chem-bla-ics

My HTML+RDFa homepage

2009-09-18T00:00:00+00:00

Finally got around to adding a few more bits to my new science homepage: egonw.github.com. Cool thing about this new page is that it is HTML+RDFa, so, my new FOAF profile is embedded in the HTML:

Down the bottom is link to extract the RDF triples:

Next, is to write a piece of code that creates HTML+RDFa+BIBO from a BibTeX file, and to write a plugin for Bioclipse to extract triples from HTML+RDFA.

Bioclipse and SPARQL end points #2: MyExperiment

2009-08-21T00:00:00+00:00

RDF and SPARQL are two really useful Open Standards. Bioclipse-RDF is a plugin for Bioclipse that provide RDF functionality, among which using remote SPARQL end points.

The MyExperiment team has set up an excellent RDF front end. For example, this is my MyExperiment account in RDF. The storage gets updated once every day (at this moment), but I’m sure that will become more often in the future. The SPARQL end point allows us to make any query against the database that their ontologies support. The above query showed up 132 workflows when I ran it today.

Gists

Now, so far I have been using Gist to share Bioclipse scripts and I wrote some Bioclipse GUI elements for downloading such gists . To annotate these gists, Delicious has been used, and a listing of Bioclipse scripts can be found under the tags bioclipse and gist.

MyExperiment also allows to share workflows, but originally only for Taverna. A recent change, however, made it possible to share other types of workflows too. And, MyExperiment itself also allows all the annotation which we may want to do.

Now, using the Bioclipse-RDF functionality, I can query the MyExperiment database and use that information do to stuff. If this stuff is a Bioclipse script, then I can just download it, as the download link of a workflow is part of the RDF too, as we will see.

Querying a SPARQL end point

As we have seen in the first article of this series , the RDF manager his a method to query a remote SPARQL end point. The complexity is mostly in formulating the SPARQL (and this one happens to be available as workflow on MyExperiment too:

This is worsened by the fact that JavaScript does not have a type of multiline Strings, so the backslashes at the end of the lines are JavaScript syntax and not part of the SPARQL. To simplify the SPARQL, I will show below the SPARQL only, and not the Bioclipse script wrapping as is done in the above code snippet.

List all Taverna 2 workflows

Listing all Taverna 2 workflows, as shown in that earlier snippet, is done with the SPARQL:

This query asks for a ?workflow and its ?title, and the workflow ?type must be of Class ContentType as defined in the mebase namespace, and we want to know the ?typetitle of that content type, because we are filtering that using a regular expression to contain “Taverna 2”. Well, if you cannot follow this, just google for SPARQL, and run one of those tutorials which are abundantly present on the web.

Finding tags used to annotate workflows

To list all tags which have likely to do with metabolomics, I can do:

And I can also list all workflows that are tagged like this. Because I could not get string matching to work, I used the tag’s URI instead:

All MyExperiments Users in Sweden

I was also interested in all MyExperiment Users in Sweden, and again, a simple SPARQL tells me where they live:

Finding Duncan and Pierre

Very easy to find users, such as Duncan:

Or Pierre, who has not listed where he lives:

My workflows

Given a user, it is also easy to get the workflows he owns. Again, I am using my URI instead of combining with a search for my account, because the MyExperiment SPARQL end point is not particularly fast:

Earlier in this series:

Bioclipse and SPARQL end points #1: DBPedia

Quality Publishing: EndNote versus InChIs

2008-04-22T00:00:00+00:00

Some publishers hesitate a bit, but others go full speed ahead into the electronic publishing era. Noel commented on my post about OA/OD inviting added value :

I heard a talk by the RSC at the ACS, saying that their RSS feeds contain InChIs now! Just thought I’d throw that out there :-)

The RSC Project Prospect is ahead of other publishers, for over a year already . Adding InChIs to RSS feeds are a cheap way of adding machine-readable chemistry to ones publishing pipeline; adding CML would allow much more detail (see this overview of CMLRSS information in my blog).

But, importantly, it allows third-parties to efficiently set up DOI-InChI tables. Cheap (Asian?) workers become rather expensive, when compared to machine mining to create such databases. Sure, the authoring becomes somewhat more expensive, but who will argue that scientists might be a bit more precise in what they publish. I, for sure, would love to see authors focus on adding InChIs to experimental sections, then that they focus on getting EndNote to put the comma, bold and upper casing in the right place, to meet journal standards.

