Searching for data and other information
Uploading and editing data
Information for reviewers
Species Distribution Models [TBD]
Georeferencing information and links
Getting involved and reporting errors
What is the mission of the REBIOMA Data Portal?
The mission of the REBIOMA web portal is to serve quality-labeled, up-to-date
species occurrence data and environmental niche models for Madagascar’s flora
and fauna, both marine and terrestrial. REBIOMA is a project of WCS-Madagascar and UC Berkeley. The REBIOMA Data Portal address is http://data.rebioma.net. For more general information about the entire REBIOMA project, go to
How does the REBIOMA Data Portal function?
REBIOMA serves species occurrence data for marine and terrestrial regions of Madagascar. Following data upload, data is automatically validated against a geographic mask and a taxonomic authority. At upload, data providers can decide whether their data will be public, private, or
shared only with selected collaborators. Data reviewers can add quality labels to
individual data records, allowing selection of data for modeling and
conservation assessments according to quality. Data users can query data in
numerous ways (see simple and advanced search). REBIOMA also serves environmental niche models
for current and future climate scenarios for terrestrial species.
Click image for full size version
What is the role of Taxonomic Review Board?
The Taxonomic Review Board is a group of scientific experts that maintain the Taxonomic authority and review species occurrence data, according to their specific taxonomic expertise. This review process, which is described in more detail below (see sections on reviewers and data quality control) is core to the mission of REBIOMA. A list of the members of the Taxonomic Review Board can be found here.
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How do I register for an account?
Anyone can browse and download public REBIOMA data without logging in. To upload data and use other advanced features, you will need to sign in to an account. To register for an account, click the link that says "Register" at the top right of the REBIOMA map view page. After you successfully fill out the registration form, a password will be sent to your email account. Use this password to sign in, at which point you may change it to a password of your choosing. See below for information on signing into your account and changing your password.
How do I sign in to my account?
After registering, sign in to your account by clicking the link named Sign in at the top of the REBIOMA map view page. Enter your email address and password into the form and click the “Submit” button to sign in to REBIOMA.
How do I change my password?
You must be signed in to change your password. If you’ve forgotten your password, see below for how to reset it. Once signed in, click the tab named User Profiles towards the top of the REBIOMA map view page. In the form, enter your old password, and a new password twice, then click the “Submit” button to make the change.
How do I reset my password if forgotten?
If you forgot your password, click the “Forgot password” tab on the Sign in page. Enter your email address in the form, click “Submit” and a new password will be sent to your email address.
By downloading and/or viewing data on the REBIOMA portal, you are agreeing to the following conditions:
Species occurrence records and models served by REBIOMA are to be utilized by individual researchers or research groups for scholarly, educational or research purposes only and not for any commercial purpose.
- If any records or models derived from these records are used in an analysis, report, presentation, etc., the provenance of the original data must be acknowledged (see "Acknowledgment" below) and the data-provider or the curatorial staff of specific institutions should be notified. Please also notify the REBIOMA project.
- The data-providers, institutions, REBIOMA, and their staff supply this data with no warranties, express or implied, concerning its fitness for any particular purpose, and are not responsible for damages, injury or loss due to the use of these data or models.
of data or models from the REBIOMA portal shall be solely responsible
for the use and presentation of the data and will ensure that the use
and presentation of the data are correct and that the data are
accurately reproduced and not taken out of context.
Publications and presentations resulting from the use of REBIOMA data or models should list the names of data providers or institutions whose data were used, and REBIOMA (http://data.rebioma.net) as the portal by which the data or models were accessed or downloaded. The citation also should list the date of access via REBIOMA. Users should also refer to individual institutional policies on proper citation of data from specific providers.
Data sharing agreement for data providers
By uploading PUBLIC or PRIVATE data, data providers agree to:
By uploading PUBLIC data, data providers additionally agree to share
Contribute data that is scientifically valid and is prepared to the highest possible standard of accuracy and completeness
Pledge to improve data quality when possible in response to feedback from REBIOMA
the appropriate experts from REBIOMA's Taxonomic Review Board to
assess the quality of the data and add comments in the comment field.
Finally, PRIVATE data providers also have the option of
allowing their data to contribute to species
distribution models while maintaining privacy for the records.
In handling the data provided by data providers or institutions, REBIOMA agrees to:
Provide tools and methods to enable data providers and institutions to provide their data to REBIOMA.
Securely cache data from data providers and/or institutions along with similar content from other sources on REBIOMA's servers.
Protect the privacy of records uploaded as PRIVATE by data providers/institutions.
the data providers ability to share their private data only with
collaborators, provided those collaborators are registered as REBIOMA
- Create and maintain a Taxonomic
Review Board that will review data records, both public and private,
according to the highest standard of scientific excellence and
Maintain the data in its original state; while original data will not be altered, REBIOMA will enable annotated fields or comments to be added.
Provide data-providers/institutions with comments or feedback received about its data objects with the goal of improving the quality of the data and thus reducing errors.
Not encourage or answer requests to provide all or major components of data providers/institutions content to other data providers. Rather, such requests for re-usage will be forwarded to the data provider/institution.
