ABRS Online Resources | AFD | Flora of Australia Online | GBIF | OZCAM
- Have our ABRS Online Resources (databases) under:
- http://www.environment.gov.au/biodiversity/abrs/online-resources/index.html
- Have the ABRS Fauna Online data under:
- http://www.environment.gov.au/biodiversity/abrs/online-resources/fauna/index.html
- Have the ABRS Flora Online data under:
- http://www.environment.gov.au/biodiversity/abrs/online-resources/flora/index.html
- Have Links from ABRS to external web-sites, including online databases at:
- http://www.environment.gov.au/biodiversity/abrs/links/index.html
Australian Faunal Directory
ABRS Faunal Taxonomic Checklists and Catalogues are contained in the Australian Faunal
Directory (AFD) under:
http://www.environment.gov.au/biodiversity/abrs/online-resources/fauna/afd/index.html
Australian Faunal Directory has more than a 120, separate Platypus databases
that have been loaded into AFD. Each of the stand-alone Platypus databases is
a prepared group prepared by experts from the Museums, Universities, Agriculture
Departments, retired Taxonomists etc. The Platypus databases are loaded into
different points of the Main Checklist of AFD. Can drill down to the group itself
by clicking on the little Platypus icon for a Group that you are interested in. Click
on the Main
Checklist which can be found on the LHS navigation bar of the higher level
AFD web pages. Can drill down the hierarchy level by clicking on the
brown octagon on the left of the checklist. For instance to find ‘Scarabaeoidea’
progress through; Arthropoda, Uniramia, Insecta, Coleoptera, Polyphaga, Scarabaeoidea
and click on the Blue Platypus icon. The square ‘S’ in a blue box is the
Statistics for the group and the yellow star opens all the levels below
the current level.
The
Groups page is a visual way of seeing each of the Groups loaded from the
Platypus databases. They are arranged in phylogenic order. Click on the Group
Name hyperlink, or the Checklist hyperlink to see the Checklist for that particular
group. The only difference between the two links is that the Checklist link
opens the entire hierarchy at once, so it can be a little slow. Can progress
down the Checklist, opening and closing levels by clicking on the Taxa Type
icons i.e. the little numbers, or symbols (‘G’ for Genus, ‘Sp’ for Species).
The ‘av’ symbol means Available Name. The Available Names include the synonyms,
plus the Valid Name as long as the Valid Name hasn’t had its Genus changed.
Note the hierarchy can include — Incertae Sedis ‘A Latin term meaning
of uncertain taxonomic position’ — Species Inquirenda ‘A Latin term
meaning a species of doubtful identity needing further investigation’. Clicking
on the hyperlink under a Species, or Subspecies name takes you into the Details
page for the Taxa.
The Details page
for each Taxonomic level provides the taxonomic nomenclature including synonymy, and can include literature citation, location and status of type material and type locality for each available name, a brief summary of geographical distribution and ecological attributes, host data, and important references on various aspects, especially biology.
The What’s new page is a way to keep up with the newly loaded Platypus groups.
The Search page allows you to do a variety of different searches. The main ones of interest are the Simple Name/Biocode Search and the Host Taxon Association Search.
- The Simple Name/Biocode works for Valid Name Species or Subspecies epithet only. Or you could use just the Genus Name or the Family Name in the search. To search on the full Valid Scientific Name you need to use the Advanced Search which has a few more steps and can be quite slow.
- The Host Taxon Association Search
is handy for a whole group i.e. ‘PSYLLOIDEA’ to see the Plant or Animal
Hosts for species in this group. Not all groups loaded into AFD have had
Host Taxon Association data included, but it worth doing a general search
by selecting your Group name of interest in the beige Taxon select-list
and choosing ‘Any’, ‘Plant’ or ‘Animal’ as your Host Type. Some examples of Groups Names
that have Host Taxon Association data are: ‘ALEYRODOIDEA’, ‘APHELENCHIDA’,
‘BUPRESTOIDEA’, ‘COCCOIDEA’ (Diaspididae host-taxon associations only),
‘FULGOROIDEA’, ‘NEMATOCERA’, ‘PAPILIONOIDEA’, ‘PENTATOMOMORPHA’, ‘PSYLLOIDEA’,
‘SCARABAEOIDEA’, ‘THYSANOPTERA’ (Thrips: Family Phlaeothripidae host-taxon associations only).
It is not recommended looking for individual Host or Taxon names, as there is not a lot of data in the system.
Practical session:
- 1) Do a Name/Biocode Search search for:
- ‘Austroaeschna muelleri’ in the ODONATA group.
Hint: Don’t put in the full Scientific Name, only the Genus OR the Species epithet.
- 2) Do an Advanced Search for the Valid Scientific Name:
- ‘Austroaeschna muelleri’ in the ODONATA group.
- 3) Drill down via the Main Checklist to go to the:
- ‘ODONATA’ group via its Platypus icon.
Hint: Odonata (dragonflies, damselflies) is under Insecta.
