University of Glasgow

Roderic Page

I\'ve been playing a little with [TreeBASE II](http://www.treebase.org),
and the more I do the more I want to pull my hair out.  
  
**Broken URLs**  
The old TreeBASE had a URL API, which databases such as NCBI made use
of. For example, the NCBI page for [*Amphibolurus
nobbi*](http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=206551)
has a link to this taxon in TreeBASE. The link is
<http://www.treebase.org/cgi-bin/treebase.pl?TaxonID=T31183&Submit=Taxon+ID>.
Now, this is a fragile looking link to a Perl CGI script, and sure
enough, it\'s broken. Click on it and you get a 404. In moving to the
new TreeBASE II, all these inward links have been severed. At a stroke
TreeBASE has cut itself off from an obvious source of traffic from
probably the most important database in biology. **Please, please, throw
in some mod_rewrite and redirect these CGI calls to TreeBASE II.**  
  
**New identifiers**  
All the TreeBASE studies and taxa have new identifiers. Why? Imagine if
GenBank decided to trash all the accession numbers and start again from
scratch. TreeBASE II does support \"legacy\" StudyIDs, so you can find a
study using the old identifier (you know, the one people have cited in
their papers). But there\'s no support for legacy TaxonIDs (such as
**T31183** for *Amphibolurus nobbi*). I have to search by taxon name.
**Why no support for legacy taxon IDs?**  
  
**Dumb search**  
Which brings me to search. The search interface for taxa in TreeBASE is
gloriously awful:  
  

::: {style="text-align:center;"}
![tbsearch.png](http://lh6.ggpht.com/_Gct8lVAxKqQ/S_u1SKH28qI/AAAAAAAAAqQ/744dg1hR9KU/tbsearch.png?imgmax=800){border="0"
width="400"}
:::

  
So, I have to tell the computer what I\'m looking for. I have to tell it
whether I\'m looking for an identifier or doing a text search, then
within those categories I need to be more specific: do I want a TreeBASE
taxon ID (new ones of course, because the old ones have gone), NCBI id,
or uBio? And this is just the \"simple\" search, because there\'s an
option for \"Advanced search\" below.  
  
Maybe it\'s just me, I get really annoyed when I\'m asked to do
something that a computer can figure out. I shouldn\'t have to tell a
computer that I\'m searching for a number or some text, nor should I
tell it what that number of text means. Computers are pretty good at
figuring that stuff out. I want **one** search box, into which I can
type \"Amphibolurus nobbi\", or \"Tx1294\" or \"T31183\" or \"206552\"
or \"6457215\" or \"urn:lsid:ubio.org:namebank:6457215\" (or a DOI, or a
text string, or pretty much anything) and the computer does the rest. I
don\'t ever want to see this:  
  

::: {style="text-align:center;"}
![tbsearch2.png](http://lh5.ggpht.com/_Gct8lVAxKqQ/S_u3RnivVXI/AAAAAAAAAqY/kjw8YGNRXww/tbsearch2.png?imgmax=800){border="0"
width="400"}
:::

  
Computers are dumb, but they\'re not so dumb that they can\'t figure out
if something is a number or not. What I want is something close to
this:  
  

::: {style="text-align:center;"}
![google.png](http://lh4.ggpht.com/_Gct8lVAxKqQ/S_u4KfQHzSI/AAAAAAAAAqg/TnNz6I-1Cug/google.png?imgmax=800){border="0"
width="400"}
:::

  
Is this really too much to ask? **Can we have a search interface that
figures out what the user is searching for?**  
  
Note to self: Given that TreeBASE [has an
API](http://sourceforge.net/apps/mediawiki/treebase/index.php?title=API),
I wonder how hard it would be to knock up a tool that took a search
query, ran some regular expressions to figure out what the user might be
interested in, then hit the API with that search, and returned the
results?  
  
My concern here is that TreeBASE II is important, very important. Which
means it\'s important to make it usable, which means don\'t break
existing URLs, don\'t make old identifiers disappear, and don\'t have a
search interface that makes me want to pull my hair out.  
  


