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1.  Structuring research methods and data with the research object model: genomics workflows as a case study 
One of the main challenges for biomedical research lies in the computer-assisted integrative study of large and increasingly complex combinations of data in order to understand molecular mechanisms. The preservation of the materials and methods of such computational experiments with clear annotations is essential for understanding an experiment, and this is increasingly recognized in the bioinformatics community. Our assumption is that offering means of digital, structured aggregation and annotation of the objects of an experiment will provide necessary meta-data for a scientist to understand and recreate the results of an experiment. To support this we explored a model for the semantic description of a workflow-centric Research Object (RO), where an RO is defined as a resource that aggregates other resources, e.g., datasets, software, spreadsheets, text, etc. We applied this model to a case study where we analysed human metabolite variation by workflows.
We present the application of the workflow-centric RO model for our bioinformatics case study. Three workflows were produced following recently defined Best Practices for workflow design. By modelling the experiment as an RO, we were able to automatically query the experiment and answer questions such as “which particular data was input to a particular workflow to test a particular hypothesis?”, and “which particular conclusions were drawn from a particular workflow?”.
Applying a workflow-centric RO model to aggregate and annotate the resources used in a bioinformatics experiment, allowed us to retrieve the conclusions of the experiment in the context of the driving hypothesis, the executed workflows and their input data. The RO model is an extendable reference model that can be used by other systems as well.
The Research Object is available at
The Wf4Ever Research Object Model is available at
Electronic supplementary material
The online version of this article (doi:10.1186/2041-1480-5-41) contains supplementary material, which is available to authorized users.
PMCID: PMC4177597  PMID: 25276335
Semantic web models; Scientific workflows; Digital libraries; Genome wide association study
2.  Preserving sequence annotations across reference sequences 
Journal of Biomedical Semantics  2014;5(Suppl 1):S6.
Matching and comparing sequence annotations of different reference sequences is vital to genomics research, yet many annotation formats do not specify the reference sequence types or versions used. This makes the integration of annotations from different sources difficult and error prone.
As part of our effort to create linked data for interoperable sequence annotations, we present an RDF data model for sequence annotation using the ontological framework established by the OBO Foundry ontologies and the Basic Formal Ontology (BFO). We defined reference sequences as the common domain of integration for sequence annotations, and identified three semantic relationships between sequence annotations. In doing so, we created the Reference Sequence Annotation to compensate for gaps in the SO and in its mapping to BFO, particularly for annotations that refer to versions of consensus reference sequences. Moreover, we present three integration models for sequence annotations using different reference assemblies.
We demonstrated a working example of a sequence annotation instance, and how this instance can be linked to other annotations on different reference sequences. Sequence annotations in this format are semantically rich and can be integrated easily with different assemblies. We also identify other challenges of modeling reference sequences with the BFO.
PMCID: PMC4108922  PMID: 25093075
3.  Developing medical educators – a mixed method evaluation of a teaching education program 
Medical Education Online  2014;19:10.3402/meo.v19.23868.
It is well accepted that medical faculty teaching staff require an understanding of educational theory and pedagogical methods for effective medical teaching. The purpose of this study was to evaluate the effectiveness of a 5-day teaching education program.
An open prospective interventional study using quantitative and qualitative instruments was performed, covering all four levels of the Kirkpatrick model: Evaluation of 1) ‘Reaction’ on a professional and emotional level using standardized questionnaires; 2) ‘Learning’ applying a multiple choice test; 3) ‘Behavior’ by self-, peer-, and expert assessment of teaching sessions with semistructured interviews; and 4) ‘Results’ from student evaluations.
Our data indicate the success of the educational intervention at all observed levels. 1) Reaction: The participants showed a high acceptance of the instructional content. 2) Learning: There was a significant increase in knowledge (P<0.001) as deduced from a pre-post multiple-choice questionnaire, which was retained at 6 months (P<0.001). 3) Behavior: Peer-, self-, and expert-assessment indicated a transfer of learning into teaching performance. Semistructured interviews reflected a higher level of professionalism in medical teaching by the participants. 4) Results: Teaching performance ratings improved in students’ evaluations.
