Default nodes and relationships

Many of the nodes and relationships have properties that represent specific characteristics. The overview below contains a description of each node or relationship, its ontology term and any properties that the item has if default import functions are used.

Edge - NCIT:C75923

The Edge node is one of the most important nodes of mako and supports most of its functionality. While it is possible to connect Taxon nodes directly, the Edge node can be connected separately to Network nodes or Property nodes, so that more complicated Edge metadata is possible. For example, Edge nodes could be connected to a Network node named Literature if they are identified via a literature analysis. Hence, this implementation expressly facilitates network meta-analyses.

name Edge nodes normally are assigned a universally unique identifier (UUID) as a name property, since edge lists and matrix formats do not contain edge identifiers.
Weight If available, Edge nodes are also assigned a weight property. Since edge weights are usually not directly comparable across network inference methods, it is recommended to use a binary representation of 1 and -1 for positively- and negatively- weighted edges.

Experiment - NCIT:C42790

The Experiment node connects all Specimen nodes to a single file.

name The name for the Experiment node is taken from the filename of the imported file, but it can also be adjusted manually.

Network - NCIT:C61377

The Network node connects all Edge nodes to a single network. An alternative version of Network nodes is also available; these have the Set label and are used to indicate results of network operations.

name The name for the Network node is taken from the filename of the imported file, but it can also be adjusted manually.

Property - NCIT:C20189

Property nodes are nodes that can be used to query specific metadata. These can be connected to any other node, but default imports connect them to Specimen and Taxon nodes.

name The name for the Property node is taken from the column name (if table-like import). For example, a column with pH values will lead to one pH property being generated.

Specimen - NCIT:C19157

Specimen nodes represent specimens or samples collected for an experiment.

name The name for the Specimen node is taken from whatever sample identifier is used by the file, e.g. column names for standard count tables.

Taxon - NCIT:C40098

Taxon nodes usually represent OTUs or ASVs, but can also represent any other biological unit.

name The name for the Taxon node is taken from whatever taxon identifier is used by the file, e.g. row names for standard count tables.

Species, Genus, Family, Order, Class, Phylum, Kingdom

NCIT:C45293, NCIT:C45292, NCIT:C45290, NCIT:C45287, NCIT:C45280, NCIT:C45277, NCIT:C45276
These nodes represent taxonomic values for these specific taxonomic levels. Taxon nodes usually represent OTUs or ASVs, but can also represent any other biological unit.

name The name for taxonomy nodes is the value usually represented in taxonomy tables. For example, the Genus node for Escherichia coli will have Escherichia as a name. When tables contain only a prefix (e.g. g__), no node is created.

LOCATED_IN

Relationships connecting Taxon nodes to Specimen nodes.

count Value of count or abundance table for a specific taxon in a specific specimen.

MEMBER_OF

Relationships connecting Taxon nodes to taxonomy nodes (Species, Genus, Family, Order, Class, Phylum and Kingdom), and also taxonomy nodes to each other. These relationships form acyclic trees with Kingdom as the root and therefore mimic taxonomic trees. By directly connecting Taxon nodes to taxonomy nodes, queries can access those directly.

PARTICIPATES_IN

Relationships connecting Taxon nodes to Edge nodes. These relationships are currently undirected, so Taxon nodes always participate in an edge, rather than being affected by another taxon.

PART_OF

Relationships connecting Sample nodes to Experiment nodes and Edge nodes to Network nodes. These relationships therefore indicate a hierarchy of file structures.

QUALITY_OF

Relationships connecting nodes to Property nodes. Usually, these relationships connect Taxon and Specimen nodes to Property nodes, but other nodes can be connected to Property nodes as well.

value Value of the Property node. For example, if pH values per sample are uploaded to the database, one pH Property node is generated and all QUALITY_OF relationships contain the pH value for that specific Specimen node.