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Integration of glycan-related databases between different research fields is essential in glycoscience. It requires knowledge across the breadth of science because most glycans exist as glycoconjugates. On the other hand, especially between chemistry and biology, glycan data has not been easy to integrate due to the huge variety of glycan structure representations. We have developed WURCS (Web 3.0 Unique Representation of Carbohydrate Structures) as a notation for representing all glycan structures uniquely for the purpose of integrating data across scientific data resources. While the integration of glycan data in the field of biology has been greatly advanced, in the field of chemistry, progress has been hampered due to the lack of appropriate rules to extract sugars from chemical structures. Thus, we developed a unique algorithm to determine the range of structures allowed to be considered as sugars from the structural formulae of compounds, and we developed software to extract sugars in WURCS format according to this algorithm. In this manuscript, we show that our algorithm can extract sugars from glycoconjugate molecules represented at the molecular level and can distinguish them from other biomolecules, such as amino acids, nucleic acids, and lipids. Available as software, MolWURCS is freely available and downloadable ( https://gitlab.com/glycoinfo/molwurcs )., Competing Interests: Declarations. Conflict of interest: The authors declare no competing interests. Kiyoko F. Aoki-Kinoshita is guest editor of ABC but was not involved in the peer review of this paper., (© 2024. The Author(s).)

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a large and highly-integrated public chemical database resource at NIH. In the past two years, significant updates were made to PubChem. With additions from over 130 new sources, PubChem contains >1000 data sources, 119 million compounds, 322 million substances and 295 million bioactivities. New interfaces, such as the consolidated literature panel and the patent knowledge panel, were developed. The consolidated literature panel combines all references about a compound into a single list, allowing users to easily find, sort, and export all relevant articles for a chemical in one place. The patent knowledge panels for a given query chemical or gene display chemicals, genes, and diseases co-mentioned with the query in patent documents, helping users to explore relationships between co-occurring entities within patent documents. PubChemRDF was expanded to include the co-occurrence data underlying the literature knowledge panel, enabling users to exploit semantic web technologies to explore entity relationships based on the co-occurrences in the scientific literature. The usability and accessibility of information on chemicals with non-discrete structures (e.g. biologics, minerals, polymers, UVCBs and glycans) were greatly improved with dedicated web pages that provide a comprehensive view of all available information in PubChem for these chemicals., (Published by Oxford University Press on behalf of Nucleic Acids Research 2024.)

The GlyCosmos Glycoscience Portal (https://glycosmos.org) and PubChem (https://pubchem.ncbi.nlm.nih.gov/) are major portals for glycoscience and chemistry, respectively. GlyCosmos is a portal for glycan-related repositories, including GlyTouCan, GlycoPOST, and UniCarb-DR, as well as for glycan-related data resources that have been integrated from a variety of 'omics databases. Glycogenes, glycoproteins, lectins, pathways, and disease information related to glycans are accessible from GlyCosmos. PubChem, on the other hand, is a chemistry-based portal at the National Center for Biotechnology Information. PubChem provides information not only on chemicals, but also genes, proteins, pathways, as well as patents, bioassays, and more, from hundreds of data resources from around the world. In this work, these 2 portals have made substantial efforts to integrate their complementary data to allow users to cross between these 2 domains. In addition to glycan structures, key information, such as glycan-related genes, relevant diseases, glycoproteins, and pathways, was integrated and cross-linked with one another. The interfaces were designed to enable users to easily find, access, download, and reuse data of interest across these resources. Use cases are described illustrating and highlighting the type of content that can be investigated. In total, these integrations provide life science researchers improved awareness and enhanced access to glycan-related information., (Published by Oxford University Press 2023.)

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves a wide range of use cases. In the past two years, a number of changes were made to PubChem. Data from more than 120 data sources was added to PubChem. Some major highlights include: the integration of Google Patents data into PubChem, which greatly expanded the coverage of the PubChem Patent data collection; the creation of the Cell Line and Taxonomy data collections, which provide quick and easy access to chemical information for a given cell line and taxon, respectively; and the update of the bioassay data model. In addition, new functionalities were added to the PubChem programmatic access protocols, PUG-REST and PUG-View, including support for target-centric data download for a given protein, gene, pathway, cell line, and taxon and the addition of the 'standardize' option to PUG-REST, which returns the standardized form of an input chemical structure. A significant update was also made to PubChemRDF. The present paper provides an overview of these changes., (Published by Oxford University Press on behalf of Nucleic Acids Research 2022.)

