Table 1. Overview over main resources used in this work.
| Data | Downloaded from | Downloaded on/Version |
| GO annotations | Gene Ontology Annotation project [4] | Nov 13, 2012 |
| Genetic interactions | Gene Ontology Annotation project | Nov 13, 2012 |
| Protein-protein interactions | Gene Ontology Annotation project | Nov 13, 2012 |
| Protein-protein interactions | STRING [21] | Dec 25, 2012/v9.0 |
| Protein-protein and genetic interactions | BioGRID [22] | Feb 20, 2013/v3.2.97 |
| Phenotype data | Model organism databases (MGI, SGD, ZFIN, FlyBase, WormBase) | Nov 11, 2012 |
| Phenotype ontologies | OBO Foundry website | Nov 13, 2012 |
| Gene Ontology | Gene Ontology website | Nov 13, 2012 |
| Mammalian Phenotype Ontology: formal definitions | https://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/mp/mp-equivalence-axioms.obo | Nov 13, 2012 |
| Human Phenotype Ontology: formal definitions | https://phenotype-ontologies.googlecode.com/svn/trunk/src/ontology/hp/hp-equivalence-axioms.obo | Nov 13, 2012 |
| Worm Phenotype Ontology: formal definitions | http://obo.cvs.sourceforge.net/checkout/obo/obo/ontology/phenotype/worm_phenotype_xp.obo | Nov 13, 2012 |
| Ascomycete Phenotype Ontology: formal definitions | http://obo.cvs.sourceforge.net/viewvc/obo/obo/ontology/phenotype/yeast_phenotype_xp.obo | Nov 13, 2012 |
| Flybase Controlled Vocabulary: formal definitions | http://code.google.com/p/phenomeblast/source/browse/trunk/phenotypeontology/obo/fly_xp.obo | Nov 13, 2012 |
The phenotype data resulting from single gene mutations and genetic interaction data for Drosophilae, Mus musculus, Saccharomyces cerevisiae, Caenorhabditis elegans and Danio rerio were downloaded from FlyBase [10], Mouse Genome Informatics [13], Saccharomyces Genome Database [9], WormBase [12], and Zebrafish Information Network (ZFIN) database [11] respectively. All phenotype data was downloaded on 11 Nov 2012. GO annotations were downloaded from the GOA website on 13 Nov 2012. The ontologies as well as the phenotype definitions were obtained from the OBO Foundry website on 13 Nov 2012. For zebrafish, we downloaded the files Morpholinos.txt and genotype_features.txt on 02 Oct 2012 from the ZFIN website. We use these files to map ZFIN genotype and Morpholino identifiers to ZFIN’s gene identifiers.