EDIT

/\ **Under construction...** _Platform components for taxonomists dealing with geographic visualisation, geocoding and predictive modelling tools_

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# Geographic Components

## Introduction

The general aim of this activity is to provide the resources and applications able to publish, visualise, and analyze the distributional information associated with taxonomic information. Taxonomists require an easy and freely available application allowing to display and/or publishes the distribution information directly from simple data sources. However, as present distributional data are far from accurate we urgently also need tools able to:

* i) examine the degree of completeness of this information,

* ii) discriminate well surveyed localities from those do not have reliable inventories, and

* iii) locate the localities in which is necessary to carry on additional surveys in order to recover the environmental and spatial variation of the area. The activity is collaboratively carried out by all the partners.

## Objectives

To provide a generic and open source software solution for the Internet Platform for Cybertaxonomy and to use this as the base for specific tools to:

* provide output for printed and on-line taxonomic publications

* visualize distributional information

* statistically analyse distributional information with regard to completeness of surveys

* identify gaps to prioritise surveys in order to obtain an unbiased set of data for environmental analysis.

### Visualise Distributional Data

### Visualise specimen & observation coordinates as simple points

See ticket#64. 

A webservice will be build that creates and returns maps (as images) showing point occurrence data.

The service will take the following parameters and generate GIS layers on the fly that will be used to create maps via WMS:

 - bbox: the bounding box defining the boundaries of the image map

 - back: the background image. Defaults to some basic physical(?) world map.

 - height: the final height of the image in pixel

 - data: a list of point coordinates with an uncertainty radius in the form of `X1,Y1,Uncert1;X2,Y2,Uncert2;X3,Y3,Uncert3;...` 

 - title: title of the image, might be blank.

An example call to the service could then look like this:

~~~

http://etaxonomy.eu/distributionmap.php/?bbox=12.21,13.45&height=600&back=1&data=21.523,34.245,100;21.789,34.887,100;22.018,34.903,100

~~~

### Visualise area distribution data

A webservice will be build that creates and returns maps (as images) showing area distribution of a taxon.

A simple example map could look like this: http://128.214.62.43/euromed/euromed_map.php?taxon=280714&size=medium

The service will take the following parameters and generate GIS layers on the fly that will be used to create maps via WMS:

 - bbox: the bounding box defining the boundaries of the image map

 - back: the background image. Defaults to some basic political(?) world map

 - height: the final height of the image in pixel

 - areas: pointer to the list of area codes and therefore area shapes being used. Defaults to TDWG areas if NULL

 - status: pointer to the list of status codes being used. The format needs to be defined.

 - data: a list area codes with distribution status codes in the form of @Area1,Status1;Area2,Status2;Area3,Status3;...@. Areas can occur multiple times?

An example call to the service could then look like this:

~~~

http://etaxonomy.eu/occurrencemap.php/?bbox=12.21,13.45&height=800&data=MOR,35;FRA,32;SIC,35;CNY-OO,35

using TDWG area codes

~~~

There needs to be separate services that allow uploading and listing of area codes+shapes and status codes.

By default TDWG areas should exist already on the mapping server and should be used if no areas parameter is given.

### Analise Distributional Data

#### Calculation service that sums up single occurrences per region

A visualisation service for regions could then be used to display colored regions instead of simple points.

## Results

### Component C5.32 eConference on Geospatial Components of the Cybertaxonomy Platform

Report of the conference available at [[e-conference20071030]].

### Components C5.35 ~~Predictive distribution modelling report~~ and C5.38 ~~Gap analysis in local inventories report~~ 

Taxonomists have to continue doing what they have done during the last three hundred years: to describe the variety of life organisms and their location. Although this colossal task is important by itself its relevance is higher now due to current need of reliable biodiversity data. In the attached report we review the available scientific information on the possibilities and usefulness of the compiled species distribution data for basic and applied purposes, two of the deliverables of EDIT Work Package 5.4 “Geographical platform components” (deliverables 5.35 ~~Predictive distribution modelling report~~ and 5.38 -Gap analysis in local inventories report-).

