The Atlas has upgraded their biocache

The Atlas has upgraded their biocache

  • By Robyn Lawrence
  •  September 9, 2011
  •  Tags:  Blogs & news Tools & Apps

The Atlas of Living Australia is pleased to announce that they have upgraded their Atlas’ biocache.

So what is the biocache, you might ask?

It’s the data store the Atlas portal uses to keep a cache of the occurrence records – sightings, specimen details, survey information – and media files (images, sound files, videos) harvested from our 280+ data set contributors.

New engine in car

Our team of mechanics (developers and systems architects) have fitted a whole new "biocache” to the Atlas.

Feature list

The Atlas presently looks the same from the home page, but like a “hotted up car”, it’s had a whole new engine fitted.

Now for the specs of our new Atlas engine

Advanced searching and facets

First off, we added an advanced search feature to the biocache that allows for faceting (or filtering) of the returned occurrence results set. Facets include among many: sensitive records, coordinate uncertainty, record issues, state conservation status and location quality. The facets / filters are customisable to only show those of interest to the user.

The advanced search can be found on the occurrence results page just above the simple text search, or by using this URL: http://biocache.ala.org.au/search#tab_advanceSearch.

Advanced search

The synonymy within the search results is now made clearer. Just press the “numbered results for” species field to see the synonymy and child taxa of the query. It also gives the original, raw scientific names used in the records before any processing occurs.
Shows Synonymy for Common Sandpiper

Map or list mode to view results

The occurrence records result set can be viewed in either list or map mode. After the results are returned, click the map button to view a simple mapping tool. Click the list button, when in the map mode, to return to the list mode.

Map Button
List Button

One of five environmental layers can be added to the map. Different coloured faceting is available to discriminate between values of a chosen variable – in the image below faceted on Dataset.

Simple Mapping Tool

Multiple record versions

We store multiple versions of each occurrence record:

  1. verbatim (original raw, unprocessed record)
  2. processed
  3. consensus (if the owner of a record has verified any flagged issues or made some edits)

The Atlas on loading the verbatim or raw records into the biocache matches the occurrence records with our taxonomic scientific name lists produced by the National Species Listing project. A whole series of editing steps are worked through to create the processed records.

Registered users of the system can mark records as having an issue, by pressing the Flag an Issue button on a single occurrence record. This will flow through to the mapping applications, allowing applications to only show records without issues. The owner of the record will be notified of the potential problem. In turn, they can verify the record is correct or edit it. This creates a third version of the record, the consensus view.

Flag an issue

Flexible data model

The data for any occurrence record or survey event can now use any of the latest Darwin Core (150+) terms as the basis for the record. This can be extended to cater for other standards such as HISPID, OBIS, MCL.

Web services

A web services layer has been added across the following applications to access the biocache data:

Applications external to the Atlas can utilise these web services for their own purposes.

For further information see: http://biocache.ala.org.au/ws

Individual sightings entered into the citizen science portal

Sightings submitted by the public are now incorporated into the Biological Data Recording System (BDRS) Citizen Science portal. This tool is being utilised by a range of naturalist groups such as Birds Australia and education departments around Australia.

When you click the menu option for “My Profile”, then “View your Sightings you have recorded” you are taken to the Advanced Review page that shows all the Citizen Science – Individual Sightings:

You can facet (filter) on your “My Records Only” to see only those personally submitted.

Like the occurrence records results set you can view in Map or List mode by clicking on the tabs. You can do a free text “Search within results” on scientific name or common name.

Citizen Science Portal

Register for an ALA account

You have to register for an ALA account in order to submit sightings. An email link is sent to you after registering, to activate your account.

Then you can add your sightings. We now have the ability to upload a single photo, sound file or video to accompany a sighting. This will help to verify the species submitted. We use creative commons licensing.

Coming soon!

Within the month, the biocache will integrated with the Spatial Portal (using the new web services) and will have access to the extended set of occurrence records. This means there will be additional fields to filter (facet) on in the Spatial Portal.

Any queries performed in the biocache and other sections of the ALA site will carry through to the Spatial Portal, and vice versa.

Improvements in data quality

We are developing methods to detect and flag potential problems in species occurrence information, including:

  • spatial outliers
  • duplicated records
  • terrestrial versus marine checking

The growing list of checks to be implemented is documented here:

Test your own uploads

A new sandbox (test) environment will be released soon. Users will be able to trial uploading their data and test how it works with the various backend tools of the Atlas.

The data is kept separate from the ALA biocache data and will be removed after a period of time. Once satisfied, users can choose to upload their data into the actual Atlas.