795e0dfc543020d5a353f1c27291d31de17992ec mspeir Sat Mar 14 12:57:37 2026 -0700 minor tweak to genark entry, no refs diff --git docs/genomeBrowserGlossary.md docs/genomeBrowserGlossary.md index cccabcb5a44..cf0abdc8fe1 100644 --- docs/genomeBrowserGlossary.md +++ docs/genomeBrowserGlossary.md @@ -1,611 +1,612 @@ --- title: "UCSC Genome Browser Glossary" --- A comprehensive reference guide to terminology used on the UCSC Genome Browser. This page covers the following topics: - [Genome Assemblies and Nomenclature](#genome-assemblies-and-nomenclature) - [Popular Genome Assemblies](#popular-genome-assemblies) - [Core Tools](#core-tools) - [Browser Interface and Interaction](#browser-interface-and-interaction) - [Main Display Elements](#main-display-elements) - [Navigation Controls](#navigation-controls) - [Mouse Interactions](#mouse-interactions) - [Position and Search](#position-and-search) - [Configuration and Settings](#configuration-and-settings) - [Views, Output, and Export](#views-output-and-export) - [Tracks and Display](#tracks-and-display) - [User Data Features](#user-data-features) - [Data Formats](#data-formats) - [Genome Browser Data and Annotations](#genome-browser-data-and-annotations) - [Gene Annotations](#gene-annotations) - [Mapping, Sequencing, and Repeats](#mapping-sequencing-and-repeats) - [Conservation and Comparative Genomics](#conservation-and-comparative-genomics) - [Variants and Clinical Data](#variants-and-clinical-data) - [Regulatory and Functional Data](#regulatory-and-functional-data) - [Table Browser](#table-browser) - [Technical Terms](#technical-terms) ## Genome Assemblies and Nomenclature **Assembly**: A genome assembly is the complete genome sequence produced after chromosomes have been fragmented, sequenced, and computationally reassembled. Assemblies are updated when new sequence data fills gaps or improved algorithms produce better results. Find supported assemblies from the [gateway page](/cgi-bin/hgGateway) or request new ones from our [assembly search page](/assemblySearch.html). -**[GenArk](https://hgdownload.gi.ucsc.edu/hubs/)**: UCSC's Genome Archive +**[GenArk](https://hgdownload.gi.ucsc.edu/hubs/)**: UCSC's repository containing thousands of additional genome assemblies beyond the main featured -assemblies. +assemblies. Search for and request new ones from +our [assembly search page](/assemblySearch.html). **Chromosome Coordinates**: Genomic positions specified as chromosome name and base position (e.g., `chr7:155,799,529-155,812,871`). UCSC uses zero-based, half-open coordinates in its databases. See [this blog post](https://genome-blog.gi.ucsc.edu/blog/2016/12/12/the-ucsc-genome-browser-coordinate-counting-systems) for details. **Scaffold / Contig**: Intermediate sequence units used in genome assembly. A contig is a contiguous stretch of assembled sequence with no gaps, while a scaffold is an ordered set of contigs joined by estimated gap lengths. In assemblies that are not fully resolved into chromosomes, sequences may be named as scaffolds (e.g., `scaffold10671`) rather than chromosomes. In chromosome-based assemblies, unplaced scaffolds appear as sequences like `chrUn_gl000220` and unlocalized scaffolds (known chromosome, unknown position) appear as `chr1_gl000191_random`. **Haplotype / Alternate Sequence**: Alternative versions of specific genomic regions representing common structural variation between individuals. In the Genome Browser, these appear as sequences with `_hap` or `_alt` suffixes (e.g., `chr6_cox_hap2`, `chr1_KI270762v1_alt`). See our [FAQ](/FAQ/FAQdownloads.html#downloadAlt) for more details. Alternate sequences can be viewed in chromosomal context using [Multi-Region mode](/goldenPath/help/multiRegionHelp.html). **Fix Sequences (Fix Patches)**: Patch sequences correct errors or improve the reference assembly without changing the coordinate system. In the UCSC Genome Browser, these sequences are identified by appending `_fix` to their names (e.g., `chr2_KN538362v1_fix`). See our [FAQ]( /FAQ/FAQdownloads.html#downloadFix) for more details. ### Popular Genome Assemblies **[hg19 (GRCh37)](/cgi-bin/hgTracks?db=hg19)**: The February 2009 human reference genome assembly from the Genome Reference Consortium. Still widely used for legacy datasets and clinical annotations. **[hg38 (GRCh38)](/cgi-bin/hgTracks?db=hg38)**: The December 2013 human reference genome assembly, the current standard for most new human genomics work. Contains improved sequence accuracy and gap filling compared to hg19. **[hs1 (T2T-CHM13)](/cgi-bin/hgTracks?db=hub_3671779_hs1)**: The telomere-to-telomere human genome assembly released in 2022, representing the first complete, gapless sequence of a human genome including centromeres and other previously unresolved regions. **[mm10 (GRCm38)](/cgi-bin/hgTracks?db=mm10)**: The December 2011 mouse reference genome assembly from the Genome Reference Consortium. **[mm39 (GRCm39)](/cgi-bin/hgTracks?db=mm39)**: The June 2020 mouse reference genome assembly, the current standard for mouse genomics. ## Core Tools **[Genome Browser](/cgi-bin/hgTracks)**: The main visualization tool that displays any portion of a genome at any scale with aligned annotation tracks showing genes, regulatory elements, conservation, variants, and other genomic features. **[BLAT (BLAST-Like Alignment Tool)](/cgi-bin/hgBlat)**: A rapid sequence alignment tool developed by Jim Kent for finding sequence matches in genomes. Faster than BLAST for closely related sequences and useful for locating mRNA/EST alignments. **[Table Browser](/cgi-bin/hgTables)**: A web interface for querying, filtering, and downloading data from the underlying MySQL databases. Allows intersection of data tables and export in multiple formats. See [below](#table-browser) for more related terms, or our [documentation](/goldenPath/help/hgTablesHelp.html). **[LiftOver](/cgi-bin/hgLiftOver)**: A tool for converting genomic coordinates between different genome assemblies (e.g., hg19 to hg38). Requires chain files that map regions between assemblies. **[In-Silico PCR](/cgi-bin/hgPcr)**: A tool for virtually testing PCR primer pairs against a genome to verify specificity and predict amplicon locations. **[Variant Annotation Integrator](/cgi-bin/hgVai)**: A tool for annotating genomic variants using multiple data sources to predict functional effects. **[Data Integrator](/cgi-bin/hgIntegrator)**: A tool for intersecting and combining data from multiple annotation tracks simultaneously. ## Browser Interface and Interaction ### Main Display Elements **Browser Graphic / Tracks Image**: The main visualization area displaying the genome and all visible annotation tracks. The image is interactive and supports mouse-based navigation. **Base Position Track / Ruler**: The coordinate ruler at the top of the browser graphic showing the genomic position scale. Clicking and dragging on the ruler activates the drag-and-select zoom feature. **Chromosome Ideogram**: A graphical representation of the entire chromosome shown above the browser graphic (for assemblies with cytological banding data). A red box indicates the currently viewed region's location on the chromosome. Can zoom to regions by dragging-and-selecting a region in the ideogram. **Scale Bar**: A reference bar in the center of the browser graphic showing the current viewing scale in bases, kilobases, or megabases. **Track Label (Long Label)**: The descriptive text displayed above each track in the browser graphic (e.g., "GENCODE V41 Comprehensive Transcript Annotation"). **Short Label**: The abbreviated track name shown in the track controls section below the browser graphic. **Track Control / Visibility Menu**: The drop-down menus below the browser graphic that control each track's display mode (`hide`, `dense`, `squish`, `pack`, `full`). **Minibutton**: The small gray button to the left of each displayed track. Clicking it opens the track's configuration/settings page. **Track Groups**: Categories that organize related tracks together below the browser graphic (e.g., "Genes and Gene Predictions," "Mapping and Sequencing," "Regulation"). ### Navigation Controls **Position/Search Box**: The text field at the top of the page where you enter coordinates, gene names, accession numbers, rsIDs, HGVS terms, or DNA sequences to navigate to specific locations. **Zoom Buttons**: Controls above and below the browser graphic for zooming in (`1.5x`, `3x`, `10x`, `base`) or out (`1.5x`, `3x`, `10x`, `100x`) on the current view. **Move Buttons**: Arrow buttons for shifting the view left or right along the chromosome while maintaining the current zoom level. **Reverse Button**: Flips the browser display to show the negative strand (3' to 5') instead of the default forward strand (5' to 3'). **Next / Prev Item Navigation**: Gray double-headed arrows that appear at the ends of track items (when enabled in configuration) allowing you to jump to the next or previous feature in that track. **Keyboard Shortcuts**: Many Genome Browser interactions can be activated using keyboard shortcuts (e.g. "vd" to view DNA sequence of current window). See all keyboard shortcuts by typing "?". ### Mouse Interactions **Right-Click Context Menu**: A context-sensitive menu that appears when you right-click on any item in the browser graphic. Options include zooming to the full item, highlighting, getting DNA sequence, viewing the details page, and accessing track configuration. **Click on Item**: Clicking on a feature (gene, SNP, etc.) in the browser graphic opens its details page with comprehensive information and external links. **Drag-and-Reorder**: Click and drag tracks vertically to rearrange their display order in the browser graphic. **Drag-and-Scroll (Pan)**: Click and drag anywhere on the browser graphic (except the ruler) to scroll the view horizontally left or right. **Drag-and-Select (Drag-and-Zoom)**: Click and drag on the ruler/base position track to select a region, then choose to zoom into that region. Hold Shift while dragging elsewhere on the image to activate this feature outside the ruler. **Highlight**: A colored vertical band that can be added to mark regions of interest. Created via the drag-and-select popup menu or right-click menu. Multiple highlights can be added with different colors. ### Position and Search **Position/Search Box**: Text entry box at the top of the main Genome Browser image. Accepts positions or one of a variety of search terms, including gene names, rsIDs, short sequences and [various other terms](/goldenPath/help/query.html). **Autocomplete**: For assemblies with gene annotations, the position search box offers autocomplete suggestions as you type gene symbols. **[Track Search](/cgi-bin/hgTracks?hgt_tSearch=track+search)**: A feature for finding tracks by searching their names, descriptions, and metadata. Accessed via the Genome Browser menu or a button below the graphic. ### Configuration and Settings **[Configure Button](/cgi-bin/hgTracks?hgTracksConfigPage=configure)**: Opens the Track Configuration page where you can adjust global display settings including image width, text size, font, and gridlines. **Track Settings Page**: The detailed configuration page for an individual track, accessed by clicking the track's minibutton or name. Allows filtering, coloring, and display customization. **Default Tracks Button**: Resets all track visibility settings to their default states for the current assembly. **Hide All Button**: Sets all tracks to hidden, clearing the display. **Image Width**: A configurable setting (in pixels) controlling the horizontal size of the browser graphic. Larger widths show more genomic territory without scrolling. **Gridlines**: Optional light blue vertical lines in the browser graphic that help align features across tracks. Can be toggled on/off in configuration. **Reset All User Settings**: Under top navigation menu "Genome Browser", clears all customizations including track visibility, custom tracks, and hubs, returning the browser to its original default state. Useful when browser configuration seems to be stuck in a broken state. ### Views, Output, and Export **Recommended Track Sets**: Under top navigation menu "Genome Browser". Allows users to enable a set of recommended tracks for tasks such as clinical variant evaluation. **View Menu**: A top navigation menu providing options like viewing DNA sequence, converting coordinates to other assemblies, and accessing PDF/PostScript output. **Get DNA**: A feature to retrieve the genomic DNA sequence for the current viewing region or for a specific track item. Accessible via the View menu or right-click context menu. **PDF/PS Output**: Options under the View menu to generate publication-quality vector graphics of the browser display. ## Tracks and Display **Track**: A horizontal row in the Genome Browser display showing a specific type of annotation data (e.g., genes, SNPs, conservation scores). Each track can be configured for different display modes. **Track Group**: A set of related tracks grouped together under the main track image, e.g. "Mapping and Sequencing" or "Comparative Genomics". **Strand (+ / -)**: The orientation of a genomic feature relative to the reference sequence. The positive (+) strand reads 5' to 3' left to right; the negative (-) strand reads 3' to 5'. In gene tracks, chevrons (arrows) within intron lines indicate the direction of transcription. **Details Page**: The information page that opens when you click on an item in the browser graphic. Displays feature-specific data such as genomic coordinates, strand, score, and links to external databases. The content varies by track type. **[Multi-Region Mode](/goldenPath/help/multiRegionHelp.html)**: A display mode that shows non-contiguous genomic regions side by side. Options include exon-only view (hiding introns), gene-only view (hiding intergenic regions), and custom regions defined by a BED file. Also supports viewing alternate haplotype sequences in chromosomal context. Accessible from the View menu or button next to position box. **[Track Collection Builder](/cgi-bin/hgCollection)**: A tool for combining multiple wiggle-type tracks (bigWig, bedGraph) from native browser data, custom tracks, or track hubs into a single configurable composite. Supports overlay methods including transparent, stacked, add, and subtract. Accessible from the My Data menu. **Filtering**: Track-level configuration that limits the displayed items to those matching specified criteria such as score thresholds, name patterns, or field values. Filter settings are available on many track settings pages and persist across sessions. Click the minibutton or "Configure" from the right-click menu to see available filter options for a specific track. ### Display Modes | Mode | Description | |------|-------------| | `hide` | Track is not displayed | | `dense` | All features collapsed into a single line | | `squish` | Features shown at reduced height | | `pack` | Features shown at full height, labeled when space permits | | `full` | Features shown at full height with all labels | **Composite Track**: A container that groups related tracks together (e.g., RNA-seq replicates), allowing them to be managed collectively. Indicated in the track groups by a folder icon. **MultiWig**: A special composite display mode that overlays multiple wiggle-format data tracks in a single graphical area. See, for example, the "Layered H3K4Me1" track under the "ENCODE Regulation" supertrack. **Supertrack**: A higher-level grouping of composite tracks or individual tracks into a collapsible folder structure. Indicated in the track groups by a folder icon. ## User Data Features **[Custom Tracks](/cgi-bin/hgCustom)**: User-uploaded annotation data displayed temporarily in the browser (expires after 48 hours of inactivity unless saved in a session). See [custom track documentation](/goldenPath/help/customTrack.html) to learn how to load your custom tracks and accepted formats. **[Track Hub](/cgi-bin/hgHubConnect#unlistedHubs)**: A collection of remotely hosted annotation files that can be connected to the browser via a `hub.txt` configuration file. Provides more stable and configurable data display than custom tracks. Will show up as its own group under the main genome browser image. See our [hub basics page](/docs/hubs/hubBasics.html) for help creating your own or our [track hub documentation](/goldenPath/help/hgTrackHubHelp.html) for a full description of the format. **[Assembly Hub](/goldenPath/help/assemblyHubHelp.html)**: A track hub that includes a custom genome assembly (in twoBit format) along with annotation tracks. **[Public Hub](/cgi-bin/hgHubConnect#publicHubs)**: A track or assembly hub provided by an external group. Will show up as its own group under the main genome browser image. Questions about track data should be directed to the hub maintainers, whose email address can be found on the description page for any track in the hub. Public hubs are required to meet a set of [guidelines](/goldenPath/help/publicHubGuidelines.html) and are reviewed by Genome Browser staff before being added to the list. **[Hub Space/Hub Upload](/cgi-bin/hgHubConnect#hubUpload)**: The UCSC Genome Browser provides up to 10 GB of space for those with Genome Browser accounts to store custom track and hub data. **[Hub Development](/cgi-bin/hgHubConnect#hubDeveloper)**: Configuration settings useful when developing a new hub. Provides an interface for checking a hub for configuration issues. **[Sessions](/cgi-bin/hgSession)**: A saved snapshot of browser configuration including track visibility settings, position, custom tracks, and hubs. Can be shared via URL. See [sessions documentation](/goldenPath/help/hgSessionHelp.html). **[Public Sessions](/cgi-bin/hgPublicSessions)**: User-created sessions made publicly available for others to view. ## Data Formats **[BED (Browser Extensible Data)](/FAQ/FAQformat.html#format1)**: A tab-delimited format for defining genomic regions. Minimum 3 columns (chromosome, start, end); can extend to 12+ columns including name, score, strand, and exon structure. **[bigBed](/goldenPath/help/bigBed.html)**: A compressed, indexed binary version of BED format enabling efficient random access for large datasets. Custom AutoSQL (.as) files allow it to be extended to any number of columns containing item details, sequence, tables, and more. **[WIG (Wiggle)](/goldenPath/help/wiggle.html)**: A format for continuous-valued data displayed as graphs (e.g., conservation scores, read coverage). **[bigWig](/goldenPath/help/bigWig.html)**: A compressed, indexed binary version of WIG format for large continuous data tracks. **[bedGraph](/goldenPath/help/bedgraph.html)**: A format for displaying continuous data where each line specifies a chromosome region and associated value. Similar to WIG but preserves original data on export. **[BAM (Binary Alignment/Map)](/goldenPath/help/bam.html)**: A compressed binary format for storing sequence alignment data. Requires a separate `.bai` index file. **[CRAM](/goldenPath/help/cram.html)**: A more compressed alternative to BAM that references an external genome sequence file. **[VCF (Variant Call