From ecological records to big data: the invention of global biodiversity

This paper is a critical assessment of the epistemological impact of the systematic quantification of nature with the accumulation of big datasets on the practice and orientation of ecological science. We examine the contents of big databases and argue that it is not just accumulated information; records are translated into digital data in a process that changes their meanings. In order to better understand what is at stake in the 'datafication' process, we explore the context for the emergence and quantification of biodiversity in the 1980s, along with the concept of the global environment. In tracing the origin and development of the global biodiversity information facility (GBIF) we describe big data biodiversity projects as a techno-political construction dedicated to monitoring a new object: the global diversity. We argue that, biodiversity big data became a powerful driver behind the invention of the concept of the global environment, and a way to embed ecological science in the political agenda.

Progress in Biomedical Knowledge Discovery: A 25-year Retrospective

OBJECTIVES

We sought to explore, via a systematic review of the literature, the state of the art of knowledge discovery in biomedical databases as it existed in 1992, and then now, 25 years later, mainly focused on supervised learning.

METHODS

We performed a rigorous systematic search of PubMed and latent Dirichlet allocation to identify themes in the literature and trends in the science of knowledge discovery in and between time periods and compare these trends. We restricted the result set using a bracket of five years previous, such that the 1992 result set was restricted to articles published between 1987 and 1992, and the 2015 set between 2011 and 2015. This was to reflect the current literature available at the time to researchers and others at the target dates of 1992 and 2015. The search term was framed as: Knowledge Discovery OR Data Mining OR Pattern Discovery OR Pattern Recognition, Automated.

RESULTS

A total 538 and 18,172 documents were retrieved for 1992 and 2015, respectively. The number and type of data sources increased dramatically over the observation period, primarily due to the advent of electronic clinical systems. The period 1992- 2015 saw the emergence of new areas of research in knowledge discovery, and the refinement and application of machine learning approaches that were nascent or unknown in 1992.

CONCLUSIONS

Over the 25 years of the observation period, we identified numerous developments that impacted the science of knowledge discovery, including the availability of new forms of data, new machine learning algorithms, and new application domains. Through a bibliometric analysis we examine the striking changes in the availability of highly heterogeneous data resources, the evolution of new algorithmic approaches to knowledge discovery, and we consider from legal, social, and political perspectives possible explanations of the growth of the field. Finally, we reflect on the achievements of the past 25 years to consider what the next 25 years will bring with regard to the availability of even more complex data and to the methods that could be, and are being now developed for the discovery of new knowledge in biomedical data.

[Rules of acupoints combination of ancient acupuncture for Xiaoke based on data mining technology]

The rules of acupoints combination of ancient acupuncture for Xiaoke are mainly explored. By retrieval on ancient literature, the database of acupuncture and moxibustion for Xiaoke is established; based on the database, association analysis between acupoints and symptoms is performed. According to the association analysis in 5 databases of Xiaoke database, Xiaoke database of kidney deficiency, Xiaoke-database of dry mnouth and thirst, Xiaoke database of difficult urination, Xiaoke database of drinking addiction, the results are mainly characterized with symptom differentiation combination, distal-local combination, local combination and front-back combination, which can nourish yin and clear heat. It is believed that establishment of TCM ancient literature database and exploration of data mining technology is a potential research orientation.

An informatics approach to chronicling the history of IMIA

With the 50th Anniversary of IMIA approaching in 2017, the IMIA Board approved the creation of a Taskforce for compiling materials and writing a history of the organization. As part of the work of the Taskforce, the authors have developed informatics tools, and begun collecting IMIA-related historical materials from its members, while soliciting participation and contributions from those involved in the early days of the organization and its predecessor IFIP-TC4. This poster describes the structure and preliminary contents of the media mining and presentation tools designed at Rutgers University for use by the IMIA History Editorial Board, being constituted to produce the 50th Anniversary publication, as well as an online archive of materials chronicling the evolution of IMIA. A major feature of the data repository is its ability to present different modalities of textual, visual and graphical (timelines, trends) summarizations for the IMIA document collection. It will be augmented with audio material, and will serve as an archival repository for historical research, including software tools for text analysis and extraction of the information entering into the 50th Anniversary volume.

[LONI & Co: about the epistemic specificity of digital spaces of knowledge in cognitive neuroscience]

In the neurosciences digital databases more and more are becoming important tools of data rendering and distributing. This development is due to the growing impact of imaging based trial design in cognitive neuroscience, including morphological as much as functional imaging technologies. As the case of the 'Laboratory of Neuro Imaging' (LONI) is showing, databases are attributed a specific epistemological power: Since the 1990s databasing is seen to foster the integration of neuroscientific data, although local regimes of data production, -manipulation and--interpretation are also challenging this development. Databasing in the neurosciences goes along with the introduction of new structures of integrating local data, hence establishing digital spaces of knowledge (epistemic spaces): At this stage, inherent norms of digital databases are affecting regimes of imaging-based trial design, for example clinical research into Alzheimer's disease.

Social Security Administration's Master Earnings File: background information

The Social Security Administration (SSA) receives reports of earnings for the U.S. working population each year. Earnings data are used to administer the Social Security programs and to conduct research on the populations served by those programs. The administrative needs of SSA and other agencies have changed over time and, as a result, there have been numerous changes to the main source of SSA's earnings data, which is known as the Master Earnings File (MEF). By documenting the history, content, limitations, complexities, and uses of the MEF (and data files derived from the MEF), this article serves as a resource for researchers who use earnings data to study work patterns and their implications. It is also a resource for policymakers and administrators who must understand the data used in administering current-law programs and the data available to inform potential changes to those programs.

The standardization of race and ethnicity in biomedical science editorials and UK biobanks

As the search for human genetic variation has become a priority for biomedical science, debates have resurfaced about the use of race and ethnicity as scientific classifications. In this paper we consider the relationship between race, ethnicity and genetics, using insights from science and technology studies (STS) about processes of classification and standardization. We examine how leading biomedical science journals attempted to standardize the classifications of race and ethnicity, and analyse how a sample of UK genetic scientists used the concepts in their research. Our content analysis of 11 editorials and related guidelines reveals variations in the guidance on offer, and it appears that there has been a shift from defining the concepts to prescribing methodological processes for classification. In qualitative interviews with 17 scientists, the majority reported that they had adopted socio-political classification schemes from state bureaucracy (for example, the UK Census) for practical reasons, although some scientists used alternative classifications that they justified on apparently methodological grounds. The different responses evident in the editorials and interviews can be understood as reflecting the balance of flexibility and stability that motivate standardization processes. We argue that, although a genetic concept of race and ethnicity is unlikely to wholly supplant a socio-political one, the adoption of census classifications into biomedical research is an alignment of state bureaucracy and science that could have significant consequences.

Twin database of the secondary school attached to the Faculty of Education of the University of Tokyo

This article profiles the historical twin databases of the secondary education school attached to the Faculty of Education at the University of Tokyo. The school was established in 1948. Every year, about 50 pairs of twins of all sex and zygosity combinations and aged 11 to 12 years take an examination, and about 10 to 20 pairs are admitted based on the results. Three independent datasets exist: one for applicants (11-12 years), one for students (12-18 years), and one for graduates (18-72 years). These three historical databases and research perspectives are introduced herein.

Developing constraints on the relative sea-level curve for the northeast of Ireland from the mid-Holocene to the present day

Tide-gauge records from the north of Ireland have been digitized to generate annual estimates of both mean-sea-level (MSL) position from Malin Head (1958-1998), and mean tidal level (MTL) from Belfast Harbour (1918-2002). Both sites exhibit substantial annual variation, but show overall long-term shallow rates of falling relative sea-level change (RSLC) that are very similar at -0.2 mma(-1) (+/-0.37 mma(-1)) for Belfast and -0.16 mma(-1) (+/-0.17 mma(-1)) for Malin. Using these rates as constraints, plus other constraints of inferred RSLC rates from the mid-Holocene, an approximation of the likely profile of RSLC rates for the northeast of Ireland since 6 ka ago is presented.

