Bio Collect User Manual Citizen Science V1.0
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Citizen Science - version 1.0
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User
Manual
Citizen Science - version 1.0
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Contents
1. About the BioCollect system ................................................................................................ 4
2. The Project Finder - Find projects that interest you .............................................................. 5
2.1. What projects are in my area? .......................................................................................... 5
2.2. Find projects by a search term or keyword ....................................................................... 5
2.3. Find projects by facets and "tags" .................................................................................... 6
2.4. Combining your filter options ............................................................................................ 7
3. Add your project to the Project Finder .................................................................................. 7
3.1. Register a user account ................................................................................................... 7
3.2 Create your project ............................................................................................................ 7
Project metadata ................................................................................................................. 8
Tell people about your project.............................................................................................. 8
How can people get involved? ............................................................................................. 9
Help people find your project ............................................................................................. 10
Add graphics to personalise your project pages................................................................. 10
Define the spatial extent of the project area ....................................................................... 11
Acknowledge Terms of Use ............................................................................................... 11
4. Set up surveys to collect your project data......................................................................... 11
4.1 Add a new survey ............................................................................................................ 11
Step 1 – Describe the survey and the dataset (survey metadata) ...................................... 12
Step 2 – Visibility ............................................................................................................... 14
Step 3 – Alerts ................................................................................................................... 15
Step 4 – Select survey form template (proforma) ............................................................... 16
Step 5 – Species configuration .......................................................................................... 17
Step 6 – Locations ............................................................................................................. 20
Step 7 – Publish the survey ............................................................................................... 22
5. Managing project members ............................................................................................... 23
6. Adding and Managing Project “Resources”........................................................................ 24
7. The Project Blog Feature ................................................................................................... 26
8. Reviewing, Editing & Accessing Data ................................................................................ 27
9. Troubleshooting – Common issues.................................................................................... 29
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1. About the BioCollect system
The BioCollect system has been developed by the Atlas of Living Australia (ALA) to support
communities and organisations in capturing and managing field-based data at source and to
facilitate the smooth flow of standardised biodiversity and other environmental data into the
ALA and other major data aggregation repositories where it can be readily accessed and used
to better understand our natural assets, as well as to improve planning, management and
protection of them into the future.
BioCollect supports both “event-based” (conventional survey/monitoring), as well as “activity-
based” styles of data recording. The activity-based model is essentially a project management
approach to collecting and managing data and the system can be used as a project
management tool for these kinds of projects. In activity-based projects, you build a
chronologically arranged schedule of associated actions aimed at achieving a planned outcome
and then record data for each activity as the plan is implemented.
The “project finder” feature of BioCollect is essentially a comprehensive searchable catalogue
of projects providing direct access and linkages to all associated project materials and
resources on all kinds of internet accessible external platforms. Projects registered in the
project finder can be set up either to use the full data collection features of BioCollect or to just
appear as a project in the catalogue. Even the later can still make use of the Blog and attached
documents and resources features to further enhance the presence of their projects. You can
also easily switch between the two options.
BioCollect can be used as a cloud-based data collection and management system in it’s own
right, but importantly it can also be used in other ways such as: providing a database back-end
to external web-apps and mobile platforms; or consolidating and mobilising historical datasets
on a standardised data schema.
One of the aims of the BioCollect system is to provide a single point of access for all
information about a project, regardless of whether BioCollect is being used to collect and
manage the project data, or not. This includes: project support materials; communication
materials and blog posts; links to mobile apps in any app store; links to external resources such
as organisation and project websites, social media channels, etc.; survey forms; project data;
and links to project contacts. It can also be your data collection and management system.
Both project and survey level descriptive information and collected data aligns with existing and
developing standards as much as possible. The system is also linked to other major project
finders around the world allowing your project to be discovered globally as well as for you to be
able to easily discover and access other people’s projects happening anywhere in the world.
BioCollect really is a single platform where you can promote your project to the world and make
it discoverable by anyone who might be interested, as well collect and manage your field
collected data from simple to quite complex data structures.
BioCollect is well supported and actively being developed by the Atlas of Living Australia and,
being an open source product which is part of the ALA’s suite of tools, it has a growing
community of practice to maintain and further develop the code-base.
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2. The Project Finder - Find projects that interest you
2.1. What projects are in my area?
Step 1. Open the filter options panel if it is not already
open.
Step 2.
Select the geographic filter option at the bottom of
the filter section.
Step 3.
Find your area of interest
Use any of the variety of tools to locate your area
of interest. Options include: the + / - to zoom in and
out on the map (left-click and drag to pan the map);
the Arrow head to zoom to your current location
(requires browser location services to be enabled);
the Circle with cross-hairs to search by street
address or locality name; and the Magnifying
glass to search by region name.
Step 4.
Define your area of interest
Use any of the variety of tools to define your area
of interest. Select a map tool and draw a circle,
square or polygon covering your location or
geographic area of interest; or the point location
tool for a specific place. Alternatively you can use
the "known area tool" (at the bottom of the tool
palette) to select your area of interest by a pre-
defined geographic shape.
Step 5.
Click "Next". The map pop-up will close and return
to the project list displaying only projects which
have all or part of the project area extent within
your defined geographic area of interest.