Another publisher who takes its job seriously is Beilstein. Stephan recently showed me some of the things they are up too, like information rich figures (yes, you’ll have access to the source, and identify the molecular structures in reaction schema). He also showed me to the RDF now by default available for all their articles. For example, for DOI:10.1186/1860-5397-3-50, the RDF is available here. It’s indicated in the HTML with:

 rel='alternate' type='text/rdf' title='RDF' href='http://www.beilstein-journals.org/bjoc/content/rdf/1860-5397-3-50.rdf'/>

There is, actually, also a lot of citation information available in the tags in the HTML, but apparently not the right stuff yet to have Zotero pick it up nicely (not sure what this Firefox plugin is actually looking for). No chemistry in the RDF it seems, but there is BIBO , FOAF and Dublin Core.

Main suggestion to Stephan, right now, would be to include InChIs in the RDF and RSS feed.

Disclaimer: Colin, behind Project Prospect, visit our group when I was still in Cologne; Stephan contributed code bits to the CDK project, e.g. this this Matrix class.

Oh, Nature is, of course, also a publisher who actively gets into electronic publishing age.

My FOAF network #5: SPARQL-ing my network

2008-03-19T00:00:00+00:00

FOAF rulez: it’s RDF. With RDF comes SPARQL. SPARQL needs a query engine, however. And there comes OpenRDF which created Sesame. I have to catch the train in about 15 minutes, so will not elaborate too much, but here are some Sesame 2.0.1 work:

> create native.
Please specify values for the following variables:
Repository ID [native]: foafRepo
Repository title [Native store]: FOAF Repository
Triple indexes [spoc,posc]:
Repository created
> open foafRepo

Creates me a new RDF storage and opens it.

foafRepo> load http://blueobelisk.sourceforge.net/people/egonw/foaf.xrdf .
Loading data...
Data has been added to the repository (606 ms)

Loads my FOAF file. Now, a simple SPARQL query that finds me all friends that now someone with the nick egonw:

foafRepo> sparql

BASE 
PREFIX foaf: 

SELECT ?s ?o
WHERE { ?s foaf:knows ?o ; foaf:nick "egonw" . }

.
Evaluating query...
+-------------------------------------+-------------------------------------+
| s                                   | o                                   |
+-------------------------------------+-------------------------------------+
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
| | |
+-------------------------------------+-------------------------------------+
13 result(s) (15 ms)

Not very pretty, but rather accurate.

More SPARQL fun later. Do try this at home, but make sure to not put a period at the end of a line in your SPARQL query! :)

My FOAF network #4: Tabulating my publications

2008-03-18T00:00:00+00:00

Richard informed me (via Planet RDF) about N3 support in Tabulator. N3 is a more compressed version of RDF/XML, which I have been using so far, but both are RDF. Now, I don’t plan to use N3 for my FOAF experimenting, but two things caught my eye in the nice blog item.

First, it has a very useful tip on .htaccess which you can use to teach Apache about MIME types, even when you do not have root access. So, I added this .htaccess file to blueobelisk.sourceforge.net/people/egonw/:

AddType application/rdf+xml;charset=utf-8 .xrdf

Now, you can also access my FOAF file with the MIME type set to application/rdf+xml. And, my bibliography too. Now, the latter becomes interesting when you have Tabulator installed in your Firefox. Instead of applying the XSLT, Firefox will now show it like this:

And, in the under the hood mode it looks like:

Now, my FOAF file does not seem to work well. Not sure what goes wrong there, but given the fact that Tabulator seems to be able to recurse into referenced RDF files, I think it nicely complements what we already have.

Wow, it seems Web3.0/WebNG is really going to happen this year!

My FOAF network #3: My publications

2008-03-10T00:00:00+00:00

As promised , I’ll write a bit about using Bibliographic Ontology Specification (BIBO) over as bibliontology.com. I have written a basic XSLT to create a HTML GUI (open the RDF source in e.g. Firefox). Really basic: it only converts articles, and even assumes some conventions I found in examples in the BIBO wiki. I have not spotted a BIBO validator yet, so guessing a bit. The BibTeX mapping examples are under discussion, but provide some insight to those who are used to using that (JabRef users, for example).