The main conclusions raised by this report are that (i) our current species distribution information is biased and insufficient for most taxonomic groups, and (ii) modelling methods can not provide reliable and useful distribution predictions if they are based in these biased of data. Therefore, we identify as a key priority for bioinformatics the development of tools to: i) examine the degree of completeness of distributional information, ii) discriminate well surveyed localities from those that do not have reliable inventories, and iii) identify sets of areas where to carry out additional surveys, in order to increase the level of coverage of the environmental and spatial variation of a given region. We encourage that these tools are made freely available and easy to use to universalize their application. A list of the available software is attached at the end of the report.

Our purpose is to use this report as a kick-off for a debate between the people interested in the utility of current taxonomic and distributional data. Such debate will be carried out in a forthcoming e-conference (EDIT deliverables 5.32 and 5.33), where the participation of taxonomists, conservationists and bioinformaticians are welcome. EDIT aims to provide resources for taxonomists and the development of these tools would be an opportunity to increase the correct use of the biological information, promoting also the participation of taxonomists in the use of their (our) own data. The e-conference is an opportunity to contrast opinions and identify key issues needed for the development of effective bioinformatic tools, such as the ones we suggest.

To download the report please click here: http://wp5.e-taxonomy.eu/blog/files_edit_wp5/2007-07-26_D5.35_&_D5.38.doc

### Component C5.36: GIS database of vectorial and raster maps freely available at the European extent

#### GIS data downloads

EDIT geoplatform (http://edit.csic.es/web/page1/page1.html) provides standard GIS layers of surface units (countries, squares, ...) to evaluate the spatial distribution of occurrence data -spatial completeness-, and standard GIS layers of environmental variables (climate, topography,...) to evaluate weather occurrence data represent adequately the gradients of environmental variation -environmental completeness-.

GIS layers of surface units include both administrative units (countries, provinces) and regular equal-area units of different sizes (UTM squares, latitudinal squares, icosahedric triangles). Administrative units exist only for terrestrial areas, while regular equal-area units cover both terrestrial and marine areas. GIS layers of regular equal-area units were elaborated by MNCN-CSIC (EDIT geoplatform, 2007), with the exception of the UTM squares of 2,500 Km2 elaborated by the European Environmental Agency (EEA, 2003).

GIS layers of environmental variables cover the main environmental issues: climate, topography, vegetation, land cover and human population. Climate data include around twenty variables (temperature, precipitation, seasonality, etc.) from Worldclim database. Topography data include elevation above sea level, from Worldclim database, and distance to coast in Km, elaborated by MNCN-CSIC (EDIT geoplatform, 2007). Vegetation data include maps of Normalized Difference Vegetation Index (NDVI) obtained from satellite images by NASA and processed at Clark Labs. Land cover data include the map of land cover categories for the world generated by the University of Maryland, Department of Geography (Global Landcover Facility), and the map of land cover categories for Europe generated by the European Commission Joint Research Centre (Global Land Cover 2000 database).

It’s possible to use different geographical extents, from the whole Earth to a selected country or region within Europe. As spatial extent is reduced / increased, analyses can be done with more / less detailed spatial resolutions. 

GIS layers in the EDIT geoplatform are all in geodetic coordinates (longitude, latitude), datum WGS84. 

A more detailed description of the GIS layers of surface units and environmental variables can be found at http://edit.csic.es/web/docs/EDIT_GIS_layers.htm

Download of Geographic Information Systems (GIS) data layers:

http://edit.csic.es/web/page1/page1.html

### Component C5.31: Formerly D5.4.2. Application for distribution maps

#### Web application - Map viewer prototype

After some time evaluating the available open-source software and the possibilities it could offer to the EDIT Geoplatform we decided to start working with Mapbuilder, a JavaScript library that provides a client-side solution for dynamically generating web pages from XML  (such as OpenGIS Consortium documents) as well as the OGC Requests (GetMap, GetFeatureInfo, GetFeature...) necessary to view and query the geo-data. 

Mapbuilder version used is 1.0.1. It works with most modern browsers (Firefox 1.0+, Internet Explorer 6.0+, Mozilla 1.3+, Navigator 6+) but we are not sure about other web browsers. You must have javascript enabled! please check it in your web browser. 