Other
options
You can now use other filters to reduce the results
further to just projects of a particular kind that
interests you (eg. birds) - follow steps below under
"2.2. Find projects by theme or keyword" and "2.3.
Find projects by facets and tags".
2.2. Find projects by a search term or keyword
Step 1.
On the project finder page, type a search term into
the search box at the top right hand corner of the
page.
Projects in the results window will update to show
only those which contain the search term in the
project information (title, aim, description, etc.) and
the count of the number of projects will adjust to
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reflect the total number of projects which contain
the search term.
Other
options
The default sort order of listed projects is the most
recent at the top, but you can easily change the
sort order by clicking on the toggle options at the
top of the list.
At the top of the results set you can choose how
many projects you want to display on the page.
Note that the higher the number selected, the
longer it will take to retrieve the projects from the
server for that page.
The default set of projects listed are only those
which Australians can participate in, ie. projects
occurring in Australia and those being undertaken
worldwide. If you want to see all projects globally
which contain your search term, simply click on the
toggle button at the top right hand side of the
results list.
The project finder provides different views of the
result set as either a GRID layout or a LIST layout.
You can toggle between these views by clicking on
the relevant view button in the top right hand
corner above the results panel. In the future a MAP
view option will also be available.
At the bottom of the results set is a page selector
which allows you to jump directly to a particular
page ahead or back, or to progress through the
result set page by page in either direction.
2.3. Find projects by facets and "tags"
Step 1.
Open the filter options panel if it is not already open
and click on facet section headers to expand the
sections and expose the facet options available.
Step 2.
Option
a.
Select filters one
-
by
-
one
Click on the linked text part of the facet option you
wish to filter by. This will automatically apply the filter
and place the selected option in the "Current filters"
section at the top of the filter panel. Projects in the
result set will also be automatically adjusted to reflect
the filtered selection. You can then select more
filters, or remove currently selected filters as
required.
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Step 2.
Option
b.
Select multiple filters at once
Click on one or more checkboxes adjacent to the
linked text part of the facet options you wish to filter
by. Then click on the button at the top of the
filter section to action the filter request.
Note: Nothing will happen until you action the
request by clicking on the button. The
selected filters will then appear in the "Current filters"
section at the top of the filter panel. Projects in the
result set will also be adjusted to reflect the filtered
selections. You can then select more filters, or
remove currently selected filters as required.
Other
options
Click on the
Clear
button at the top of the filter
section to clear all filter selections and search terms
and return to the default view.
Hover over t
he
Question mark
in the black circle to
see a tool tip describing each facet category.
2.4. Combining your filter options
TIP All three of the above methods work together and
you can combine any or all of them in any
combination to quickly narrow-down the result set
to only projects which might be of interest to you -
GIVE IT A GO!
3. Add your project to the Project Finder
3.1. Register a user account
Before you start you will need to have an active user account with the Atlas of Living Australia to
register a project. If you already have an active ALA user account you can simply login and
create your project. If you don't have an active ALA user account you can Click here or "Login"
in the menu to set up your user account.
NOTE: The ALA will send you an email with a link to activate your new account. Sometimes this
email can be trapped by spam filters and sent to your junk folder. Please check this folder if you
don't receive the activation email within a few minutes.
3.2 Create your project
In order to get your project onto the project finder you will need to register it into the system.
This involves entering some simple information about the project so that you can explain to
others what you are doing and aiming to achieve, where it is, what kind of project it is, how
people can participate in it, etc.
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Most of the project registration form is self-explanatory, but in this section we describe a few of
the more important aspects which might not be so obvious.
It should only take a few brief minutes to get your project into the system.
Project metadata
Select the type of project. This should always be
Citizen
Science Project
If you are just registering your project in the project finder
[select "No"], or if you want to use this system as your
project database and collect your data with the BioCollect
tools [select "Yes"].
The BioCollect system which sits behind the project finder is a
powerful and flexible field data capture and management facility
which can streamline data recording and the re-use of data by
others in scientific research, resource management and policy
areas. Please consider this option.
Start typing the name of your organisation and look in the
results box which will appear below the search bar. As you
type more of the name the number of matching
organisations from the existing database will reduce.
When you see your organisation appear in the list, select it
and then proceed with project registration.
Every project has to be run by someone and therefore this is a
mandatory field. There are many organisations in the system
already and we encourage you to select your organisation from the
existing list if it is there, as this is beneficial to you.
If your organisation is not on the existing list, you will be prompted
to add it after you have fully searched the existing list.
If you have searched and scrolled through all potential matching
names, you will see a green button appear prompting you to create
an entry for your organisation. This will open a pop-up window for
you to enter and save a few simple details. Note that you will likely
lose any information already entered on the form when you are
returned to the page. You will need to re-enter the information if this
is the case.
Tell people about your project
These fields are the key information that communicates
your project to the world. The "Project name" and "Aim" in
particular appear on the project finder and, together with
the logo image will be the first thing that people see. Try
to include a concise name (title) and describe the aim in a
way that makes the project interesting to people browsing
the site - after all, you are wanting people to think "That
looks like and interesting project", encouraging them to
open it to have a look. With the description you have more
space to explain all about your project, use keywords in
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the description as much as possible as that will help the
project come up in searches.
