nodalpoint.org - Semantic web - Comments

RDFs

cariaso — Fri, 11 Apr 2008 22:45:40 -0400

I came across this old thread, and thought I'd point out that these days SNPedia does have the sacred RDFs thanks to the semantic-mediawiki.org extension. Today the most obvious benefit is that the SNPedia:FAQ is able to maintain some live counts about the site. The RDFs aren't yet connected to any others, but one baby step at a time it looks a bit more semantic. It seems only a matter of time until it can leverage SPARQL and perhaps the Halo browser.

What, exactly, is the point of Elsevier?

Duncan — Wed, 02 Apr 2008 07:26:07 -0400

I've been waiting for this special issue on semantic biomedical mashups for a while now. The latest scheduled production date is September 2008, which makes it exactly one whole year from Call for papers to publication. Damn thats quick, faster than a speeding glacier! Those hot hot research results must be popping of the printing press at an alarming rate!

Which makes me wonder, what, exactly is the point of Elsevier? Why does it take them so long to publish? Some, in the Open-Access publishing community have suggested this kind of publishing is a slow and expensive way to assign copyright to information that should be in the public domain, while lining shareholders pockets. As a young scientist, I'm completey baffled as to why it should take this long to shuffle a few emails and Word documents around the internet in order to publish.

Anyway, enough of the griping. Every now and then, a pre-print pops up in the Journal of Biomedical informatics feed from PubMed. So while you're waiting for Elsevier, you can read one of the first papers in the special issue below.

Carole Goble and Robert Stevens (year unknown) State of the nation in data integration for bioinformatics, Journal of Biomedical Informatics, officially published sometime before the heat-death of the Universe (but don't hold your breath). DOI:10.1016/j.jbi.2008.01.008, pubmed.gov/18358788

Cladistics

nuin — Tue, 08 Jan 2008 10:09:16 -0500

That's already a cult. A couple of more years it will be a completely new religion.

Religious War or Religious Cult?

Duncan — Tue, 08 Jan 2008 05:56:30 -0500

Theres lots of good stuff in the Open Lab 2007 winning entries but I particularly liked this: Academia is a [religious] cult. Sometimes the semantic web seems more like a religious cult than a scientific endeavour :)

Call for (more) Semantic Web Testimonials

Duncan — Mon, 10 Dec 2007 08:15:20 -0500

In addition to rather old and tired looking semantic web testimonials, Lee Feigenbaum is asking for more, see forwarded message below.

So if you've a SPARQL in your eye, these people would like to hear from you.

======

Dear W3C Colleagues,

I'm writing to you as a representative of an organization that is a W3C member whom I believe to be involved in research and/or development surrounding Semantic Web technologies. (My apologies if I'm mistaken.) In particular, I'm writing in reference to the SPARQL query language and protocol, which has recently been published as a W3C Proposed Recommendation, and is scheduled to be published as a W3C Recommendation in January.

In anticipation of sharing this achievement with the public, we are looking to gather a substantive collection of testimonials in support of SPARQL. I'm including below a note from Janet Daly of the W3C Communications Team which includes more details and guidelines about testimonials.

This is a great opportunity to help with outreach for a key semantic web technology to the rest of the world. At the same time, testimonials are an excellent vehicle for advertising your organization's support of W3C Semantic Web technologies as well as any products that your company might have that implement or use SPARQL.

The deadline for testimonials is Jan 8, 2008.

For more detailed information on the testimonial process, including examples, guidelines, and much more, please see Janet Daly's note below.

thanks,
Lee Feigenbaum
On behalf of the RDF Data Access Working Group

PS If you think you might provide a testimonial, I'd appreciate a heads-up note, just to help me track our status. Thanks!

~~ more information from Janet:

Dear DAWG participants,

Please accept my late congratulations for the set of SPARQL Proposed Recommendations.

In anticipation of a successful completion of the review period, W3C is preparing for announcements around SPARQL Recommendations, or standard. As part of the celebration, we will be issuing a press release and would like to include a testimonial sheet from W3C Member implementors and others.

We will have a draft press release available in the next week for your review. The document will be available to those with Member access. It will not be made public until the actual announcement date. Our current plans are to issue an announcement in early January; we're making efforts to get this draft to you well in advance of the date in deference to the scheduling difficulties of the end of the calendar year.

The guidelines for testimonials are at the bottom of this email. Deadlines for sending those documents to w3t-pr@w3.org is currently 7 January 2008.