Provide search, visualization, mapping and modeling functions for the data at the REBIOMA web-portal.
If requested by a data provider or institution, show further
information provided by that institution/data provider such as:
project descriptions weblinks, abstract, use restrictions, etc. on its list of Content Partners.
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The Darwin Core is a body of data standards that provides a stable reference for sharing information on biological diversity. It includes a glossary of terms (e.g. fields, columns, attributes, or concepts) that provide reference definitions, examples, and commentaries. The Darwin Core is primarily based on taxa and their occurrence in nature as documented by observations, specimens, and samples. Many projects, including REBIOMA, currently use Darwin Core standards for structuring the format of the biological data they provide. Click here for more information on Darwin Core. Click here for a full list of Darwin Core terms (e.g. fields). The REBIOMA database schema uses a subset of these terms, in addition to some REBIOMA specific terms that are defined below. For a full list of REBIOMA terms (i.e. database field or column names) click here.
In order to be used in species distribution models, data that is uploaded to REBIOMA must pass several automated validation tests. First, data must be in the proper comma-delimited format, and several required fields must be present, as described in Uploading data. The next test is geographic. Because REBIOMA focuses only on Madagascar land and sea, REBIOMA tests each locality record against a land-sea mask for Madagascar. Finally, REBIOMA checks the validity of each record’s species name against the REBIOMA taxonomic authority, as described below.
Data quality control
REBIOMA has implemented a peer-review process by taxonomic experts (the Taxonomic Review Board) to enhance data quality. There may be more than one taxonomic expert assigned to each record. Likewise, a single taxonomic expert might have multiple taxonomies that s/he has agreed to review.
Each occurrence record in REBIOMA is given one of three review states: "unreviewed", "reliable" and "questionable". As there may be multiple reviewers for a given record, "reliable" and "questionable" indicate the average of all reviews up to that point in time. A tie, that is to say, a record that has received an equal number of "reliable" and "questionable" reviews, is defined as "reliable" overall. Importantly, this review system ensures that only the highest quality records are included in species distribution models.
The general review process is as follows. After data are successfully uploaded to REBIOMA by a data owner, the records are marked as "unreviewed" and the appropriate reviewer(s) are notified by email that they have new records to review. Reviewers can then login to the portal and review these records, by giving them each a "reliable" or "questionable" review, with appropriate comments. This changes the record's status to "reviewed" and triggers a notification email to the data owner, who may then respond to the comments by downloading the data under review and making any necessary adjustments to the reviewed records as s/he sees fit. Changes by the data owner are then re-uploaded, and this triggers re-evaluation of the records by the appropriate data reviewer. Important note: In order for the data reviewer to be notified that the data owner has made changes, the data owner must download the data, edit the data in a text-editor or spreadsheet, and then re-upload the data, without altering the REBIOMA-id. If changes are only made in detail view, for example, the data reviewer may have no way to know that the record has been altered and needs to be re-reviewed. Once the data receive an overall "reliable" review, they may then pass into species distribution models.
The REBIOMA taxonomic authority is a list of valid names and synonyms for Madagascar species. When a user uploads a new species record to REBIOMA, the species name (composed of the required input fields Genus and SpecificEpithet, as well as the optional InfraspecificEpithet, see below for additional information) is checked against the taxonomic authority. If the name matches, or is a valid synonym, the record is “validated”. If not, the record is maintained, but does not pass validation. Record owners may then make appropriate corrections to the record so that it passes validation. Furthermore, users can suggest additional valid names and synonyms by contacting the site managers. In addition, users may click here to view the current REBIOMA taxonomic authority.
VerbatimSpecies is a term (or field) added to species locality data that is uploaded to REBIOMA, and is an important concept related to data validation. REBIOMA automatically derives the value of the VerbatimSpecies by concatenating the values in the required input fields Genus and SpecificEpithet, as well as the optional InfraspecificEpithet, if present. This value is used in the validation process as described below
AcceptedSpecies is a term (or field) added to species locality data that is uploaded to REBIOMA, and is an important concept related to data validation. When a user uploads a new record, REBIOMA compares the value for VerbatimSpecies to a list of VerbatimSpecies in the REBIOMA Taxonomic Authority. If the VerbatimSpecies is found in the list, the associated AcceptedSpecies as well as all of the values of the accepted higher ranks are added to the record. Having both AcceptedSpecies and VerbatimSpecies concepts in the database allows for synonymy. There may be duplicate AcceptedSpecies in the taxonomic authority (for synomyms of the same species), but VerbatimSpecies is always unique (for a given higher taxonomy).
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REBIOMA has several different user "roles" to provide different types of functionality and levels of access to the data portal. There are currently three roles: Public user, Researcher and Reviewer. Public users do not need to register to use the portal, whereas Researchers and Reviewers must register. Each role is described in greater detail below. In addition, references are made to these roles in terms of specific portal functions throughout the help pages.
The public user role is simply the default view of the portal available to all anonymous users. No registration or sign-in is required to view or use basic portal features, including maps and environmental overlays, search, browse or download data, models and environmental data. By registering for an account, however, users have additional capabilities for interacting with the database and portal, as described below.
