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Housekeeping & Self References Semantics and Ontologies Standards

This site now listed in Nature Blogs, and the reason behind my keyword choices

Last week when scanning through Friendfeed, someone mentioned Nature Blogs. A number of my friends and fellow friendfeeders (1,2,3,4,5,6,etc.) already have their blogs registered there. I took the plunge and submitted my request last week, and this site was accepted for inclusion in the list this week. You can find it listed under the bioinformatics category. In honor of that occasion, I've decided to post a summary of the tags I chose to mark this blog with on Nature Blogs, and the reasons for them. (The obvious one, bioinformatics, wasn't necessary as far as I could tell because that is the top-level category I've placed the site into.)

  • data integration: It is the main focus of my research, and one of the biggest challenges facing bioinformatics and the life sciences in general. So many formats, so little time! Reconciling these using brute force, standardization, semantics, and sneakiness are what it's all about.
  • ontologies: I like ontologies for many reasons, not the least their potential for reconciling the many different ways of defining and naming things in our lives. We need a common ground from which to perform successful integration and analysis, and I think a well-written ontology (or set of them) is a beautiful thing. They are a major tool in my research bag of tricks. Not only that, but I also help develop a community-driven ontology for describing life-science experiments (OBI).
  • workshops: my method of remembering what goes on in workshops and conferences is to take notes, and I can be a pretty fast typist. I enjoy blogging on each lecture at such an event as they happen, and you'll notice a lot of workshop and conference posts on this site. They are mainly written while the speaker is speaking, with a minimum (if any) of later editing. However, if any speaker reads my notes and would like to suggest areas where I made a mistake, I am more than happy to make those sorts of changes. One of my favorite ways of blogging.
  • systems biology: that's the field in which my bioinformatics research is applied, which makes it an immediately-applicable tag for this blog. But try to define it and, as with so many things in this world, you could get as many definitions as there are people. (Ok, perhaps a slight exaggeration for dramatic effect.) So, I'll not try to define it today, and just say that my posts often deal with work in this field.
  • science outreach: My Mom is a teacher, my Dad was a teacher and remains working in Education. If it wasn't so much hard work, I'd consider it as a career myself. 🙂 However, I do enjoy trying to pass on my enjoyment of and interest in the sciences. Some of my more recent posts talk about the work I'm doing with the Teacher Scientist Network. Outreach is just fantastic, especially when explaining science to kids, and it's something I like to talk about in this site, when the opportunity arises.
  • standards: Perhaps it's because I spent years working at the EBI, where they provide databases and services in specific syntaxes. Perhaps it's just the way my personality is. Whatever the reason, I really enjoy working with data standards. I'm lucky enough to be directly involved with two at the moment (FuGE and OBI), and peripherally involved in other efforts such as SBO (by peripherally I mean that I've nagged them in the past about the whys and wheretofores of various aspects of their ontology) and MIGS (I was involved in the initial work on the checklist, and provided advice on FuGE). I'm a bit of a standards fiend, and try to remind myself that not everyone finds them as interesting (though everyone should at least find them relevant!).

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Data Integration In The News

Two Journal Special Issues: Big Data, and Semantic Mashups for Bioinformatics

Both of these special issues are worth a look, as some of the papers look pretty interesting. I'll spend a little time in a later post on any articles I find particularly relevant.

  • Semantic Mashup of Biomedical Data Special Issue of the Journal of Biomedical Informatics. This includes a review article by Carole Goble and Robert Stevens: State of the nation in data integration for bioinformatics
  • Nature's Big Data Sepcial Issue. The article entitled "How do your data grow?" was one of the many articles in this issue that I enjoyed. It's interesting to note that these problems in management and curation of big data are only now getting special attention in Nature. When I worked at the EBI, it was common knowledge among the database curators that 1) it would be very difficult for them to find other work as curators if they left the EBI, and 2) the time and high skill level it takes to annotate and curate biological database entries means that it is very difficult to get high coverage in such databases. It's nice to finally see some recognition of all the work the biocurators do by a journal such as Nature. Finally, there are high-profile articles stating that curation begins at home, with the researcher, and that curation needs much more support from researcher-level all the way up to the level of the database curators.

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