I've been playing a little with TreeBASE II, and the more I do the more I want to pull my hair out.
<strong>
 Broken URLs
</strong>
The old TreeBASE had a URL API, which databases such as NCBI made use of. For example, the NCBI page for
<em>
 Amphibolurus nobbi
</em>
has a link to this taxon in TreeBASE.

TreeBASE II makes me pull my hair out

> You can\'t just ask customers what they want and then try to give that
> to them. By the time you get it built, they\'ll want something new. -
> [Steve Jobs](http://www.quotationspage.com/quote/38352.html)

  
It\'s Friday, so time for either a folly or a rant. BHL have put another
user survey into the field <http://www.surveymonkey.com/s/BHLsurvey>. I
loathe user surveys. They don\'t ask the questions I would ask, then
when you see the results, often the most interesting suggestions are
ignored (see the [Evaluation of the User Requirement Survey Oct-Nov
2009](http://planetposter.de/bhl/praha2009.htm)). And we\'ve been here
before, with EDIT (see this [TAXACOM
message](http://markmail.org/message/nyneolwjt7w6w5qe) about the
moribund [Virtual Taxonomic Library](http://taxonlib.org/)). Why go to
the trouble of asking users if you aren\'t going to deliver?  
  
I suspect surveys exist not to genuinely help figure out what to do, but
as an internal organisational tool to convince programmers what needs to
be done, especially in large, multinational consortia where the
programmers might be in a different institution, and don\'t have any
particular vested interest in the project (if they did, they wouldn\'t
need user surveys, they\'d be too busy making stuff to change the
world).  
  
So, what should BHL be doing? There\'s lots of things to do, but for me
the core challenges are *findability* and *linkage*. BHL needs to make
its content more findable, both in terms of bibliographic metadata and
search terms (e.g., taxa, geographic places). It also needs to be much
more strongly linked, both internally (e.g., cross referencing between
articles where one BHL article cites another BHL article), and
externally (to the non-BHL literature, for example, and to
nomenclators), and the external links need to be reciprocal (BHL should
link to nomenclators, and nomenclators should point back to BHL).  
  
There are immediate benefits from improved linkage. Users could navigate
within BHL content by citation links, for example, in the same way we
can in the recent literature. If BHL cleaned up its metadata and had a
robust article-level OpenURL resolver it could offer services to
publishers to add additional links to their content, driving traffic to
BHL itself. Better findability leads to better links.  
  
One major impediment to improving things is the quality of the OCR text
extracted from BHL scans. There have been various automated attempts to
extract metadata from OCR scans (e.g., \"A metadata generation system
for scanned scientific volumes\"
[doi:10.1145/1378889.1378918](http://dx.doi.org/10.1145/1378889.1378918)),
but these have met with mixed success. There\'s a lot of scope for
improving this, but I suspect a series of grad student theses on this
topic may not be the way forward (grad students rarely go all the way
and develop something that can be deployed). Which leaves crowd
sourcing. Given the tools already available for correcting Internet
Archive-derived book scans (e.g., Wikisource [discussed in an earlier
post](http://iphylo.blogspot.com/2010/03/setting-up-local-wikisource.html)),
it seems to me the logical next move for BHL is to dump all their
content into a Wikisource-style environment, polish the tools and
interface a bit, and encourage the community to have at it. Forming and
nurturing that community will be a challenge, but providing BHL can
demonstrate some clear benefits (e.g., generating clean pages with new
taxon names, annotated illustrations, OpenURL tools for publishers to
use), then I think the task isn\'t insurmountable. It just needs some
creativity (e.g., why not engage EOL users who land on BHL content to go
one step further and clean it up, or link with Wikipedia and Wikispecies
to attract users interested in actively contributing?).  
  
I doubt any of this will be in any user survey\...  
  


It's Friday, so time for either a folly or a rant. BHL have put another user survey into the field http://www.surveymonkey.com/s/BHLsurvey. I loathe user surveys.

Messaggi di Rogue Scholar

TreeBASE II makes me pull my hair out

Where next for BHL?