The main function of the researcher role is to allow researchers to upload locality data to be included in species distribution models. In addition, Researchers can collaborate with other researchers and engage with data Reviewers in the data validation and data quality review processes to improve data quality. The Researcher role requires account registration.
The reviewer role is critical to data quality review process and thus the success of the REBIOMA mission. Reviewers, also known as the Taxonomic Review Board, review records that are uploaded to the REBIOMA portal, according to their taxonomic specialty. As such, reviewers have special filters and tools to help them find, comment on and review occurrence records. These tools are described in additional detail below, under the section titled "Information for reviewers". Reviewers are typically invited to join the Taxonomic Review Board by a member of the REBIOMA team; however volunteers with taxonomic expertise are always welcome, please contact us.
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Searching for data and other information
To search for a location by geographic name, in Map view, enter the name in the search box that sits on the map itself, and then click “Go”. This tool currently searches names in the GoogleMaps gazetteer, so not all names will necessarily be included or found. Also, the Google gazetteer is only able to return a single location for a given name.
Quick search for occurrence data
There are many ways to search for occurrence data (also referred to as "species locality data", or "records") in REBIOMA. The default
way is to use the “quick” search box in Map or List view, located towards the top left under the
occurrences tab below the REBIOMA logo, to the right of the words "for taxon". Type a species latin name (genus plus species, or genus, or species, e.g. "Lemur catta") into the search box, and the portal will return, by default, "All Reliable Reviews" - that is to say records that have received a review of "reliable", that match that name. If there are no matches, then either there are no records in the database for that species, or there are no "Reliably Reviewed" records yet for that species. To find records for a species, you may have to change the "search filter" options, or try an "advanced search". Both methods are described below. To search all records (within a given search filter), simply leave the search box blank.
Quick search filters
Quick search filters are useful for limiting the total set of records being searched. There are a total of four filters that can be applied: 1) Occurrence filter, 2) Validation error filter, 3) Sharing filter, and 4) Privacy filter. Not all filters may be visible at one time, but the "Occurrence filter" always shows and is always applied to searches. In addition, this is the only filter that is visible to "public" (i.e. anonymous) users. All filters, when visible, are combined with a boolean "and". This is joined to terms the user has typed in the search text box by a "starts with", followed by "contains" search within the field "AcceptedSpecies". Finally, all of this is combined with whatever advanced search terms are added, again, using boolean "and". For example, setting the "Occurrence filter" to "All Occurrences" and typing "catta" in the search text box returns All occurrences that contain the term "catta". Similarly, setting the "Occurrence filter" to "All Reliable Reviews" and typing "Eulemur fulvus" in the search text box returns All reliably reviewed occurrences that start with the term "Eulemur fulvus". See below for an advanced search example.
Occurrence filter options are described in the table below:
||This filter searches within
| All Reliable Reviews
|| All occurrences that have been given a review of reliable
| All Questionable Reviews
|| All occurrences that have been given a review of questionable
| All Awaiting Review
|| All occurrences that have not yet been reviewed
| All Invalidated
|| All occurrences that have failed automatic validation
| All Occurrences
|| All public occurrences
| TRB Occurrences to Review
|| Occurrences pending user review
| TRB Reliable Reviews
|| Occurrences the user has given a review of reliable
| TRB Questionable Reviews
|| Occurrences the user has given a review of questionable
| My Overall Reliable Occurrences
|| User occurrences that have been given a reliable review
| My Overall Questionable Occurrences
|| User occurrences that have been given a questionable review
| My Awaiting Review
|| User occurrences that have not yet been reviewed
| My Invalidated
|| User occurrences that have failed automatic validation
| My Occurrences
|| User occurrences both public and private
Validation error filter options are useful for finding records that have validation errors and are described in the table below:
|Validation error filter
||This filter searches within
|All validation errors
||All occurrences with validation errors
||All occurrences with year collected validation errors
||All occurrences with genus validation errors
||All occurrences with specific epithet validation errors
||All occurrences with decimal latitude validation errors
||All occurrences with decimal longitude validation errors
||All occurrences with taxonomic classification validation errors
Sharing filter options are described in the table below. Only registered users can share data with collaborators
||This filter searches within
|All shared and unshared
||All occurrences without regard to sharing
|Shared with me
||All occurrences that are shared with the user
Privacy filters apply only to data that the registered user owns with one exception: As specified in the data sharing agreement, data reviewers can search for private data that they do not own, but are authorized to review, using the "My Occurrences to Review" filter described above. Privacy filter options are described in the table below.
||This filter searches within
|Public and private
||All user occurrences without regard to privacy
||The user's public occurrences
||The user's private occurrences
To conduct an advanced search, click the
link named "Advanced Search" just to the right of the "Search" button from either Map or List view.
This opens the advanced search page, which also contains detailed
instructions. Advanced search allows you to construct complex queries
using combinations of fields and boolean search types and conditions.
Click here to see a full list of searchable fields. Note that the selected quick search filters, shown in the drop-down list in the upper right part of
the screen ("All Occurrences", etc.), also apply to advanced searches.
Terms are specified in a text box for each specified database field,
and then searched so that they are included or excluded from the set,
with the following search conditions: Starts with, exact match, contains, in, empty.