Again congratulations on work well done. We look forward to having your participation in the Recommendation announcement.

Kind regards,

Janet Daly, W3C Communications Team

Guidelines for Testimonials

Supporting Testimonial Statements along W3C Press Releases

The Communications Team invites the Membership to participate in a press announcement by submitting supporting testimonial statements. Testimonials are not translated by W3C, but submission of testimonials in multiple languages is encouraged.

Please note that the press release itself is expected to be multilingual (at least available in English, French and Japanese).

Testimonial Guidelines

A testimonial must

contain a statement of support for the W3C and the technology we are promoting in this release;
be grammatically correct;
be attributed to an individual in the submitter's organization (name, title, org)

A testimonial should

contain an explanation of why the news is important to the Web or to specific communities, extolling the virtues and features not before enjoyed;
include a commitment for support of the spec in existing or future products and/or services

A testimonial may

include product announcements which support the technology now or plans to support later;
be in a language other than English.

A testimonial must not

contain criticisms of the technology that may undermine the success of the specification;
contain links to sites outside of W3C;
criticize other products or services;
exceed 100 words.

(note to self, this doesn't sound very "scientific"?)

Upon request by journalists, we would also pass on contact information of companies who have contributed testimonials.

Questions and Follow-up

If your marketing team has any questions, please have them phone Janet Daly (voice: +1 617.253.5884) or send mail to w3t-pr@w3.org.

shmontology

cariaso — Sun, 02 Dec 2007 14:15:11 -0500

big upfront design is suicide.

DBpedia has written rdfs for the existing wikipedia templates. I should have no problem creating rdfs for the snpedia ones. For the moment I'm keeping flexibility by writing all my queries in python. In time I'll carve the stable 80% into an rdf, and be able to use sparql.

From this web page you can play with wikipedia semantic queries.
http://wikipedia.aksw.org/index.php?qid=13

Mike Cariaso * Bioinformatics Software * http://www.cariaso.com

Dude, Where's Your Ontology?

Duncan — Sun, 02 Dec 2007 12:56:54 -0500

Hello Mike, had a look at SNPedia and the semantic wiki. Couldn't find the (sacred?) ontology (RDF / OWL / Whatever) anywhere, is it publicly available? Maybe I didn't look hard enough...

Anne Cregan at the University of New South Wales, Australia has kindly drawn my attention to an article in the December 2007 issue of Scientfic American "The Semantic Web In Action" which claims corporate applications of the semantic web are well under way, and consumer uses are emerging... haven't read it yet, but looks like it might be interesting.

Its written by Lee Feigenbaum (IBM), Ivan Herman (W3C), Tonya Hongsermeier , Eric Neumann and Susie Stephens .

warning believer

cariaso — Fri, 30 Nov 2007 12:21:28 -0500

A solution is a web with both, where some websites are more semantic than others. The semantic web lacks commercial success, because it has no place to put advertising. Best Buy has no motivation to make a semantic web site. But NCBI definitely does.

My own solution has been to ensure that data I produce is semantic friendly. The data is written onto wiki pages. The whole site becomes a semantic book about one topic. humans can edit it, but programs can crawl and query it. Humans and bots work together, on mix of wikipedia and relational database.

A public example is at
http://www.snpedia.com/index.php?title=SNPedia
which tracks human genetic variations and the tests for them

and these slides explaining a semantic wiki based LIMS
http://bioteam.net/wikilims.html

These are baby steps towards a full semantic web, but I've found them extremely powerful.

The algorithmic simplicity of ontologies solves many important problems, but fails miserably for much of the real world. Tag systems adapt better to the real world. Both can be modeled semantically, and should be.

Mike Cariaso * Bioinformatics Software * http://www.cariaso.com

Content

alf — Thu, 19 Apr 2007 05:34:45 -0400

If you can define more precisely the types of content you'll want to log, that would make it easier to point to useful plugins/modules.

use a blog to follow a project of bioinformatics

dalloliogm — Wed, 18 Apr 2007 09:18:02 -0400

I would like to do the same thing as you with notepress: use a blog to follow a project of bioinformatics.

I'm a last-year degree student and I have to follow a short period of practice of six-months in a research laboratory; the project I will work on is an analysis of the secundary structure of some genes in yeast.
Since I'm fond of Internet and the web 2.0 stuff, my head laboratory agreed to let me work slower on my project, allowing me to spend more time on deciding how to organize it and how to present it.
I've also had had to present a seminar a few weeks ago, you can find it here: http://genome.imim.es/~giovanni/ .

so I'm trying with a wordpress blog running on my local computer: I'm using it to collect all the resources on Internet, the workflows I'm using and to take note of the progresses I make.
Actually I'm not very good with the technical part, as I'm not sure I've understood very well what COinS is and I've not tried Drupal yet (I will study ;) ).