Contact information is not mandatory, but is extremely
useful as it will help potential participants to engage with
the project.
All projects have to start sometime, but they may or may
not have an end date. If your project is on-going, just
leave the end date empty. Other projects which are run as
a campaign or event will likely have an end date and this
should be filled in as this helps people wanting to
participate in projects to know whether it is still open to
participate in.
This field allows you to give profile to other organisations
involved in your project. For those organisations
themselves, this also provides them with their own mini-
website of projects that they are associated with, which
they can use to promote their participation.
These two fields are used to support global project search
and filtering, enabling your project to only be presented to
people who can physically participate in the project based
on where they are. Putting yourself in the shoes of the
potential participant, would you want to be presented with
projects that there is no way you can participate in them?
These fields in combination allow for projects to be pre-
filtered automatically.
How can people get involved?
This section allows you to highlight to people how they can participate in the project, as well as
to tag the project with information categories which will help people searching for projects of
interest to them. Selecting appropriate categories will help to make your project discoverable to
people that you want to become involved in it.
This field provides the opportunity to connect your project
with potential participants. Explain in simple terms what
people need to do to participate.
Types of science help people to filter the large pool of
potential projects down to areas or domains of scientific
interest.
Tags are another tool to help people filter projects down to
things which interest them. These are pre-defined
classifying terms which reflect certain characteristics of the
project.
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These fields are used to inform potential participants about
what tools and equipment need to be provided or used in
order to participate in the project and what tasks
participants are expected to do as their participation in the
project.
Help people find your project
If you have another website for your project, you can add a
website URL to allow people to navigate from the project
page to it.
If your project has mobile apps, you can add links to the app
download pages in the relevant app stores. This allows
people to access them directly without having to separately
search through the app stores themselves.
These will be displayed on the “About” page.
If your project or organisation has social media or other
resource channels, this field allows you to add them to your
project, thus providing a single point of access for all
information related to your project, making user access
comprehensive and easy.
These will be displayed on the “About” page.
The “Keyword” field allows you to add specific terms that
you think people might use to search for the project. This
can include acronyms, abbreviations, themes and
categories, locality names, subject area, etc.
Add graphics to personalise your project pages
The project logo is displayed on the project finder and
makes your project more identifiable and attractive to
potential participants. We strongly encourage you to add a
logo image to represent your project.
Also add attribution for use of the image.
A feature graphic can be added to your project to add visual
appeal to the main project “About” page.
For best results you should use a high resolution image and
scale it to approx. 1500px wide by 500px high.
Also add attribution for use of the image.
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Define the spatial extent of the project area
The project area represents the extent of the geographic
area which will contain all of the project data.
The map will be displayed on the “About” page and the
polygon is used for geographic searching for projects, as
well as in the MAP view of projects to display the coverage
and distribution of projects in the project finder and
organisation pages.
NOTE: See section1.1 above for a description of the
different tools available for defining the project area.
Acknowledge Terms of Use
The checkbox to acknowledge that you have read and
accept the terms of use is initially disabled until you click on
the link and open the ToU page. Please read the terms of
use as it contains important information about how the ALA
treats your project information and data, as well as your
responsibilities as a project owner.
Your use of the BioCollect system is conditional on your
acceptance of the terms of use.
The Atlas of Living Australia which owns and operates the
BioCollect system is an open infrastructure and promotes
open data principles. The default license used and which
applies to public domain data in BioCollect is the Creative
Commons Attribution 3.0 (CC-BY 3.0), though CC-BY 4.0,
CC-zero or CC-BY-NC licenses are also acceptable.
4. Set up surveys to collect your project data
This BioCollect system is much more than just a project register to promote your project to the
world and make it discoverable, it also provides powerful and flexible set of tools for you to
capture and manage your project data, as well as a blog facility for you to communicate your
events and achievements to your community and a "Resources" facility for you to provide
additional materials and linked information to your community about your project. BioCollect,
including the project finder, is hosted and supported by the Atlas of Living Australia.
4.1 Add a new survey
A project can have zero, only one or multiple surveys. Each survey can be configured differently
and collect different data. The process to set up and configure surveys is described below:
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After successfully creating your project (if you selected
“Yes” for the question to use BioCollect to capture your
project data), you will see a pop-up page with this diagram
and some other information about setting up a survey.
Click “Continue” to move to the first step in creating a
survey.
Click on the “Add Survey” button.
This will bring up a template focused on Step 1 described
below.
After completing and saving the form template for Step 1 a
“Select survey” will appear beside the “Add Survey” button.
This allows you, when you have multiple surveys, to select
the particular one that you want to review or edit
configuration settings for.
To add another survey, simply click “Add Survey” and
repeat the Steps listed below, as appropriate for the new
survey.
Step 1 – Describe the survey and the dataset (survey metadata)
Properly describing the survey and dataset is important to informing potential participants about
what the survey is about and is critical in providing descriptive and contextual information to
users of the data on matters which help them to determine bias and limitations in the data and
its suitability for their requirements, particularly for people who have not been involved in the
data collection activities. This is a key aspect of making citizen science data more useful
and credible in mainstream scientific applications.
