Biomine Explorer networks

Biomine Explorer is built on top of Biomine which supports three organism sets called biomine, human, and plants. Each organism set has a corresponding large heterogeneous network compiled from different sources.

The biomine organism set contains data about:
  1. human (Homo sapiens)
  2. mouse (Mus musculus)
  3. rat (Rattus norvegicus)
  4. fruit fly (Drosophila melanogaster)
  5. nematode (Caenorhabditis elegans)
The human organism set contains data about:
  1. human (Homo sapiens)

(Note that this is a subset of the biomine organism set.)

The plants organism set contains data about:
  1. arabidopsis (Arabidopsis thaliana)
  2. potato (Solanum tuberosum)
  3. rice (Oryza sativa)
  4. tomato (Solanum lycopersicum)
  5. tobacco (Nicotiana tabacum)
  6. beet (Beta vulgaris)
  7. cacao tree (Theobroma cacao)
  8. pearl millet (Pennisetum glaucum)
  9. bread wheat (Triticum aestivum)
  10. green algae (Chlamydomonas reinhardtii)
  11. black cottonwood (Populus trichocarpa)
  12. wine grape (Vitis vinifera)

Each network name has a prefix which marks its organism set (biomine_, plants_ and human_). Typically, there is only one (the latest) network available for each organism set. However, as the system is updated and maintained regularly, there may be more than one network present for each organism set. In such case just select the latest one and ignore the rest.

Data sources

The following tables contain information about network sizes and integrated data sources.


biomine_3_oct_2018

nodes: 1,520,673
links: 32,761,889
database version timestamp
TAXON 1.13 2018-07-31
UniProt 2018_08 2018-09-12
GO 2018-10-01_03:10 2018-10-01
EntrezGene 2018-10-01 2018-10-01
MIM 2018-10-01 2018-10-01
InterPro 70.0 2018-09-13
SwissProt 2018_08 2018-09-12
Trembl 2018_08 2018-09-12
HomoloGene 68 2014-05-06
STRING 10.5 2017-05-14
PubMed 2018-10-03 2018-10-03

human_3_oct_2018

nodes: 874,241
links: 8,666,287
database version timestamp
TAXON 1.13 2018-07-31
UniProt 2018_08 2018-09-12
GO 2018-10-01_03:10 2018-10-01
EntrezGene 2018-10-01 2018-10-01
MIM 2018-10-01 2018-10-01
InterPro 70.0 2018-09-13
SwissProt 2018_08 2018-09-12
Trembl 2018_08 2018-09-12
HomoloGene 68 2014-05-06
STRING 10.5 2017-05-14
PubMed 2018-10-03 2018-10-03

plants_2_aug_2018

nodes: 1,740,270
links: 4,125,274
database version timestamp
TAXON 1.13 2018-07-31
GO 2018-07-30_02:59 2018-07-30
EntrezGene 2018-08-01 2018-08-01
GoMapMan 2018-08-01 2018-08-01
CNN 2018-08-01 2018-08-01
PubMed 2018-08-01 2018-08-01