So, if I understood the specs enough, the following should be valid BIBO (at least it is valid RDF):

<?xml-stylesheet type="text/xsl"
                 href="http://blueobelisk.sourceforge.net/people/egonw/bibo2xhtml.xsl"
                 ?>

      xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
      xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
      xmlns:bibo="http://purl.org/ontology/biblio/"
      xmlns:dc="http://purl.org/dc/elements/1.1/"
      xmlns:dcterms="http://purl.org/dc/terms/"
      xmlns:foaf="http://xmlns.com/foaf/0.1/"
>

   rdf:about="urn:issn:1471-2105">
    BMC Bioinformatics
  
   rdf:about="http://dx.doi.org/10.1186/1471-2105-8-59">
    Bioclipse: an open source workbench for chemo- and bioinformatics
    2007-02-22
     rdf:resource="urn:issn:1471-2105"/>
    8
    10.1186/1471-2105-8-59

         rdf:resource="http://purl.org/ontology/bibo/roles/author" />
         foaf:name="Ola Spjuth"/>
        1
      
         rdf:resource="http://purl.org/ontology/bibo/roles/author" />
         foaf:name="Tobias Helmus"/>
        2
      
         rdf:resource="http://purl.org/ontology/bibo/roles/author" />
         foaf:name="Egon Willighagen"/>
        3
      
         rdf:resource="http://purl.org/ontology/bibo/roles/author" />
         foaf:name="Stefan Kuhn"/>
        4
      
         rdf:resource="http://purl.org/ontology/bibo/roles/author" />
         foaf:name="Martin Eklund"/>
        5
      
         rdf:resource="http://purl.org/ontology/bibo/roles/author" />
         foaf:name="Johannes Wagener"/>
        6
      
         rdf:resource="http://purl.org/ontology/bibo/roles/author" />
         foaf:name="Peter Murray-Rust"/>
        7
      
         rdf:resource="http://purl.org/ontology/bibo/roles/author" />
         foaf:name="Christoph Steinbeck"/>
        8
      
         rdf:resource="http://purl.org/ontology/bibo/roles/author" />
         foaf:name="Jarl Wikberg"/>
        9

There are some things notable about this markup:

It is very verbose, even for XML standards!
It’s RDF from the ground up
it reuses many other ontologies

Particularly, the authors section is very verbose. However, it also nicely reuses FOAF here. This makes it really powerful. For example, I could have used this bit:

  
     rdf:resource="http://purl.org/ontology/bibo/roles/author" />
     rdf:resource="http://blueobelisk.sourceforge.net/people/egonw/foaf.xml#me"/>
    3
  

This would semantically link this publication to whatever information I have on myself published in my FOAF file.

Now, the reason why I have not done this yet, is that the XSLT did not properly load the XML from my foaf file:

 name="foafURI" select="substring-before(bibo:contributor/@rdf:resource, '#')"/>
 name="authorID" select="substring-after(bibo:contributor/@rdf:resource, '#')"/>
 name="foafDoc" select="document($foafURI)"/>
 select="$foafDoc//foaf:Person[@rdf:ID=$authorID]"/>

The XSLT processor xsltproc (version 1.1.22 on Ubuntu 8.04) gives this error: warning: failed to load external entity "http://blueobelisk.sourceforge.net/people/egonw/foaf.xml". But, if I make it a relative, it does work. Both with xsltproc as well as with Firefox online.

Another reason not to do it like that, is that one looses control of the citation content. What I will do soon, is use this set up, making researcherid.com obsolete (see also these three blogs):

   foaf:name="Egon Willighagen">
     rdf:resource="http://blueobelisk.sourceforge.net/people/egonw/biblio.xml#me"/>
  

Just in case you are wondering, “why the ### does he not simply use BibTeX?”, the answer is RDF. No RDF, no SPARQL, no GLORY. Just thing how easy it will become to run a queries like:

which of those I have published with, run a blog
which of those I have published with are going to that conference in Boston in September?
which of those I have published with have friends who published about topics around these keywords
etc…

All that becomes very easy now.