The “Name” field is the human readable identifier for the
survey. It should be descriptive, but brief and concise.
The “Description field allows you to elaborate on the title
and provide more information and context about the survey
to readers.
These fields display on the survey listing page and are the
main entry point into the survey form.
The survey data should be credited to someone or
something when it is used and cited by downstream users
of the information.
This field is auto-populated with a concatenation of the
project and survey names, however it is editable and you
can replace the entry with something else or append to it
with something else.
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This attribution will travel with the data in downstream use
and credit given to this source when it is used and cited in
publications – an important aspect of the CC-BY license.
Sampling method is critical in data users being able to
assess dataset suitability for their purpose. It helps in
understanding sampling bias and limitations which may/may
not make the data compatible with the user’s intended
application for it.
Ideally methods should be standardised and selectable from
a controlled list, but such a list is not yet available. Until it is,
just type in the method used for sampling.
All surveys must have a commencement date and may/may
not have an end date.
NOTE: These dates are not just informative, they actually
control the availability of the survey for data entry – ie. Data
entry will only be available on and after the start date and on
or before the end date. The earliest and latest records in a
bulk-loaded dataset must also be within the configured date
range for the survey.
When you create a survey it is automatically restricted to
being accessible only by project members. If you want to
open it up to the public to enter data, you will need to check
the tick-box on this field.
You can configure surveys to allow discussion threads and
commentary on individual records in the view mode. This
can be useful as part of a suite of measures to improve data
quality and species identification.
This field is disabled by default and you will need to check
the tick-box to enable it.
Attaching a logo image for each survey is highly
recommended as it makes your project page more visually
appealing to users and also helps users to visually identify
individual surveys and what they are about without having to
read.
Supplementary Information
This field allows you to provide specific and detailed
information to users of the data about how it should be
used, any constrains and limitations in the data, special
usage conditions, etc.
This is currently a manually set date field to indicate to data
users the currency of the dataset. In the future this will auto-
populate from the most recent create/edit action from the
audit log.
The organisation which is running the project is assumed to
be the legal dataset owner and auto-populates this field.
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However it is editable and can be changed if the legal owner
is another entity.
It is important to check and correct this as appropriate as
the legal ownership statement will accompany the dataset
as it is accessed and used by other people.
This is the Creative Commons attribution license, default
and non-editable at this stage, as specified in the Terms of
Use. However, in the future other suitable CC open data
licenses will also be available as selectable options, with
CC-BY 3.0 still as the default.
Step 2 – Visibility
Visibility configuration allows you to decide how and when the survey data is made publicly
visible and accessible.
There are three record visibility options currently available:
1. Public on submission (default) – As it says, records are
publicly visible as soon as they are submitted/received
into the system.
2. Public after a specified number of days after
submission – This option caters to the situation where
you want to withhold records from public view for a
period of time until you’ve had a chance to review them
and correct any anomalies (ie. It provides an
opportunity to moderate records before they go into the
public domain). The maximum number of withholding
days is 180 (6 months) and this applies to individual
records.
3. Public after a specified future date – This option caters
to situations where it is important to retain data visibility
to within the project membership only for a certain
period of time, such as researchers needing to publish
their work before they publish the raw data, datasets
containing culturally sensitive information, etc. This
option allows a forward date to be set up to 12 months
in advance and, within this period, the date can be
manually moved further in advance.
NOTES:
Data which is subject to embargo are only visible to
project members.
All data which is not under embargo is publicly visible.
Data is expected to go into the public domain under a
CC-BY license at some point.
Records are always editable by the submitter and all
member of the project who have an “Administrator”
role.
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Treatment of “sensitive species” records
BioCollect treats the visibility of sensitive species in the
same manner as the main Atlas of Living Australia – ie. All
species records are sent to the ALA sensitive data service
for instructions on how to treat the public view of record
spatial precision for that species in that location. Spatial
denaturing rules for all listed sensitive species are provided
by each state, territory and commonwealth environment
agency.
Limitations
1. Embargoing individual records or whole datasets
indefinitely is not currently supported.
2. Releasing individual records into the public domain
after a moderation process is not currently
supported.
Plans are being made to implement appropriate
mechanisms to deal with current limitations, whilst still
preserving the spirit of public infrastructure for public data.
Step 3 – Alerts
The Alerts tab allows you to configure automatic notifications to nominated email accounts
whenever certain species are recorded in that survey. This feature is still very basic, but is
planned to be significantly enhanced in the future with more “trigger” options, as well as more
“response” options.
The feature is optional in survey configuration and you can just skip through it if you don’t wish
to set an alert.
Start typing the scientific or common name of a species and
a list of names containing that text string will appear in a
drop-down list below the input box.
As you type more characters the list of options will reduce.
When you see the name that you are looking for in the list,
click on it to select it.
You can add as many species names as you wish to
receive notification of.
If a species is listed above as an “alert species”, the system
has to know where you want the alert notification to be sent
to.
You can send alert notifications to one or more email
addresses.
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NOTES
Input is not case sensitive, but it is spelling sensitive –
ie. A spelling error will not return the required species
name.
It is not currently possible to have different notification
addresses for different species. Notifications of any
listed species are sent to all listed addresses.
