Glycans have a critical role in health and disease. As a direct result, there is keen interest to identify and increase glycan data in bioinformatics databases like ChEBI and PubChem, and in connecting them to biomedical resources at the EMBL-EBI and NCBI. GlyTouCan is a comprehensive archival database that contains over 118,000 glycans, obtained primarily through batch upload from glycan repositories, submissions from glycoprotein databases, and individual laboratories. In many instances, the glycan structures deposited in GlyTouCan may not be fully defined or have supporting experimental evidence or biological source content. Databases like ChEBI and PubChem were designed to accommodate complete atomistic structures with well-defined chemical linkages. As a result, they cannot easily accommodate the structural ambiguity inherent in many glycan database representations. Consequently, there is a need to organize glycan data coherently to improve the connectivity across the major NCBI, EMBL-EBI, and glycoscience databases. This paper outlines a workflow developed in collaboration between GlyGen, ChEBI, and PubChem to improve the visibility and connectivity of glycan data across these resources. GlyGen hosts a subset of glycans (~29,000) from the GlyTouCan database and has submitted valuable glycan annotations to the PubChem database and registered or mapped over 10,500 (including ambiguously defined) glycans into the ChEBI database. The integrated glycans were prioritized based on links to PubChem and connectivity to glycoprotein data. The pipeline provides a blueprint for how glycan data can be harmonized between different resources. The current PubChem, ChEBI, and GlyTouCan mappings can be downloaded from GlyGen(https://data.glygen.org).