The geo-data is stored in PostGIS, a database with a consolidated spatial extension able to make spatial queries (intersect, point-in-polygon, calculate distances, centroids), reproject data, etc. and "usual" queries, including statistical functions. On the next steps we will take profit of both possibilities to statistically analyze geo-referenced data in order to locate well surveyed localities...

The link between data (PostGIS) and web-application (Mapbuilder) is done through GeoServer. It takes the requests and sends a response: a beautiful image (after applying styles). 

The URL of the web application is: http://edit.csic.es:8080/edit_geo/prototype/edit.html

This web application is not definitive at all. In fact, it lacks of two main issues:

- Complete interactivity: user doesn't insert data and the analysis (point-in-polygon) to get biological information is not done "on-the-flight". We will have to work with programming (PHP probably) to send the parameters to a spatial SQL function (Contains) to be executed in PostGIS. 

- Complete interoperatibility:

* 1) legend images are static. We will have to manage to interactively generate a legend according to the data the user inserts. MapBuilder doesn't provide the possibility to interactively construct legends. MapServer can be a good solution. 

* 2) legend images are not OGC compliant. It means that they cannot be viewed through any other OGC compliant web-application. For example, you can try to view our geoserver data through the Intergraph WMS Viewer  (http://www.wmsviewer.com/main.asp): If in “Edit Servers” you insert http://edit.csic.es:8080/geoserver/wms you can check all the WMS layers we are serving. Using the adequate style for each layer, you can see the data as if you were in our application, but you cannot see the legends (left side of the page, next to Layers). If instead of our server you insert, for examle  http://devgeo.cciw.ca/cgi-bin/mapserv/windatlas?  and check any of the layers, you will can see a Legend. You can check also to get the legend inserting, as an URL to the browser, the following:  http://devgeo.cciw.ca/cgi-bin/mapserv/windatlas?SERVICE=WMS&VERSION=1.1.1&REQUEST=GetLegendGraphic&LAYER=roughnesslength&FORMAT=image%2Fgif

### Component C5.37 ~~Application to examine inventory completeness~~ & C5.39 ~~Application to map inventory completeness~~ 

#### Demo: Spatial completeness of biodiversity data

The objective of the demo is to make an idea of one of the functions of the future application: the analysis of spatial completeness.

The URL of the web application where you can see the demo is: http://edit.csic.es:8080/edit_geo/prototype/edit.html

In this demo, it’s supposed that the user has already:

* 1.- selected the extent for the analysis (Iberian Peninsula is used as example)

* 2.- submitted his file of point sample data (Jorge M. Lobo's data on Iberian Scarabaeidae are used as example)

* 3.- selected a taxonomic level from those included in his data file (genus is used as example)

* 4.- selected a GIS layer of surface units (UTM squares of 2500 sq.km. are used as example)

* 5.- choosed or clicked on “perform anaysis of spatial completeness”

Then, three different maps are displayed:

* Map of sampling effort (number of records in each square)

* Map of taxonomic richness (number of genera in each square)

* Map of inventory uncertainty. Inventory uncertainty in each surface unit is based not only on the number of taxa (S) and the number of records (N), but also on the relative frequency of the taxa (FrSp = Fr1, ...., FrS). In this example, inventory uncertainty (IU) is measured as the probability of missing some of the taxa:

 IU = 1 - ∏Sp (1-(1-FrSp)N)

The map of inventory uncertainty indicates the “red” surface units where is necessary to carry on additional surveys in order to recover the spatial variation of the area, or where data on absences should be recorded.

A review of the available scientific information on the possibilities and usefulness of the compiled species distribution data for basic and applied purposes is available for download at http://wp5.e-taxonomy.eu/blog/files_edit_wp5/2007-07-26_D5.35_&_D5.38.doc.

## Geo Webservice Api

The webservice Api is available at [[MapRestServiceApi]]

## Free GIS software links

Links to main Geographic Information Systems (GIS) free software:

* DIVA-GIS http://www.diva-gis.org/

* Quantum GIS http://qgis.org/

* gvSIG http://www.gvsig.gva.es/

* SEXTANTE http://www.sextantegis.com/

* SAGA GIS http://www.saga-gis.uni-goettingen.de/

* uDig http://udig.refractions.net/