To begin, start typing the name of the first field to search, for
example "Accepted Family". When you find the name of the field you want
to search within, click it to reveal additional options. Select terms
to search on, and whether they should be "included" or "excluded" from
the set. Included terms are typed in the text box to the left, excluded
terms are typed in the text box to the right. Next, use the radio
buttons to select the search conditions ("starts with", etc.) described
above. Click the "Add search term" button to add this to the advanced
search query. Additional queries can be constructed and added in this
way. Finally, click the "Search" button to execute the search. See
below for an additional example.
- "Starts with" searches for terms within the specified field that
start with that term. For example, seaching "all occurrences" for
records with an "accepted family" that "starts with" that "includes"
the term "mu" will currently return records from the families Mugilidae
and Muridae (at least).
- "Exact match" is self-explanatory and returns or excludes only exact matches with the specified terms.
- "Contains" returns or excludes records that contain the specified
term anywhere within the specified field. For example, searching for
records that "contain" "lemur" in the "Accepted Family" field returns records from both families "Lemuridae" and "Lepilemuridae" (plus any others that contain the term "lemur").
- "In". Use "in" to build a query of terms joined by commas. For example,
to search for records from two or more genera at once, you could add
"Accepted Genus", then type "boophis,accipiter" and click the "in"
radio button. This will return all records from the genera Boophis and
- "Empty". Searches on blank or null values in the database for a
specified field. For example, use "empty" to search for records that do
not have a "State Province" value.
Advanced search example
To exclude a particular genus from a family search, do the following. Click the "advanced search" link. Make sure the "All Occurrences" filter is selected from the list box to the right of this link. In the text box next to "Add a search field" type "Accepted Family" and return. Then, under where it says "Search in Accepted Family", in the text box to the right of the word "Include" type "Lemuridae", click the "exact match" radio button and click the "Add search term" button. The term you have added will appear in the list in the upper right part of the screen. Next, in the text box next to "Add a search field" type "Accepted Genus" and return. Under where it says "Search in Accepted Genus", in the text box to the right of the word "Exclude" type "Eulemur", click the "exact match" radio button and click the "Add search term" button. You should now see two search criteria listed to the top right of the screen under "Search criteria".
Finally, to apply the criteria in an advanced search click the "Search" button. This will return all records from the family "Lemuridae" excluding the genus "Eulemur" (at the time of writing all public records from the following genera are returned: lemur, hapilemur, prolemur, varecia).
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Map view is the default view for browsing REBIOMA data and conducting quick searches. Once a search is complete, results are displayed on the map, and in the panel to the left of the map, 10 results at a time. Each icon and each record in the list to the left represents one locality record in REBIOMA. The total number of results is displayed just above the map, towards the right side of the page. Users may browse through the results, 10 records at a time, by clicking “next” or “last” in this same area (or “first” and “last” if dealing with a set of records other than the first). Each balloon icon on the map represents one record from the set. For a given set of 10 records displayed, letters are also assigned to common species. For example, multiple icons with the letter “A” in a given set represent multiple records for a single species. Individual record icons may be turned on or off by clicking the checkboxes next to each record in the list to the left of the page. Clicking an individual icon displays additional details for that record in a pop-up window.
List view is accessed by clicking the link named “List” on the top right of the grey bar above the map. This provides a tabular view of the search results and includes additional details about the record set not available in map view.
Detail view is detailed view of the data for one single locality record. Detail view can be accessed from three different locations on the REBIOMA portal. In map or list view, when a set of records is displayed after a successful search, choose a single record in the list of results. Each REBIOMA id number listed is a link to the detail view for that single record. In map view, click on a map balloon icon for one record displayed after a successful search. On the popup window that displays you will see a link to detail view for that record. If you are the owner of the record (i.e. you uploaded the data), detail view offers several in-place editing features. See editing for details.
Map view allows users to view several different environmental and vegetation cover layers as overlays on the map interface. Some, but not all of these layers are used in the species distribution modeling routines. To display an individual layer, choose it by name from the list box on the map that says “Select Layer…”. To clear all layers, select the entry in the list box that says “—Clear layers –“. After a layer is added to the map, a legend is added to the map that shows the range of values and colors displayed for that layer. Users may click directly on the map to display values at that location. In addition, additional information is available on the selected layer by clicking the “Details” link in the legend. This displays a popup window showing summary statistics for the layer in question. It also provides a link to a metadata summary for that layer. Click the “Close” button to return to the application. More complete metadata for all layers can be found here. In addition, ascii grid files for the layers can be downloaded here, and these include standard FGDC and ESRI metadata in xml and html format.
Anyone may download public data from REBIOMA as a comma-delimited table (.csv file) with or without logging in. To download data, first search for data of interest. When you have the results you wish to download, click the link labeld "CSV", towards the top right of the page in either Map or List view. By default, all records are rendered as a comma-delimited table (.csv file), not only the 10 records that are visible on any one page of results. Large tables may take some time to produce and made available to download. After clicking the "CSV" link, you are then given a choice of delimiters to use in the csv table. Choose "comma" or "semi-colon" depending on the language preferences of your operating system. Finally, click the "Download" button to begin the download. Most web-browsers will then offer you the option to open the file directly or save to disk.