Our results demonstrate the success of a 5-day education program in embedding knowledge and skills to improve performance of medical educators. This multimethodological approach, using both qualitative and quantitative measures, may serve as a model to evaluate effectiveness of comparable interventions in other settings.
PMCID: PMC3969510  PMID: 24679671
faculty development; medical education; medical teacher; educational theory; collaborative feedback
4.  Automated workflow-based exploitation of pathway databases provides new insights into genetic associations of metabolite profiles 
BMC Genomics  2013;14:865.
Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) that associate with clinical phenotypes, but these SNPs usually explain just a small part of the heritability and have relatively modest effect sizes. In contrast, SNPs that associate with metabolite levels generally explain a higher percentage of the genetic variation and demonstrate larger effect sizes. Still, the discovery of SNPs associated with metabolite levels is challenging since testing all metabolites measured in typical metabolomics studies with all SNPs comes with a severe multiple testing penalty. We have developed an automated workflow approach that utilizes prior knowledge of biochemical pathways present in databases like KEGG and BioCyc to generate a smaller SNP set relevant to the metabolite. This paper explores the opportunities and challenges in the analysis of GWAS of metabolomic phenotypes and provides novel insights into the genetic basis of metabolic variation through the re-analysis of published GWAS datasets.
Re-analysis of the published GWAS dataset from Illig et al. (Nature Genetics, 2010) using a pathway-based workflow (, confirmed previously identified hits and identified a new locus of human metabolic individuality, associating Aldehyde dehydrogenase family1 L1 (ALDH1L1) with serine/glycine ratios in blood. Replication in an independent GWAS dataset of phospholipids (Demirkan et al., PLoS Genetics, 2012) identified two novel loci supported by additional literature evidence: GPAM (Glycerol-3 phosphate acyltransferase) and CBS (Cystathionine beta-synthase). In addition, the workflow approach provided novel insight into the affected pathways and relevance of some of these gene-metabolite pairs in disease development and progression.
We demonstrate the utility of automated exploitation of background knowledge present in pathway databases for the analysis of GWAS datasets of metabolomic phenotypes. We report novel loci and potential biochemical mechanisms that contribute to our understanding of the genetic basis of metabolic variation and its relationship to disease development and progression.
PMCID: PMC3879060  PMID: 24320595
Genome-wide association; Metabolite; Genotype-phenotype prioritization; Bioinformatics; Pathway databases
5.  Competence-based curriculum development for general practice in Germany: a stepwise peer-based approach instead of reinventing the wheel 
BMC Research Notes  2013;6:314.
Improving postgraduate medical training is one important step to attract more medical students into general practice. Keeping pace with international developments moving to competence-based curricula for general practice training, the aim of this project was to develop and implement such a curriculum in Germany.
A five-step, peer-based method was used for the curriculum development process including panel testing and a “test version” of the curriculum for the pilot implementation phase. The CanMEDS framework served as a basis for a new German competence-based curriculum in general practice training. Four curricula from European countries and Canada were reviewed and, following required cultural adaptions, key strengths from these were integrated. For the CanMEDS “medical expertise” element of the curriculum, the WONCA ICPC-2 classification of patient’s “reason for encounters” was also integrated.
Altogether, 37 participants were involved in the development process representing 12 different federal states in Germany, and including an expert advisor from Denmark. An official “test version” of the curriculum consisting of three parts: medical expertise, additional competencies and medical procedures was established. A system of self-assessment for trainees was integrated into the curriculum using a traffic light scale. Since March 2012, the curriculum has been made freely available online as a “test version”. In 2014, an evaluation is planned using feedback from users of the test model as a further stage of the implementation process.
The first German competence-based curriculum for general practice training has been developed using a pragmatic peer controlled approach and implementation is being trialed with a “test version” of the curriculum. This model project and its peer-based methodology may support competence-based curriculum development for other medical specialties both inside and outside Germany.
PMCID: PMC3751065  PMID: 23937795
Curriculum development; General practice; Physician shortage; CanMEDS
6.  Speeding up research with the Semantic Web 
Orphanet Journal of Rare Diseases  2012;7(Suppl 2):A11.
