GrassPortal - User Guide

Getting Started

Datasets

First check that the dataset you wish to use is selected. There are currently two datasets in GrassPortal:

Occurrence Data: field observations of grasses e.g. herbarium specimens.
Species Data: global grass species checklist.

The active dataset is displayed at the top left of the display under the GrassPortal logo (here the "Occurrence Data" dataset is active):

Dataset selection

To change the active datset click on the "Other Datasets" tab and select the required dataset:

This results in the active dataset display changing (from "Occurrence Data" to "Species Data" in this case):

Searching

GrassPortal allows users to construct both simple keyword searches, and more complex searches built up from multiple concepts. Two areas of the screen are related to search:

1. Search concepts are arranged in a tree on the left of the display. This is used to put together advanced searches using specific concepts.

Concepts can be browsed either by clicking on
branches of the tree ("+") or by typing search
terms in the box and clicking "Filter".

2. Click on the "Search" tab to display the current search, and to refine and customise it (click on the "Help" tab to return here).

Concept Searching

To perform a concept search browse the "Concept" tree on the left-hand side of the screen to locate the desired search concept (e.g. Genus) and click on the desired concept:

The search concept box appears on the right-hand side of the screen in the "Search" pane:

The "Any" radio button is selected by default which will return all instances of the concept when the "Search" button is clicked. More specific searches can be done by selecting a different radio button (e.g. "Exact") in the concept box and typing a search term in the box underneath the radio buttons:

Suggestions are displayed as you type (with the number of records matching that term in brackets) in decreasing order of the number of records matching that term. A suggested term may be slected by moving the mouse pointer over it and clicking it to select it. At this point click a "Search" button to perform the search using a single concept or additonal concepts may be added to build up a more complex search:

The above is an example of a concept search using three concepts. When more than one concept is used in this way the search is performed using a logical AND operation i.e. in the above example the search is for all instances of the genus Poecilostachys that have been identified to species level and were recorded in the country Tanzania. A search for records that match the concepts of the genus Poecilostachys AND the genus Echinochloa would return zero results as there cannot be any records for instances of a plant that is in the genus Poecilostachys AND in the genus Echinochloa.

Logical OR operations are performed by clicking on the "[or]" next to a selected concept. A concept search for the genus Poecilostachys OR the genus Echinochloa would return all the records that match both genera.

Keyword Searching

In the "Search" pane type keyword(s) in the box; and click a "Search" button.

Search Results

Search results are shown in a table in the righthand "Results" pane. Click the "Search" tab to continue refining your search.

Record Information

Full record data can be obtained for any result by double clicking on the "Occurrence ID" in the "Results" pane:

Hover Help

Throughout GrassPortal holding the mouse pointer over an item will cause hover help to be displayed in a box that appears:

Above is the hover help provided when the mouse pointer is held over the "Species" concept in the concept tree browser area.

Visualise Results

In the top right of the display the area vertically labeled "Visualise Results" can be clicked on to display bar charts and pie charts of the results of a search:

The above is what is displayed in the "Visualise Results" area following a search for C3 or C4 using the "Photosynthetic pathway" search concept and the "Species Data" dataset.

Map of Results

When using the "Occurrence Data" dataset, search results are plotted onto a map located in the bottom pane of the righ-hand side of the display (the example below is for a search for any instances of the genus Echinochloa using the "Occurrence Data" dataset and the genus search concept to search for eactly Echinochloa):

Full zoom control is provided. The number of records are regionally summarised by the coloured circles showing the number of records returned for that area.

Downloading Results

Search results may be downloaded. Click on the "Download" button in the bottom left-hand corner of the "Results" pane. The results are saved as a Comma Separated Variable (CSV) file that may be opened using e.g. Microsoft Excel.