Commenting on data
Anyone may comment on a particular data record, whether or not they are logged in. These comments do not affect the record or the models derived from the record, but may be taken into account (or not) by the review board during data quality labeling. To comment on a record, search for data of interest, and in Detail view, enter a comment in the blank field below the map, where it says "Enter your comments". When complete, click the "Submit" button. Please be polite and considerate when commenting. Comments cannot be removed, except by the REBIOMA development team. If you see Spam, offensive or inappropriate comments, please report them.
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Comma-delimited data (.csv format)
You can upload your own data to REBIOMA and keep it private or make it publicly accessible. This is the primary method for entering data into REBIOMA. Uploaded data should follow these format specifications defined below. You must be signed-in to upload data. You are the owner of data that you upload to REBIOMA, and only you can make changes to it.
Occurrence data are uploaded to REBIOMA in a comma separated format (CSV) file. A
header row (the first row in the file) is required. It must contain, in
any order, comma separated column names. Column names and values may be
surrounded by double quotes ("). Column names or values that have
commas in them MUST be surrounded by double quotes. Column names that
match any of the terms found in the Sample, SamplingEvent, Location, Taxon, or Identification sections of the Simple Darwin Core will be understood and uploaded. Column names not found among these
terms will be ignored in the upload and will not be accessible from
The header row must contain all of the following required terms. If any of these terms are missing, the upload will fail:
Following are the contents of a simple (and valid) CSV file that contains a
required header row and a single row of data without spaces between
Some additional aids and sample files to assist with Data Upload to REBIOMA:
- Click here for a template .csv with the minimum required fields. Save (export) this file to a local directory, then paste data in.
- Click here
for a sample .csv file with test data and fields in the required
format, ready to upload to REBIOMA. Save (export) to your computer,
REBIOMA allows data providers to select from among several levels of access and privacy. Data providers can specify that their data is open access (i.e. public), private, or can be shared with selected collaborators. If you decide that your data should be private, you can make two further choices: whether these private occurrence points can still contribute to species distribution models for that species (assuming they are of sufficient data quality), and whether or not you wish to allow others to know that you have submitted data, even though the data is not public. To keep your data private, click the radio-button labeled “Private” during data upload. To allow private data to contribute to species models, click the check box just to the right of the "Private" label that says "Is modeling OK?". To show your email address, click the check box next to "Show email in records?". Note: Selecting "show email" for private data has no effect, as all data marked "Private" cannot be seen by the public. For additional information on data use policies, see the data use agreement.
Uploading both public and private records
If you have a dataset that contains some records that can be public and others that must remain private, you can handle this in two ways. One method is mostly done outside of REBIOMA. First, separate your data into a public and a private .csv file. Upload each file separately and use the public/private radio-button to set the privacy of each file to public or private as needed. The second way is to upload all of the data at once as private data, and then search for the records (use the "My occurrences" search filter and any other necessary advanced search terms) that are to be public and change them from private to public. See editing data below for additional information.
Changing the privacy status of a record or set of records
You must be logged in and the owner of the records for this to be an option. Search for the records whose status you wish to alter using "My Occurrences" as your primary search filter. Change to List view. Select the records whose status you wish to alter. Next, from the drop down list that starts with "Select an action", select "Make public". If you have more than 10 records and do not wish to page through every set to apply this action, you may select the check box next to the label "Apply this action to all n results". If you have searched and found 1000 records for example, this will make all 1000 records in the set public. Other actions that can be applied in this way include "Make private", "Show my email", "Hide my email", etc. See the section on Editing for additional details.
Sharing and collaboration
During the upload
process, you have the option of sharing the records you are uploading
with collaborators. Collaborators must have a REBIOMA account. To share
records with collaborators, you must first search for them and add them
to your "collaborator list". To do this, first sign in,
and then click on the "User Profiles" tab. This tab is in the upper
left of the screen, under the REBIOMA logo, just to the right of the
"occurrences" tab. Towards the bottom of this screen, click the link
labeled "Search for collaborators". This opens a collaborator search
form. Search for collaborators by name, email or institution. Check the names of the
collaborators you would like to add, and then select "Add
Collaborators" from the drop down list labeled "Select an action" to
add them to your collaborator list.
Once collaborators are in your collaborator list, you can then select them to share records with during data upload.
To share records, upload data as normal, however before clicking the
"Upload" button, check boxes next to collaborators with whom you want
to share this data. You can also share records after upload. To do
this, search for the data of interest, select the records you want to
share, and then under the list box labeled "Select an action" select
"Share/Unshare records". This will open a window that allows you to
share records with collaborators you choose from your collaborator
Collaborators do not have any special rights to edit the data you share with them. They can, however, see private data that is not visible to a public visitor to the website. As with all other data, however, only the owner can edit or make changers. In this sense, collaboration is a way of organizing groups of people to search for and view otherwise private data, and to allow collaborators to easily find data of mutual interest, by searching on data using the "shared with me" filter.
