University of Glasgow

Roderic Page

OK, second rant of the day. One of my favourite online specimen
databases is [AntWeb](http://www.antweb.org/). For a while the ability
to harvest data from this database using the venerable DiGIR protocol
hasn\'t been possible, due to various issues at the California Academy
of Sciences. Well, now it\'s back, and \"accessible\" using [TAPIR
(TAPIR - TDWG Access Protocol for Information
Retrieval)](http://www.tdwg.org/dav/subgroups/tapir/1.0/docs/tdwg_tapir_specification_2009-02-05.htm).
Accessible, that is, if you like horrifically over-engineered, poorly
documented standards. OK, at lot of work has gone into TAPIR, there\'s
lots of [great code on
SourceForge](http://sourceforge.net/projects/digir/), and there\'s lots
of documentation, but I\'ve really struggled to get the most basic tasks
done.  
  
For example, let\'s imagine I and want to retrieve the information on
the ant specimen
[CASENT0100367](http://www.antweb.org/specimen.do?name=casent0100367)
(note how trivial this is via a web browser, just append the specimen
name to **http://www.antweb.org/specimen.do?name=**). After much
clenching of teeth struggling with the TAPIR documentation and the TAPIR
client software, I finally found [an email by Markus
Döring](http://lists.tdwg.org/pipermail/tdwg-tapir/2008-April/000493.html)
that gave me the clue. If I\'m going to construct a URL to retrieve this
specimen record, I need to include the URL of an XML document that
serves as a template for the query. Since one doesn\'t exist, I have to
create it and make it accessible to the TAPIR server (i.e., the AntWeb
TAPIR server needs to access it, so I have to place this XML document on
my web server). The template (shown below) lives at
<http://bioguid.info/tapir/dwc_catalog_number.xml>:  

``` prettyprint

                xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
                xmlns:xs="http://www.w3.org/2001/XMLSchema" 
                xsi:schemaLocation="http://rs.tdwg.org/tapir/1.0
                                    http://rs.tdwg.org/tapir/1.0/schema/tapir.xsd
                                    http://www.w3.org/2001/XMLSchema
                                    http://www.w3.org/2001/XMLSchema.xsd">
  Scientific name in query
  Query for a Scientific Name. Based on http://rs.tdwg.org/tapir/cs/dwc/1.4/template/dwc_sci_name_range.xml, found in email by Markus Döring http://lists.tdwg.org/pipermail/tdwg-tapir/2008-April/000493.html
  
  
    
        
        
    
  
```

  
Now I can write my query:
[http://www.antweb.org/tapirlink/www/tapir.php/antweb  
op=search  
&start=0  
&limit=1  
&template=http://bioguid.info/tapir/dwc_catalog_number.xml  
&name=casent0100367](http://www.antweb.org/tapirlink/www/tapir.php/antweb?op=search&start=0&limit=1&template=http://bioguid.info/tapir/dwc_catalog_number.xml&name=casent0100367)  
So, the AntWeb server is going to read this query, and call my web
server to get the query template to figure out what I actually want. Am
I the only person who thinks that this is insane? Can anybody imagine
going through these hoops to access a GenBank record, or a PubMed
record?  
  
Perhaps it\'s me, and my obsession with linking individual data records
(rather than harvested lots of records, or federated search). But it
strikes me that harvesting is a simple task and not many people will be
doing it (at least, not on the scale of GBIF), and federated search is a
non-starter as our community can\'t keep data providers online to save
themselves.  
  
In many ways I think TAPIR (and DiGIR before it) missed what for me is
the most basic use case, namely I have a specimen identifier and I want
to get the record for that specimen. These services make it much harder
than it needs to be. It\'s a symptom of our field\'s inability to
deliver simple tools that do basic tasks well, rather than overly
general and highly complex tools that are poorly documented. Of course,
retrieving individual records woud be easy if we have resolvable GUIDs
for specimens, but we\'ve singularly failed to deliver that, so we are
stuck with very clunky tools. There\'s got to be a better way\...


OK, second rant of the day. One of my favourite online specimen databases is AntWeb. For a while the ability to harvest data from this database using the venerable DiGIR protocol hasn't been possible, due to various issues at the California Academy of Sciences.

Messaggi di Rogue Scholar

Accessing specimens using TAPIR or, why do we make this so hard?