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical database at the U.S. National Institutes of Health. Visited by millions of users every month, it plays a role as a key chemical information resource for biomedical research communities. Data in PubChem is from hundreds of contributors and organized into multiple collections by record type. Among these are the Protein, Gene, Pathway, and Taxonomy data collections. Records in these collections contain information on chemicals related to a given biological target (i.e., protein, gene, pathway, or taxon), helping users to analyze and interpret the biological activity data of molecules. In addition, annotations about the biological targets are collected from authoritative or curated data sources and integrated into the four collections. The content can be programmatically accessed through PubChem's web service interfaces (including PUG View). A machine-readable representation of this content is also provided within PubChemRDF., Competing Interests: Declaration of interests The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Published by Elsevier Ltd.)

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a popular chemical information resource that serves the scientific community as well as the general public, with millions of unique users per month. In the past two years, PubChem made substantial improvements. Data from more than 100 new data sources were added to PubChem, including chemical-literature links from Thieme Chemistry, chemical and physical property links from SpringerMaterials, and patent links from the World Intellectual Properties Organization (WIPO). PubChem's homepage and individual record pages were updated to help users find desired information faster. This update involved a data model change for the data objects used by these pages as well as by programmatic users. Several new services were introduced, including the PubChem Periodic Table and Element pages, Pathway pages, and Knowledge panels. Additionally, in response to the coronavirus disease 2019 (COVID-19) outbreak, PubChem created a special data collection that contains PubChem data related to COVID-19 and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)., (Published by Oxford University Press on behalf of Nucleic Acids Research 2020.)

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a key chemical information resource for the biomedical research community. Substantial improvements were made in the past few years. New data content was added, including spectral information, scientific articles mentioning chemicals, and information for food and agricultural chemicals. PubChem released new web interfaces, such as PubChem Target View page, Sources page, Bioactivity dyad pages and Patent View page. PubChem also released a major update to PubChem Widgets and introduced a new programmatic access interface, called PUG-View. This paper describes these new developments in PubChem.

PubChem ( https://pubchem.ncbi.nlm.nih.gov ) is a key chemical information resource, developed and maintained by the US National Institutes of Health. The present chapter describes how to find potential multitarget ligands from PubChem that would be tested in further experiments. While the protocol presented here uses PubChem's Web-based interfaces to allow users to follow it interactively, it can also be implemented in computer software by using programmatic access interfaces to PubChem (such as PUG-REST or E-Utilities).

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, launched in 2004 as a component of the Molecular Libraries Roadmap Initiatives of the US National Institutes of Health (NIH). For the past 11 years, PubChem has grown to a sizable system, serving as a chemical information resource for the scientific research community. PubChem consists of three inter-linked databases, Substance, Compound and BioAssay. The Substance database contains chemical information deposited by individual data contributors to PubChem, and the Compound database stores unique chemical structures extracted from the Substance database. Biological activity data of chemical substances tested in assay experiments are contained in the BioAssay database. This paper provides an overview of the PubChem Substance and Compound databases, including data sources and contents, data organization, data submission using PubChem Upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access. It also gives a brief description of PubChem3D, a resource derived from theoretical three-dimensional structures of compounds in PubChem, as well as PubChemRDF, Resource Description Framework (RDF)-formatted PubChem data for data sharing, analysis and integration with information contained in other databases., (Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.)

PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, developed and maintained by the US National Institutes of Health (NIH). PubChem contains more than 180 million depositor-provided chemical substance descriptions, 60 million unique chemical structures and 225 million bioactivity assay results, covering more than 9000 unique protein target sequences. As an information resource for the chemical biology research community, it routinely receives more than 1 million requests per day from an estimated more than 1 million unique users per month. Programmatic access to this vast amount of data is provided by several different systems, including the US National Center for Biotechnology Information (NCBI)'s Entrez Utilities (E-Utilities or E-Utils) and the PubChem Power User Gateway (PUG)-a common gateway interface (CGI) that exchanges data through eXtended Markup Language (XML). Further simplifying programmatic access, PubChem provides two additional general purpose web services: PUG-SOAP, which uses the simple object access protocol (SOAP) and PUG-REST, which is a Representational State Transfer (REST)-style interface. These interfaces can be harnessed in combination to access the data contained in PubChem, which is integrated with the more than thirty databases available within the NCBI Entrez system., (Published by Oxford University Press on behalf of Nucleic Acids Research 2015. This work is written by (a) US Government employee(s) and is in the public domain in the US.)