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

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

I. An Overview of the Library Support Process Used at the Joint Genome Institute Production Genomics Facility

I. AN OVERVIEW OF THE LIBRARY SUPPORT PROCESS USED AT THE JOINT GENOME INSTITUTE PRODUCTION GENOMICS FACILITY Cathe Adam, Karli Ikeda, Sandy Huynh, Jayadevi Krishnakumar, Jim Fey, Diane Bauer, Sanna Anwar, Mansi Chovatia, Nicole Shapiro, Miranda Harmon-SmithLibrary support is the first step in production sequencing at the Joint Genome Institute s (JGI) Production Genomics Facility (PGF). The goal of library support is to generate 384 well glycerol stock plates of each library for a given project. These plates are then passed on to the Sequencing Prep group for Rolling Circle Amplification. Transformation stocks of the 3, 8, and 40kb libraries for a given project are received into library support from cloning technology. The stocks are stored at -80oC until plated. Libraries are plated according to priority. The colonies produced from a plating event are then picked using robotic colony pickers and are inoculated into 384-well destination plates containing LB/glycerol + antibiotic. The destination plates are grown overnight and visualized on a Spectramax Optical Density reader to identify wells without growth. Wells containing no growth are aspirated and replaced with colony growth from a "fix source" plate generated from the same library. The destination plates are then sealed and stored at -80oC until sent to the Sequencing Prep area for Rolling Circle Amplification (RCA). This poster will elaborate on these steps in the library support process and detail further the project tracking and management, plating and picking procedures and the instruments that are utilized throughout these steps

I. An Overview of the Library Support Process Used at the Joint Genome Institute Production Genomics Facility

I. AN OVERVIEW OF THE LIBRARY SUPPORT PROCESS USED AT THE JOINT GENOME INSTITUTE PRODUCTION GENOMICS FACILITY Cathe Adam, Karli Ikeda, Sandy Huynh, Jayadevi Krishnakumar, Jim Fey, Diane Bauer, Sanna Anwar, Mansi Chovatia, Nicole Shapiro, Miranda Harmon-SmithLibrary support is the first step in production sequencing at the Joint Genome Institute s (JGI) Production Genomics Facility (PGF). The goal of library support is to generate 384 well glycerol stock plates of each library for a given project. These plates are then passed on to the Sequencing Prep group for Rolling Circle Amplification. Transformation stocks of the 3, 8, and 40kb libraries for a given project are received into library support from cloning technology. The stocks are stored at -80oC until plated. Libraries are plated according to priority. The colonies produced from a plating event are then picked using robotic colony pickers and are inoculated into 384-well destination plates containing LB/glycerol + antibiotic. The destination plates are grown overnight and visualized on a Spectramax Optical Density reader to identify wells without growth. Wells containing no growth are aspirated and replaced with colony growth from a "fix source" plate generated from the same library. The destination plates are then sealed and stored at -80oC until sent to the Sequencing Prep area for Rolling Circle Amplification (RCA). This poster will elaborate on these steps in the library support process and detail further the project tracking and management, plating and picking procedures and the instruments that are utilized throughout these steps