So I was looking for some interesting plugins for wordpress: in particular, I would like to find something to manage reviews on articles and resources on Internet, and maybe to implement a connotea/citeulike/other(zotero when it will have social bookmarking utilities?) account, but I believe I won't find very much :(

What kind of thing are you

alf — Tue, 17 Apr 2007 05:13:20 -0400

What kind of thing are you trying to do? There's a COinS plugin for Wordpress that does a little bit of this, but it's not proper structured blogging. You might be better off using Drupal and defining your own CCK content types.

Structure Blogging Plugin

dalloliogm — Mon, 16 Apr 2007 10:43:15 -0400

Hi,
I was trying out this plugin, but it seems that it doesn't work anymore, it is not compatible with wordpress 2.1 and the developers aren't going to continue it (http://mail.structuredblogging.org/mailman/private/structuredblogging-di...).

Moreover, the page referred for the other plugin Notepress, is not avaible any more http://projects.hubmed.org/track/notepress :(

---

http://genome.imim.es/~giovanni

Taxonomy is dead...long live taxonomy!

Duncan — Thu, 29 Mar 2007 12:45:40 -0400

Thanks for the links. The whole HTTP URIs issue is a bit of a hot potato...and a philosophical quagmire.

If you're looking for more feedback on bioguid, there are lots of people interested in and using various biological identifiers over at http://lists.w3.org/Archives/Public/public-semweb-lifesci/

LSIDs, talk, and database inconsistencies

Roderic Page — Thu, 29 Mar 2007 09:55:59 -0400

Duncan, it's not a stupid question at all, especially as I glossed over this in the blurb about the site. Basically, I think LSIDs are probably a dead end, in that they don't play nice with current Semantic Web tools, which expect HTTP URIs. Hence, cool tools like Disco-Hyperdata Browser can't use LSIDs directly. Now, you could argue that if we use an HTTP proxy (like my own lsidres.org) to resolve the LSID, then we can use Semantic Web tools, but this is a hack. Furthermore, it doesn't work with tools like Disco. There are also issues with representing concepts and things with URIs (the infamous httpRange-14 problem, see my del.icio.us bookmarks tagged with 303 for some background). If we use HTTP URIs, then we can easily use 303 redirects to handle URIs that don't point to documents.

The other issue for me is that LSIDs are non-trivial to set up (you need to fuss with SRV records in the DNS, or convince your systems admin to do this). The fact that so few LSIDs are "real", in the sense that you can resolve them wiht the LSID protocol speaks volumes. None of the LSIDs in the Uniprot RDF dumps are real, for example. If the only way to make LSIDs semi-usable is to put an HTTP proxy in front of them, then why go to all the hassle of supporting the LSID resolution protocol in the first place? As much as I get the arguments that URNs have advantages, and HTTP may disappear one day, I just don't see that LSIDs give us want we want right now. Having said that, they did a huge service by getting people in my community to think about RDF, and then the Semantic Web, which is where the real action is.

bioguid.info will soon start supporting LSIDs, I just need to bolt on my resolver code from lsidres.org, and write some XSL to transform the RDF into the form that I'm using (I'm trying to use a consistent vocabulary to that I can meaningfully integrate RDF from multiple sources). So, soon you'll be able to resolve a LSID in the same way as a DOI, etc.

A version of the talk I gave at Manchester is on my iSpecies blog here. For some related ideas more specifically on identifiers and what happens when you link stuff together, see my posts on inconsistences within GenBank, and discovering that GenBank has sequences for species but doesn't know it (near the end of this post)..

relationship to LSID?

Duncan — Fri, 23 Mar 2007 08:39:07 -0400

Hi Rod, I hope this isn't a stupid question, but can you explain a little more of the relationship between BioGUIDs and LSID? This isn't clear from browsing the site. Are you re-using any of the LSID infrastructure? Or is this a completely seperate effort?

On a related note, I remember you gave a talk here in Manchester about a year ago on biological identifiers, a "wisdom of the crowds" type presentation which had some nice examples of different types of identifiers in bioinformatics and problems with what they identify (NCBI taxonomy etc). Do you have the slides of this, or subsequent talks along the same lines?