You must be signed in and the owner of data that you want to edit. To edit a single record, search for the record(s) that you want to change. Then, in Detail view, simply click on the value for many of the displayed fields, in order change the values. Note: not all fields are editable. Values that can be editable will be black in Detail view. Values that you cannot edit through the web portal will be light grey, and include "Rebioma-Id", "Time Created", and other database critical fields. Similarly, you may click and hold the icon in the small map to move the record to a new location, but be aware that this also changes the permanent latitude and longitude values for this record. To save changes, click the “Save changes” button towards the bottom of the page. Changes should be made with caution, as they update the corresponding permanent record in REBIOMA. Finally, if you have signed in to REBIOMA, you may also comment on any record that is publicly viewable (whether or not you are the owner).
You can also bulk edit certain attributes for multiple records. First search for the records that you want to change. Then, in List
view, select the record(s) that you want to apply changes to. You may
also select all records, by clicking the check box towards the top of
list view labeled "Apply action to all n results". Available actions
are listed in the "Select an action" list box, and include delete, make
public, make private, certify, uncertify, show my email, hide my email
and share/unshare. These actions are described in more detail below
Finally, data editors will want to save any changes before navigating to another page or record. Because of the dynamic nature of the website, any unsaved changes may be lost if you leave the Detail view of the record being edited.
- Delete: This permanently deletes selected records from the REBIOMA database, and cannot be undone.
- Make public: This makes all selected records public.
- Make private: This makes all selected records private.
- Show my email: This shows the owner's email on all selected records.
- Hide my email: This hides the owner's email on all selected records.
- Share/unshare: This shares or unshares selected records, reversing their current shared/unshared state.
You have records that you have already uploaded to REBIOMA that you have improved (or wish to alter) and you want to re-upload these data. There are two options. One, data may be downloaded from REBIOMA, edited and re-uploaded. You must be the owner of the data to successfully re-upload. Data providers wishing to re-upload data should be careful not to alter or delete the values in the field named "Id", otherwise, REBIOMA will treat the re-uploaded data as new data, and the records will then be duplicated in the database. If data providers with to simply alter some of the fields for a given record, and have this record replace the old record, then make sure to keep the "Id" unchanged, and re-upload the data. REBIOMA will then replace the old record with this new one, based on the "Id". An second way to edit and replace data in REBIOMA is to search and download the data of interest, then delete the records through the REBIOMA portal. Data providers can then be sure there will be no record duplication. This is not at all the recommended method, however, as records that are deleted will lose any comments or quality labeling that have been added by outside users or reviewers. Once these same data are re-uploaded, they will have to be completely reviewed from the beginning as if they had never been uploaded.
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Information for reviewers
Finding your occurrences to review
If you are a member of the Taxonomic Review Board and have agreed to review records for a particular taxonomic group, you should expect to receive periodic emails notifying you when new records within your taxonomic speciality are uploaded to the REBIOMA portal. Follow these steps to find your occurrences to review. First, register and sign in to the REBIOMA web portal (http://data.rebioma.net). Next, select "My Occurrences to review" from the "Occurrence" filter. If you don't select or enter anything else, and click the "search" button, this will return all of your records to review. If on the other hand, you want to search for a subset of records to review, you may use "quick" or "advanced" search tools to find your records to review. An example: To find a record by REBIOMA id #12345, first select "My Occurrences to review" from the "Occurrence" filter. Leave the "taxon" search text box blank. Next, click the "advanced search" link. In the text box that says "Add a search field:", type "Rebioma Id". Next, in the text box that says "Search In Rebioma Id", type the Rebioma Id number (e.g. 12345 in our example) and click the equals ("=") radio button. Then click the "Add Search Criteria" button. Finally, click "Search" and this will return (in our hypothetical example) one record with the Rebioma id# 12345.
Aids for reviewing
Once a set of records to review has been found (described above), reviewers can then review records in either List or Detail view. See below for suggested best practices for how to assess the overall quality of individual records. The reviewer must assign one of two quality labels to reviewed records: "reliable" or "questionable". If no choice is made, the record remains unreviewed. If there is more than one reviewer for a given record, the overall review is calculated as the average of all reviews given up to that point, with ties (e.g. same number of "reliable" and "questionable" reviews) equal to "reliable". Only overall "reliably" reviewed records are included in species distribution models. Data owners are automatically notified by email when records are given a review of "questionable". They may then address the changes and re-upload the data for further review.
To review a record or set of records, search "My Occurrences to Review", then go to list view and select the record or records you wish to review by checking the check-boxes next to each record. You may also click the "Select All" link to select all records on a page. Next, in the action list box, select "Review as Reliable" or "Review as Questionable" as applicable. The portal will then ask you to enter a comment. If you have selected multiple records, this same comment will apply to each. See below for additional notes on review comments.
Submitting your comments
The comments you submit while reviewing a record may be the only way to communicate your assessment of a record or set of records to a data owner. As such, it is very important that you be as specific as possible so that the data owner can address any issues raised and be able to correct problems. There are two ways to comment on records. The first is specific to the review process. After selecting records in List view, they may be "reviewed" with the "action" list box (select "Review as Reliable" or "Review as Questionable" from the drop-down list). The portal will then ask you to enter a comment for the reviewed records. If you have selected multiple records, this same comment will apply to each selected record. In addition, as with all records in Detail view, any user may enter comments on an individual record.
