James A. Overton: Timeline

I build smarter software for science. Here's a list of my projects, my resumé, my curriculum vitae, and some stuff I think is interesting.
An Ontology for Major Histocompatibility Restriction2016-01-12 09:00 ESTontology, MRO, toolsA paper describing our new ontology for MHC is now online. Major histocompatibility complex is an important part of the adaptive immune system, and MRO helps users search the IEDB for experiments involving different classes of MHC molecules. We use ROBOT templates to build MRO, and I think it's a good example of cutting edge ontology development. You can browse the project source code at https://github.com/IEDB/MRO.
The Command Line2015-12-12 11:30 ESTtoolsOn Thursday I gave a presentation to the UofT Coders, a group of graduate students in science at the University of Toronto who are working together to improve their computer skills. It's part of the Study Group initiative from the Mozilla Science Lab. I talked about the Unix command line: what it does, how it works, and why it's great.
New OBO PURL system2015-11-27 12:00 ESTontology, OBO, toolsOn Monday I deployed a new system for managing Persistent URLs (PURLs) for the OBO community. It uses Git for configuration management and Apache for serving the URLs. I'm pleased with the GitHub and Travis CI integration for automatically testing all pull requests.
OBI Assay Templates2015-11-27 11:45 ESTontology, OBI, tools, ROBOTThe most recent release of the Ontology for Biomedical Investigations uses templates to define about half of the OBI assays. Template spreadsheets make it much easier to edit large sets of terms using the same pattern. The IEDB team put a lot of work into new template files and we use ROBOT to translate the templates into OWL format.
In memory of Cesare Romagnoli2015-11-04 12:15 ESTphilosophy, ontologyLast week my friend and colleague Cesare died. I owe my career to our collaboration, and miss him dearly. I shared some of my memories of him on the Rotman Institute blog.
EDN-LD: A simple linked data tool2015-05-20 10:15 EDTlinked data, tools, EDN-LDLast night I presented a new project at the Clojure Toronto Meetup. EDN-LD is designed to make working with linked data simple, by using standard Clojure data structures and the standard toolkit for working with those structures. Instead of navigating a hierarchy of Java classes, you just use strings, keywords, maps, and sets to work with your data, then convert the results to a standard RDF format for other tools to use. I've been using predecessors of EDN-LD in my work at IEDB for a few years now, and now it's time to share.
MHC Restriction Ontology2015-05-20 09:45 EDTontology, immunology, MROOn Friday the IEDB team shared a preliminary version of a new ontology. Major histocompatibility complex (MHC) is a family of protein complexes that plays a crucial role in presenting molecules for recognition by immune cells. Those molecules might be harmless pieces of a healthy cell, or they could be fragments of a virus, infectious bacterium, or toxin. MRO is not ready for wide use yet (our term identifiers are UNSTABLE -- DON'T reuse them), but we're already using it to drive our Allele Finder.
ROBOT is an OBO Tool2015-05-20 09:30 EDTontology, OBO, tools, ROBOTFor the last few months I've been working on a new project with Chris Mungall's team at BerkeleyBOP. ROBOT is a command-line tool for working with OBO ontologies, designed to be a friendlier and more modular replacement for OWLTools. It's open source, runs on Windows, Mac OS X, and Linux, and builds on OWLAPI to do the heavy lifting. ROBOT is still in early development, but it's ready to try. We'd love to hear your thoughts.
BD2K Workshop Slide2015-02-26 18:00 ESTontology, OBO, fundingThe National Institutes of Health's Big Data to Knowledge (BD2K) program has a number of parts. I was invited to their Workshop on Community-Based Data and Metadata Standards Development this week, and contributed to a panel on tools. Here's my slide. We need better tools that specialize the linked data stack, and don't require us to keep reinventing the wheel. But good tools need good ergonomics and long-term maintenance, and that costs money.
OBI Assay Patterns2015-02-23 13:00 ESTOBI, OWLA quarter of the terms in the Ontology for Biomedical Investigations are assays, and they need to be cleaned up. The IEDB team has been working on restructuring they assays we've defined. I presented some of that work on the OBI call today.
STREAM Workshop2015-02-19 12:00 ESTphilosophy, science, explanationYesterday I gave a presentation on my explanation work for the Studies of Translations, Ethics, and Medicine (STREAM) group at McGill University in Montreal. We had a good discussion about extracting structured knowledge from publications, and it was great to see my friend Spencer Hey.
Relation Ontology Core2015-02-12 10:00 ESTOBO, ROOver the past month I've put in a lot of hours into adding documentation to the core terms in the OBO Relation Ontology Now we have a new RO Core release.
PSA 2014 Presentation2014-11-07 18:00 CSTphilosophy, science, PSAToday I presented some of my work on explanation at the Philosophy of Science Association conference. The talk went pretty well, I think, and it was great to see so many old friends.
ontoden-deploy2014-10-30 10:30 EDTontology, OBO, toolsI spent a couple of days this week using Ansible and Vagrant to get Ontobee and OntoFox running in a virtual machine. The code is up on GitHub.
OBO Technical Workshop2014-10-07 12:00 CDTontology, OBO, workshop, ICBOWe created a Google Doc to track the discussions in our workshop at ICBO 2014 in Houston this morning.
OBO Tutorial v0.12014-10-03 16:39 EDTontology, OBO, tutorial, ICBOThere's a lot to cover, and it's not done yet, but I've made substantial additions to the OBO tutorial, and I'm calling it "v0.1".
OBI Term Guidelines2014-09-08 16:09 EDTontology, OBI, tutorialI wrote some new guidelines for submitting terms to OBI. Most of the advice applies to any OBO ontology.
OBO Tutorial2014-09-03 15:23 EDTontology, OBO, tutorial, ICBOI've started writing a tutorial for scientists working with OBO ontologies. It's about half done now, and we'll be using some of this material in the OBO Tutorial at ICBO 2014.
OBI Release 2014-08-182014-08-25 15:14 EDTontology, OBI, releaseThis OBI release includes three new terms.
C.S. Peirce and the Philosophy of Medical Imaging2014-07-17 12:00 EDTphilosophy, radiology, Peirce, conference, presentationThis morning Cesare, Nick, and I presented on Peirce and radiology at the The Charles S. Peirce International Centennial Congress. The breadth and scope of the presentations here is impressive!
Ontology and Imaging Informatics Workshop2014-06-25 15:00 EDTontology, radiologyHeiner Oberkampf and I just presented his recent work applying OBI to radiology reports. You can download our slides and see the full workshop schedule.
OBO Tutorial and Workshop at ICBO 20142014-06-21 10:00 EDTontology, OBO, ICBOI'm helping to organize a Tutorial and Workshop on Open Biomedical Ontologies at the 5th International Conerence on Biomedical Ontologies.
Rotman GRA Grant2014-05-22 17:00 EDTphilosophy, radiology, PeirceGillian, Cesare, and I are grateful to the Rotman Institute for funding a graduate research assistant position for our project "The Ontology and Epistemology of Medical Imaging". We're even happier that Nick Nash has accepted our invitation to join the project!
BFO Classes-Only Version2014-05-03 16:23 EDTontology, BFO, releaseI helped arrange today's release of BFO, with a new classes-only version.
The perils of managing OWL in a version control system2014-04-01 15:37 EDTontology, OBO, toolsChris Mungall has sparked a good discussion about how OWL/XML doesn't play nicely with version control systems.
OBI Release 2014-03-292014-04-01 12:16 EDTontology, OBI, releaseA new version of OBI has been released -- not an April Fool's joke!
Ontohub Hackathon2014-03-29 15:15 EDTontology, Ontohub, toolsToday I worked on deployment automation for the Ontohub project as part of the OntoLog hackathon.
OBI Release Process2014-03-17 19:47 EDTontology, OBI, releaseOBI has adopted a new process for more frequent releases. I'm the first OBI "release manager".
OBI Release 2013-10-252013-11-01 14:38 PSTontology, OBI, releaseThis is the first release of OBI to use the new build tool, and the first to include OBI Core.
OBO Foundry Technical Working Group2013-10-21 15:30 PSTontology, OBO, TWGThe Working Group coordinates on the infrastructure and technical policies of the OBO Consortium. Today I'm its newest member.
OBI Build Tool2013-04-06 11:35 EDTontology, OBI, toolsI've written a new build tool for testing and releasing OBI.
BFO 1.2 Proposal2013-01-07 15:35 ESTontologyI think that the Basic Formal Ontology needs to release a version 1.2 ...
Dissertation2012-06-25 20:02 EDTphilosophy, gradschoolOne month ago I successfully defended my doctoral dissertation...
Submission2013-03-19 19:40 EDTphilosophy, science, gradschoolToday I submitted my doctoral dissertation...
Philosophy of Science2011-10-27 15:34 EDTphilosophy, scienceWhat is philosophy of science, exactly?
About this Site2011-10-26 08:17 EDTsoftware, languagesIt's been a long time coming, but I've finally updated my homepage...