PMCID: PMC3504542
7.  Video-assisted feedback in general practice internships using German general practitioner's guidelines  
Introduction: The planned modification of the Medical Licenses Act in Germany will strengthen the specialty of general practice. Therefore, medical students should get to know the daily routine of general practitioners during their academic studies. At least 10% of students should get the possibility to spend one quarter of the internship, in the last year of their academic studies, in a practice of family medicine.
The demonstrated teaching method aims at giving feedback to the student based on video recordings of patient consultations (student-patient) with the help of a checklist.
Video-feedback is already successful used in medical teaching in Germany and abroad.
This feasibility study aims at assessing the practicability of video-assisted feedback as a teaching method during internship in general practice.
Teaching method: First of all, the general practice chooses a guideline as the learning objective. Secondly, a subsequent patient – student – consultation is recorded on video. Afterwards, a video-assisted formative feedback is given by the physician. A checklist with learning objectives (communication, medical examination, a structured case report according to the guideline) is used to structure the feedback content.
Feasibility: The feasibility was assessed by a semi structured interview in order to gain insight into barriers and challenges for future implementation. The teaching method was performed in one general practice. Afterwards the teaching physician and the trainee intern were interviewed.
The following four main categories were identified: feasibility, performance, implementation in daily routine, challenges of the teaching concept.
The results of the feasibility study show general practicability of this approach. Installing a video camera in one examination room may solve technical problems. The trainee intern mentioned theoretical and practical benefits using the guideline. The teaching physician noted the challenge to reflect on his daily routines in the light of evidence-based guidelines.
Conclusion: This teaching method supports quality control and standardizing of learning objectives during the internship in general practice by using general practice guidelines. The use of a checklist enhances this method in general practice. We consider the presented teaching method in the context of the planned modification of the Medical Licenses Act is part of quality control and standardisation of medical teaching during general practice internships. In order to validate these presumptions, further, evaluation of this method concerning the learning objectives using the guidelines of general practice need to be carried out.
PMCID: PMC3525913  PMID: 23255963
Video feedback; general practice; guideline; evidence based medicine; internship
8.  Train the Trainer for general practice trainer - a report of the pilot within the programme Verbundweiterbildungplus 
Background: Since 2008 the Verbundweiterbildungplus programme of the Competence Centre General Practice Baden-Wuerttemberg offers continual improvement with regards to content and structure of general practice training. The programme uses the didactical concept of the CanMEDs competencies, which were developed in Canada, as a postgraduate medical training framework. Train the trainer (TTT)-programmes are an additional important element of these contentual optimisations of postgraduate training. Within this article we describe the conception and evaluation of the first TTT-workshop within the programme Verbundweiterbildungplus.
Methods: The conception of the first TTT-workshop was influenced by results of a survey of general practitioner (GP) trainers and by experiences with teaching GP trainers involved in medical undergraduate teaching. A questionnaire was designed to get a self-assessment about organisational and didactic aspects oriented on the CanMEDs competencies of postgraduate medical training. In addition, the workshop was evaluated by the participants.
Results: The workshop lasted 12 teaching units and included the following elements: introduction into the CanMEDs competencies, feedback training, fault management, legal and organisational aspects of post graduate training. From the 29 participating trainers 76% were male and on average 57 years old. The evaluation showed a good to very good acceptance of the workshop. Initial self-rating showed the need of improving in the fields of determining learning objectives, providing formative feedback and incorporation of a trainee. Most trainers rated themselves as very good in procure CanMEDs competencies with the exclusion of the competencies “Manager“ and “Scholar“.
Conclusion: A TTT-programme is an important method to improve GP training which has not been used in Germany so far. Such a GP TTT-programme should highlight especially training in providing feedback and teaching in management aspects. Results of this article add information that can be used for developing TTT-programmes also in other specialties.
PMCID: PMC3374139  PMID: 22737198
General Practice; Train the Trainer; Feedback Training; Management; Postgraduate Medical Training
9.  Students' performing of practical research tasks for their scientific qualification - an approach within the family practice internship in undergraduate education 
Background: Future physicians should be educated in evidence-based medicine. So it is of growing importance for medical students to acquire both practical medical and basic research competencies. However, possibilities and concepts focusing on the acquisition of basic practical research competencies during undergraduate medical studies in Germany are rare. Therefore the aim of this article is to develop a didactic and methodological concept for research-based teaching and learning based on the initial results from the block placement in general practice.
