Survey-based naming conventions for use in OBO Foundry ontology development

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data

Ontologies and Information Extraction

This report argues that, even in the simplest cases, IE is an ontology-driven process. It is not a mere text filtering method based on simple pattern matching and keywords, because the extracted pieces of texts are interpreted with respect to a predefined partial domain model. This report shows that depending on the nature and the depth of the interpretation to be done for extracting the information, more or less knowledge must be involved. This report is mainly illustrated in biology, a domain in which there are critical needs for content-based exploration of the scientific literature and which becomes a major application domain for IE

Ontology population for open-source intelligence: A GATE-based solution

Open-Source INTelligence is intelligence based on publicly available sources such as news sites, blogs, forums, etc. The Web is the primary source of information, but once data are crawled, they need to be interpreted and structured. Ontologies may play a crucial role in this process, but because of the vast amount of documents available, automatic mechanisms for their population are needed, starting from the crawled text. This paper presents an approach for the automatic population of predefined ontologies with data extracted from text and discusses the design and realization of a pipeline based on the General Architecture for Text Engineering system, which is interesting for both researchers and practitioners in the field. Some experimental results that are encouraging in terms of extracted correct instances of the ontology are also reported. Furthermore, the paper also describes an alternative approach and provides additional experiments for one of the phases of our pipeline, which requires the use of predefined dictionaries for relevant entities. Through such a variant, the manual workload required in this phase was reduced, still obtaining promising results

Enactivism, other minds, and mental disorders

Although enactive approaches to cognition vary in terms of their character and scope, all endorse several core claims. The first is that cognition is tied to action. The second is that cognition is composed of more than just in-the-head processes; cognitive activities are externalized via features of our embodiment and in our ecological dealings with the people and things around us. I appeal to these two enactive claims to consider a view called “direct social perception” : the idea that we can sometimes perceive features of other minds directly in the character of their embodiment and environmental interactions. I argue that if DSP is true, we can probably also perceive certain features of mental disorders as well. I draw upon the developmental psychologist Daniel Stern’s notion of “forms of vitality”—largely overlooked in these debates—to develop this idea, and I use autism as a case study. I argue further that an enactive approach to DSP can clarify some ways we play a regulative role in shaping the temporal and phenomenal character of the disorder in question, and it may therefore have practical significance for both the clinical and therapeutic encounter