Frank Gibson has posted again in our ongoing conversation about using FUGE as a data model for laboratory notebooks. We have also been discussing things by email and I think we are both agreed that we need to see what actually doing this would look like. Frank is looking at putting some of my experiments into a FUGE framework and we will see how that looks. I think that will be the point where we can really make some progress. However here I wanted to pick up on a couple of points he has made in his last post. Read more »

Posted: April 20th, 2008 under FuGE, biosysbio2008, data formats, data model, format.
Comments: 4

And other big words I learnt from mathematicians…

The observant amongst you will have realised that the title of my previous post pushing a boat out into the area of semantics and RDF implied there was more to come. Those of you who followed the reaction [comments in original post, 1, 2, 3] will also be aware that there are much smarter and more knowledgeable people out there thinking about these problems. Nonetheless, in the spirit of thinking aloud I want to explore these ideas a little further because they underpin the way I think about the LaBLog and its organization. As with the last post this comes with the health warning that I don’t really know what I’m talking about. Read more »

Posted: April 8th, 2008 under FuGE, data formats, data model, format, indexing, ontologies, semantics, tagging.
Comments: 3

Frank Gibson has continued the discussion that kicked off here and has continued here [1, 2, 3, 4] and in other places [1, 2] along the way. Frank’s exposition on using FuGE as a data model is very clear in what it says and does not say and some of his questions have revealed sloppiness in the way I originally described what I was trying to do. Here I will respond to his responses and try to clarify what it is that I want, and what I want it to achieve. I still feel that we are trying to describe and achieve different things, but that this discussion is a great way of getting to the bottom of this and achieving some clarity in our description and language. Read more »

Posted: March 30th, 2008 under FuGE, data formats, data model, definitions, format, glueware, metadata, ontologies, rdf, semantics, tools, xml.
Comments: none