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GrassPortal - User Guide

Contents:

Getting started

Datasets

Searching

Keyword Searching

Concept Searching

Search Results

Record Information

Hover Help

Visualise Results

Map of Results

Downloading Results

 

 

 

 

 

 

 

 

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).

search pane


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.

keyword search

 

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.

LabelData TypeComment/DescriptionDatasource
1. Frequently used concepts
a. SpeciesstringAccepted scientific binomial species name (Genus species) e.g. Poa annua.Kew Grassbase Nomencalture database (http://www.kew.org/data/grasses-syn).
b. Photosynthetic pathwaystringType of photosynthetic pathway (C3 or C4) used by each species.
c. Botanical countrystringBotanical country, e.g. Arizona, New Mexico, OregonKew GrassBase nomenclature database (http://www.kew.org/data/grasses-syn).
d. Mean annual temperaturefloatMean annual temperature (degrees C) for the period 1961-1990http://badc.nerc.ac.uk/data/cru/
e. SubfamilystringSubfamily (taxonomic rank below Family and above Tribe).
g. PrecipitationfloatMean annual precipitation (mm) for the period 1961-1990http://badc.nerc.ac.uk/data/cru/
Life history (categorical description)stringLife history strategy (annual or perennial).Character #1 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
2. TaxonomySearch by taxonomic rank.
a. SpeciesstringAccepted scientific binomial species name (Genus species) e.g. Poa annua.Kew Grassbase Nomencalture database (http://www.kew.org/data/grasses-syn).
b. GenusstringGenus (taxonomic rank below Subtribe and above Species) e.g. Poa.
c. SubtribestringSubtribe (taxonomic rank below Tribe and above Genus).
d. TribestringTribe (taxonomic rank below Subfamily and above Subtribe).
e. SubfamilystringSubfamily (taxonomic rank below Family and above Tribe).
3. Phylogeny
Phylogeny (Long Name)string
Phylogeny (Short Name)string
4. Plant traits
a. Morphological charactersMorphological characteristics of each species.Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Culm habit (categorical description)stringCategorical description of culm habit.Character #29 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Culm height (cm)Height (cm) of culms (stems that support the inflorescences).Character #33 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
High (cm)doubleUpper limit to the normal range of culm height (cm).Character #33 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Low (cm)doubleLower limit to the normal range of culm height (cm).Character #33 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Max (cm)doubleMaximum culm height (cm) - extreme value.Character #33 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Min (cm)doubleMinimum culm height (cm) - extreme value.Character #33 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Inflorescence type (categorical description)stringCategorical 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.Character #229 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Leaf size (length x width)
Length (cm)
High (cm)doubleUpper limit to the normal range of leaf blade length (cm).Character #165 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Low (cm)doubleLower limit to the normal range of leaf blade length (cm).Character #165 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Max (cm)doubleMaximum leaf blade length (cm) - extreme value.Character #165 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Mean (cm)doubleMean length of the leaf blades (cm).Character #165 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Min (cm)doubleMinimum leaf blade length (cm) - extreme value.Character #165 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Width (cm)
High (cm)doubleUpper limit to the normal range of leaf blade width (cm).Character #166 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Low (cm)doubleLower limit to the normal range of leaf blade width (cm).Character #166 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Max (cm)doubleMaximum leaf blade width (cm) - extreme value.Character #166 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Mean (cm)doubleMean width of the leaf blades (cm).Character #166 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Min (cm)doubleMinimum leaf blade width (cm) - extreme value.Character #166 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Life history (categorical description)stringLife history strategy (annual or perennial).Character #1 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Match ConfidencedoubleConfidence (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%.Internal to the GrassPortal system.
Pericarp (categorical description)stringCategorical description of the pericarp (tissue developing from the ovary and surrounding the seed) of the caryopsis (seed).Character #1018 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Plant density (categorical description)stringGrowth habit of the plant.Character #4 from Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Species description (Kew GrassBase URL)stringURL linking to a full taxonomic description of the species.Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Species identifier (Kew numeric ID)intUnique species identifier (numeric ID) from the Kew GrassBase morphological descriptions database.Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
Species identifier (Kew URN reference)stringUnique species identifier (URN reference) from the Kew GrassBase morphological descriptions database.Kew GrassBase - the Online World Grass Flora - descriptions (http://www.kew.org/data/grasses-db.html).
