalent of a column heading that you see when listing the records in your database. Tap on the field that you want to edit. For example, if you tap on ‘DOB’ from the surgical logbook database, you can see that its ‘Field Type’ is ‘Date’ (Figure 3). This means that changing the value of this date in a record will bring up a calendar.


Figure 3 The date of birth field in HanDBase

If you had selected ‘Text’ instead, you would have to write ‘01/26/1976’ for a patient’s whose date of birth is 26 January 1976. This might seem faster, but it means that running the filters feature is practically useless for ‘DOB’.

You will not be able to filter patients born before 1975, for example, as the database does not treat ‘DOB’ as a date.
Similarly, the ‘Age’ field is an integer, which means that the database treats it as a whole number. This is useful because the surgical logbook database will prevent you writing ‘67.5’ or ‘67a’ by mistake, which keeps your data clean. It also means you can see the sum of that field’s data when you run a report on the database.

As you can see, designing a database can be complicated at the start. Fortunately, HanDBase’s website has excellent explanations of all of the field types, as well as excellent tutorials that walk you through setting up your own database []. The RSM course that we run every year [] also provides hands-on training.

Citation: Al-Ubaydli M, Paton C. The Doctor’s PDA and Smartphone Handbook Databases. J R Soc Med. 2006 Jan;99(1):20-3.