User and Developer Interaction with Editable and Readable Ontologies

The process of building ontologies is a difficult task that involves collaboration between ontology developers and domain experts and requires an ongoing interaction between them. This collaboration is made more difficult, because they tend to use different tool sets, which can hamper this interaction. In this paper, we propose to decrease this distance between domain experts and ontology developers by creating more readable forms of ontologies, and further to enable editing in normal office environments. Building on a programmatic ontology development environment, such as Tawny-OWL, we are now able to generate these readable/editable from the raw ontological source and its embedded comments. We have this translation to HTML for reading; this environment provides rich hyperlinking as well as active features such as hiding the source code in favour of comments. We are now working on translation to a Word document that also enables editing. Taken together this should provide a significant new route for collaboration between the ontologist and domain specialist.Comment: 5 pages, 5 figures, accepted at ICBO 2017, License update

Ontological imagination: transcending methodological solipsism and the promise of interdisciplinary studies

This text is a presentation of the notion of ontological imagination. It constitutes an attempt to merge two traditions: critical sociology and science and technology studies - STS. By contrasting these two intellectual traditions, I attempt to bring together: a humanist ethical-political sensitivity and a posthumanist ontological insight. My starting point is the premise that contemporary world needs new social ontology and new critical theory based on it in order to overcome the unconsciously adapted, “slice-based” modernist vision of social ontology. I am convinced that we need new ontological frameworks of the social combined with a research disposition which I refer to as ontological imagination

Electracy: the Internet as fifth estate

This account of an experimental approach to apparatus invention is offered as an introduction to apparatus study in general (grammatology), and electracy as the digital apparatus in particular. The approach is that of the Florida Research Ensemble (FRE), working through the EmerAgency, a virtual consultancy developed to translate Arts & Letters pedagogy into institutional consulting. The term 'electracy' (modeled on 'literacy,' a portmanteau of 'electricity' and Derrida's 'trace') was adopted to clarify that digital technologies are not reducible to a 'media literacy,' but include, besides technological innovations, inventions in the dimensions of institution formation and related skill sets, and identity behaviors individual and collective (ethics and politics). Current members of the FRE include Gregory Ulmer (University of Florida), John Craig Freeman (Emerson College), Barbara Jo Revelle (University of Florida), Jack Stenner (University of Florida), Jan Holmevik (Clemson University)

htsint: a Python library for sequencing pipelines that combines data through gene set generation

Background: Sequencing technologies provide a wealth of details in terms of genes, expression, splice variants, polymorphisms, and other features. A standard for sequencing analysis pipelines is to put genomic or transcriptomic features into a context of known functional information, but the relationships between ontology terms are often ignored. For RNA-Seq, considering genes and their genetic variants at the group level enables a convenient way to both integrate annotation data and detect small coordinated changes between experimental conditions, a known caveat of gene level analyses. Results: We introduce the high throughput data integration tool, htsint, as an extension to the commonly used gene set enrichment frameworks. The central aim of htsint is to compile annotation information from one or more taxa in order to calculate functional distances among all genes in a specified gene space. Spectral clustering is then used to partition the genes, thereby generating functional modules. The gene space can range from a targeted list of genes, like a specific pathway, all the way to an ensemble of genomes. Given a collection of gene sets and a count matrix of transcriptomic features (e.g. expression, polymorphisms), the gene sets produced by htsint can be tested for 'enrichment' or conditional differences using one of a number of commonly available packages. Conclusion: The database and bundled tools to generate functional modules were designed with sequencing pipelines in mind, but the toolkit nature of htsint allows it to also be used in other areas of genomics. The software is freely available as a Python library through GitHub at https://github.com/ajrichards/htsint

Augmenting design deliberation with Compendium: the case of collaborative ontology design

and other research output

Ontology Summit 2008 Communiqué: Towards an open ontology repository

Each annual Ontology Summit initiative makes a statement appropriate to each Summits theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology repository is a facility where ontologies and related information artifacts can be stored, retrieved and managed." We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies