Category Archives: Databases

Updated CV

For my upcoming evaluation, I put together an updated CV. On the off chance that it might interest someone, here it is.

Well, it’s not just an exersize in narcissism. I really struggled to figure out how to divide up the various kinds of projects I have been working on, in the “Scholarship” section. I settled on the following.

  • Book chapter (peer reviewed)
  • Conferences
  • Edited works. Includes my digital republication of the Origin of Species.
  • Invited lecture.
  • Ontology.
  • Bibliography.
  • “Evolution Resources” column in Evolution: Education and Outreach.
  • Book reviews.
  • Web presence. Blogs, twitter.
  • Development. I am the BibDesk release engineer. Lapsed, apparently. Seriously, though, I will get to the next release soon.
  • Computing. Applications, including svn, Emacs, other development tools.

I have no idea what this will mean to the Dean, the Provost, or the evaluation committee. Nor will I find out, either, except by way of a “thumbs up” or “thumbs down.”

It’s important to differentiate these different kinds of works according to their nature and purpose, rather than lumping them together as “web publications” or “software.” Look, we don’t put journal articles, posters, and books in the same category because they are all printed materials (or at least, used to be). In fact, some of the digital works do more or less the same thing as their print analogs, for instance, bibliographies. Whether in print or in the form of a BibTeX database, a collection of bibliographic records serve the same essential functions.

One thing that is clear, whatever other confusions there may be, is that I need to publish papers in the usual places, peer-reviewed periodicals, whether online or in any other form.

I’d be interested to hear about how other people in the Humanities working on digital projects have represented them to their administrators.

Files for Pratt LIS 663

Tonight I am guest lecturing at Pratt Institute School of Information and Library Science. The topic is ontology. This post is mainly for the students; they will be able to find the lecture notes and the “Make your own ontology” worksheet here.

The worksheet is HERE.

The lecture notes are HERE.

OBO Foundry announces approved ontologies

The OBO Foundry has just announced that a set of ontologies have been reviewed, and have been found to be compliant with OBO Foundry principles. The approved ontologies include the following.

CHEBI
Chemical Entities of Biological Interest
GO
Gene Ontology
PATO
Phenotypic Quality Ontology
PRO
Protein Ontology
XAO
Xenopus Anatomy Ontology
ZFA
Zebrafish Anatomy Ontology

These ontologies are intended to represent a broad range of biological phenomena without overlapping with one another, and so are intended to be used in a modular fashion by a variety of researchers. Developing these ontologies helps the research community as a whole by improving these multi-purpose classification tools.

Other ontologies are being reviewed at present, and it is anticipated at the Foundry that these will also be approved, pending revision.

The OBO Foundry has announced that ”we will be publishing a revised set of principles which will be applied in future reviews in the period following the February 2010 OBO Foundry meeting,” noting that ”At every stage, these are best conceived as a set of guidelines designed to promote evolutionary improvement in the ontologies; like the ontologies themselves, these principles will always be subjected to further review in the future.”