DNA fingerprinting on trial: the dramatic early history of a new forensic technique

The early history of "DNA fingerprinting" in the UK might have been different were it not for the accounts of two dramatic courtroom trials, made by the participants and the media, in the mid-1980s. But these reports, which misrepresented the importance DNA evidence had in the trials, left a strong impression on the British public and on judges on both sides of the Atlantic. These trials, widely considered to be the first "victories" for DNA fingerprinting, have been frequently cited as proof of the utility and reliability of the technique, in both the UK and beyond. But in reality, it was the threat of DNA evidence being used rather than the integrity or validity of it that resolved these cases. At that time, DNA fingerprinting was still in its infancy, an untried and untested technology.

Sanitary policing and the local state, 1873-1874: a statistical study of English and Welsh towns

This article examines local sanitary policing in extra-metropolitan English and Welsh towns and cities in the period 1873-4. It combines two parliamentary returns, one focusing on the appointments by towns of sanitary officers (inspectors of nuisances and medical officers), the other listing the number of nuisance cases and modes of resolutions. The article uses these databases to examine the identification of nuisances in terms of region, town type, mode of government, population, and salary of inspector. It considers also the effects of tenure and job security on nuisances identification, the effects of town wealth, and differences in the resolution of nuisance allegations by town type and region. The article shows a remarkable and perhaps unexpected sanitary activism, but also a considerable variability by region, town size, and town type.

Virtues of a worldwide congenital heart surgery database

The rationale for a congenital heart surgery database lies in the organized manner in which information can be compiled to accomplish programmatic evaluation, monitor clinical outcomes, comply with governmental requirements, perform retrospective and prospective clinical studies, and participate in local, national, and global improvement strategies. The task of inaugurating an effective congenital heart surgery database has taken many years and involved concurrent development efforts at multiple sites. Two such efforts took place in North America with the Society of Thoracic Surgeons Congenital Heart Surgery Database, and in Europe with the European Congenital Heart Defects Database. These initial efforts provided the impetus for development of an international congenital heart surgery database that would allow scientific exchanges on an international scale and promote multi-institutional evaluation of congenital heart surgery. Sample outcome templates from the Society of Thoracic Surgeons and the European Association for Cardio-thoracic Surgery's accepted minimum database data set are reviewed for the specific diagnostic entry ventricular septal defect, to familiarize the reader with potential available data summaries and outcome analyses, including risk stratification, when data harvest is performed. In Europe, the agreed upon minimum data set are now collected as part of the Pediatric European Cardiac Surgical Registry, while in North America users of the CardioAccess database and users of the minimum data set downloaded from the Society of Thoracic Surgeons web site are being notified of plans for a 2002 data harvest incorporating the minimum database data set. It is likely that the extant voluntary, minimal data set congenital heart surgery database will be replaced by a mandated system required by states, provinces, and countries. Data collection schemes and data validation programs will become standardized, which will result in improved data quality and uniform congenital heart center participation. As participation with valid data approaches 100% of congenital heart centers, the power and importance of the database increases exponentially. Reliable information can be used to assess residency/fellowship programs, resource allocation, major therapeutic trends, manpower issues, and in the end, all initiatives that will require accurate information.

The European Congenital Heart Defects Surgery Database experience: Pediatric European Cardiothoracic Surgical Registry of the European Association for Cardio-Thoracic Surgery

The initial purpose of collecting data on the outcome of congenital heart surgery procedures across Europe was to make possible comparison of results and definition of mortality and morbidity risk factors as well as targeting research activities. The European Congenital Heart Surgeons Foundation, established in 1992, created the European Congenital Heart Defects Database, precursor to today's Pediatric European Cardiothoracic Surgical Registry. In 1999, initiatives of the Society of Thoracic Surgeons and the European Association for Cardio-Thoracic Surgery resulted in a series of conferences aimed at arriving at a standardized nomenclature and reporting strategies as a foundation for an international database. In April 2000 the International Congenital Heart Surgery Nomenclature and Database Project published a minimum dataset of 21 items and lists of 150 diagnoses, 200 procedures, and 32 complications, as well as 28 extracardiac anomalies and 17 preoperative risk factors. Since January 2000 the Pediatric European Cardiothoracic Surgical Registry has officially operated from the Department of Cardiothoracic Surgery at the Children's Memorial Health Institute in Warsaw, Poland, under the auspices of the European Association for Cardio-Thoracic Surgery and the responsibility of Bohdan Maruszewski. As of March 2001, 84 cardiothoracic units from 33 countries had registered in the database and data on almost 4,000 procedures have been collected. Participation in the database is free of charge through the internet for all participants. Development of data validation protocols is a work in progress.