Best practices for reviewers and record owners
Below are a few suggestions for items to check during record review
- Location: Does the species seem to be far outside of known or expected range? If so, is additional documentation necessary?
- Rarity: Is this a record for a rare species with very few known records? Is additional documentation needed to confirm?
- Collection date: Does the collection date seem to fall within an expected range? Accurate collection date is very important for modeling distributions across different eras, and documenting changes over time
Reviewers and data providers are encouraged to communicate outside of the REBIOMA portal to discuss data review and related issues. Working within the portal architecture, however, the most reliable and automated procedure to communicate and correct errors or problems identified during the review process is as follows:
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- User A uploads data within Reviewer B's taxonomic speciality
- Reviewer B reviews the data and finds one record in need of additional details. S/he flags this record with a "questionable" review
- User A receives an email notification about the record needing additional information
- User A logs into REBIOMA and adds a new comment to the record. The comment contains the additional information requested by the reviewer.
- ** Important: In order to ensure that Reviewer B is notified of this change, User A must download the record and then re-upload it, without changing or deleting the REBIOMA id.
- After successful re-upload, Reviewer B will automatically receive email notification of the changed record. S/he then returns to the portal and reviews the changes, and may update the review at this point
Species Distribution Models
One of the key features of the REBIOMA web portal is its support of species distribution models, created from taxonomically valid and quality reviewed occurrence data. The specification that guided the development of the modeling routines used in REBIOMA can be found here. This is a working document and includes details and discussion on
modeling features that have been implemented in REBIOMA, as well as some additional features that have not been implemented yet.
To summarize, species distribution models are produced only from valid, quality reviewed occurrence records. MaxEnt is used to produce continuous distribution models from the occurrence records and environmental data for several eras: past (1950), current (2000), and future (2080). In constructing training data, we attempt to correct for both sample and era bias. The models are trained, and results are subjected to statistical validation. Only models that pass this validation step are projected to the eras listed above.
The main steps in the modeling process are as follows:
From all occurrences, select species with at least 8 reliably reviewed, non-duplicate records
For each species occurrence, extract and save appropriate climate and forest cover values in a sample file under two scenarios: Climate only, and Climate plus forest.
Create background sample files for each species scenario consisting of 10,000 points, with the following constraints: Select 10,000 points randomly from within sampled cells (i.e. a “mask” of all sampled cells for all species) to correct for spatial sampling bias. Selecting background data in the same proportion per era as it was collected to correct for temporal sample bias.
The next step is to run Maxent with replicates. We do not project the models at this stage. Run either 4 or 10 replicates to evaluate model depending on the total number of samples. If total samples are > 8 but < 20, run 4 replicates. If samples are >= 20, run 10 replicates. For every species, we now have two potential models, one including climate and forest cover variables, one with climate only.
For a given species, if the mean training AUC minus standard error (SE) > 0.5 (for the 4 or 10 models produced by cross validation), then we produce (“project”) the full models using all the samples.
If the species passes validation, then produce the model using 100% of the data (no cross-validation). This step produces the lambdas that we will use in projection.
- Full set of models to project:
For each model, select the correct “lambda” scenario (climate only scenario, or climate plus forest scenario), and project onto the matching climate layers, and forest (if relevant) for past, present and future climate.
- 1950 distribution, climate only
- 1950 distribution including climate and forest cover
- 2000 distribution, climate only
- 2000 distribution including climate and forest cover
- 2080 distribution, climate only
- 2080 distribution including climate and forest cover (“conservative”, where 2080 forest cover = 2005 forest cover)
- 2080 distribution including climate and forest cover (“dire”, where 2080 forest cover remains in protected areas only)
To view all available models, in Map view, click on the "Models" button. This opens a dialogue that shows models available at this time. Models are listed in alphabetical order by scientific name (genus and species), ten at a time. To view an additional page of ten models, click the small arrow link next to the number of models displayed (e.g. 1-10 of 321 >). Or, to find a model for a particular species, you may want to search for that species.
To view individual model scenarios, click the "plus" (+) button next to an individual species name, e.g. Anochetus grandidieri. This will expand the view to show all available model "scenarios" for that species. Each model scenario shows a prediction for the species distribution at a given time (either 1950, 2000, or 2080), under certain assumptions (distribution modeled using climate as a predictor, or distribution modeled using climate and forest cover as a predictor). For a description of the climate and forest cover variables used in the modeling process, look at the layer descriptions on the environmental layers metadata page. We are currently modeling terrestrial species distributions to seven different era/environment scenarios: 1950 distribution, climate only; 1950 distribution including climate and forest cover; 2000 distribution, climate only; 2000 distribution including climate and forest cover; 2080 distribution, climate only; 2080 distribution including climate and forest cover (“conservative”, where 2080 forest cover = 2005 forest cover); 2080 distribution including climate and forest cover (“dire”, where 2080 forest cover remains in protected areas only).