Methods: Connecting medical didactic approaches with classic educational control measures (knowledge, acceptance and transfer evaluation, process evaluation, and outcome evaluation).
Results: We describe the steps for implementing a research task into the block placement in general practice. Also stressed is the need to develop didactic material and the introduction of structural changes. Furthermore, these steps are integrated with the individual educational control measures. A summary serves to illustrate the learning and teaching concept (Block Placement Plus).
Conclusion: The conceptualisation of the Block Placement Plus leads to changes in the daily life routine of medical education during the undergraduate block placement in general practice. The concept can in principle be transferred to other courses. It may serve as an instrument for teachers within the framework of a longitudinal curriculum for the scientific qualification of medical students.
PMCID: PMC3149465  PMID: 21818234
research competencies; undergraduate medical education; general practice
10.  myExperiment: a repository and social network for the sharing of bioinformatics workflows 
Nucleic Acids Research  2010;38(Web Server issue):W677-W682.
myExperiment ( is an online research environment that supports the social sharing of bioinformatics workflows. These workflows are procedures consisting of a series of computational tasks using web services, which may be performed on data from its retrieval, integration and analysis, to the visualization of the results. As a public repository of workflows, myExperiment allows anybody to discover those that are relevant to their research, which can then be reused and repurposed to their specific requirements. Conversely, developers can submit their workflows to myExperiment and enable them to be shared in a secure manner. Since its release in 2007, myExperiment currently has over 3500 registered users and contains more than 1000 workflows. The social aspect to the sharing of these workflows is facilitated by registered users forming virtual communities bound together by a common interest or research project. Contributors of workflows can build their reputation within these communities by receiving feedback and credit from individuals who reuse their work. Further documentation about myExperiment including its REST web service is available from Feedback and requests for support can be sent to
PMCID: PMC2896080  PMID: 20501605
11.  BioCatalogue: a universal catalogue of web services for the life sciences 
Nucleic Acids Research  2010;38(Web Server issue):W689-W694.
The use of Web Services to enable programmatic access to on-line bioinformatics is becoming increasingly important in the Life Sciences. However, their number, distribution and the variable quality of their documentation can make their discovery and subsequent use difficult. A Web Services registry with information on available services will help to bring together service providers and their users. The BioCatalogue ( provides a common interface for registering, browsing and annotating Web Services to the Life Science community. Services in the BioCatalogue can be described and searched in multiple ways based upon their technical types, bioinformatics categories, user tags, service providers or data inputs and outputs. They are also subject to constant monitoring, allowing the identification of service problems and changes and the filtering-out of unavailable or unreliable resources. The system is accessible via a human-readable ‘Web 2.0’-style interface and a programmatic Web Service interface. The BioCatalogue follows a community approach in which all services can be registered, browsed and incrementally documented with annotations by any member of the scientific community.
PMCID: PMC2896129  PMID: 20484378
12.  Does GPs' self-perception of their professional role correspond to their social self-image? - A qualitative study from Germany 
BMC Family Practice  2010;11:10.
There is a decline in the relative numbers of general practitioners in Germany. Earlier research showed that the professional relationship between general practitioners and specialists is overshadowed by conflicts which could influence medical students not to choose a career in general practice. The aim of the study is to analyse potential discrepancies between general practitioners' self-perception of their professional role and their social self-image in relation to medical specialists and to identify potential barriers that might prevent medical students from becoming a general practitioner.
A qualitative study design consisting of 16 interviews with general practitioners was chosen. Data analysis was carried out using the qualitative content analysis by Philipp Mayring.
There is a discrepancy between general practitioners' professional self-perception and how they perceive they are viewed by specialists. General practitioners communicate a positive self-perception of their professional role. While general practitioners think that specialists in outpatient care have a positive view on general practice, it is assessed to be negative by specialists working in hospitals and as medical teachers.