Step 4 – Select survey form template (proforma)
Along with the survey metadata (step 1), form selection is the most important step in configuring
the survey. This is essentially the proforma into which survey data will be collected. Form
selection is important as it affects other configuration options such as species selection (step 5)
This is currently a simple select-list of proformas which have
already been developed and in use by someone else.
We believe that data collection requirements for a particular
situation (eg. Weed management) in one area is not so
different to requirements for the same situation in another
area. We also don’t believe in “reinventing the wheel” and
that re-using a proforma developed for one person’s
situation is better than a bespoke rebuild for every situation.
Scroll through the list to find an existing proforma which
might suit your needs. If none of the existing proformas fit
your requirements, please contact the Atlas of Living
Australia (support@ala.org.au), including your contact
details, and you will be contacted to discuss your specific
requirements.
New proformas can be developed for most data collection
requirements – see Notes below.
TIP
S
A survey cannot be published without having a proforma
associated with it.
Rather than change an existing form for the current survey it
is better to end-date the current survey (see step 1 above)
and create a new survey. This way existing data remains
valid for the survey that it was collected for. It doesn’t matter
that there might be significant overlap in the data collected
as equivalent data between the two surveys can still be
viewed and analysed as if they were part of the same
survey anyway.
NOTE
S
Users are encouraged to re-use existing proformas for
common situations as much as possible. This facilitates
more effective data aggregation, analysis and downstream
use, and is ultimately simpler for everyone. However, we
understand that there are many situations which call for
bespoke requirements and these can be accommodated in
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most cases. The ALA is happy to work with project owners
in such cases.
Once data records have been made using the selected
form, you cannot change the form without “unpublishing” the
survey and allowing the system to delete the data. This is
because changing the form could significantly affect the
structure, meaning and even visibility/accessibility of
existing data records (see TIP 2 above).
Step 5 – Species configuration
The species configuration feature allows you to restrict the taxonomic reference list for each
species field in a form – it is dependent on the proforma selected (which is why this step is after
the selection of the proforma). The default setting is that species fields are not configured, but
they must be configured in order to publish the survey.
The usefulness of this feature is perhaps best explained by using a few examples:
1. A survey of a single species (eg. koala, platypus, or rare bird) – Pre-populates the
species field for every record and makes it non-editable, thus reducing data entry effort
and the risk of data quality issues.
2. A survey of a specific group of taxa (eg. Reptiles, amphibians, or fungi) – Configuration
allows for a relatively small subset of taxa for the recorder to choose from and these are
very specifically targeted to the purpose of the particular survey.
3. A survey of a specific set of taxa that are likely to be found in a particular area (eg. –
Like in case 2, the taxonomic reference in this case is a subset of all species, but it is
further filtered down to only those likely to be in a particular area. This level of
configuration flexibility further reduces the risk of false-positives being recorded.
4. A survey of a set of particular parasitic plants occurring in a particular range of host
plants (eg. Mistletoe species occurring in eucalypts) – Configuration allows for the
species field for parasite species to be different to the species field for eucalypt species
and neither look-up list to include species which are not mistletoe or eucalypt species.
By restricting the list of available species for specific fields in specific surveys you can, to some
reasonable degree, manage issues around input errors, false-positives and mis-identifications of
species and thus significantly improve data quality and identification confidence. This is very
important!
If the selected form does not have a species field, then this step is not applicable.
If the selected form template contains one or more species
fields, each field will be displayed on this page using the
field label from the form.
By default the field(s) will not be configured, yet they must
be in order to publish the survey.
Click on the “configure/view” link – see below for the
configuration process.
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You can change the way that species names appear on
forms and data records via this configuration setting.
Options include:
Scientific name (common name)
Common name (scientific name)
Scientific name
Common name
Configuring
“Lists” of species
There are three options available for configuring the species reference list:
a) All species
This uses the ALA species name look-up service in the
species field of the data collection form. As you start
typing the scientific or common name of a species it will
searches for that text string in the name of all species
names held in the ALA across all taxa and without any
geographic constraint.
This is the least preferred configuration option in most
cases as it provides the least support for taxonomic data
quality control. For example it is easy to record marine
animals on land.
b) Single species
Whilst the configuration process uses the ALA species
name look-up service to select the species of interest, in
the data collection form the species name will be auto-
populated and it will not be editable, thus assuring
taxonomic data quality.
Simply start typing the scientific or common name of the
species of interest and when it appears in the select list,
click on it. Then click “Apply”.
c) Selection or group of species
This is likely to be the most common configuration
setting for species fields and is the most complex to set
up, but it does provide the best DQ outcomes where a
selection of multiple species option is required for a
species field.
A species list can contain any selection of species that
you require, such as: all species occurring in a particular
taxon group (eg. Frogs) or multiple groups (eg. Insects,
arachnids and crustaceans); all species of all taxon
groups recorded in a particular area; selected species of
selected taxon groups occurring in a particular area; or a
selection of individual species/taxa with no particular
spatial or taxonomic theme at all.
