Taxonomic cross-mapping tools
Chang Liu, Andrew Jones & Richard White, Cardiff University School of Computer Science & Informatics
The things which you can test at present are a subset of the elements that Andrew and Chang plan to demonstrate in Berlin. The demo is in a number of pieces, for good development reasons, that are not seamlessly integrated. We are moving towards a more seamless integration, but the primary objective is to test the methodology and seek feedback, not produce a polished system at this stage. Indeed, the various requirements probably preclude a single "turn-key" approach.
Updates
-
7 September 2011: Four additional cross-maps comparing CoL Annual Checklist editions against the NCBI Taxonomy checklist have been added. The cross-maps currently available are listed in section 2 below and are accessible from the "Version 2" demo link.
Cross-mapping services for test and demonstration
Introduction
1. Checklist importing and preparation for i4Life cross-mapping
Currently the following types of checklists can be imported into the "checklist repository".
- Catalogue of Life Annual Checklists 2005 to 2010
- NCBI Taxonomy
Although our current focus is on the cross-map creation and export processes listed below, it is hoped to add the Red Data List to this set of import data types before the Berlin meeting. This will make it possible to create a "mapping" between an edition of the CoL and the currently available Red List. DwC-A import will also be added.
- A web-accessible instance of the data preparation program will appear here
- You can examine the raw checklist repository database tables using the
phpMyAdmin web tool
(opens in a new tab or window).
The versions of the repository are named "CR" followed by the date of creation, in the form "CR20110904".
2. i4Life cross-mapping tool test versions
The demo cross-mapping tools use as their source data the following databases, created as described above:
CR20110904Droseraceae, CR20110904Solanum,
CR20110904Gracillariidae, CR20110904Phasmida
and infer the following taxonomic relationships:
isTaxCongruentWith, isTaxIncludes
The test subset data sets are described further in a brief text note.
The following cross-maps have been generated:
- Droseraceae
- ac2008 vs ncbi
- ac2009 vs ncbi
- ac2008 vs ac2009 (only
isTaxCongruentWith inferred)
- Solanum
- ac2008 vs ac2009 (has
isTaxIncludes relationship)
- Gracillariidae
- ac2008 vs ncbi
- ac2007 vs ac2008
- Phasmida
- ac2007 vs ncbi
- ac2008 vs ncbi
3. i4Life cross-mapping web services
- A page listing the methods available in the service
(under the heading "CrossMap")
- Test SOAP client
(paste the address
http://litchi.cs.cf.ac.uk:8080/axis2/services/CrossMap?wsdl
of the WSDL file
into the box provided, or use the following direct links)
For the first service, "searchNames", you need to provide:
searchNames.dataset (there is only one OWL file deployed on the web service: CoL20110607Solanum.owl.
So in order to invoke the web service, the only "dataset" parameter accepted is "CoL20110607Solanum".
searchNames.keyword (a taxon (in the genus Solanum, such as Solanum woodburyi), for which any crossmapped taxa will be reported)
searchNames.relType (isTaxCongruentWith or isTaxIncludes)
This page is now hosted on ice9.tk
by Richard White, last edited on 24th March 2018