BTW, this is how I link to my bibliography from my FOAF:

 rdf:resource="http://blueobelisk.sourceforge.net/people/egonw/biblio.xml"/>

My FOAF network #2: XSLT for a HTML GUI

2008-03-08T00:00:00+00:00

Because the ACS meeting where Henry will present something about FOAF in chemistry, is nearing very fast now (here’s the first blog it this series ), it becomes urgent to beef up the Blue Obelisk FOAF network, now consisting of 7 members. All do now show up in the FOAFExplorer:

Now, to make sure that my FOAF is in order, I set up the regular XML/RDF toolchain, using xmllint to validate the XML and RDF syntax, and XSLT to convert the FOAF to human readable HTML. Using the ?xml-stylesheet? syntax this also provide the basic HTML GUI when accessing the FOAF file using Firefox. BTW, I had to rename the file to make the SourceForge web server aware that the file is an XML file, so that it nicely sets the MIME type.

BTW, I suggest all to validate your FOAF with this RDF validator, because some of us got some work to do to make them valid:

Mine is having some encoding issue
Henry’s has some 8 errors

The others are actually fine.

While the XSLT is getting along quite nicely, I got serious other work to do. The Strigi-based FOAF indexer is sort of working, gets FOAF documents recursively, but I want it to index our publications and presentation slides too. Now, FOAF has a foaf:publications tag, which I thought might be suited. But after chatting with (new) friends on the #foaf IRC channel (the log), it became clear that the scope of that element is to point to some other file (foaf:Document) which lists the publications, such a HTML output created from BibTeX.

That is, the following syntax is not quite what appears to be intended:

   rdf:about="http://dx.doi.org/10.1186/1471-2105-8-59">
    Bioclipse: an open source workbench for chemo-
      and bioinformatics
     rdf:resource="#me"/>
  

The Bibliontology was suggested and seem a rather good candidate to draft a separate but RDF/OWL-based publication list. The server was down at the time of writing, but the Google cache showed the scope nicely. The Google group is active and the server should go back online shortly.

OK, enough for now. More will follow in this series shortly. Such as a HTML GUI for my publication list in Bibliontology format.

Jane, find me interesting journals, please.

2008-03-01T00:10:00+00:00

Bioinformatics just published a paper from Schuemie and Kors (Erasmus University/NL, BioSemantics group): Jane: suggesting journals, finding experts (doi:10.1093/bioinformatics/btn006):

Jane (Journal/Author Name Estimator) is a freely available web-based application that, on the basis of a sample text (e.g. the title and abstract of a manuscript), can suggest journals and experts who have published similar articles.

Having just gone into a different research field, I appreciate Jane as a useful tool to learn to find my way around in relevant literature. Based on, for example, the abstract of an article I find interesting, it finds me appropriate journals and authors. The next screenshot shows the results for the abstract of the Blue Obelisk paper (doi:10.1021/ci050400b):

The Show articles feature as well as the journal annotation are rather useful to get a quick overview of what is being suggested. The list of authors seems, at first sight, populated by co-authors, and lacks any form of annotation. Room for FOAF here ? They used PubMed as content provider, and text mining to align articles, but nothing really semantic, despite the group’s name. The output does not seem to provide semantics either.

My FOAF network #1: the FOAFExplorer

2007-10-26T00:00:00+00:00

In this series I will introduce the technologies behind my FOAF network. FOAF means Friend-of-a-Friend and

[t]he Friend of a Friend (FOAF) project is creating a Web of machine-readable pages describing people, the links between them and the things they create and do.

My FOAF file (draft) will give you details on who I am, who I collaborate with (and other types of friends), which conferences I am attending, what I published etc. That is, I’ll try to keep it updated. BTW, FOAF is a RDF language.

FOAFExplorer

Pierre has done some excellent FOAF work in the past, and developed the MyFOAFExplorer, and also developed a tool to create a FOAF network based on the PubMed database, called SciFOAF. The latter is neat, but does not allow putting all this personal details in the FOAF files. However, the output could be a starting point.

Back to FOAFExplorer, this is what the FOAFExplorer shows for my network:

I’m a bit lonely, even though I have linked to two friends in my FOAF file, of which one has a FOAF file too (Henry):

   rdf:ID="HenryRzepa">
    Henry Rzepa
     rdf:resource="http://www.ch.ic.ac.uk/rzepa/rzepa.xrdf"/>
  


   rdf:ID="PeterMurrayRust">
    Peter Murray-Rust
    926d6f8ed367bdded26353a05e80b4f0ce18230d...
  

I guess the FOAFExplorer does not browse into my network. More on that in later items in this series.