Continue progressing under the hierarchy once you have entered the Odonata group and find the species:
‘Austroaeschna muelleri’
Hint - The hierarchy is: ODONATA, EPIPROCTOPHORA, AESHNOIDEA, TELEPHLEBIIDAE
- 4) Use the Groups page to go to the same species:
- ‘Austroaeschna muelleri’ which is part of the ODONATA (dragonflies, damselflies) group.
- 5) Do a Host Taxon Association Search to look for Plant hosts using the:
- ‘SCARABAEOIDEA’ group.
Note the blue plant host details on the left and the beige taxa on the right of the HTML table.
Drill into the taxa details for the taxon ‘Anoplognathus multiseriatus’.
Look at its distribution and that its host plant is ‘Banksia serrata’.
Keep this web-page active as we will be using these species and other Host Taxa
associations in other searches.
Flora of Australia Online
Flora of Australia Online at: http://www.environment.gov.au/biodiversity/abrs/online-resources/flora/main/index.html
There are three main entry points on the internet to the Flora of Australia Online
data.
However they can all be accessed from any of the Flora of Australia Online
web-pages. The first one, Flora of Australia Online covers the vascular
flora: Volumes 2 to 48 of the hard-copy version of Flora of Australia.
The second one, Volume 49 Flora of Australia Online has information
on Norfolk Island, Lord Howe Island, Admiralty Island Group, Balls Pyramid
etc. The third one, Volume 50 Flora of Australia Online has information
on the Coral Sea Islands Territories, Christmas Island, Cocos (Keeling) Island,
Macquarie Island, Heard Island etc.
The What’s published & What’s online?
web page lists by families whether the volume that contains the family has
been published and whether that hard-copy volume has been loaded online into
one of the three Flora of Australia online datasets.
It it best to consult this page before searching, as only half the published
volumes for the Flora of Australia have been loaded online.
There is a Search Instructions page and a page for
Abbreviations & Contractions (as used in the published volumes of the Flora of Australia).
There is a Search
Page for Flora of Australia Online. Note you change the Volumes
to search on, to Volume 49 or Volume 50 from here.
There are three options for searching:
- Quick Name Search, in which you type a single word.
- Normal Search, in which you type in at least one of Family, Genus, Species etc.
Note the wildcard is an asterisk.
- Refined Search, that allows you to do Quick Name Search or a Normal Search
but additionally, specify extra text to search for within the Non-standard
fields i.e. NOT Family, Genus, Species, Subspecies BUT fields like Author,
Habitat.
You can also ‘Limit Display Results’ by choosing the fields to display in the Search Results.
There are two different Sort Orders for the Results:
- The default is ‘As in the published volumes’ (i.e. usually in taxonomic
order).
- The other option is ‘Alphabetical’.
There are three main types of Search Results:
- Standard Flora Display. This produces a replica of all information as published
in the Flora of Australia hard-copy volume. From the Standard Display
there are hyperlinks to take you to the images for which we have copyright
permission (line art of the plants and distribution maps). Keys are embedded within
the Standard Display at the appropriate rank, usually at Family and Genus Level.
You can also go to the Hierarchical Display from here.
- Hierarchical. This gives a checklist of ranks and taxa names starting from the higher
order. To display all available ranks in the hierarchy, as shown here, you
must choose the default option for Sort Order i.e. ‘As in the published
volumes’. If you choose Sort Order ‘Alphabetical’ only the ranks of family,
genus, species and infraspecific taxa will display. If you click on the
icon to the left of the name in the hierarchy you expand the list of names
to show those at the next lower rank. If you click on the taxon name you
goto into the Standard Flora Display for that taxon.
- Names list. There are 3 types of display – Names List to Genus Level, to Species Level and to Infraspecific
Level. In this display type you get the Taxa name, the Author, the Publication details.
Demonstration:
- 1) Search for:
- ‘Acacia implexa’ which in AFD was the host plant in the PSYLLOIDEA group for the species ‘Acizzia lidgetti’.
Practical Session:
- 1) Search using all the different options for:
- ‘Banksia serrata’ which was the host plant in the SCARABAEOIDEA group for the species ‘Anoplognathus multiseriatus’.
- 2) Keys:
- Find the Key that shows how to key out the characteristics for ‘Banksia serrata’.
Global Biodiversity Information Facility (GBIF) and Australian Biodiversity Information Facility (ABIF)
GBIF Communications Portal online at: http://www.gbif.org/
has information and documents about GBIF, tools, the various sub-programmes of GBIF, grants,
upcoming events, latest news.
GBIF Data Portal online at: http://www.gbif.net/
has the search facilities for searching specimens and observations from databases
throughout the world that have installed one of the GBIF compatible Data Providers
(i.e. wrapper) onto their databases. Points on the map of the world are also displayed
if point data, latitudes and longitudes have been included in the records. Currently GBIF
supports the DiGIR and the BioCASE Data Providers. The DiGIR Data Provider supports the
Darwin Core2 XML schema. The BioCASE, Data Provider supports the ABCD XML schema. The Taxonomic Names or Checklist
data is provided by the Catalogue of Life Consortium that include organisations such as
Species 2000 and ITIS. So far, ABRS has contributed
‘PULMONATA’ taxonomic names data to the Catalogue of Life Consortium.
