Sign in or Join FriendFeed
FriendFeed is the easiest way to share online. Learn more »
Science Semantics

Science Semantics

Topics related to the semantic description of research process and scientific data/knowledge.
Mike Chelen
@PLoS Is there an API for #PLoS or @PLoSONE? There was talk of RDF support, has this been documented? /cc @BoraZ @p_binfield
Here is the old blog post discussing RDF: http://www.plos.org/cms... - Mike Chelen
Maybe using a 3rd party site, such as PubMed, HubMed, Mendeley or Citeulike is the best alternative? - Mike Chelen
No API yet (its still on our list...) however the articles are all tagged with RDFa for the Dublin Core elements. See: http://www.dragishak.com/?p=78 - Peter Binfield
The RDFa looks good! Had the best luck using the GetN3 addon. If search results had similar markup, then RDFa could supply all the needed API features. - Mike Chelen
Mike - our API is coming soon... - Peter Binfield
Peter: How exciting to hear! Look forward to learning the details as they are announced. Any idea when release date or documentation will be available? - Mike Chelen
Now live :) - Peter Binfield from Android
Egon Willighagen
Egon Willighagen
Egon Willighagen
Mike Chelen
SWiM -- A Semantic Wiki for Mathematical Knowledge Management - arXiv.org > cs > arXiv:1003.5196 - http://arxiv.org/abs/1003.5196
"SWiM is a semantic wiki for collaboratively building, editing and browsing mathematical knowledge represented in the domain-specific structural semantic markup language OMDoc. It motivates users to contribute to collections of mathematical knowledge by instantly sharing the benefits of knowledge-powered services with them. SWiM is currently being used for authoring content dictionaries, i. e. collections of uniquely identified mathematical symbols, and prepared for managing a large-scale proof formalisation effort." - Mike Chelen from Bookmarklet
A prototype is running the software at http://wiki.openmath.org/ - Mike Chelen
Mike Chelen
Fwd: "Wikipedia for academic research". Post a summary of your research to increase its impact. http://acawiki.org/Home (via http://friendfeed.com/plosone...)
it looks like semantic mediawiki? - Mike Chelen
ah thanks, interesting to see which extensions they are using - Mike Chelen
Noteworthy: so far, 18 summaries of articles in PLoS Biol., 12 in PLoS Med. (None in PLoS ONE). - Jim Till
Perhaps noteworthy: the vast majority of edits in the last thirty days are by two people. It's hard to build critical mass... http://acawiki.org/index... - Andrew Su
the site looks pretty new, sometimes starting fresh produces the best results, although it can be useful to find some existing data to import initially - Mike Chelen
The site launched this week. The PLoS articles were seeded using the Editor Summaries that PLoS Bio and PLoS Med routinely publish - Peter Binfield
Peter: wondering if the data was converted from another format, or does PLoS supply RDF directly? is there any description of the process used? - Mike Chelen
We didnt work with them on this (other than to have some early meetings). I suspect they just copied and pasted... However, it can be extracted from our XML file of course. - Peter Binfield
Yes, it's copy and paste at present. A better workflow would be a good enhancement to Semantic MediaWiki if anybody's looking for a project! - Jodi Schneider
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
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
Mike Chelen
"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
Mike Chelen
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
Mike Chelen
Egon Willighagen
Mike Chelen
Mike Chelen
Mike Chelen
Bioinformatics applications for next generation sequencing on SEQwiki - http://seqanswers.com/wiki...
Mike Chelen
USGS National Water Information System (NWIS) Water-Quality Web Services - http://qwwebservices.usgs.gov/
"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
Mike Chelen
National Water Information System (NWIS) Water-Quality Web Services WQX-Outbound XML schema documentation - http://qwwebservices.usgs.gov/schemas...
these things are really long and detailed ;) - Mike Chelen
Mike Chelen
Mike Chelen
Fwd: NCBO BioPortal: Ontology of homology and related concepts in biology Ontology - similarity - http://bioportal.bioontology.org/visuali... (via http://friendfeed.com/the-lif...)
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
Richard Klancer
I find myself agreeing with David Karger's position in http://groups.csail.mit.edu/haystac... The NIH reviewer's comments seem to suggest a doughnut hole -- predefined ontologies are too rigid but bottom-up ontologies are too risky to fund? Does anyone have any opposing thoughts?
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
Mike Chelen
"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
Mike Chelen
Using Javascript and Greasemonkey for Chemistry - BlueObelisk - http://blueobelisk.sourceforge.net/wiki...
"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
Mike Chelen
"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
Mike Chelen
"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
Mike Chelen
Mike Chelen
Mike Chelen
Semantic e-Science (2009 Fall) - Tetherless World Wiki - http://tw.rpi.edu/wiki...
"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
What else would be recommended besides RDF? Having learned some basics of XML it is next on my list, especially since there are finally more sites providing RDF and also heard good things about SPARQL. - Mike Chelen
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. - Chris Granade
Mike Chelen
Allyson Lister
Just wanted to say hi. Noticed this room when searching for "semantics" in room names, and thought I'd put in my 2 cents' worth. :)
Other ways to read this feed:Feed readerFacebook