KG-Hub-building and exchanging biological knowledge graphs.

MOTIVATION: Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains, but a coherent solution for constructing, exchanging, and facilitating the downstream use of KGs is lacking. RESULTS: Here we present KG-Hub, a platform that enables standardized construction, exchange, and reuse of KGs. Features include a simple, modular extract-transform-load pattern for producing graphs compliant with Biolink Model (a high-level data model for standardizing biological data), easy integration of any OBO (Open Biological and Biomedical Ontologies) ontology, cached downloads of upstream data sources, versioned and automatically updated builds with stable URLs, web-browsable storage of KG artifacts on cloud infrastructure, and easy reuse of transformed subgraphs across projects. Current KG-Hub projects span use cases including COVID-19 research, drug repurposing, microbial-environmental interactions, and rare disease research. KG-Hub is equipped with tooling to easily analyze and manipulate KGs. KG-Hub is also tightly integrated with graph machine learning (ML) tools which allow automated graph ML, including node embeddings and training of models for link prediction and node classification. AVAILABILITY AND IMPLEMENTATION: https://kghub.org

The Gene Ontology knowledgebase in 2023

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project

INCATools/whelk: Release 1.1.2

<h2>What's Changed</h2> <ul> <li>Fix some compiler warnings. by @balhoff in https://github.com/balhoff/whelk/pull/163</li> <li>Fix loophole in disableBottom option. by @balhoff in https://github.com/balhoff/whelk/pull/181</li> </ul> <h3>Dependency updates</h3> <ul> <li>Update sbt to 1.5.4 by @scala-steward in https://github.com/balhoff/whelk/pull/147</li> <li>Update sbt-scalajs to 1.6.0 by @scala-steward in https://github.com/balhoff/whelk/pull/146</li> <li>Update scala-library to 2.13.6 by @scala-steward in https://github.com/balhoff/whelk/pull/143</li> <li>Update utest to 0.7.10 by @scala-steward in https://github.com/balhoff/whelk/pull/142</li> <li>Update sbt-pgp to 2.1.1 by @scala-steward in https://github.com/balhoff/whelk/pull/133</li> <li>Update sbt to 1.5.7 by @scala-steward in https://github.com/balhoff/whelk/pull/162</li> <li>Update sbt-native-packager to 1.9.0 by @scala-steward in https://github.com/balhoff/whelk/pull/156</li> <li>Update sbt-scala-native-crossproject, ... to 1.1.0 by @scala-steward in https://github.com/balhoff/whelk/pull/151</li> <li>Update scowl to 1.4.0 by @scala-steward in https://github.com/balhoff/whelk/pull/150</li> <li>Update sbt-pgp to 2.1.2 by @scala-steward in https://github.com/balhoff/whelk/pull/149</li> <li>Update build and scala versions. by @balhoff in https://github.com/balhoff/whelk/pull/164</li> <li>Update sbt to 1.5.8 by @scala-steward in https://github.com/balhoff/whelk/pull/166</li> <li>Update scala-library to 2.13.8 by @scala-steward in https://github.com/balhoff/whelk/pull/167</li> <li>Update sbt-native-packager to 1.9.9 by @scala-steward in https://github.com/balhoff/whelk/pull/173</li> <li>Update sbt-scala-native-crossproject, ... to 1.2.0 by @scala-steward in https://github.com/balhoff/whelk/pull/175</li> <li>Update sbt-scala-native to 0.4.4 by @scala-steward in https://github.com/balhoff/whelk/pull/174</li> <li>Update sbt to 1.6.2 by @scala-steward in https://github.com/balhoff/whelk/pull/178</li> <li>Update owlapi-distribution to 4.5.21 by @scala-steward in https://github.com/balhoff/whelk/pull/172</li> <li>Update scowl to 1.4.1 by @scala-steward in https://github.com/balhoff/whelk/pull/176</li> <li>Update sbt-scalajs to 1.10.0 by @scala-steward in https://github.com/balhoff/whelk/pull/177</li> <li>Update owlapi-distribution to 4.5.22 by @scala-steward in https://github.com/balhoff/whelk/pull/180</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/balhoff/whelk/compare/v1.1.1...v1.1.2</p&gt

balhoff/arachne: Release 1.2.1

<p>Changes to logging framework.</p&gt

phenoscape/homology-annotations-demo: Release 1.0.1

Added license

INCATools/relation-graph: Release 2.3.2

<h2>What's Changed</h2> <ul> <li>Cleanup. by @balhoff in https://github.com/INCATools/relation-graph/pull/171</li> <li>Update zio, zio-streams, zio-test, ... to 2.0.13 by @scala-steward in https://github.com/INCATools/relation-graph/pull/199</li> <li>Update sbt to 1.8.2 by @scala-steward in https://github.com/INCATools/relation-graph/pull/180</li> <li>Update apache-jena-libs to 4.8.0 by @scala-steward in https://github.com/INCATools/relation-graph/pull/200</li> <li>Update scalafmt-core to 3.7.3 by @scala-steward in https://github.com/INCATools/relation-graph/pull/196</li> <li>Update scribe-slf4j to 3.10.7 by @scala-steward in https://github.com/INCATools/relation-graph/pull/185</li> <li>Update sbt-native-packager to 1.9.16 by @scala-steward in https://github.com/INCATools/relation-graph/pull/192</li> <li>Update sbt-pgp to 2.2.1 by @scala-steward in https://github.com/INCATools/relation-graph/pull/176</li> <li>Update sbt-git to 2.0.1 by @scala-steward in https://github.com/INCATools/relation-graph/pull/175</li> <li>Update zio, zio-streams, zio-test, ... to 2.0.19 by @scala-steward in https://github.com/INCATools/relation-graph/pull/232</li> <li>Update scalafmt-core to 3.7.17 by @scala-steward in https://github.com/INCATools/relation-graph/pull/234</li> <li>Update apache-jena-libs to 4.10.0 by @scala-steward in https://github.com/INCATools/relation-graph/pull/231</li> <li>Update scala-library to 2.13.12 by @scala-steward in https://github.com/INCATools/relation-graph/pull/226</li> <li>Update scribe-slf4j to 3.12.2 by @scala-steward in https://github.com/INCATools/relation-graph/pull/224</li> <li>Update sbt to 1.8.3 by @scala-steward in https://github.com/INCATools/relation-graph/pull/203</li> <li>Update sbt to 1.9.7 by @scala-steward in https://github.com/INCATools/relation-graph/pull/235</li> <li>Update version and dependencies. by @balhoff in https://github.com/INCATools/relation-graph/pull/236</li> </ul> <p><strong>Full Changelog</strong>: https://github.com/INCATools/relation-graph/compare/v2.3.1...v2.3.2</p&gt

Demonstration code for paper submission to the Bio-ontologies SIG Phenotype Day at ISMB 2014

<p>This software is cited within the paper:</p> <p>Presence-absence reasoning for evolutionary phenotypes<br> James P. Balhoff, T. Alexander Dececchi, Paula M. Mabee, and Hilmar Lapp</p> <p>submitted to Bio-ontologies SIG Phenotype Day at ISMB 2014</p

phenoscape/Phenex: Beta release 1.21-beta.2

Fixes launch problem