Link discovery and interactive exploration in biological databases
Good news, everyone! A new database biomine_10_jun_2021 is now available. It was prepared almost two years ago but because of a hard to find issue in the cache subsystem it was not possible to make it publicly available. It took a long time to resolve the issue due to lack of time but now we will be able to prepare up-to-date versions of all three databases (biomine, human, and plants). Stay tuned.
Biomine networks are finally available for download! Three latest network are available in the Downloads tab. The largest one has 35+ million edges and 1.5+ million nodes. The format of the data is very simple, each line contains both nodes, link type and link goodness. These networks are ideal for testing graph algorithms on a large scale, and for developing new knowledge extraction methods from graphs.
A paper describing Biomine Explorer has finally been published! It is an applications note paper in the journal Bioinformatics. Here is the link to the online version (open access): Interactive exploration of heterogeneous biological networks with Biomine Explorer. If you use Biomine Explorer in your research, this paper should be used as a reference to Biomine Explorer.
There are two important updates to the advanced visualization interface. First, all nodes now have direct links to data sources. The links are available in node context menus and the linked page will open in a new tab, Second, when expanding the selection it is now possible to group new nodes. This is especially useful when there is a set ot Article nodes which clutter the graph. The option is available in the Controls section in the advanced visualization interface.
The web page and the server got a bunch of updates. The page should now load much faster because a caching backend was set up. There is now also a "How to" page which explains how to use Biomine Explorer search and visualization interfaces.
The search interface received an update: the network size got two additional sizes, XXL and XXXL which translates into 150 and 200 vertices. This is useful for users who are not afraid of large, crowded Biomine networks. Needless to say, this is only an approximation and the returned graphs may be smaller or larger. The API also uses the updated size range.
The API Python example also received an update: by using the requests library the example is now simpler and works in Python 2 and 3 without modifications.
The biomine and human databases have been updated! After more than 2 years of fixing bugs and updating the networks, there are two new databases: biomine_3_oct_2018 and human_3_oct_2018.
There is another very important update: the server which hosts Biomine Explorer now supports HTTPS.
Three new plants have been added: green algae (Chlamydomonas reinhardtii), black cottonwood (Populus trichocarpa) and wine grape (Vitis vinifera) The updated plants database is called plants_2_aug_2018. The old plant database plants_1_jul_2016 was retired and is no longer available.
Two new plants have been added: pearl millet (Pennisetum glaucum) and bread wheat (Triticum aestivum). The updated plants database is called plants_26_jan_2018.
A new data source called CNN has been added for Arabidopsis thaliana! CNN is an abbreviation for "comprehensive knowledge network" which is a hand-crafted network, compiled from different sources. It was prepared by dr. Živa Ramšak from the National Institute of Biology, Ljubljana, Slovenia. The updated plants database is called plants_18_jan_2018.
A small bug was fixed which caused that in some special cases the search result was not returned (the server returned 404 error instead of the graph).
The search interface has changed! It now supports three types of search:
All three types were already supported by Biomine but were not enabled by Biomine Explorer. Its interface now provides two query lists (source and target) where query terms can be added or imported. Please see the "How to use" tab to get more information.
All databases were updated. The latest databases are: biomine_1_jul_2016, human_1_jul_2016 and plants_1_jul_2016. Due to changes in OMIM licence some OMIM data (textual descriptions) is not available anymore. Updates of OMIM in Biomine are expected to become less frequent because each academic OMIM download is granted only upon a formal request.
Graph visualisation has been updated to show a thick green border around query nodes. They are now easily distinguishable from the rest of the graph. There were also few fixes as well such as proper formatting of query terms in the search interface.
All databases were updated! The latest databases are: biomine_13_jan_2016, human_13_jan_2016 and plants_13_jan_2016. Also, few additional fixes were implemented in the user interface.
Happy anniversary! It's been exactly one year since the Biomine Explorer went online.
There is a huge number of updates in the web interface! Biomine Explorer now supports user management and private graph repositories for each user. Anonymous sessions are of course still available (and default) but advanced users who need to store and manage a larger number of graphs will find new features very useful. A short list of what's new:
Biomine Explorer graph visualization interface was updated with the latest version of the vis.js library. There were few minor updates and fixes as well.
There is a new type of database which contains only data about human: human_16_oct_2015. It is a subset of the biomine database. However, because it is built separately some nodes and links may differ because of newer data sources.
The Biomine Explorer, Biomine core software and the host OS moved to 64-bit and to a much faster machine! This is indeed a huge improvement - process memory limitations on 32-bit systems were causing troubles on every update. Because of hardware updates user queries should now run much faster. Enjoy!
Both biomine and plants organism sets were updated so now we have two shiny new databases: biomine_23_sep_2015 and plants_23_sep_2015. See the Databases tab for more info.
The suggestion input field was modified to accept longer text. This is neccessary if you want to search for certain entities which have very long names (e.g., potato genes). Also, few new options were added to the advanced graph view (colouring of neighbour nodes and expand option in context menu).
The advanced graph interface just got nice Bootstrap context menus for nodes and edges! One thing which remains on the todo list is linking to the original data sources. This will require a little bit of additional work as some of the links are now different as in the original Biomine.
Two new organisms were added to Biomine plants organism set: sugar beet and cacao. The latest plants database which includes new organisms is called plants_12_jan_2015. Also, there was a brief downtime due to a human error and trouble with the database server but everything is up and working again.
The updated Biomine Explorer and the Biomine backend are now online! There is a new web search interface and graph visualization and manipulation plus numerous internal fixes and updates. Please report bugs and comments to email@example.com.
The first working public set of databases were prepared. The latest are biomine_6_jan_2015 for the biomine organism set and plants_6_jan_2015 for the plants organism set.