Format)](/goldenPath/help/vcf.html)**: A standard format for storing genetic variant data including SNPs, insertions, and deletions. **[PSL](/FAQ/FAQformat.html#format2)**: A format for storing sequence alignments, commonly used for BLAT output and mRNA/EST alignments. **[GenePred](/FAQ/FAQformat.html#format9)**: A table format used to represent gene prediction and transcript structure data. Fields include transcript name, chromosome, strand, transcription start/end, coding region start/end, exon count, and exon coordinates. An extended version (genePredExt) adds gene name and coding region status fields. **[MAF (Multiple Alignment Format)](/FAQ/FAQformat.html#format5)**: A format for storing multiple sequence alignments across species. **[interact / bigInteract](/goldenPath/help/interact.html)**: A format for displaying pairwise interactions between genomic regions, drawn as arcs or half-rectangles connecting two loci. Suitable for chromatin interaction data such as ChIA-PET and promoter-enhancer links. The bigInteract binary version is used for track hubs. **[HAL (Hierarchical Alignment Format)](/FAQ/FAQformat.html#format12)**: A graph-based binary format for storing multiple genome alignments organized according to a phylogenetic tree. Unlike MAF, HAL allows reference-free querying with respect to any genome in the alignment. Native output format of the Progressive Cactus alignment pipeline. **[twoBit](/FAQ/FAQformat.html#format7)**: An efficient binary format for storing genomic sequence data. See our [format page](/FAQ/FAQformat.html) for a full listing of track and data types. ## Genome Browser Data and Annotations ### Gene Annotations **[GENCODE](https://www.gencodegenes.org/)**: The reference gene annotation for human and mouse genomes, combining manual curation with computational predictions. Includes protein-coding genes, non-coding RNAs, and pseudogenes. **[RefSeq](https://www.ncbi.nlm.nih.gov/refseq/)**: NCBI's curated collection of reference sequences for genes, transcripts, and proteins. **[Ensembl Genes](https://www.ensembl.org/)**: Gene predictions from the Ensembl project, available for many species. **UCSC Genes**: UCSC's gene track built by integrating data from RefSeq and GenBank among other sources with extensive metadata and external database links. Now retired and replaced by GENCODE genes. **Transcript / Isoform**: A transcript is a single RNA molecule produced from a gene. Many genes produce multiple transcripts (isoforms) through alternative splicing, alternative promoters, or alternative polyadenylation. In the browser, each isoform is drawn as a separate line within a gene track, which is why a single gene may appear as multiple stacked items. **Exon**: A coding or untranslated region of a gene that is retained in the mature mRNA after splicing. Displayed as thick boxes in gene tracks. **Intron**: A region within a gene that is removed during RNA splicing. Displayed as thin lines connecting exons. Chevrons indicate direction of transcription. **UTR (Untranslated Region)**: Portions of mRNA at the 5' and 3' ends that do not code for protein. Displayed as half-height boxes in gene tracks. **CDS (Coding Sequence)**: The portion of a gene or mRNA that codes for protein, from start codon to stop codon. ### Conservation and Comparative Genomics **[phastCons](/goldenPath/help/phastCons.html)**: A conservation scoring method that calculates the probability that each base is in an evolutionarily conserved element, using a phylogenetic hidden Markov model. Scores range from 0 to 1. Typically found alongside phyloP scores and a Multiz multiple alignment. **phyloP**: A conservation scoring method that measures evolutionary rates at individual bases compared to a neutral model. Positive scores indicate conservation; negative scores indicate faster-than-expected evolution. Typically found alongside phastCons scores and a Multiz multiple alignment. **Multiz**: An algorithm for creating multiple genome alignments from pairwise alignments. Subsequent multiple alignments are displayed in the Genome Browser in MAF format. Typically found alongside phastCons and phyloP scores. **[Chain](/goldenPath/help/chain.html)**: A series of gapless aligned blocks between two genomes, representing alignable regions. **[Net](/goldenPath/help/net.html)**: A hierarchical arrangement of chains representing syntenic (same genomic context) alignments between genomes, with the highest-scoring chains filling each region. More details about net construction can be found in [this FAQ](/FAQ/FAQtracks#tracks24). **Conservation Track**: A composite track displaying multiple species alignments and conservation scores (phastCons and phyloP) computed from those alignments. ### Mapping, Sequencing, and Repeats **[RepeatMasker](http://www.repeatmasker.org/)**: A program