Constraint-Guided Workflow Composition Based on the EDAM Ontology

Methods for the automatic composition of services into executable workflows need detailed knowledge about the application domain, in particular about the available services and their behavior in terms of input/output data descriptions. In this paper we discuss how the EMBRACE data and methods ontology (EDAM) can be used as background knowledge for the composition of bioinformatics workflows. We show by means of a small example domain that the EDAM knowledge facilitates finding possible workflows, but that additional knowledge is required to guide the search towards actually adequate solutions. We illustrate how the ability to flexibly formulate domain-specific and problem-specific constraints supports the workflow development process

Perspectives on automated composition of workflows in the life sciences [version 1; peer review: 2 approved]

Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the “big picture” of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic process of workflow development than we know today. We believe that this can lead to more robust, reusable, and sustainable workflows in the future.Stian Soiland-Reyes was supported by BioExcel-2 Centre of Excellence, funded by European Commission Horizon 2020 programme under European Commission contract H2020-INFRAEDI-02-2018 823830. Carole Goble was supported by EOSC-Life, funded by European Commission Horizon 2020 programme under grant agreement H2020-INFRAEOSC-2018-2 824087. We gratefully acknowledge the financial support from the Lorentz Center, ELIXIR, and the Leiden University Medical Center (LUMC) that made the workshop possible. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscriptPeer Reviewed"Article signat per 33 autors/es: Anna-Lena Lamprecht , Magnus Palmblad, Jon Ison, Veit Schwämmle , Mohammad Sadnan Al Manir, Ilkay Altintas, Christopher J. O. Baker, Ammar Ben Hadj Amor, Salvador Capella-Gutierrez, Paulos Charonyktakis, Michael R. Crusoe, Yolanda Gil, Carole Goble, Timothy J. Griffin , Paul Groth , Hans Ienasescu, Pratik Jagtap, Matúš Kalaš , Vedran Kasalica, Alireza Khanteymoori , Tobias Kuhn12, Hailiang Mei, Hervé Ménager, Steffen Möller, Robin A. Richardson, Vincent Robert9, Stian Soiland-Reyes, Robert Stevens, Szoke Szaniszlo, Suzan Verberne, Aswin Verhoeven, Katherine Wolstencroft "Postprint (published version

Synthesis of Scientific Workflows: Theory and Practice of an Instance-Aware Approach

The last two decades brought an explosion of computational tools and processes in many scientific domains (e.g., life-, social- and geo-science). Scientific workflows, i.e., computational pipelines, accompanied by workflow management systems, were soon adopted as a de-facto standard among non-computer scientists for orchestrating such computational processes. The goal of this dissertation is to provide a framework that would automate the orchestration of such computational pipelines in practice. We refer to such problems as scientific workflow synthesis problems. This dissertation introduces the temporal logic SLTLx, and presents a novel SLTLx-based synthesis approach that overcomes limitations in handling data object dependencies present in existing synthesis approaches. The new approach uses transducers and temporal goals, which keep track of the data objects in the synthesised workflow. The proposed SLTLx-based synthesis includes a bounded and a dynamic variant, which are shown in Chapter 3 to be NP-complete and PSPACE-complete, respectively. Chapter 4 introduces a transformation algorithm that translates the bounded SLTLx-based synthesis problem into propositional logic. The transformation is implemented as part of the APE (Automated Pipeline Explorer) framework, presented in Chapter 5. It relies on highly efficient SAT solving techniques, using an off-the-shelf SAT solver to synthesise a solution for the given propositional encoding. The framework provides an API (application programming interface), a CLI (command line interface), and a web-based GUI (graphical user interface). The development of APE was accompanied by four concrete application scenarios as case studies for automated workflow composition. The studies were conducted in collaboration with domain experts and presented in Chapter 6. Each of the case studies is used to assess and illustrate specific features of the SLTLx-based synthesis approach. (1) A case study on cartographic map generation demonstrates the ability to distinguish data objects as a key feature of the framework. It illustrates the process of annotating a new domain, and presents the iterative workflow synthesis approach, where the user tries to narrow down the desired specification of the problem in a few intuitive steps. (2) A case study on geo-analytical question answering as part of the QuAnGIS project shows the benefits of using data flow dependencies to describe a synthesis problem. (3) A proteomics case study demonstrates the usability of APE as an “off-the-shelf” synthesiser, providing direct integration with existing semantic domain annotations. In addition, a manual evaluation of the synthesised results shows promising results even on large real-life domains, such as the EDAM ontology and the complete bio.tools registry. (4) A geo-event question-answering study demonstrates the usability of APE within a larger question-answering system. This dissertation answers the goals it sets to solve. It provides a formal framework, accompanied by a lightweight library, which can solve real-life scientific workflow synthesis problems. Finally, the development of the library motivated an upcoming collaborative project in the life sciences domain. The aim of the project is to develop a platform which would automatically compose (using APE) and benchmark workflows in computational proteomics