Label	Data Type	Comment/Description	Datasource
1. Taxonomy		Search by taxonomic rank.
a. Species	string	Accepted scientific binomial species name (Genus species) e.g. Poa annua.
b. Genus	string	Genus (taxonomic rank below Subtribe and above Species) e.g. Poa.
c. Subtribe	string	Subtribe (taxonomic rank below Tribe and above Genus).
d. Tribe	string	Tribe (taxonomic rank below Subfamily and above Subtribe).
e. Subfamily	string	Subfamily (taxonomic rank below Family and above Tribe).
Synonym	string
2. Phylogeny	string
Phylogeny (Long Name)	string
Phylogeny (Short Name)	string
3. Plant traits
a. Morphological characters		Morphological characteristics of each species	http://www.kew.org/data/grasses-db.html
Culm Habit (Categorical Description)	string	Categorical description of culm habit.	http://www.kew.org/data/grasses-db.html
Culm height (cm)		Height (cm) of culms (stems that support the inflorescences).
High (cm)	double	Upper limit to the normal range of culm height (cm).	http://www.kew.org/data/grasses-db.html
Low (cm)	double	Lower limit to the normal range of culm height (cm).	http://www.kew.org/data/grasses-db.html
Max (cm)	double	Maximum culm height (cm) - extreme value.	http://www.kew.org/data/grasses-db.html
Min (cm)	double	Minimum culm height (cm) - extreme value.	http://www.kew.org/data/grasses-db.html
Inflorescence Type (Categorical Description)	string	Categorical description of the inflorescence (cluster of flowers arising from the main stem). Refers to the true inflorescence (i.e. above uppermost sheath) in a compound system.	http://www.kew.org/data/grasses-db.html
Leaf size (length x width)
Length (cm)
High (cm)	double	Upper limit to the normal range of leaf blade length (cm).	http://www.kew.org/data/grasses-db.html
Low (cm)	double	Lower limit to the normal range of leaf blade length (cm).	http://www.kew.org/data/grasses-db.html
Max (cm)	double	Maximum leaf blade length (cm) - extreme value.	http://www.kew.org/data/grasses-db.html
Mean (cm)	double	Mean length of the leaf blades (cm).	http://www.kew.org/data/grasses-db.html
Min (cm)	double	Minimum leaf blade length (cm) - extreme value.	http://www.kew.org/data/grasses-db.html
Width (cm)
High (cm)	double	Upper limit to the normal range of leaf blade width (cm).	http://www.kew.org/data/grasses-db.html
Low (cm)	double	Lower limit to the normal range of leaf blade width (cm).	http://www.kew.org/data/grasses-db.html
Max (cm)	double	Maximum leaf blade width (cm) - extreme value.	http://www.kew.org/data/grasses-db.html
Mean (cm)	double	Mean width of the leaf blades (cm).	http://www.kew.org/data/grasses-db.html
Min (cm)	double	Minimum leaf blade width (cm) - extreme value.	http://www.kew.org/data/grasses-db.html
Life History (Categorical Description)	string	Life history strategy (annual or perennial).	http://www.kew.org/data/grasses-db.html
Match Confidence	double	Confidence (0-100%) of the matching between species name in the morphological characters database, and the database of accepted names. Since both databases come from Kew, this should always be 100%.
Pericarp (Categorical Description)	string	Categorical description of the pericarp (tissue developing from the ovary and surrounding the seed) of the caryopsis (seed).	http://www.kew.org/data/grasses-db.html
Plant Density (Categorical Description)	string	Growth habit of the plant.	http://www.kew.org/data/grasses-db.html
Species description (Kew GrassBase URL)	string	URL linking to a full taxonomic description of the species.
Species identifier (Kew numeric ID)	int	Unique species identifier (numeric ID) from the Kew GrassBase morphological descriptions database.
Species identifier (Kew URN reference)	string	Unique species identifier (URN reference) from the Kew GrassBase morphological descriptions database.
b. Photosynthetic pathway	string	Type of photosynthetic pathway (C3 or C4) used by each species.
4. Distribution
Expert-determined species ranges		Search by Biodiversity Information Standards (Taxonomic Databases Working Group or TDWG) defined area.
a. Continent	string	Continent, e.g. Northern America	Kew GrassBase nomenclature database (http://www.kew.org/data/grasses-syn).
b. Region	string	Region, e.g. Southwestern U.S.A, South-Central U.S.A	Kew GrassBase nomenclature database (http://www.kew.org/data/grasses-syn).
c. Botanical country	string	Botanical country, e.g. Arizona, New Mexico, Oregon	Kew GrassBase nomenclature database (http://www.kew.org/data/grasses-syn).
d. Basic recording unit	string	Basic TDWG geographic recording unit.	Kew GrassBase nomenclature database (http://www.kew.org/data/grasses-syn).
TDWG level 1 code	int	TDWG level 1 code for continent (single digit integer, e.g. 2). For text descriptions of continents, use "a. Continent" instead.	TDWG level 1 code for continent (integer, 1-9). For text descriptions of continents, use "a. Continent" instead.
TDWG level 2 code	int	TDWG level 2 code for region (two-digit integer, e.g. 22). For text descriptions of regions, use "b. Region" instead.	Kew GrassBase nomenclature database (http://www.kew.org/data/grasses-syn).
TDWG level 3 code	string	TDWG level 3 code for botanical country (three-letter code), equating in most cases to political units, except that large countries are broken into smaller units, and small countries grouped. For text descriptions of botanical country, use "c. Botanical country" instead.	Kew GrassBase nomenclature database (http://www.kew.org/data/grasses-syn).
TDWG level 4 code	string	TDWG level 4 code for the basic recording unit of plant distributions (two-letter code appended onto level 3 codes). Not currently supported.	Kew GrassBase nomenclature database (http://www.kew.org/data/grasses-syn).

Contents:

Getting started

Datasets