A Brief History Of Sciences

(Introduction copied from DBPedia): Wikipedia is the by far largest available encyclopedia on the Web. Wikipedia has the problem that its search capabilities are limited to full-text search, which only allows very limited access to this valuable knowledge-base.Semantic Web technologies enable expressive queries against structured information on the Web. The Semantic Web has the problem that there is not much RDF data online yet and that up-to-date terms and ontologies are missing for many application domains. The DBPedia project approaches both problems by extracting structured information from Wikipedia and by making this information available on the Semantic Web. A major feature of DBPedia is to enable sophisticated queries against Wikipedia using SPARQL. Extracting structured information from Wikipedia leads to quite astonishing query answering possibilities.

In February, the dbpedia dataset was available for download.

For example, here are the N3 statements about Francis Crick that were extracted from wikipeda with dbpedia.

<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/name> "Francis Crick" .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/image>        "FrancisHarryComptonCrick.jpg" .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/caption>      "Francis Harry Compton Crick" .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/birth_date>   "1916068"^^<http://www.w3.org/2001/XMLSchema#Date> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/birth_place>  <http://en.wikipedia.org/wiki/Weston_Favell> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/birth_place>  <http://en.wikipedia.org/wiki/Northamptonshire> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/birth_place>  <http://en.wikipedia.org/wiki/UK> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/residence>    <http://upload.wikimedia.org/wikipedia/commons/a/ae/Flag_of_the_United_Kingdom.svg> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/residence>    <http://en.wikipedia.org/wiki/UK> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/residence>    <http://upload.wikimedia.org/wikipedia/commons/a/a4/Flag_of_the_United_States.svg> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/residence>    <http://en.wikipedia.org/wiki/USA> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/nationality>  "[[Image:Flag_of_the_United_Kingdom.svg|20px|]]  [[England|English]]" .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/death_date>   "20040728"^^<http://www.w3.org/2001/XMLSchema#Date> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/death_place>  <http://en.wikipedia.org/wiki/San_Diego> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/death_place>  <http://en.wikipedia.org/wiki/California> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/death_place>  <http://en.wikipedia.org/wiki/USA> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/field>        <http://en.wikipedia.org/wiki/Biophysics> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/work_institution>     <http://en.wikipedia.org/wiki/Salk_Institute> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/alma_mater>   "[[University College London]][[University of Cambridge]]" .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/doctoral_advisor>     <http://en.wikipedia.org/wiki/Max_Perutz> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/doctoral_students>    "None" .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/known_for>    "[[DNA|DNA structure]], [[consciousness]]" .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://3ba.se/wikipedia/attributes/prizes>       "[[Image:Nobel.png|20px]] [[Nobel Prize for Physiology or Medicine|Nobel Prize]] (1962)" .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://en.wikipedia.org/wiki/Template:infobox_scientist> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://www.w3.org/1999/02/22-rdf-syntax-ns#label>        "Francis Crick" .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://en.wikipedia.org/wiki/Category:Nobel_laureates_in_Physiology_or_Medicine> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://en.wikipedia.org/wiki/Category:English_neuroscientists> .
<http://en.wikipedia.org/wiki/Francis_Crick>      <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://en.wikipedia.org/wiki/Category:English_humanists> .

Iv' been playing with this source of data to build a dynamic timeline of scientists. The person choosen was the one where I could find a date of birth/death (some people didn't have this information or the date was not parseable (e.g. "[[March 11]], [[1922]] ([[Istanbul]], [[Turkey]])") ord I only used the predicates that could be used to find the date. For example here are a few predicates that could be used to find the date of birth:

http://3ba.se/wikipedia/attributes/birth_date
http://3ba.se/wikipedia/attributes/birthdate
http://3ba.se/wikipedia/attributes/Birthdate
http://3ba.se/wikipedia/attributes/date_birth
http://3ba.se/wikipedia/attributes/datebirth
http://3ba.se/wikipedia/attributes/date_of_birth
http://3ba.se/wikipedia/attributes/dateofbirth
http://3ba.se/wikipedia/attributes/DateOfBirth
http://3ba.se/wikipedia/attributes/DATE_OF_BIRTH
http://en.wikipedia.org/wiki/Category:1945_births>
(...)

I also used relationships between persons that could be found in the database. e.g.:

<http://en.wikipedia.org/wiki/Hermann_Joseph_Muller>    <http://3ba.se/wikipedia/attributes/teachers>   <http://en.wikipedia.org/wiki/Thomas_Hunt_Morgan> .

The result is a java application called WikiStory.
It requires JAVA Webstart 1.6. You can use the following command line:

javaws http://www.urbigene.com/wikistory/wikistory.jnlp

Selecting one or more category will select all the people that belong to it.
Clicking on a person in the timeline will load the page from wikipedia.