Seamless Coarse Grained Parallelism Integration in Intensive Bioinformatics Workflows

To be easily constructed, shared and maintained, complex in silico bioinformatics analysis are structured as workflows. Furthermore, the growth of computational power and storage demand from this domain, requires workflows to be efficiently executed. However, workflow performances usually rely on the ability of the designer to extract potential parallelism. But atomic bioinformatics tasks do not often exhibit direct parallelism which may appears later in the workflow design process. In this paper, we propose a Model-Driven Architecture approach for capturing the complete design process of bioinformatics workflows. More precisely, two workflow models are specified: the first one, called design model, graphically captures a low throughput prototype. The second one, called execution model, specifies multiple levels of coarse grained parallelism. The execution model is automatically generated from the design model using annotation derived from the EDAM ontology. These annotations describe the data types connecting differents elementary tasks. The execution model can then be interpreted by a workflow engine and executed on hardware having intensive computation facility

Bioscientific data processing and modeling

Computer Systems, Imagery and Medi

Ontologies4Chem: The landscape of ontologies in chemistry

For a long time, databases such as CAS, Reaxys, PubChem or ChemSpider mostly rely on unique numerical identifiers or chemical structure identifiers like InChI, SMILES or others to link data across heterogeneous data sources. The retrospective processing of information and fragmented data from text publications to maintain these databases is a cumbersome process. Ontologies are a holistic approach to semantically describe data, information and knowledge of a domain. They provide terms, relations and logic to semantically annotate and link data building knowledge graphs. The application of standard taxonomies and vocabularies from the very beginning of data generation and along research workflows in electronic lab notebooks (ELNs), software tools, and their final publication in data repositories create FAIR data straightforwardly. Thus a proper semantic description of an investigation and the why, how, where, when, and by whom data was produced in conjunction with the description and representation of research data is a natural outcome in contrast to the retrospective processing of research publications as we know it. In this work we provide an overview of ontologies in chemistry suitable to represent concepts of research and research data. These ontologies are evaluated against several criteria derived from the FAIR data principles and their possible application in the digitisation of research data management workflows