Software development, nomenclature schemes, and mapping strategies for an international pediatric cardiac surgery database system

The field of congenital heart surgery has the opportunity to create the first comprehensive international database for a medical subspecialty. An understanding of the demographics of congenital heart disease and the rapid growth of computer technology leads to the realization that creating a comprehensive international database for pediatric cardiac surgery represents an important and achievable goal. The evolution of computer-based data analysis creates an opportunity to develop software to manage an international congenital heart surgery database and eventually become an electronic medical record. The same database data set for congenital heart surgery is now being used in Europe and North America. Additional work is under way to involve Africa, Asia, Australia, and South America. The almost simultaneous publication of the European Association for Cardio-thoracic Surgery/Society of Thoracic Surgeons coding system and the Association for European Paediatric Cardiology coding system resulted in the potential for multiple coding. Representatives of the Association for European Paediatric Cardiology, Society of Thoracic Surgeons, European Association for Cardio-thoracic Surgery, and European Congenital Heart Surgeons Foundation agree that these hierarchical systems are complementary and not competitive. An international committee will map the two systems. The ideal coding system will permit a diagnosis or procedure to be coded only one time with mapping allowing this code to be used for patient care, billing, practice management, teaching, research, and reporting to governmental agencies. The benefits of international data gathering and sharing are global, with the long-term goal of the continued upgrade in the quality of congenital heart surgery worldwide.

[The Beilstein CrossFire Information System and its use in pharmaceutical chemistry]

The Beilstein CrossFire database system is one of the most popular, most extensive, and most accomplished systems presenting information about chemical substances, including drugs, and covering the basic identification, physico-chemical, ecological, and pharmacological data. The present article offers an overview of historical evaluation of the Beilstein CrossFire database system, beginning from its founder Prof. Friedrich Conrad Beilstein till the most recent prospects about the connection of classical data with full-text databases. The article also offers a review of the development of electronic information systems in the Slovak Republic, a definition of basic functionality of the Beilstein CrossFire database system, and an example of targeted selection of active substances structurally similar to novel COX-2 inhibitors having an approved anti-inflammatory activity.

Bioinformatics goes back to the future

The need to turn raw data into knowledge has led the bioinformatics field to focus increasingly on the manipulation of information. By drawing parallels with both cryptography and artificial intelligence, we can develop an understanding of the changes that are occurring in bioinformatics, and how these changes are likely to influence the bioinformatics job market.

Three decades of research on computer applications in health care: medical informatics support at the Agency for Healthcare Research and Quality

The Agency for Healthcare Research and Quality and its predecessor organizations-collectively referred to here as AHRQ-have a productive history of funding research and development in the field of medical informatics, with grant investments since 1968 totaling $107 million. Many computerized interventions that are commonplace today, such as drug interaction alerts, had their genesis in early AHRQ initiatives. This review provides a historical perspective on AHRQ investment in medical informatics research. It shows that grants provided by AHRQ resulted in achievements that include advancing automation in the clinical laboratory and radiology, assisting in technology development (computer languages, software, and hardware), evaluating the effectiveness of computer-based medical information systems, facilitating the evolution of computer-aided decision making, promoting computer-initiated quality assurance programs, backing the formation and application of comprehensive data banks, enhancing the management of specific conditions such as HIV infection, and supporting health data coding and standards initiatives. Other federal agencies and private organizations have also supported research in medical informatics, some earlier and to a greater degree than AHRQ. The results and relative roles of these related efforts are beyond the scope of this review.

