The PEIMAN2 R package provides functions and mined database from UniProt for single enrichment analysis (SEA) and protein set enrichment analysis (PSEA) in a list of proteins. The database is updated regularly with monthly changes in UniProt/SwissProt repository.
The NIMAA R package provides a comprehensive set of methods for performing nominal data mining. It employs bipartite networks to demonstrate how two nominal variables are linked and then places them in the incidence matrix to proceed with network analysis.
CINNA is an R package that has been written for centrality analysis in network science. It can be useful for assembling, comparing, evaluating, and visualizing several types of centrality measures.
IMMAN R package provides a way to overlay different PPINs to mine conserved common networks between diverse species. This approach is useful to reconstruct Interolog Protein Network (IPN) integrated from several Protein-Protein Interaction Networks (PPINs).
UNaProd 1.2 is a systematic collection of information concerning natural products used in Iranian traditional medicine (ITM). To generate this database, one of the most authentic resources in this school of medicine, Makhzan-al-Advieh, has been used. Compiled by Mohammad Hossein Aghili Khorasani (Shirazi) in 1769 A.D., this encyclopedia of materia medica is a semi-structural resource in the Persian language. UnaProd was created using both text mining and manual editing methods and is currently host to 3411 monographs in 16 attributes of remarks, identity, Mizaj, actions and medicinal uses, adverse effects, refinement, substitute, dosage, pronunciation, synonyms, origin, common name, and scientific name. This database has been linked to the CMAUP database for molecular features, and to IrGO (Iranian traditional medicine General Ontology) for Mizaj.
Iranian traditional medicine (also called Persian Medicine), is an elaborate holistic system of healing grounded in a philosophical basis. The numerous concepts and their intricate relationships are described in numerous textbooks by scholars. However, embracing the totality of this rich school of thought is challenging due to the large amount of data in various time periods and ambiguities resulting from a lack of consensus or semantic change and the evolution of word usage. In order to arrange for an explicit, shared, and common understanding of Iranian traditional medicine concepts and facilitate connection with contemporary medicine to offer the potential for future research, the ontology of the key concepts mentioned in descriptions of materia medica is extracted. Subontologies include Mizaj, actions, disease, organ, and weight unit based on the 3411 monographs described in Makhzan-al-Adviah, an encyclopedia of materia medica compiled by Mohammad Hossein Aghili Khorasani in the 18th century. Iranian traditional medicine general ontology (IrGO) will enable the reuse of the knowledge in this field, make the assumptions explicit, and finally gain new knowledge by analyzing the concepts and their relationships.