that screens DNA sequences for interspersed repeats and low-complexity regions. The RepeatMasker track is one of the most prominent default tracks, displaying repeat classes including SINEs, LINEs, LTR elements, DNA transposons, simple repeats, and satellites. Items are color-coded by repeat class and shaded by divergence from the repeat consensus. **GC Percent**: A track showing the percentage of guanine (G) and cytosine (C) bases across the genome, calculated in fixed-size windows. Regions with higher GC content are drawn more darkly. High GC content is generally associated with gene-rich areas of the genome. **Mappability**: Tracks indicating how uniquely short sequences (k-mers) at each position can be mapped back to the genome. Regions with low mappability contain repetitive sequences where sequencing reads cannot be confidently placed, which is important for interpreting read coverage and variant calls. **Synteny**: Conservation of gene order and genomic organization between species. Syntenic regions share a common ancestral arrangement. The concept is central to the Chain and Net comparative genomics tracks, where Net tracks specifically display the highest-scoring syntenic alignments between two genomes. ### Variants and Clinical Data **SNP (Single Nucleotide Polymorphism)**: A single base position where different alleles exist in a population. **[dbSNP](https://www.ncbi.nlm.nih.gov/snp/)**: NCBI's database of genetic variation, displayed as SNP tracks in the browser. **rsID**: A reference SNP identifier from dbSNP (e.g., `rs12345`). **[ClinVar](https://www.ncbi.nlm.nih.gov/clinvar/)**: NCBI's database of clinically significant genetic variants and their relationship to disease. **[gnomAD (Genome Aggregation Database)](https://gnomad.broadinstitute.org/)**: A resource of exome and genome sequencing data from large populations, providing allele frequencies. **HGVS Nomenclature**: A standardized system for describing sequence variants (e.g., `NM_004006.2:c.4375C>T`). Accepted in the position/search box. ### Regulatory and Functional Data **[ENCODE (Encyclopedia of DNA Elements)](/ENCODE/)**: A consortium project identifying all functional elements in the human genome, including regulatory regions. **cCRE (Candidate Cis-Regulatory Element)**: Regions identified by ENCODE as potential regulatory elements based on epigenomic data. **DNase Hypersensitivity**: Regions of open chromatin accessible to DNase I enzyme, indicating potential regulatory activity. **ChIP-seq**: Chromatin immunoprecipitation followed by sequencing, used to identify protein-DNA interactions. **CpG Islands**: Genomic regions with high frequency of CpG dinucleotides, often found near gene promoters. **[GTEx (Genotype-Tissue Expression)](/gtex.html)**: A project providing gene expression data across multiple human tissues. **[FANTOM5](https://fantom.gsc.riken.jp/5)**: A project mapping transcription start sites and promoter activity across cell types and tissues. ## Table Browser **[Intersection](/goldenPath/help/hgTablesHelp.html#Intersection)**: A Table Browser feature that combines data from two tracks by finding overlapping genomic regions. For example, intersecting a gene track with a conservation track returns only the genes that overlap conserved elements. Supports both simple (two-table) and multiple intersection modes. **Data Format Description (Schema)**: A page describing the structure of a track's underlying data — its columns, data types, and example values. Found via the "Data schema/format description and download" link on track description pages, or via the "describe table schema" button in the Table Browser. Also provides a download link for the dataset. ## Technical Terms **Byte-Range Requests**: HTTP feature required for hosting bigBed, bigWig, and BAM files, allowing the browser to fetch only the portion of a file needed for the current view. **MariaDb/MySQL**: The relational database system underlying the Genome Browser's data storage. **[REST API](/goldenPath/help/api.html)**: A programming interface for retrieving Genome Browser data in JSON format. **[trackDb](/goldenPath/help/trackDb/trackDbHub.html)**: A configuration file (`trackDb.txt`) that defines track properties in a track hub, including display settings, colors, and metadata. **AutoSql**: A schema definition format used to describe custom fields in Genome Browser tables and bigBed files. **hubCheck**: A command-line utility for validating track hub configuration files. Available from our [download server](https://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads). See the [hubCheck documentation](/goldenPath/help/hgTrackHubHelp.html#Compatibility) and related [blog post](https://genome-blog.gi.ucsc.edu/blog/how-portable-is-your-track-hub-use-hubcheck-to-find-out/).