Enabling Data-Guided Evaluation of Bioinformatics Workflow Quality

Bioinformatics can be divided into two phases, the first phase is conversion of raw data into processed data and the second phase is using processed data to obtain scientific results. It is important to consider the first “workflow” phase carefully, as there are many paths on the way to a final processed dataset. Some workflow paths may be different enough to influence the second phase, thereby, leading to ambiguity in the scientific literature. Workflow evaluation in bioinformatics enables the investigator to carefully plan how to process their data. A system that uses real data to determine the quality of a workflow can be based on the inherent biological relationships in the data itself. To our knowledge, a general software framework that performs real data-driven evaluation of bioinformatics workflows does not exist. The Evaluation and Utility of workFLOW (EUFLOW) decision-theoretic framework, developed and tested on gene expression data, enables users of bioinformatics workflows to evaluate alternative workflow paths using inherent biological relationships. EUFLOW is implemented as an R package to enable users to evaluate workflow data. EUFLOW is a framework which also permits user-guided utility and loss functions, which enables the type of analysis to be considered in the workflow path decision. This framework was originally developed to address the quality of identifier mapping services between UNIPROT accessions and Affymetrix probesets to facilitate integrated analysis1. An extension to this framework evaluates Affymetrix probeset filtering methods on real data from endometrial cancer and TCGA ovarian serous carcinoma samples.2 Further evaluation of RNASeq workflow paths demonstrates generalizability of the EUFLOW framework. Three separate evaluations are performed including: 1) identifier filtering of features with biological attributes, 2) threshold selection parameter choice for low gene count features, and 3) commonly utilized RNASeq data workflow paths on The Cancer Genome Atlas data. The EUFLOW decision-theoretic framework developed and tested in my dissertation enables users of bioinformatics workflows to evaluate alternative workflow paths guided by inherent biological relationships and user utility

A process model in platform independent and neutral formal representation for design engineering automation

An engineering design process as part of product development (PD) needs to satisfy ever-changing customer demands by striking a balance between time, cost and quality. In order to achieve a faster lead-time, improved quality and reduced PD costs for increased profits, automation methods have been developed with the help of virtual engineering. There are various methods of achieving Design Engineering Automation (DEA) with Computer-Aided (CAx) tools such as CAD/CAE/CAM, Product Lifecycle Management (PLM) and Knowledge Based Engineering (KBE). For example, Computer Aided Design (CAD) tools enable Geometry Automation (GA), PLM systems allow for sharing and exchange of product knowledge throughout the PD lifecycle. Traditional automation methods are specific to individual products and are hard-coded and bound by the proprietary tool format. Also, existing CAx tools and PLM systems offer bespoke islands of automation as compared to KBE. KBE as a design method incorporates complete design intent by including re-usable geometric, non-geometric product knowledge as well as engineering process knowledge for DEA including various processes such as mechanical design, analysis and manufacturing. It has been recognised, through an extensive literature review, that a research gap exists in the form of a generic and structured method of knowledge modelling, both informal and formal modelling, of mechanical design process with manufacturing knowledge (DFM/DFA) as part of model based systems engineering (MBSE) for DEA with a KBE approach. There is a lack of a structured technique for knowledge modelling, which can provide a standardised method to use platform independent and neutral formal standards for DEA with generative modelling for mechanical product design process and DFM with preserved semantics. The neutral formal representation through computer or machine understandable format provides open standard usage. This thesis provides a contribution to knowledge by addressing this gap in two-steps: • In the first step, a coherent process model, GPM-DEA is developed as part of MBSE which can be used for modelling of mechanical design with manufacturing knowledge utilising hybrid approach, based on strengths of existing modelling standards such as IDEF0, UML, SysML and addition of constructs as per author’s Metamodel. The structured process model is highly granular with complex interdependencies such as activities, object, function, rule association and includes the effect of the process model on the product at both component and geometric attributes. • In the second step, a method is provided to map the schema of the process model to equivalent platform independent and neutral formal standards using OWL/SWRL ontology for system development using Protégé tool, enabling machine interpretability with semantic clarity for DEA with generative modelling by building queries and reasoning on set of generic SWRL functions developed by the author. Model development has been performed with the aid of literature analysis and pilot use-cases. Experimental verification with test use-cases has confirmed the reasoning and querying capability on formal axioms in generating accurate results. Some of the other key strengths are that knowledgebase is generic, scalable and extensible, hence provides re-usability and wider design space exploration. The generative modelling capability allows the model to generate activities and objects based on functional requirements of the mechanical design process with DFM/DFA and rules based on logic. With the help of application programming interface, a platform specific DEA system such as a KBE tool or a CAD tool enabling GA and a web page incorporating engineering knowledge for decision support can consume relevant part of the knowledgebase