Science Semantics

it looks like semantic mediawiki? - Mike Chelen

here is a guide to import data (TSV, tab separated values) to Semantic MediaWiki with a script: http://semantic-mediawiki.org/wiki... and some extensions for XML import: http://semantic-mediawiki.org/wiki... - Mike Chelen

"The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. The groups developing ontologies who have expressed an interest in this goal are listed below, followed by other relevant efforts in this domain." - Mike Chelen from Bookmarklet

"The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data." - Mike Chelen from Bookmarklet

sourceforge project page: https://sourceforge.net/project... - Mike Chelen

"OSCAR3 (Open Source Chemistry Analysis Routines) is software for the semantic annotation of chemistry papers. The modules OPSIN (a name to structure converter) and ChemTok (a tokeniser for chemical text) are also available as standalone libraries." - Mike Chelen from Bookmarklet

"USGS and EPA are working together to provide scientists and policy-makers an easier way to integrate access to their large water-quality databases. A common suite of web services allow for the automated sharing of water monitoring data via a common format and terminology. Initial web services are now available. A web service is a computer-to-computer protocol that allows for the direct sharing of information. The services will provide the ability to combine data from USGS's NWIS and EPA's STORET systems. The services will produce data formatted according to the Water Quality Exchange (WQX) Outbound XML schema, which has been developed collaboratively by EPA and USGS. Applications such as internet portals can use the web services to access data from both NWIS and the STORET Warehouse without needing an authorized database connection." - Mike Chelen from Bookmarklet

made a basic YQL open data table for this service, see http://friendfeed.com/watergo... for example - Mike Chelen

these things are really long and detailed ;) - Mike Chelen

"Semantic web atlas of postgenomic knowledge" - Mike Chelen from Bookmarklet

And this happens to have a snapshot of the NMRShiftDB too :) (by yours truly, feature requests most welcome :) - Egon Willighagen

I tend to agree although I take an even more radical position - which is that we need the tools that will help local ontologies be created as needed - and ideally these tools could be attempting the integration problem by seeking out similar data and descriptions elsewhere (which may be useful for the end user) and solving the "cut and paste" problem one step at a time, probably with... more... - Cameron Neylon

I can't comment on your funding question, but I definitely agree with everything Karger says in his post with regards to identifier resolution. Let the chips fall where they may, mint different identifiers for the same thing, write incompatible ontologies, mix your semantics, put it on the web in any format you like. As long as it is there, we will sort it out. - Greg Tyrelle

"This is version 1.0 of the NCBI Brief Article DTD This DTD was written to accommodate the submission of simple articles into the NCBI Rapid Research Notes database." - Mike Chelen from Bookmarklet

"Using JavaScript and/or Greasemonkey, it's possible to add a lot of value to existing web pages. JavaScript is a scripting language that runs in a web browser and which can alter the html of the web page you're viewing (for example). This means that information from other web pages, or from a web service, can be added to a particular web page. Greasemonkey is a Firefox extension that can run a Javascript program automatically on pages that you visit. It also contains additional JavaScript functions for common tasks. In the examples below, we show how it is possible to identify PDB codes contained in the text of normal web pages and to add a link beside each PDB code that displays the protein structure in Jmol. A more sophisticated example identifies DOIs on a page, looks them up on Chemical Blogspace, and adds a link if there are any blogs that discuss that paper." - Mike Chelen from Bookmarklet

We havent' done much with it recently... I should make some now scripts... - Egon Willighagen

"Today's web is built predominantly for human consumption. Even as machine-readable data begins to appear on the web, it is typically distributed in a separate file, with a separate format, and very limited correspondence between the human and machine versions. As a result, web browsers can provide only minimal assistance to humans in parsing and processing web data: browsers only see presentation information. We introduce RDFa, which provides a set of XHTML attributes to augment visual data with machine-readable hints. We show how to express simple and more complex datasets using RDFa, and in particular how to turn the existing human-visible text and links into machine-readable data without repeating content." - Mike Chelen from Bookmarklet

"This page allows you to submit a webpage URL and have the taxon names within the page automatically identified and linked up to projects which have information about those names. This demo uses the NameTag API" - Mike Chelen from Bookmarklet

wiki: http://www.bioontology.org/wiki... - Mike Chelen

"Science has fully entered a new mode of operation. E-science, defined as a combination of science, informatics, computer science, cyberinfrastructure and information technology is changing the way all of these disciplines do both their individual and collaborative work." - Mike Chelen from Bookmarklet

Technically speaking, RDF isn't XML-based, but rather has a serialization to XML. I've not done much with RDF, but in learning it, I found Notation3 to be very useful. - Christopher Granade

I would amend that to read, "Anything but a data model that can be used in a very simple way is likely to be fatally flawed when recording an experiment." I have heard some describe FuGE (http://fuge.sf.net) as complex, but because you can pick and choose what aspects you use, you can still be FuGE-compliant while at the same time keeping things simple! :) - Allyson Lister

Where can I find examples of FuGE used to describe a simple experiment? - William Moore

What I'm looking for is a simpler version of this, that can be used to describe a low-throughput experiment, and can be understood by scientists in the lab. - William Moore

So why doesn't ISA-Creator write FuGE-ML? I look forward to playing with ISACreator when it comes out (Scheduled for Jan 2009). - William Moore

The EXPLAN format looks like a nice simple "format" for a protocol. http://usefulchem.wikispaces.com/EXPLANS A good starting place for a "semantic" experiment? - William Moore