The negatively influenced social self-image may originate particularly from "badmouthing" general practitioners at universities and in hospitals. "Badmouthing" demonstrates the importance of the consideration of psychological aspects in medical teachers and hospital specialists acting as role models. Negative comments should be considered as an important factor in influencing medical students and trainees' career choices. These aspects should be more integrated in future medical education curricula.
PMCID: PMC2834633  PMID: 20132534
13.  Structuring and extracting knowledge for the support of hypothesis generation in molecular biology 
BMC Bioinformatics  2009;10(Suppl 10):S9.
Hypothesis generation in molecular and cellular biology is an empirical process in which knowledge derived from prior experiments is distilled into a comprehensible model. The requirement of automated support is exemplified by the difficulty of considering all relevant facts that are contained in the millions of documents available from PubMed. Semantic Web provides tools for sharing prior knowledge, while information retrieval and information extraction techniques enable its extraction from literature. Their combination makes prior knowledge available for computational analysis and inference. While some tools provide complete solutions that limit the control over the modeling and extraction processes, we seek a methodology that supports control by the experimenter over these critical processes.
We describe progress towards automated support for the generation of biomolecular hypotheses. Semantic Web technologies are used to structure and store knowledge, while a workflow extracts knowledge from text. We designed minimal proto-ontologies in OWL for capturing different aspects of a text mining experiment: the biological hypothesis, text and documents, text mining, and workflow provenance. The models fit a methodology that allows focus on the requirements of a single experiment while supporting reuse and posterior analysis of extracted knowledge from multiple experiments. Our workflow is composed of services from the 'Adaptive Information Disclosure Application' (AIDA) toolkit as well as a few others. The output is a semantic model with putative biological relations, with each relation linked to the corresponding evidence.
We demonstrated a 'do-it-yourself' approach for structuring and extracting knowledge in the context of experimental research on biomolecular mechanisms. The methodology can be used to bootstrap the construction of semantically rich biological models using the results of knowledge extraction processes. Models specific to particular experiments can be constructed that, in turn, link with other semantic models, creating a web of knowledge that spans experiments. Mapping mechanisms can link to other knowledge resources such as OBO ontologies or SKOS vocabularies. AIDA Web Services can be used to design personalized knowledge extraction procedures. In our example experiment, we found three proteins (NF-Kappa B, p21, and Bax) potentially playing a role in the interplay between nutrients and epigenetic gene regulation.
PMCID: PMC2755830  PMID: 19796406
14.  SigWin-detector: a Grid-enabled workflow for discovering enriched windows of genomic features related to DNA sequences 
BMC Research Notes  2008;1:63.
Chromosome location is often used as a scaffold to organize genomic information in both the living cell and molecular biological research. Thus, ever-increasing amounts of data about genomic features are stored in public databases and can be readily visualized by genome browsers. To perform in silico experimentation conveniently with this genomics data, biologists need tools to process and compare datasets routinely and explore the obtained results interactively. The complexity of such experimentation requires these tools to be based on an e-Science approach, hence generic, modular, and reusable. A virtual laboratory environment with workflows, workflow management systems, and Grid computation are therefore essential.
Here we apply an e-Science approach to develop SigWin-detector, a workflow-based tool that can detect significantly enriched windows of (genomic) features in a (DNA) sequence in a fast and reproducible way. For proof-of-principle, we utilize a biological use case to detect regions of increased and decreased gene expression (RIDGEs and anti-RIDGEs) in human transcriptome maps. We improved the original method for RIDGE detection by replacing the costly step of estimation by random sampling with a faster analytical formula for computing the distribution of the null hypothesis being tested and by developing a new algorithm for computing moving medians. SigWin-detector was developed using the WS-VLAM workflow management system and consists of several reusable modules that are linked together in a basic workflow. The configuration of this basic workflow can be adapted to satisfy the requirements of the specific in silico experiment.
As we show with the results from analyses in the biological use case on RIDGEs, SigWin-detector is an efficient and reusable Grid-based tool for discovering windows enriched for features of a particular type in any sequence of values. Thus, SigWin-detector provides the proof-of-principle for the modular e-Science based concept of integrative bioinformatics experimentation.
PMCID: PMC2533338  PMID: 18710516

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