- User interfaces
- API documentation
- Install new OBM Server guide
- PWA application
- Mobile application documentation
- Developer hints
- Frequently Asked Questions
- What is OpenBioMaps?
- What is OpenBioMaps consortium?
- How can I contact the consortium?
- How can I create/find a new database-project?
- How can I upload data?
- How can I access data?
- How can I sign up for an OpenBioMaps project?
- Is there a programmable interface for developers?
- What language support is available?
- How can I contribute to OpenBioMaps?
- Should I pay for anything?
- How and where does the OpenBioMaps store the data?
- Is there any backup solution?
- I lost my password, how can I get a new one?
- Pink squares appear on the map page
- What is the RUM?
- Is it possible to assign a DOI to databases?
- Where can I find the list of the existing OpenBioMaps servers?
- How to use the OpenBioMaps mobile app?
- Where can I find the OpenBioMaps R package?
- What data download options are there?
Frequently Asked Questions¶
What is OpenBioMaps?¶
OpenBioMaps is a software and services platform for managing biological data. It can be used on its own or as a service. It can be used to create database-based projects that can be used simultaneously by multiple users with different devices and access privilege levels. If you do not wish to maintain your own server, you can use it as a service, as some institutions also operate servers that host research or citizen-science projects for no charge.
What is OpenBioMaps consortium?¶
OpenBioMaps is a consortium of public institutions and social organizations. Their aim is to develop OpenBioMaps software and maintain freely available services based on it. The members of the consortium are equal partners and they have all contributed to achieving this objective in some ways. The partnership can be extended, if the parties wishing to join are willing to accept the system’s fundamentals, satisfy the specified conditions set and the partners accept the new member.
Current OpenBioMaps partners:
University of Debrecen
contact: Dr. Miklós Bán
Danube-Ipoly National Park Directorate
contact: Zsolt Baranyai
Eötvös Loránd University
contact: Dávid Ritter
WWF World Wildlife Fund for Nature Hungary
contact: Katalin Sipos
Eszterházy Károly University
contact: Dr. Erika Pénzesné Kónya
Milvus Group Association
contact: Edgár Papp
Danube-Dráva National Park Directorate
contact: Ákos Gáborik
Fertő-Hanság National Park Directorate
contact: Gábor Takács
The OpenBioMaps consortium was established on September 1, 2015. The OpenBioMaps Consortium Agreement will be available here.
How can I create/find a new database-project?¶
If you are already a member of a project on a server, you can use the web interface to create a new database project on the same server. This is a simple process that can be done by filling in a form.
How can I upload data?¶
Simply answered: using data upload forms. Or perhaps using any PostgreSQL client, although this solution is only recommended for occasional imports of large amounts of data.
How can I access data?¶
Via the web interface with map or text queries.
Using a PostgreSQL client.
Using the OpenBioMaps R package.
Using data sharing via the web interface.
Data export via the web interface.
How can I sign up for an OpenBioMaps project?¶
Registration requires an invitation. Any registered member can invite new users. In addition, by default, an invitation request form is available from the login interface, which can be filled in by new hosts to request an invitation to join a project. In addition, there is an OpenID module that allows registration and login with a Google Account.
For more information on registration and invitations, please contact the creators or administrators of the database you wish to join.
Is there a programmable interface for developers?¶
Yes. The Project Data Service (PDS) allows you to query projects and user data on a per-project basis through URL requests from databases.
For more information visit the API documentation.
What language support is available?¶
There are no language restrictions, but the OpenBioMaps is currently available in Hungarian, English Romanian, Spanish, and partially in Russian. Additional languages or translations can be added through the https://translate.openbiomaps.org interface.
Each project can have individual language settings and associated translations.
How can I contribute to OpenBioMaps?¶
By creating/establishing a database project
Uploading data to a database project
By creating a new OpenBioMaps server
Hosting database-project on your server
Adding new languages or improving existing translations
Should I pay for anything?¶
All components and services of OpenBioMaps are completely free of charge, but some of the development is not voluntary work, i.e. we pay the developers, so all support for the development is gratefully accepted!
How and where does the OpenBioMaps store the data?¶
Each OpenBioMaps server stores the data in its own database and file system.
Is there any backup solution?¶
No centralized backup, as there is no centralized data management in OpenBioMaps. Each server has its own backup solution, but some servers use each other’s storage capacity for archiving.
I lost my password, how can I get a new one?¶
Don’t worry, it’s very easy to get a new password.
Follow the “lost password” link on the login page.
There you can enter your login email address. Once you submit it, you will receive an email from the system containing a link that you can follow to log in to your account and set a new password.
Pink squares appear on the map page¶
This may be due to some kind of configuration error, which may be related to the map layers or the settings of the data queries.
What is the RUM?¶
RUM is an acronym for database openness classes:
Read - Upload - Modify
Each element can have a value of [-] or  or [+].
[-] is not public,  is partially public and the [+] is public
and the colors are: [-] black,  red and [+] green
<font color=”red”>R</font><font color=”green”>U</font>M partial public read, public upload and no public modify
Is it possible to assign a DOI to databases?¶
Yes, all databases in a finalized state can receive a DOI using the DataCite DOI Service.
All databases have a DOI metadata page like:
Our DOI prefix in DataCite is: 10.18426
The DOI suffixes are automatically generated and they are unique.
In every database, it is possible to assign additional DOI-s for datasets.
Where can I find the list of the existing OpenBioMaps servers?¶
The servers that have registered can be found in the OpenBioMaps database at https://openbiomaps.org/projects/openbiomaps_network.
How to use the OpenBioMaps mobile app?¶
On Iphone or Android (currently, only the Android version works). Users need to be logged in on their own server to access the data upload forms available in their project. After logging in and downloading the forms, the app can be used offline. The current base map is Google-based and only works offline if the target area is downloaded for offline use from the Google Terrain Map application.
The mobile application lists the servers that are registered in the https://openbiomaps.org/projects/openbiomaps_network database.
Where can I find the OpenBioMaps R package?¶
For now, only available as a developer package here: https://github.com/OpenBioMaps/obm.r
What data download options are there?¶
Using csv, kml, json, and other modules where available
Using bookmarks and permanent links
Using the R package