The positive/negative associations are statistical associations we curated from literature/ references. They are also known as “co-occurrence patterns” - i.e. two microbes tend to show up together more often than expected by random (positive association), or never show up together (negative association). You can read the specific algorithms used to compute these values (i.e. what are the null models used to estimated the random chance).
MicrobiomeNet is designed to help detect biologically interpretable co-occurrence patterns based on the metabolic capacities defined by their GEMs