The web-pages for Australian Biodiversity Information Facility (ABIF)
is online at: http://www.abif.org/index.htm.
The ABIF
site is being developed to become a data portal that provides access to checklists
of species names, allows for searching of those specimens and observations
contained in the biological collections of ABIF
participants and has a range of analytical tools. In order for ABIF
participants to contribute their datasets a Data Provider has to be set up.
We at ABRS
have set up a ABIF
DiGIR
Data Provider for the Australian Faunal Directory to serve out Valid
Species and Valid Sub-species derived data. The basis of these records
are derived as the data is not based on actual specimens or observations
in the field, but based on literature searches and summaries of the specimen
collections. We also have on the ABIF
Data provider a dataset of 100,000 Land Mollusc specimens from the Australian
museums and the Chicago Field Museum. In addition, we host for the Queensland
Museum a dataset of around 4,500 dung beetles collected in New Caledonia.
In Australia there are currently five other data providers besides ABIF.
Look on the ABIF
web-pages under Data Providers for further information.
Demonstration:
- 1) Using the GBIF Data Portal search for:
-
‘Lepanus pisoniae’ which is a another taxon involved in Host-Taxon
associations for the SCARABAEOIDEA group. Its host plant is ‘Pisonia umbellifera’.
- You can restrict the Country to ‘Australia’ if you like.
- Click on the returned species ‘Lepanus pisoniae’ hyperlink.
- See how in the Specimens/observations section shows the various Data Providers
that contain data for ‘Lepanus pisoniae’. In this case the AFD data
through the ABIF
DiGIR Data Provider and ANIC specimen data.
- Normally if the Catalogue of Life consortium has provided matching Taxonomic
Names data, this will be shown at the top of the page in the Species section,
that includes Synonyms and the Higher Taxonomy.
- Click on the ‘down’ arrows takes you to a download page, so you can get
a download of the data in a couple of different formats.
- Click on the ‘+’ at the bottom of the page, in the Total line. This will
take you to a page that shows all the records from each of the Data providers.
Hopefully the Map Server is working and will show the point data provided
by ANIC for the Latitudes and Longitudes.
- For more details of a particular record you can click on the Record ID or
Scientific Name hyperlink. When you goto the Details page, for data from AFD
we have provided the URL of the record in the Notes section.
- Show how the ANIC data is also available through
APPD,
which is the same data as available through the GBIF Data Portal.
Practical Session:
- 1) Search using the GBIF Data Portal for:
- ‘Anoplognathus multiseriatus’ which was the taxon in the SCARABAEOIDEA group that is found on the host plant ‘Banksia serrata’.
Online Zoological Collections of Australian Museums (OZCAM)
OZCAM online at:
http://www.ozcam.org/
Similar in functionality to Australia’s
Virtual Herbarium (AVH).
Also similar to Australian Plant Pest Database (APPD).
So far only these groups loaded:
- Mammals
- Reptile and amphibians
- Fish
- Dung beetles
- Barnacles
- Molluscs (Type specimens only - in progress)
- Vertebrates (Type specimens only)
Some Features of OZCAM 1.5
- On the map, the query point function allows you to view the data for an individual record (moving to a new view of the data).
- On the map, you can zoom in or out to see more or less detail (adjusting the current view).
- Can redraw the map using different data layers (adjusting the current view) and then press the Pan/Redraw function.
- The Advanced Display page allows data to be displayed and downloaded in various formats, including html and xml.
- Public access which will allow users to perform queries but the returned
results will not provide access to full location data and the latitudes
and longitudes will be ‘fuzzed’ randomly within 10 minutes. A disclaimer
will draw the users attention to these points.
- Club access which is password protected provides access to all available
information.
- Spatial Regional Querying will be added which will allow users to draw an area and
query on that user defined region. This feature does not work currently.
- On the returned mapping page, an information button will appear beside the name of each returned taxon that will allow the user to query other data sources for additional information on the returned taxon name. For example, automatic Google searches, Species Bank searches, GBIF searches etc.
- Streamlining of available data sources to be searched. Queries will now be directed at institutions rather than individual data sources within each institutions.
- A GBIF project to database Vertebrate and Molluscan Type specimens together with images is in progress.
Demonstration:
- 1) Using the Mapping facility of OZCAM search for:
- ‘Potorous’.
Practical Session:
- 1) Search using OZCAM for:
- Species which are part of the pest family ‘SCARABAEIDAE’ that can be also
found in Australian Plant Pest Database (APPD).
Hint: Some Genus examples to try out: ‘Onthophagus’, ‘Amphistomus’.
Please Note: APPD has restricted password protected access. Generally, only plant health or quarantine specialists and collection curators from contributing agencies have access to the database.
If you have access to APPD, have a look to see if the distribution maps between APPD and OZCAM coincide.
- 2) Search OZCAM
using the ‘Data’ Display Format to look for ‘Fur Macki’; a Holotype specimen with associated image that can be enlarged.
Return to: Online Resources