To view an individual species model on the map interface, click the check box next to a model scenario. This will display the continuous species distribution model on the map. The range of colors indicates the strength of the model prediction for a given area. Warmer colors (to bright red) indicate better predicted conditions for that species, during that era. Darker colors (to dark blue) indicate less favorable conditions for that species during that era. Note that MaxEnt does not directly predict probability of occurrence, rather the result is generally interpreted as a prediction of habitat suitability. For additional information on MaxEnt, check the MaxEnt website for tutorials and publications.
To view details for individual models produced by MaxEnt, click the link formed by the scenario name (e.g. 1950 Climate Forest). This will open up an .html page, in a new window, showing the model results as reported by MaxEnt. This includes, for example, an analysis of commission and ommission, the ROC and AUC curves, and other details that can help to interpret the model result.
There are several reasons why a model for a particular species may not be present here. One, there may not be any occurrence records for that species on the data portal. Two, there may be occurrence records, but the species name may not match a valid taxonomic name according to our Taxonomic Authority. Three, there may be an insufficient number of records, or an insufficient number of quality reviewed records. Models are only produced for species for which there are at least eight, reliably reviewed, non-duplicate (per grid cell) records. Finally, the model may have failed statistical validation (see the section on "model validation" here).
Searching for models
Searching for models is similar to simple search for species occurrences. To begin, click on the models tab, next to the results tab on the left side of the screen. Then type the name of a species scientific name in the text box next to the word "Models". You can type an entire binomial scientific name, a genus name, a species name, or just the beginning of a genus or species name. Hit "Enter" to return the model results that match your search term. For example, typing "darwin", results in models for both Camponotus darwinii and Pachycondilla darwinii, plus any other genus or species name starting with Darwin.
To download all model results for a particular species, click the link named "Download" next to a species model name on the models tab. This link will download all individual models for that species, including the model results as ascii and .html files. The download includes a file named "citation.txt" that includes a recommended citation, as well as additional information about the models produced, such as the number of public and private occurrence records that went into the model The download also includes a csv file of the public occurrence records themselves. To download the results of a single model scenario only, click the "Download" link next to the model scenario of interest.
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Georeferencing information and links
Many of the records in REBIOMA and similar databases were collected before the advent of GPS. The Biogeomancer project provides tools for georeferencing data and specimens that cannot otherwise be tied to a latitude-longitude coordinate. Read more about Biogeomancer and georeferencing here.
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Getting involved and reporting errors
What to do if things go wrong
As with any large and complex system, things will sometimes not work as
expected. A few things to try first if you receive an error or a
strange result. One, try again with the latest version of the Mozilla
Firefox web browser. While REBIOMA portal will work in other browsers,
it has been most extensively tested in and works best in Firefox. Two,
clear data from your browser cache, log out of REBIOMA (if logged in),
close the browser, and try again. If none of these simple suggestions
work, see below for how to report an error to the REBIOMA development
Report unexpected results, errors and bugs
Please use the issue tracking system to report any bugs or unexpected
results to us, and we will do our best to resolve them. To submit an
error report, click on the link to the upper right of the screen
labeled "Code site”.
This will open a new browser window on the REBIOMA Google code site. In
the upper left of this page, click the "New Issue" link. In the
"Template" list box, select the category that most appropriately
defines your problem (usually "User defect report" is fine) and then
fill out the description of the issue. When complete, click submit
issue. Thank you for helping to make REBIOMA a better web portal!
Make suggestions for enhancements
Please feel free to recommend new enhancements or tools that you would
like to have available. We will do our best to accommodate you, to the
extent possible, based on what works with the existing software
platform and site logic, and what is within our budget (Link to Make
Donation). You can also use the issue tracking system to request
enhancements. To submit an enhancement request,
click on the link to the upper right of the screen labeled "Code site”.
This will open a new browser window on the REBIOMA google code site. In
the upper left of this page, click the "New Issue" link. In the
"Template" list box, select "User enhancement request". When complete,
click submit issue. Thank you
for helping to make REBIOMA a better web portal!
REBIOMA Developer's portal
REBIOMA is an open source project and all of the code may be found here
on the REBIOMA google code site. Check out this site for additional
information on getting involved as a developer, submitting issues or
enhancement requests, checking out source code and related topics.
REBIOMA Google group
REBIOMA also has a google group page here. Anyone may request to sign up for the group to ask questions, start a discussion or get more involved.
Other ideas? Questions? Contact us!
Concerning the taxonomic authority: rebiomawebportal [at] gmail [dot] com
Concerning the web portal: rebiomawebportal [at] gmail [dot] com
Concerning the source code or integrating new code: rebiomawebportal [at] gmail [dot] com
Concerning Darwin Core: rebiomawebportal [at] gmail [dot] com
Concerning species modeling: rebiomawebportal [at] gmail [dot] com
Concerning the overall REBIOMA project: rebiomawebportal [at] gmail [dot] com
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- We are actively encouraging individual scientists to upload their datasets.
- We have formulated the leadership of the Taxonomic Review Board, and those leaders will be forming core groups of reviewers for their selected taxonomic groups.
- We plan to implement additional features within the Species Modeling routine.
- See http://www.rebioma.net for further information about the project
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