Kenneth Harrison Uttley (1901-1972). Historian to the diseases of Antigua, British West Indies

Dr Kenneth Harrison Uttley (1901-1972) served as the Chief Medical Officer in Antigua, British West Indies, from 1955 until 1966. During this time, Dr. Uttley personally reviewed and tabulated an island-wide governmental demographic database of all births, deaths and causes of death during the preceding 100 years. This database was the result of a Compulsory Birth and Death Registration Ordinance enacted as one of several Colonial Poor Laws in 1856. His efforts resulted in the publication of a total of 30 papers in American and British medical journals. Many of these papers reviewed historical demographic trends in births, fertility rates, neonatal deaths, infant mortality and early childhood mortality rates. Others focussed on the historical epidemiology of specific diseases such as neonatal tetanus, leprosy, tuberculosis and malaria. This is the first complete bibliographical account of Uttley's contributions to the history of diseases in the West Indies in general and Antigua in particular. Dr Uttley also served as an ordained priest in the Anglican Church and, upon retirement from the Colonial Medical Services, returned to England to serve as the Vicar of Purton, Oxfordshire.

A brief history of the formation of DNA databases in forensic science within Europe

The introduction of DNA analysis to forensic science brought with it a number of choices for analysis, not all of which were compatible. As laboratories throughout Europe were eager to use the new technology different systems became routine in different laboratories and consequently, there was no basis for the exchange of results. A period of co-operation then started in which a nucleus of forensic scientists agreed on an uniform system. This collaboration spread to incorporate most of the established forensic science laboratories in Europe and continued through two major changes in the technology. At each step agreement was reached on which systems to use. From the beginning it was realised that DNA databases would provide the criminal justice systems with an efficient way of crime solving and consequently some local databases were created. It was not until the introduction of the amplification technology linked to the analysis of short tandem repeats that a sufficiently sensitive and robust system was available for the formation of efficient and effective DNA databases. Comprehensive legislation enacted in the UK in 1995 enabled forensic scientists to set up the first national DNA database which would hold both personal DNA profiles together with results obtained from crime scenes. Other countries quickly followed but in some the legislation has severely restricted the amount and type of data which can be retained and, therefore, effectiveness of the databases is limited. The widespread use of commercially produced multiplex kits has produced a situation in which nearly all European laboratories are using compatible systems and there is, therefore, the potential for the introduction of a pan-European DNA database. However, the exchange of results between countries is hampered by the various legislations which currently exist.

The Perinatal Database of the Netherlands

OBJECTIVE

In the Netherlands, the Perinatal Database of the Netherlands (Landelijke Verloskunderegistratie, LVR) was set up in 1982 for secondary care obstetric departments on a voluntary participation basis, its main goal being quality monitoring. At the outset of the database, 70% of Dutch obstetric departments participated immediately. This percentage has now increased to almost 100%. How the LVR was set up, its aims, participation, general function and some aspects of the reliability are described in this article.

RESULTS

Assessment of the reliability of the data on a number of points found that the frequency of various types of nearly all errors has decreased during the existence of the LVR, with the exception of a complete registration of the first-week mortality.

CONCLUSIONS

The quality of the data has improved over the years. More reliable figures for the first-week mortality would be available if the LVR data were linked to those of the Neonatal Database of the Netherlands (Landelijk Neonatale Registratie, LNR), so that the condition of each child is known up to and including 28 days after birth. Improvements in the reliability of other items can be attained by implementing more checks during the data input stage and by making the data more accessible to the gynaecologists, in order to further increase motivation to record the data.

The protein data bank. Bridging the gap between the sequence and 3D structure world

The protein data bank (PDB), at Brookhaven National Laboratory, is a database containing information on experimentally determined three-dimensional structures of proteins, nucleic acids, and other biological macromolecules, with approximately 9000 entries. The PDB has a 27-year history of service to a global community of researchers, educators, and students in a wide variety of scientific disciplines. Data are easily submitted via PDB's WWW-based tool AutoDep, in either PDB or mmCIF format, and are most conveniently examined via PDB's WWW-based tool 3DB Browser. Collaborative centers have been, and continue to be, established worldwide to assist in data deposition, archiving, and distribution.