There are several ways to create and select lists
containing groups of species. The ALA species lists tool
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(https://lists.ala.org.au) is used to create and hold the
defined list of species used for this config setting. You
can either:
I. Select and use an existing list which has been
previously created (“Choose from existing
species lists” option);
II. Create a new list directly in the lists tool and then
select and use it in your survey config. (“Choose
from existing species lists” option); or
III. Create a new list directly via the BioCollect
interface and “Apply” it to the species config in
context (“Create new species lists” option).
See scenarios I and II above.
Start typing the name of the required list in the search
bar. You will notice the list of lists below automatically
start filtering.
Note that this is automatically searching for a species name
within existing lists and the automatic filtering reflects lists
with species names containing the search string (ie. Not the
names of lists themselves).
When you have typed in a term contained in the name
of the required list, click on the “search” button.
You will now see a list of lists containing the search term
within the name of the list.
Notes:
Click on the column headers in the list of lists to change the
sort order and direction of short-listed items.
If your required species list appears, click on the “Add”
button on the right hand side of the page to select it.
Notes:
The name of the selected list will appear below the
configuration type select box.
You can select more than one list in your configuration.
Click on the “Apply” button to finalise the configuration and
return to the “Species” configuration tab.
See scenario III above. This instruction only applies to
creating a new species list from within BioCollect itself.
Give your new list a unique but descriptive short name to
help both you and others easily search for and identify it in
the list of lists. Ideally the name will be a short summary of
what it is and where it applies.
See the names of some others in the list of lists for examples.
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In most cases “
LOCAL_LIST
” should be selected for this.
Provide a longer description of what this new list is, what it
contains and what it is for. This will assist anyone else who
might want to use the list too.
You can search for and select species to add them to the
list. This method works reasonably well for relatively small
lists of species, but is not ideal for larger lists as populating
it can take a while.
NOTE: If you have a large list or want to use your own set
of common names, it would be better to bulk upload your list
directly into the ALA lists tool (https://lists.ala.org.au) and
then configure it to the species field via the method
described above – “Choose from existing species lists”.
Click on the “Create new species list” button to complete the
process and associate it with the species field configuration.
Click on the “Apply” button to select the species list for the
particular species field.
Repeat the configuration process for each species field on
the selected survey proforma.
Step 6 – Locations
The “Locations” tab allows you to define the geographic scope for data recording in the survey.
You may want to scope the survey to a smaller area within the overall project area, or perhaps
to a set of specific observation/monitoring sites which have been pre-defined.
This column lists sites which have been specified as
associated with the survey. The area defined for the project
will automatically be listed here by default, but you can
include other specific sites which will appear in a select-list
above the map in the data entry form.
Options for adding sites are described below.
If you wish to remove associated sites from this list (ie. Dis-
associate them from the survey), click on the arrow to move
them into the right hand column. For example, after defining
other specific sites for the survey, you can remove the
project area as it is no longer relevant to the survey.
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TIPS:
A survey must have at least one site associated with
it.
Two or more associated sites will be displayed on the
form as a select-list above the map.
The default view of the map in the form will zoom to
the extent of the sites associated with the survey.
This column lists sites which are associated with the project,
but not with the survey. For example, sites may have been
created for another survey within the project and are listed
here in this column.
You can easily choose existing sites and simply click on the
left-arrow to move them into the left hand column to
associate them with the survey.
Allows you to manually create a site which appears in a
select-list above the map in the data entry form.
A site must have a name and a spatial definition as either a
point or a polygon. If it is a polygon it will have a “footprint”
shape and a calculated centroid point, whereas points only
have a latitude and longitude.
You can also add a description of the site (eg. Where it is
relative to other local features, bearing and distance from an
obvious fixed feature, or distance along a road from a fixed
reference point, etc.) and a type. In most cases the type
should be selected as “Monitoring point”.
Use the any of the variety of zoom, pan, layer selection and
drawing tools to locate and spatially define the site.
Instead of creating a new site, you can select and use a site
which has already been created for a different project.
Since each site has a unique identifier, this is a good option
when you want to take a site-based view of data from
multiple surveys and projects – the best way to do this is to
re-use an existing site.
After clicking on this button you will be presented with a list
of all sites in the system. You can search and filter them to
find the one that you are looking for and a map showing site
locations is also shown on that page.
When you find the one (or many) that you are looking for,
click the “Add” button adjacent to the site name in the list.
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If you have many sites to load and have them in a GIS
system already, BioCollect supports bulk upload from an
ESRI SHP file format. This can also be very useful if your
site(s) has a complex footprint which is difficult to replicate
by hand-drawn polygon.
The SHP file must be in a .ZIP container file which also
includes other files such as the PRJ and DAT files
(projection format and sites data table respectively). The
coordinate reference system (CRS) used in the projection
should be EPSG:4326 (WGS84 decimal lat/long).
This option allows users entering data into forms to add new
sites to the list of available sites in the drop-down site
selection list above the map. These will be added to any
sites already associated with the survey.
If enabled, additional tools are displayed in the tool palette
in the map feature.
This feature is disabled by default.
NOTES
Sites can be edited to fine-tune point or boundary details,
but this SHOULD NOT be done after the site has already
been used for a data point in any survey as it will change
the coordinate and footprint details of the existing record(s).
Step 7 – Publish the survey
“Publishing” the survey is the final step in the survey set-up
process.
