TitleDispositions, capacities, abilities. Towards a classification of the powers of living beings
In my talk I want to investigate the active and passive powers of living beings. Usually, abilities are classified as dispositions to voluntary action. I want to argue, first, that a broader concept of abilities is necessary both in the case of human beings and in the case of other animals. Second, abilities are not a species of dispositions.
TitleThe Pragmatics and Formality of Authoring Ontologies
In this talk I will explore ideas of pragmatics and formality in our approaches to authoring biomedical ontologies. Formality can come from the philosophical approach to ontology development, from the area of knowledge representation, ontological analysis used and the rigor of the method applied in the ontology development. I will advocate a moderately pragmatic approach for one's philosophical rigor and being much more formal, but not always so, on the representational side. I will illustrate both my pragmatics and formality with some recent work on normalising the Molecular Function sub-ontology of the Gene Ontology. This shows that the functions of gene products are very few; that upper ontologies can be of practical use and avoiding 'distinctions that make no difference'. Fully normalising the GO's molecular function ontology shows some reasonable insights in the biology and again demonstrates how a formal KR language can help. Even here, to make it work sensibly, pragmatics also come into play. The formality of using a language with strict semantics can be demonstrated, aided by some ontological rigor, but with some representational compromises or pragmatics to make the reasoning with the ontology sensible. At the end of the talk I will give a set of guidelines that I use that help me decide whether or not to be pragmatic or formal when authoring an ontology.
(listing according to author notification on Aug 25, 2016; ordered by surnames of first authors)
Deep Learning meets Semantic Web: A feasibility study with the Cardiovascular Disease Ontology and PubMed citations
Mercedes Arguello Casteleiro, George Demetriou, Warren Read, Maria Jesus Fernandez-Prieto, Diego Maseda-Fernandez, Goran Nenadic, Julie Klein, John Keane and Robert Stevens
A document-centric approach for developing the tolAPC ontology
Aisha Blfgeh, Jennifer Warrender, Catharien Hilkens and Phillip Lord
Challenges and opportunities for system biology standards and tools in medical research
Matthias König, Anika Oellrich, Dagmar Waltemath, Richard Jb Dobson, Tim Jp Hubbard and Olaf Wolkenhauer
Querying standardized EHRs by a Search Ontology XML extension (SOX)
Stefan Kropf, Alexandr Uciteli, Kerstin Denecke and Heinrich Herre
Towards standardized evidence descriptors for metabolite annotations
Daniel Schober, Reza M. Salek and Steffen Neumann
A Whiteheadian approach to data and knowledge
Sebastian Siemoleit and Heinrich Herre
Risk Identification Ontology (RIO): An ontology for specification and identification of perioperative risks
Alexandr Uciteli, Juliane Neumann, Kais Tahar, Kutaiba Saleh, Stephan Stucke, Sebastian Faulbrück-Röhr, André Kaeding, Martin Specht, Tobias Schmidt, Thomas Neumuth, Andreas Besting, Frank Portheine and Heinrich Herre
A modelling pattern for multi-track dispositions for life-science ontologies
Adrien Barton and Ludger Jansen
FAIRDOM approach for semantic interoperability of systems biology data and models
Olga Krebs, Katy Wolstencroft, Natalie Stanford, Norman Morrison, Martin Golebiewski, Stuart Owen, Quyen Nguyen, Jacky Snoep, Wolfgang Mueller and Carole Goble
Qualitative assessment of annotations using SNOMED CT
Jose Antonio Miñarro-Giménez, Catalina Martínez Costa and Stefan Schulz
Extracting process graphs from medical text data
Ontological interpretation of biomedical database annotations
Filipe Santana Da Silva, Ludger Jansen, Fred Freitas and Stefan Schulz
Scope and Goals
Medicine, biology and life sciences produce hardly manageable and comprehensible amounts of data, information, and knowledge. Their computer-based retrieval, processing, integration, as well as their conceptual foundation, interpretation and application presents ever new challenges to existing methods of knowledge representation, data bases, and data analysis. In the life sciences, enormous data sets are being produced in connection with biological and medical experiments, aiming to unravel biological interconnections for a better understanding in order to offer patients the best possible therapies. Data management and data processing in the life sciences ranges from the best possible integration and usage of distributed, heterogeneous data to the best possible obfuscation of medical data.
This integrated workshop covers the overall spectrum of biomedical information management, from experimental data acquisition and preprocessing, across analysis, structuring and interpretation of data, up to developing structured representations of knowledge, in particular in the form of ontologies, with their various applications. The aims of this workshop are to exchange ideas, to discuss new results and applications as well as to inspire cooperation. The workshop has an interdisciplinary character. It fosters the collaboration between ontologists, computer scientists, bio-informaticians, medical information scientists, applied logicians, as well as the cooperation with physicians, bio-chemists, and biometricians. Scientists, professionals as well as students in academia and industry are welcome to share knowledge and experience at ODLS.
