update to social semantic tagging list

A while back I started to keep track of social semantic tagging projects (other than mine) in a post. Since then, I've continued to add to the list in that post - most recently today. Its starting to feel downright crowded in here - not the feeling you want to have when trying to wrap up the last project for your dissertation.

fret fret

freebase ED and sparql

So what do you do when the two papers you would like to finish and submit are sitting in the hands of co-authors?  Kayaking? Sleeping?  Surfing? today, no.  Hacking? today, yes.

While I wait, I decided to finally start working on bridges between freebase and our semantic tagging repository for ED for use after the data is collected. To get started, I wrote the code to answer this question: "what URIs have been tagged with the organism classification X or any of the sub classifications of X".  For example, has anyone tagged anything with magnoliopsida or any of its lower classifications, such as arabidopsis?

To do this, I needed to utilize the 'Higher classifications' (or of course 'Lower classifications') property of the Organism Classification Type.  Unfortunately, there is, thus far, no such thing as a generic transitive property in freebase as far as I can tell, so I built a brute force, recursive query that implements it myself.  I send the following with the '???' replaced with my starting point (e.g. 'magnoliopsida') to freebase as the rest of the URL starting with http://www.freebase.com/api/service/mqlread?queries= .

{"q1":{"query":
 [{
 "higher_classification" : "???",
 "name" : null,
 "guid" : null,
 "type" : "/biology/organism_classification"
 }]
}}

Freebase responds with the lower classifications of my query and then I repeat the process with these until either a maximum depth is reached or it bottoms out. If you know a better way to do this please let me know.

Once I have all of the guids for all of the lower classifications of my query, I send these over to get URIs tagged with any of them via a SPARQL query like this:

prefix tag: 
prefix rdfs: 
select ?tagging ?tag
where {
{
?tagging tag:associatedTag ?tag .
?tag rdfs:isDefinedBy http://www.freebase.com/view/guid/9202a8c04000641f8000000000516f8d
}
UNION
{
?tagging tag:associatedTag ?tag .
?tag rdfs:isDefinedBy http://www.freebase.com/view/guid/9202a8c04000641f800000000003be00
}
UNION
{?
tagging tag:associatedTag ?tag .
?tag rdfs:isDefinedBy http://www.freebase.com/view/guid/9202a8c04000641f800000000572e4660
}
}

The query has as many UNIONs as topics to check for. (Note that you have to put URIs in SPARQL queries inside angle brackets - blogger was making this difficult for me to include). It works well enough, but if there are too many, I hit the max URL size limit (HTTP 414) so I set it up to send them in chunks and then reassemble the results.

Hacky? Yes. Successful for demo purposes? so far..

Any ideas about optimizing such activities most appreciated.

On the todo list:

1. Assemble the must-tag list of web services for the upcoming biomoby/ED jamboree
2. Build up an API-like library of queries like the above and normal queries like 'get all the URIs tagged by user X' so that we can more easily put up reasonable human interfaces for users of ED2.0. (Thanks to those that have already started using it!).  Note that any developers out there already have access to all of the data needed to build ED applications via HTTP calls to freebase and to our repository.  The library I speak of will be used by us and probably made public, but the real idea is for external developers to utilize SPARQL/MQL directly as that provides the most flexibility.
3. Create mappings between bio-ontology classes and freebase topics.  Likely follow Shawn Simister's model for approaching this integration.  (He has some excellent ideas about SPARQL/MQL integration).
4. Prepare for kayaking trip tomorrow
5. Graduate before they cut off my funding...

Peter (Google) and Christine (the librarians)

I was very lucky to have my new wife with me at SciFoo for many reasons, not the least of which is that she is much better at socializing than I am and thus managed to introduce me to many people I would never normally have met.  One of those people was Christine Borgman, Professor & Presidential Chair in Information Studies at UCLA.  While I was struggling to explain my work on the Entity Describer project to her, she noticed Peter Norvig walk by and dragged him over to join our conversation.  I guess she must have known him from somewhere but I'm not sure where.  Anyway, I didn't realize this at the time, but Peter is head of research at Google.  Ahem... did I mention that SciFoo interactions could be somewhat intimidating?  So there I am, standing between two giants of modern information science trying to explain what it was I was doing there but mostly trying to get some insight into their respective thoughts on the organization of the world's information. It wasn't a long discussion, but here are the basics.

The main question that I posed to them was whether or not and how semantic tagging (a la ED) is or might be useful.  On the surface, the answer from Peter was no and the answer from Christine was yes.  However, the truth of the matter is that they were really talking about supporting different functions for the end user - though this fundamental difference became a little lost during the conversation.  Google is principally focused on providing the best possible results, to the most people, given the least amount of information in the query - that is, keyword based search of the entire Web.  Library-science is typically much more concerned with providing the capacity for people to make very specific requests using much more sophisticated queries that operate over much smaller collections of information (e.g. the library of congress). The fact that there is some overlap in the information needs of the users of these different kinds of systems often brings up the desire for combative  comparison, but I think that, in reality, there is clearly no need for combat because they are simply too different in the functions that they intend to provide.