b. Photosynthetic pathwaystringType of photosynthetic pathway (C3 or C4) used by each species.
5. Distribution
Expert-determined species rangesSearch by Biodiversity Information Standards (Taxonomic Databases Working Group or TDWG) defined area.
a. ContinentstringContinent, e.g. Northern AmericaKew GrassBase nomenclature database (http://www.kew.org/data/grasses-syn).
b. RegionstringRegion, e.g. Southwestern U.S.A, South-Central U.S.AKew GrassBase nomenclature database (http://www.kew.org/data/grasses-syn).
c. Botanical countrystringBotanical country, e.g. Arizona, New Mexico, OregonKew GrassBase nomenclature database (http://www.kew.org/data/grasses-syn).
d. Basic recording unitstringBasic TDWG geographic recording unit.Kew GrassBase nomenclature database (http://www.kew.org/data/grasses-syn).
TDWG level 1 codeintTDWG level 1 code for continent (single digit integer, e.g. 2). For text descriptions of continents, use "a. Continent" instead.Kew GrassBase nomenclature database (http://www.kew.org/data/grasses-syn).
TDWG level 2 codeintTDWG 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 codestringTDWG 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 codestringTDWG 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).
Geo-referenced point occurrencesGlobal Biodiversity Information Facility geo-referenced point distribution datahttp://data.gbif.org
Authorstring
b. GenusstringGenus (taxonomic rank below Subtribe and above Species) e.g. Poa.
Basis of Recordstring
Collector Namestring
Coordinate Precisionstring
Countrystring
Country Fullnamestring
Countystring
Data Providerstring
Datasetstring
Date CollecteddateTime
Geospatial Issueint
Identification DatedateTime
Identifierstring
Latitudestring
LocalitystringCollection Locality
Longitudestring
Norm Latitudefloat
Norm Longitudefloat
Normalised GBIF Scientific NameScientific Name assigned in GBIFhttp://data.gbif.org
Occurrence idint
Original GBIF Scientific NamestringScientific Name assigned in GBIFhttp://data.gbif.org
Phylogeny (Long Name)string
Phylogeny (Short Name)string
Provider Countrystring
Regionstring
Species Namestring
State Provincestring
6. Environment
ClimateGlobal mean annual climate variables for the period 1961-1990 from the University of East Anglia Climate Research Unit half degree TS 3.0 datasethttp://badc.nerc.ac.uk/data/cru/
a. Cloud coverfloatMean annual cloud cover (%) for the period 1961-1990http://badc.nerc.ac.uk/data/cru/
b. Minimum annual temperaturefloatMean annual minimum temperature (degrees C) for the period 1961-1990http://badc.nerc.ac.uk/data/cru/
c. Maximum annual temperaturefloatMean annual maximum temperature (degrees C) for the period 1961-1990http://badc.nerc.ac.uk/data/cru/
d. Mean annual temperaturefloatMean annual temperature (degrees C) for the period 1961-1990http://badc.nerc.ac.uk/data/cru/
e. Diurnal temperature rangefloatMean annual diurnal temperature range (degrees C) for the period 1961-1990http://badc.nerc.ac.uk/data/cru/
f. Mean annual vapour pressurefloatMean annual vapour pressure in hectopascals (hPa) for the period 1961-1990http://badc.nerc.ac.uk/data/cru/
g. PrecipitationfloatMean annual precipitation (mm) for the period 1961-1990http://badc.nerc.ac.uk/data/cru/
h. Number of wet daysfloatMean annual number of wet days for the period 1961-1990http://badc.nerc.ac.uk/data/cru/
i. Number of frost daysfloatMean annual number of frost days for the period 1961-1990http://badc.nerc.ac.uk/data/cru/
Fire occurrencefloatMean burnt area of 1 degree grid cells for the period 1961-1990http://www.cefe.cnrs.fr/fe/staff/Florent_Mouillot.htm
Land cover typestringLandcover Label
Soil quality for crop productionIIASA Harmonized World Soil Database - soil qualities for crop production datasethttp://www.iiasa.ac.at/Research/LUC/External-World-soil-database/HTML/SoilQuality.html?sb=10
Soil Excess Salts IndexintIndex based on soil salinity, soil sodicity and soil phases influencing salt conditionshttp://www.iiasa.ac.at/Research/LUC/External-World-soil-database/HTML/SoilQuality.html?sb=10
Soil Nutrient Availability IndexintIndex based on soil texture, soil organic carbon, soil pH, and total exchangeable baseshttp://www.iiasa.ac.at/Research/LUC/External-World-soil-database/HTML/SoilQuality.html?sb=10
Soil Nutrient Retentrion Capacity IndexintIndex based on soil Organic carbon, soil texture, base saturation, cation exchange capacity of soil and of clay fractionhttp://www.iiasa.ac.at/Research/LUC/External-World-soil-database/HTML/SoilQuality.html?sb=10
Soil Oxygen Availability to Roots IndexintIndex based on soil drainage and soil phases affecting soil drainagehttp://www.iiasa.ac.at/Research/LUC/External-World-soil-database/HTML/SoilQuality.html?sb=10
Soil Rooting ConditionsintIndex based on soil textures, bulk density, coarse fragments, vertic soil properties and soil phases affecting root penetration and soil depth and soil volumehttp://www.iiasa.ac.at/Research/LUC/External-World-soil-database/HTML/SoilQuality.html?sb=10
Soil ToxicityintIndex based on amount of calcium carbonate and gypsumhttp://www.iiasa.ac.at/Research/LUC/External-World-soil-database/HTML/SoilQuality.html?sb=10
Soil Workability (constraining field management)intIndex based on soil texture, effective soil depth/volume, and soil phases constraining soil management (soil depth, rock outcrop, stoniness, gravel/concretions and hardpans)http://www.iiasa.ac.at/Research/LUC/External-World-soil-database/HTML/SoilQuality.html?sb=10
Tree coverintAVHRR remote-sensed tree cover (%) of 1km grid cells across the globehttp://glcf.umiacs.umd.edu/data/treecover/

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