Submission of contributions
Wed, June 22, 2016
Thu, August 25, 2016
Submission of camera-ready version
Thu, September 15, 2016! strict, UTC-12 !
Registration for ODLS
Sun, September 18, 2016 *
Thu-Fri, September 29–30, 2016
* At least one author of each accepted submission must register by September 18, 2016.
For registration, please send an email to firstname.lastname@example.org and pay the contribution towards expenses by bank transfer (see below).
In the email one should be able to read / find the following information:
first name, last name, and email address of the registrant(s)
possibly a preferred shorthand of the affiliation (to be used on the name badge)
possibly a billing address as required by your affiliation (otherwise the Confirmation of Registration and Participation may contain only your affiliation in the address field)
if applicable, indication of being a student or of membership in GI, GMDS or IAOA
if applicable, the title of the submission that the registrant presents
joining the dinner on Thursday, Sep 29: yes / maybe / no
The registration period opened on Thursday, September 01, 2016. Registrations and, if necessary, cancellations shall be made by Sunday, September 18, 2016, please.
Concerning the presentation of accepted submissions it is expected that at least one of the authors will participate in the workshop. Presenting authors should register as early as possible and should specify which paper they will present.
Interested parties (without contribution to any submission) are equally welcome to participate.
Contribution towards Expenses
Every participant is charged a contribution towards expenses, which amounts to
30 EUR regular,
25 EUR for members of GI, GMDS or IAOA,
20 EUR for students.
It covers mainly catering during the breaks of both days, excluding dinner. One lunch at the campus cafeteria might be included, depending on the available budget.
Payment by bank transfer: (replace <name> by the name for whom the payment is made)
special rate (incl. breakfast) is 65 EUR per person and night with booking code: «Leibniz Institut für Pflanzenbiochemie»
Here is some travel info how you get to IPB from Ankerhof to the IPB by Tram:
Take the Tram line 4 or 5 from Saline towards Kröllwitz and get off at Weinberg Campus Station, see at the HAVAG map . The ride takes around 6 minutes. You can buy the ticket right in the Tram when you enter, but there are also ticket machines at the stations. Although there are week tickets, you might still consider to buy 2 one-way tickets («Einzelfahrkarte») each day (one costs 2 Euros), or even better, since you are going less than 4 stations a trip, you can pay less (1.40 EUR) for a short range ticket («Kurzstrecke»). So that is probably what you want. In any case you want the 1 Zone Stadt Halle Tarif when you look-up the ticket in the machine.
Submissions to the workshop can be abstracts of 1–2 pages or papers of 4–6 pages (any such length is equally welcome; 6 pages is the strict maximum, including references).
Contributions in English are highly recommended, but submissions in German can also be accepted. Besides original submissions, abstracts on work accepted for and possibly already presented at other events can likewise be accepted.
The preferred file format for submissions is PDF, other admitted formats are Microsoft Word (DOC and DOCX) and Postscript (PS). Please use the corresponding template for submissions, either the Microsoft Word template or the LaTeX template, for which there is a sample file. (NB: The Word template has been substantially revised for ODLS 2016 and there is a minor change in the LaTeX sample file, while the LaTeX template is unchanged since 2010. For more details or for originally related files, see the ODLS series page.)
Accepted abstracts and papers will be made available electronically by the date of the workshop. After the workshop, authors of selected submissions will be invited to submit revised and extended versions to the Journal of Biomedical Semantics (JBSM). These manuscripts must then be written in English and will be re-reviewed.
The following topics are of (equal) relevance for the workshop. Submissions regarding other related topics are likewise welcome.
Ontologies and ontological analysis in biology, medicine and clinical research, e.g.
Ontologies for biological or medical phenotypes
Ontologies for biochemistry, neuro-biology, ecology
Process ontologies in systems biology and medicine
Ontologies for the specification of clinical trial data
Foundational ontologies (with indicated applications in life sciences),
e.g. of time and space, properties, roles, functions, material objects
Medical terminologies and their applications
Linking ontologies to terminologies, models and data standards
Methods and tools for the development, management and application of ontologies, e.g.
Ontology crossreferencing, mapping, integration and evolution
Quality assurance, best practices and evaluation of ontologies
Provenance, audit and evidence ontologies in life sciences
Ontology learning and refinement, e.g. by text mining
Ontology portals and libraries
Integrative data semantics
Semantic or ontology-based data annotation, enrichment, analysis and interpretation
Data management methods and systems in biology, medicine and health care, e.g. for
Heterogeneity and integration of data, including of Linked Data and Big Data
Management, retrieval and sharing of big data and/or complex data sets
Curation, analysis and visualization of data in life sciences
Omics-data for diagnosis and therapy
Biomedical metadata and metadata management
Generic transformation of clinical data into Semantic Web standards
Data protection of clinical data
Text mining and transformation of unstructured into structured data
Use of biomedical ontologies in text mining
Applications of biomedical ontologies in the Semantic Web, for Linked Open Data or Big Data
Life sciences applications enabled by the Semantic Web or Linked Open Data