When you click on the “Publish” button the system will run a
validation test to ensure that all mandatory configuration
settings have been completed. If they haven’t a message
will appear advising what is missing. Publishing will not be
possible until these issues have been resolved. Goto the
relevant tab(s), fix the missing configurations, then return to
the Publish tab to try publishing the survey again.
When the publishing process is successful, a green
“success” message will be displayed and then the view will
automatically redirect to the survey list page (“Surveys” tab).
You can then go ahead and start entering data into the
form.
If you want to remove a survey from the survey list page you
can “Unpublish” it. This does not hide data which has
already been made public, it simply hides the survey and it’s
associated proforma.
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NOTES
Surveys must be published in order to be accessible for
data entry. Until it is “published”, a survey will not be visible
on the survey list page (“Surveys” tab).
5. Managing project members
BioCollect allows project Administrators to add “members” to their project. Members can be
given permissions in the project which allow them to access project features and content that
non-members cannot access.
Members are added to the project by users with an “Administrator” role via the “Admin” tab.
Must be a valid and active account with the Atlas of Living
Australia.
There are three available permissions which apply within a
project:
1. Administrator – This role is very powerful and gives
holders full access and editorial rights to all aspects of
the project, including editing of project and survey
metadata pages, editing of any record within project
surveys, ability to create and edit survey configurations,
ability to add and edit blog items and resource items,
add and edit project members and their permissions,
etc. The person who creates a project is automatically
assigned as an Administrator of the project.
2. Editor – This is a dedicated member role which
provides READ access to all aspects of the project and
EDIT access only to data records which they
create/submit themselves. The role does not have edit
access to other contributor records, not any other
aspect of the project.
3. Project participant – This role is essentially an honorary
project member role for the purpose of data record
entry only and is automatically assigned to public (non-
member) contributors to the project (ie. When the
public participation checkbox is ticked in the step 1
survey configuration page). Permissions for this role
are effectively the same as those for EDITOR.
Permissions are hierarchical in nature - higher levels include
all of the permissions of the levels below.
Members can only have one permission and this applies at
the project level, not the survey level. Therefore this
permission applies to all data visibility and data editing
rights for all surveys within the project.
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Administrators can easily edit the permission level
assigned to any member of the project, including other
administrators.
A project must have at least one member with
Administrator level permission.
A project can have multiple Administrators and all
administrators have full access to all editorial features
of the project – ie. They can modify any project content
and edit any record.
NOTES
There is no limit to the number of members in a project
– just remember though that project administrators are
responsible for managing the list.
In order to be a member of a project all users must
have an active ALA user account.
6. Adding and Managing Project “Resources”
Project “Resources” are essentially documents and other media items which are attached to a
project as additional project information. Resources are added to the project by users with an
“Administrator” role via the “Admin” tab and are visible to users via the “Resources” tab.
Types of resources can include: “how to …” instructions and guides; identification support tools
such as downloadable field guides; audio files of bird calls to aid species identification, or verbal
history stories of indigenous knowledge; project posters and promotional materials; presentation
slide packs; progress reports; videos hosted on youtube or vimeo; database files; safety guides;
and much more.
From the resources editing feature (“Admin > Resources”),
click on the “Attach document” button.
A “Document” is essentially any digital artefact that can be
attached to the project and can include video clips stored in
Title and description are important as they help to identify
the document in the list of resources, with the title being the
link to open the document for viewing.
The document should be attributed to the person/entity who
is the legal rights holder of it.
The “Document type” allows you to specify it as an
information artefact or a video. This affects other choices
below.
You should also include a usage license for the artefact,
especially if the default CC-BY 3.0 license should not apply.
If you do not include a license, CC-BY 3.0 will be assumed.
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You can make individual documents selectively visible to
the public or members as required. By default documents
will only be visible to project members. If you want them to
be publicly visible you will need to explicitly check the
“settings” checkbox to do so.
In order to protect the rights of any individuals mentioned in
text or displayed in images contained in artefacts which are
put into the public domain, you are required to make a
declaration that you are responsible for the privacy
concerns of any affected individuals.
Size limit of 5MB per item.
Formats include: PDF, DOC, DOCX, XLS, XLSX, PPT,
PPTX, MP3, AVI, and many others.
Supported formats can be viewed in-situ on the “Resources”
page in an in-built media viewer.
Click the “Save” button to upload and store the resource
artefact. It will then be visible on the project “Resources” tab
according to the visibility rules assigned to the document.
Document type options There are currently two types of resource artefacts
available, but this may be extended in the future to include
additional types.
Information The “information” type covers pretty much anything that is
not an embedded video.
If you want to use a video as a resource, you can do so by
selecting the “Embedded video” document type and then
copying into the input box, the ‘embed code’ which are
provided by the video channel that holds the video.
This will allow the video to play inside the in-built media
player in BioCollect.
Supported video channels are youtube and vimeo.
These controls enable deletion and editing of the
document/artefact.
Editing it will open the same pop-up used to submit the
document, where you can edit the metadata associated with
it, including the public visibility setting.
This feature allows the document/artefact to be
downloaded.
NOTES
All materials attached to projects must comply with the Atlas
of Living Australia and BioCollect Terms of Use. All
breaches of this condition will be treated seriously and may
result in appropriate response actions being taken.