The early days of bioinformatics publishing

A brief history of the early days of publishing in the bioinformatics field is presented.

History, implementation, and current status of the National Spinal Cord Injury Database

OBJECTIVE

To summarize a 25-year history of the Model Spinal Cord Injury Program and the coexistent National Spinal Cord Injury Database and provide the status of the Database with a discussion of the strengths and weaknesses.

DESIGN

Inception cohort.

SETTING

Model spinal cord injury systems throughout the United States.

RESULTS

As of September 1998, the National Spinal Cord Injury Database included abbreviated registry records on 6,085 new patients, more complete initial injury and hospitalization records on 18,969 new patients, and 78,627 annual follow up records on those persons. Although stability and continuity of the Database has been a priority since it was started, some changes were needed to meet the changes in health care, health care policy, and new technology.

CONCLUSION

This large database can now provide a wealth of information about short- and long-term outcomes, provide data on which future health care policies can be evaluated, and act as a source for answers to future research questions.

The Danish Cancer Registry--history, content, quality and use

The Danish Cancer Registry is a population-based registry containing data on the incidence of cancer throughout Denmark since 1943. Reporting of cancer was made mandatory by administrative order in 1987. Details of individual cases of cancer are available according to the 7th revision of the International Classification of Diseases (ICD) for all years, and according to the ICD-O since 1978. A core data set is kept on each individual which includes date of birth, sex, date of cancer diagnosis, method of verification, date of death and cause of death. This paper describes the history of the registry, its data sources and its procedures, including quality control and access to data. Integration of both research activities and registration since the inception of the Registry has maintained the completeness and validity of the data for 1943-1996.

Some reflections on the early days of sequence searching

Russell Doolittle is a biocomputing pioneer who was among the first to use computers in the 1960s to compare sequences. He contributed to the discovery of unforeseen sequence similarities, such as the relationship between v-src and v-mos. Doolittle's reflection demonstrates the enormous advances made in bioinformatics, soft- and hardware, and the concurrent explosion in data storage and acceleration of communication. Today's advanced technology was not available at the beginning of Doolittle's career, when no databases existed, and researchers knew by heart most of the sequences which had been published.

An efficient delivery of historical information for the Mendelian Inheritance in Man database

The ability to manage information with regard to changes in a database is critical for quality control. This information can also provide audit trails about the time of the change and the person who made the change. In addition, historical information can provide the proper context in which to interpret the relationships between the current and past data. In most genomic databases, only the most recent copy of the information is presented to the user, thereby losing the audit trail and the historical context. Therefore, we have constructed a delivery mechanism for the historical information in the Mendelian Inheritance in Man database. Furthermore, this feature was designed to optionally display only the changes so that the user can bypass the unchanged portions of the text. It was anticipated that technical problems would influence the acceptance of this information delivery. However, the involvement of the editorial staff became the critical factor.

The Society of Thoracic Surgeons National Database status report

This report describes the development of the first known national surgical database designed for the practicing community cardiothoracic surgeon. Acceptance by members of The Society of Thoracic Surgeons has been gratifying. The number of patients on the system has grown from 116,109 at the end of 1991 to an anticipated 350,000 to 450,000 by the end of 1993. At the time of this report, 842 surgeons were participating, and more than 1,200 will be on the system by the end of 1993. A risk stratification system has been incorporated into the software, which predicts each patient's risk based on the individual surgeon's past experience. Trend analyses demonstrate a substantial increase in the number of patients at increased risk for perioperative death for coronary artery bypass operations over the past 5 years, while observed mortality has remained relatively constant. Programs are available for adult and congenital heart disease, lung cancer, and esophageal cancer, and modules for mediastinal tumors, pleural disorders, and benign pulmonary disease will soon be added. We anticipate that growth will continue as the need for practice profile data increases because of reimbursement issues.

Clinical research databases--a historical review

The increasing importance of computer-stored databases for clinical research prompted a historical review of their evolution over the past three decades. The special problems associated with the computer processing of clinical research data were reviewed, and the various types of clinical research registers and databases were described.