BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs.

SUMMARY: Knowledge graphs are an increasingly common data structure for representing biomedical information. These knowledge graphs can easily represent heterogeneous types of information, and many algorithms and tools exist for querying and analyzing graphs. Biomedical knowledge graphs have been used in a variety of applications, including drug repurposing, identification of drug targets, prediction of drug side effects, and clinical decision support. Typically, knowledge graphs are constructed by centralization and integration of data from multiple disparate sources. Here, we describe BioThings Explorer, an application that can query a virtual, federated knowledge graph derived from the aggregated information in a network of biomedical web services. BioThings Explorer leverages semantically precise annotations of the inputs and outputs for each resource, and automates the chaining of web service calls to execute multi-step graph queries. Because there is no large, centralized knowledge graph to maintain, BioThings Explorer is distributed as a lightweight application that dynamically retrieves information at query time. AVAILABILITY AND IMPLEMENTATION: More information can be found at https://explorer.biothings.io and code is available at https://github.com/biothings/biothings_explorer.

BioThings Explorer: a query engine for a federated knowledge graph of biomedical APIs.

Knowledge graphs are an increasingly common data structure for representing biomedical information. These knowledge graphs can easily represent heterogeneous types of information, and many algorithms and tools exist for querying and analyzing graphs. Biomedical knowledge graphs have been used in a variety of applications, including drug repurposing, identification of drug targets, prediction of drug side effects, and clinical decision support. Typically, knowledge graphs are constructed by centralization and integration of data from multiple disparate sources. Here, we describe BioThings Explorer, an application that can query a virtual, federated knowledge graph derived from the aggregated information in a network of biomedical web services. BioThings Explorer leverages semantically precise annotations of the inputs and outputs for each resource, and automates the chaining of web service calls to execute multi-step graph queries. Because there is no large, centralized knowledge graph to maintain, BioThing Explorer is distributed as a lightweight application that dynamically retrieves information at query time. More information can be found at https://explorer.biothings.io, and code is available at https://github.com/biothings/biothings_explorer.

MyGeneset.info: an interactive and programmatic platform for community-curated and user-created collections of genes.

Gene definitions and identifiers can be painful to manage-more so when trying to include gene function annotations as this can be highly context-dependent. Creating groups of genes or gene sets can help provide such context, but it compounds the issue as each gene within the gene set can map to multiple identifiers and have annotations derived from multiple sources. We developed MyGeneset.info to provide an API for integrated annotations for gene sets suitable for use in analytical pipelines or web servers. Leveraging our previous work with MyGene.info (a server that provides gene-centric annotations and identifiers), MyGeneset.info addresses the challenge of managing gene sets from multiple resources. With our API, users readily have read-only access to gene sets imported from commonly-used resources such as Wikipathways, CTD, Reactome, SMPDB, MSigDB, GO, and DO. In addition to supporting the access and reuse of approximately 180k gene sets from humans, common model organisms (mice, yeast, etc.), and less-common ones (e.g. black cottonwood tree), MyGeneset.info supports user-created gene sets, providing an important means for making gene sets more FAIR. User-created gene sets can serve as a way to store and manage collections for analysis or easy dissemination through a consistent API.

BioThings SDK: a toolkit for building high-performance data APIs in biomedical research.

SUMMARY: To meet the increased need of making biomedical resources more accessible and reusable, Web Application Programming Interfaces (APIs) or web services have become a common way to disseminate knowledge sources. The BioThings APIs are a collection of high-performance, scalable, annotation as a service APIs that automate the integration of biological annotations from disparate data sources. This collection of APIs currently includes MyGene.info, MyVariant.info and MyChem.info for integrating annotations on genes, variants and chemical compounds, respectively. These APIs are used by both individual researchers and application developers to simplify the process of annotation retrieval and identifier mapping. Here, we describe the BioThings Software Development Kit (SDK), a generalizable and reusable toolkit for integrating data from multiple disparate data sources and creating high-performance APIs. This toolkit allows users to easily create their own BioThings APIs for any data type of interest to them, as well as keep APIs up-to-date with their underlying data sources. AVAILABILITY AND IMPLEMENTATION: The BioThings SDK is built in Python and released via PyPI (https://pypi.org/project/biothings/). Its source code is hosted at its github repository (https://github.com/biothings/biothings.api). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

ChlamBase: a curated model organism database for the Chlamydia research community.

The accelerating growth of genomic and proteomic information for Chlamydia species, coupled with unique biological aspects of these pathogens, necessitates bioinformatic tools and features that are not provided by major public databases. To meet these growing needs, we developed ChlamBase, a model organism database for Chlamydia that is built upon the WikiGenomes application framework, and Wikidata, a community-curated database. ChlamBase was designed to serve as a central access point for genomic and proteomic information for the Chlamydia research community. ChlamBase integrates information from numerous external databases, as well as important data extracted from the literature that are otherwise not available in structured formats that are easy to use. In addition, a key feature of ChlamBase is that it empowers users in the field to contribute new annotations and data as the field advances with continued discoveries. ChlamBase is freely and publicly available at chlambase.org.