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7. The Project Blog Feature
The Blog feature allows you to communicate real-time and run-time information about your
project to your community and the wider public. Blog articles can include items such as: updates
on project progress; exciting or notable things associated with the project (eg. Exciting
discoveries, highlighting contributors and contributions, project milestones and achievements,
etc.); up-coming events and promotions; and much more.
Blog articles are added to the project by users with an “Administrator” role via the “Admin” tab
and are visible to users via the “Blog” tab.
From the blog editing feature (“Admin > Blog”), click on the
“New entry” button.
Select an appropriate content type. Options are:
1. News & Events – up-coming events and project
activities, discoveries, findings, contributor profiles, etc.
2. Project stories – highlight stories from the project,
progress tracking and milestone reports, achievements,
etc.
The date on which the blog article is released. This auto-
populates with today’s date, but can be edited.
The headline title of the article.
The blog article can have a feature image which can be one
of two ways:
1. Select type – This uses a standard info-graphic as
an image to represent the type of article. Options
include: Important, News, Star, and Information.
2. Attach image – Click on the “+ Attach” button, find
the image that you want to use for the article,
“Submit” the image.
This is the main content area. You can either type into this
text area or use the markdown editor to include emphasis
formatting and other elements to your article.
The URL link allows you to hook the blog article into a
tweet, facebook entry, youtube clip, a related article on your
company website, or some other related external resource.
This will appear as an active link in the blog article.
When you’ve completed your blog article, click the “Create”
button to publish it.
NOTES:
You can easily edit content after publishing it.
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8. Reviewing, Editing & Accessing Data
From any of the access points to a data review page you can easily review, edit and access
your data. Depending on your permission level in the project, you can also edit other data too.
Action buttons will display to the right of records if the user has permission to apply them.
Apply search and filters to reduce the results to only those
that you require. See section 2 above for guidance on how
to do this.
Action button:
Click on the “View” button to see a read-only version of an
individual record.
It is currently not possible to switch to edit mode from this
view.
Action button :
Click on the “Edit” button to open the selected record in
“edit” mode. This will allow you to amend data and then
save the changes.
Action button :
Click on the “Delete” button to remove a particular record
from the database.
By default records are displayed in a list format in reverse
chronological order (ie. Most recent first).
Clicking on a species name will open (new tab) the page for
that species in the ALA.
Clicking on the survey name will open the survey form
template for entering a new record for that survey.
Clicking on the project name will switch the view to the
selected project data page.
Records displayed in the list respect the search and filter
settings used.
Records can be displayed geographically on a map and are
clustered according to the zoom level of the view.
As you zoom into an area of the map clustering break down
into smaller clusters until only individual records are
displayed (shown as blue dots).
Clicking on a blue dot will display a dialogue box with links
which take you either to a read-only view of the record or to
the project associated with the record.
Records displayed on the map respect the search and filter
settings used.
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NOTE: Currently the map will only display the first 10,000
records returned. If you need specific records in an
area, please apply additional filters to reduce the
result set to less than 10,000 records.
Images associated with records can be viewed in a gallery
format.
Clicking on an image will open it in a pop-up viewer.
The links below the image can then take you to a read-only
view of the record associated with the image, or to the
project associated with the record.
Images displayed on the gallery reflects the records
returned from the search and filter settings used.
The “Download” option allows you to access raw data. This
will produce a zip file containing the following:
Project metadata
Survey metadata
Survey data
Thumbnail images associated with records and url
links to the full resolution images
SHP formatted file containing spatial geographies of
projects and records, both points and polygons.
Records included in the download respect the search and
filter settings used.
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9. Troubleshooting – Common issues
Below is a guide to troubleshooting some of the more commonly reported issues:
Problem
Cause/Solution
Can’t see my survey on the
survey list page (“Surveys”
tab)
The survey has either not yet been “published”, or it has
been “unpublished”.
Goto “Admin > Survey settings”, select the appropriate
survey from the drop-down list. Goto the “Publish” tab and
click on the button.
Can see my survey on the
survey list page (“Surveys”
tab), but can’t access the
survey form –
button.
There are three possible causes of this:
1. The user is not logged in.
2. Today’s date is outside the date range specified in the
survey configuration – See “Admin > Survey settings >
Step 1”.
3. User permission does not allow access to the survey.
This is more likely to be the case where a non-member
of the project is trying to access the survey and the
setting to “Allow public to enter data“ has not been
enabled in “Admin > Survey settings > Step 1”. This
may be a legitimate setting for the survey and if the
user is to be allowed access to the survey they should
be added as a project member.
I can’t access the “Admin”
features of my project. The most likely scenario is that you are not logged in.
If your project has other users with the “Administrator”
permission it is possible that one of them could have
changed your permission level in the project.
How do I update my project
information? Goto “Admin > Project info” and click on the “Edit” button.
Make changes as required, scroll to the bottom of the page
and click “Save”.
How can I change my project
to use BioCollect for collecting
data?
Goto “Admin > Project info” and change the setting of the
second field in the template () from “No” to “Yes”.
Scroll to the bottom of the page and click “Save”.
“Admin > Survey settings” and follow the survey set-up
process described in section 4.