The timeline can also be saved as a SVG picture. If you're using Firefox, you can see an example Here

See also:

http://www.wikitimescale.org/index.php
http://meta.wikimedia.org/wiki/EasyTimeline
http://www.futureswatch.org/Timeline.htm
http://www.todayinsci.com/
http://www.perseus.tufts.edu/
http://dandelife.com/
http://www.timelineindex.com/content/home.php








Pierre

Tips: Sending Batch Invitations to Nature-Network.

A few minutes ago, I was looking for an quick method to send batch invitations to join Nature Network to my colleagues. I found a solution using the cURL utility.

1. Open firefox



2. log in to Nature Network



3. the site stores a cookie called '_session_id' on your browser. Open your Cookie Panel: Tools -> Options -> Privacy -> Cookies". Note the value of the cookie _session_id associated to the site network.nature.com



4. use cURL to send the form.
   

   
    curl -L -b '_session_id=THE_VALUE_OF_YOUR_COOKIE' -d 'referral[name]=Name' -d 'referral[email]=nobody.nowhere@mycompagny.com' -d 'referral[message]=this is an invitation to another social network'  -d 'commit=send'  'http://network.nature.com/referrals/create?locality='
   

   
   
   the option -L is used to follow any http redirection, -b set a cookie, -d set a key/value from the original html form. You can automatize this process using a simple loop over your addresses.
   

This solution worked fine at the time I wrote this post.

Pierre

network.nature.com is alive

.
A quick post: it seems that the global scientific social network network.nature.com global (previously known as Nature Network Boston) is now alive. I created two groups Bioinformatics and Semantic Web for the Life Sciences.

Pierre

New blog: Beginning Python for Bioinformatics

Beginning Python for Bioinformatics is a new blog about... (guess what). The author's aim is to convert the book Beginning Perl for Bioinformatics into pyhton.

See also: Python course in Bioinformatics

Pierre

Social Genealogy

From the FAQ: Geni is a unique approach to solving the problem of genealogy, which is the question of how everyone is related. Geni lets you create a family tree through our fun simple interface. When you add a relative's email address, he or she will be invited to join your tree. That relative can then add other relatives, and so on. Your tree will continue to grow as relatives invite other relatives. Each family member has a profile which can be viewed by clicking their name in the tree. This helps family members learn more about each other and stay in touch. Family members can also share information and work together to build profiles for common ancestors. Geni is a private network. Only the people in your tree can see your tree and your profile. Geni will not share your personal information with third parties.

See also, my previous post about how to draw pedigrees using DOT.

Pierre

Share your graph using swivel

Yesterday I found Many Eyes a service used to create and share some graphs to visualize your data, and his morning,Deepak also found Swivel which seems to be a similar product. However wile you have to copy and paste your data in ManyEyes, you can upload a csv file with Swivel.

I tried to create the same graph I did with openeyes and dbSNP yesterday, but I was not able to create a graph which could compare two columns in the same data-set, and moreover swivel doesn't stop to say "Swivel has not started swiveling this data yet. It'll be worth the wait".... and I've not time to investigate this further....


Pierre

Create your Visualizations with IBM's Many Eyes

Many Eyes is a new social tool from IBM used to create a custom dynamic visualization (bar chart,treemap, block histogram, bubble chart, line graph, network diagram, pie, scatterplot, stack, GIS ...) charts from your data. The graphics are plotted via a java applet. I've tested it using the snp data from the UCSC: for example, I've running the following query in the snp table:
select chrom as "chromosome",molType,class ,func as "function",avg(avHet),min(avHet),max(avHet),count(*) as "count" from snp126 where avHet>0 and valid!="unknown" group by chrom,molType,class,func

which group the snps features by chromosome, class ,etc... and I've displayed it as a treemap using Many Eyes

Pierre

BioSysBio 2007

FYI: Several presentations from BioSysBio 2007 are available on google-video:

http://video.google.com/videosearch?q=BioSysBio

Pierre

Nature Network Reloaded

Nature Network Boston(NNB) is a networking tool for scientists in the Boston area. It was created last year and I was little bit disappointed when I compared it to www.linkedin.com or www.openbc/xing.com.


Today I received this mail from NNB:

(...)
Thank you for setting up the Bioinformatics and Semantic Web groups on Nature Network Boston. I know it's been a while, but I finally have news about the website to report.

At the end of February/early March, Nature Network Boston will become part of a new website called Nature Network, which will be global in scope so we will be inviting scientists from all over the world to use the site. NNB will become a local channel within Nature Network (with local news and events).

Groups will still be there. On Nature Network, they will be labeled as either global or local (Boston-based) in scope. When we go live with Nature Network, all existing groups on NNB will, by default, be labeled a Boston group.

The other new thing going live in early March: each group will get its own discussion forum, so that group members can post messages and respond to each other. I'll send you another email in a few weeks with more details about how to be a moderator in your group forums.



Great ! I'm impatient to see this :-)

Launch of BMC Systems Biology

BMC Systems Biology, the first open access journal focussed solely on the entire emerging subject of systems biology, has just published its first articles.