My interpretation is that Google isn't really concerned with intentionally provided meta-data in the name of end-user, full-Web search because the scale that they operate on seems to render any such indexing by one or even a number of parties almost laughably shallow in its characterization of both the nature of any particular item and its expected relevance to a query.  When you have literally millions of people passively voting and indexing every item of the Web through their decisions to link to it or not, you have very sophisticated algorithms for understanding the text in the pages generating and receiving those links and to top it off you record and process millions of people's behavior when faced with your search results, why should you care what some person or institution says the item is about?  The fact that they (among other search engines) beat out the directory-based approach to finding information on the Web is a clear demonstration that automatic indexing and link based relevance ranking do a better job than meta-data based classification - for the problem of Web scale search.  Google clearly doesn't need human semantic indexers to succeed, though, as Peter said, they certainly use all of the information that exists.  If there happen to be good indexes online (as Connotea turned out to be be for a fairly brief window), then their algorithms will certainly find them and use them - if not, no worries, the algorithms will take advantage of the 'normal' data on the Web and do just fine thank you. 

From the library-science professional perspective, this attitude is clearly annoying.  If human indexing isn't really necessary to find things, what is the point of the field that has devoted itself to the creation of effective ways for people to categorize things for retrieval?  For example, there is a lot of annoyance that the Google Books initiative seems to ignore most, if not all of the meta-data already associated with the books that they are scanning and indexing.  This means that meta-data, even as basic as volume numbers, is inaccessible for searching.  For the library professional that is trained to both search through and construct careful and precise classification structures,the inability to even search for a specific volume of a book is infuriating - particularly knowing that it is well within Google's power to incorporate such abilities into their system.

So on the one side we have the perspective that there is still value in the careful, intentional use of meta-data in the search and retrieval process while on the other side we are quite happy to let the intersection of algorithm and massive passive indexing do the work.  I guess, as is the usual answer, I'd suggest that both sides provide useful functions that are both worth keeping and advancing.  A detailed classification system, either constructed intentionally through the work of professional labor or semi-intentionally through the work of social taggers, provides functionality that is clearly different than what can be achieved by automatic indexing; however, it may not provide any help whatsoever in improving a full-Web-scale keyword-based search.  The essence of the power of intentional classification is the precision of the queries that it enables.  For example, if I want only version 3 of "The Devil's Rights and the Redemption" and thats it or I want only those items that have been tagged as with bioinformatics and to_read by Jaa, there is really no way ( AFAIK) to accomplish this without the intentional recording and utilization of meta-data about those resources.

So, though Peter and Google may have little direct use for ED and its semantic meta-data generating and consuming brethren emanating from the library and information sciences, there are still clearly meaningful applications of such work.  It just happens that providing effective search over the contents of the entire Web based on a string like 'Britney Spears' isn't really one of them.

I'm ok with that.

another year older -My 2008 Research In Progress seminar

I just finished giving my annual Research in Progress seminar for the iCAPTURE Heart and Lung research institute where I "work".  In the talk, titled "The social construction of a semantic web for the life sciences" which might someday be the title of my thesis, I describe results from comparisons of different approaches to the indexing problem (like MEDLINE versus Connotea ..) and use those results to motivate the Entity Describer project.  I also spent a short digression on my experiences with "publishing" the ideas for that project on my blog and encouraging the younger grad students to do the same thing with their work.

I think that, in general, the talk was well received, but we will see if it actually produces any new users ;) !

On the Entity Describer front, I should point out that we have a couple new people working on various aspects of it and that their work will be described on the ED developer blog.  (Throw out a comment for our most active contributer Paul!).  I will continue to write about the project here, but it is my hope that the other site will be a better source for more technical commentary as the project unfolds over time.

Feelin groovy today (despite the ongoing onslaught of "Junuary" in YVR.

updates to ED

Since the last post, we've made a couple minor changes to the ED interface based on feedback we've received. Changes visible in the current version were intended to meet these objectives

1. clear separation between normal user created tags and semantic tags 
2. easier access to previously added user tags
3. easier to add many semantic tags to the same post

We also noticed that several new users were tagging exclusively with private posts.  To clarify the fact that private posts don't go into our database and that the semantics of the tags added to private posts are therefore inaccessible, we've added a warning message that appears whenever private bookmarks are posted through the system.  In the words or Eddie, the javascript guru of this project, 

"... go private they will,

annoy them we must ..."

We may at some point expand the ED functionality to support private bookmarks, but for now, we think its fair that if people would like to use a free, social system they share openly.  Private bookmarks will still be posted to Connotea as they currently are without ED and the non-sharing users will still benefit from the semantic tags during the process of tagging.

I've also gone ahead and added ED to the growing list of semantic tagging projects that I am beginning to compile.